MS/MS fragmentation-guided search of TMG-chitooligomycins and their structure-activity relationship in specific β-N-acetylglucosaminidase inhibition.

PubMed

Usuki, Hirokazu; Yamamoto, Yukihiro; Kumagai, Yuya; Nitoda, Teruhiko; Kanzaki, Hiroshi; Hatanaka, Tadashi

2011-04-21

The reducing tetrasaccharide TMG-chitotriomycin (1) is an inhibitor of β-N-acetylglucosaminidase (GlcNAcase), produced by the actinomycete Streptomyces anulatus NBRC13369. The inhibitor shows a unique inhibitory spectrum, that is, selectivity toward enzymes from chitin-containing organisms such as insects and fungi. Nevertheless, its structure-selectivity relationship remains to be clarified. In this study, we conducted a structure-guided search of analogues of 1 in order to obtain diverse N,N,N-trimethylglucosaminium (TMG)-containing chitooligosaccharides. In this approach, the specific fragmentation profile of 1 on ESI-MS/MS analysis was used for the selective detection of desired compounds. As a result, two new analogues, named TMG-chitomonomycin (3) and TMG-chitobiomycin (2), were obtained from a culture filtrate of 1-producing Streptomyces. Their enzyme-inhibiting activity revealed that the potency and selectivity depended on the degree of polymerization of the reducing end GlcNAc units. Furthermore, a computational modeling study inspired the inhibitory mechanism of TMG-related compounds as a mimic of the substrate in the Michaelis complex of the GH20 enzyme. This study is an example of the successful application of a MS/MS experiment for structure-guided isolation of natural products.

"Polymeromics": Mass spectrometry based strategies in polymer science toward complete sequencing approaches: a review.

PubMed

Altuntaş, Esra; Schubert, Ulrich S

2014-01-15

Mass spectrometry (MS) is the most versatile and comprehensive method in "OMICS" sciences (i.e. in proteomics, genomics, metabolomics and lipidomics). The applications of MS and tandem MS (MS/MS or MS(n)) provide sequence information of the full complement of biological samples in order to understand the importance of the sequences on their precise and specific functions. Nowadays, the control of polymer sequences and their accurate characterization is one of the significant challenges of current polymer science. Therefore, a similar approach can be very beneficial for characterizing and understanding the complex structures of synthetic macromolecules. MS-based strategies allow a relatively precise examination of polymeric structures (e.g. their molar mass distributions, monomer units, side chain substituents, end-group functionalities, and copolymer compositions). Moreover, tandem MS offer accurate structural information from intricate macromolecular structures; however, it produces vast amount of data to interpret. In "OMICS" sciences, the software application to interpret the obtained data has developed satisfyingly (e.g. in proteomics), because it is not possible to handle the amount of data acquired via (tandem) MS studies on the biological samples manually. It can be expected that special software tools will improve the interpretation of (tandem) MS output from the investigations of synthetic polymers as well. Eventually, the MS/MS field will also open up for polymer scientists who are not MS-specialists. In this review, we dissect the overall framework of the MS and MS/MS analysis of synthetic polymers into its key components. We discuss the fundamentals of polymer analyses as well as recent advances in the areas of tandem mass spectrometry, software developments, and the overall future perspectives on the way to polymer sequencing, one of the last Holy Grail in polymer science. Copyright © 2013 Elsevier B.V. All rights reserved.

Tandem mass spectrometry: analysis of complex mixtures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singleton, K.E.

1985-01-01

Applications of tandem mass spectrometry (MS/MS) for the analysis of complex mixtures results in increased specificity and selectivity by using a variety of reagent gases in both negative and positive ion modes. Natural isotopic abundance ratios were examined in both simple and complex mixtures using parent, daughter and neutral loss scans. MS/MS was also used to discover new compounds. Daughter scans were used to identify seven new alkaloids in a cactus species. Three of these alkaloids were novel compounds, and included the first simple, fully aromatic isoquinoline alkaloids reported in Cactaceae. MS/MS was used to characterize the chemical reaction productsmore » of coal in studies designed to probe its macromolecular structure. Negative ion chemical ionization was utilized to study reaction products resulting from the oxidation of coal. Possible structural units in the precursor coal were predicted based on the reaction products identified, aliphatic and aromatic acids and their anhydrides. The MS/MS method was also used to characterize reaction products resulting from coal liquefaction and/or extraction. These studies illustrate the types of problems for which MS/MS is useful. Emphasis has been placed on characterization of complex mixtures by selecting experimental parameters which enhance the information obtained. The value of using MS/MS in conjunction with other analytical techniques as well as the chemical pretreatment is demonstrated.« less

Hydrogen Exchange Mass Spectrometry

PubMed Central

Mayne, Leland

2018-01-01

Hydrogen exchange (HX) methods can reveal much about the structure, energetics, and dynamics of proteins. The addition of mass spectrometry (MS) to an earlier fragmentation-separation HX analysis now extends HX studies to larger proteins at high structural resolution and can provide information not available before. This chapter discusses experimental aspects of HX labeling, especially with respect to the use of MS and the analysis of MS data. PMID:26791986

Structural correlates of subjective and objective memory performance in multiple sclerosis.

PubMed

Pardini, Matteo; Bergamino, Maurizio; Bommarito, Giulia; Bonzano, Laura; Luigi Mancardi, Gian; Roccatagliata, Luca

2014-04-01

Subjective and objective memory deficits represent a frequent and ill-understood aspect of multiple sclerosis (MS), and a significant cause of disability and quality of life reduction. The aim of the study is to verify the role of hippocampal and temporal associative fibers' damage in MS-related memory complaints. To reach this aim, 25 patients with low disability relapsing-remitting MS and 19 healthy controls were included in the study. All subjects underwent 3D T1 structural imaging and Diffusion Tensor Imaging. Additionally, MS patients underwent neuropsychological evaluation of objective (Selective Reminding Test and Spatial Recall Test) and of subjective (Perceived Deficit Questionnaire, Retrospective and Prospective Memory Subscales) memory deficits. Normalized hippocampal volume (NHV) and mean Fractional Anisotropy (FA) for the uncinate fasciculus (UF) and for the ventral division of the cingulum bundle (VCB) were calculated for all subjects. We showed that, compared to controls, MS subjects presented with reduced right NHV and with reduced mean FA bilaterally in the UF and the VCB. In the MS group, verbal memory scores correlated with left NHV, spatial memory scores correlated with right NHV, while perceived retrospective and prospective memory deficits correlated with left VCB and left UF mean FA respectively. Our data confirm an early involvement of memory-related brain structures in MS patients. Our data suggest that verbal and nonverbal memory as well as perceived retrospective and prospective memory deficits are related to alterations of discrete anatomical structures in the low-disability phase of MS. Copyright © 2013 Wiley Periodicals, Inc.

Relationship between Structural and Functional Assessment of the Visual System in Mildly Disabled Relapsing-Remitting Multiple Sclerosis Patients

PubMed Central

Huseyinoglu, Nergiz; Ekinci, Metin; Ozben, Serkan; Buyukuysal, Cagatay

2014-01-01

Abstract Studies that explored the anterior visual pathway in the patients with multiple sclerosis (MS) have demonstrated contradictory results about the correlation between structural and functional status of optic nerve and retina. We aimed to investigate the functional and structural findings in our cohort of mildly disabled relapsing-remitting MS patients. A total of 134 eyes (80 eyes of the patients with MS and 54 eyes of the control group) were investigated. Eyes of MS patients were divided into two groups—as eyes with history of optic neuritis (ON group) and without history of optic neuritis (NON group). Ophthalmological investigation including visual evoked potentials, standard automated perimetry, and optical coherence tomography were performed for all participants. Retinal and macular thicknesses were significantly decreased in ON and NON groups compared with controls. Also, visual evoked potential latencies and visual field loss were worse in the both MS groups compared with control group. We did not find any correlation between visual evoked potentials and retinal or macular thickness values but visual field parameters were correlated between retinal and macular layer loss in the NON group. According to our results and some previous studies, although both functional and structural changes were detected in patients with MS, functional status markers do not always show parallelism (or synchrony) with structural changes, especially in eyes with history of optic neuritis. PMID:27928266

Process and Formulation Effects on Protein Structure in Lyophilized Solids using Mass Spectrometric Methods

PubMed Central

Iyer, Lavanya K.; Sacha, Gregory A.; Moorthy, Balakrishnan S.; Nail, Steven L.; Topp, Elizabeth M.

2016-01-01

Myoglobin (Mb) was lyophilized in the absence (Mb-A) and presence (Mb-B) of sucrose in a pilot-scale lyophilizer with or without controlled ice nucleation. Cake morphology was characterized using scanning electron microscopy (SEM) and changes in protein structure were monitored using solid-state Fourier-transform infrared spectroscopy (ssFTIR), solid-state hydrogen-deuterium exchange-mass spectrometry (ssHDX-MS) and solid-state photolytic labeling-mass spectrometry (ssPL-MS). The results showed greater variability in nucleation temperature and irregular cake structure for formulations lyophilized without controlled nucleation. Controlled nucleation resulted in nucleation at ~ −5 °C and uniform cake structure. Formulations containing sucrose showed better retention of protein structure by all measures than formulations without sucrose. Samples lyophilized with and without controlled nucleation were similar by most measures of protein structure. However, ssPL-MS showed the greatest pLeu incorporation and more labeled regions for Mb-B lyophilized with controlled nucleation. The data support the use of ssHDX-MS and ssPL-MS to study formulation and process-induced conformational changes in lyophilized proteins. PMID:27044943

UPLC-QTOF-MS/MS-guided isolation and purification of sulfur-containing derivatives from sulfur-fumigated edible herbs, a case study on ginseng.

PubMed

Zhang, Li; Shen, Hong; Xu, Jun; Xu, Jin-Di; Li, Zhen-Ling; Wu, Jie; Zou, Ye-Ting; Liu, Li-Fang; Li, Song-Lin

2018-04-25

In this study, a novel ultra-performance liquid chromatography coupled with quadrupole/time-of-flight mass spectrometry (UPLC-QTOF-MS/MS)-guidance strategy was proposed for preparation of sulfur-containing derivatives in sulfur-fumigated edible herbs. Being versatile in both chromatographic separation and mass spectrometric detection, UPLC-QTOF-MS/MS was inducted into each experimental step for multifaceted purposes including finding, tracking, purity determination and structural elucidation of targeted compounds as well as UPLC-HPLC chromatographic conditions transplantation, whereby the isolation and purification procedures were greatly facilitated. Using this strategy, a new sulfur-containing ginsenoside Rg 1 derivative (named compound I) was obtained from sulfur-fumigated ginseng. The chemical structure of compound I was elucidated to be (3β, 6α, 12β)-3, 12-dihydroxydammar-25-ene-6, 20-diylbis-β-d-glucopyranoside, 24-sulfonic acid by QTOF-MS/MS, 1 H-NMR and 13 C-NMR analysis, and its generation mechanisms by sulfur-fumigation were accordingly discussed. The research deliverable suggests that the UPLC-QTOF-MS/MS-guidance strategy is promising for targeted preparation of sulfur-containing derivatives from sulfur-fumigated edible herbs. Copyright © 2017 Elsevier Ltd. All rights reserved.

Structural Analysis of Titan's Tholins by Ultra-High Resolution Mass Spectrometry

NASA Astrophysics Data System (ADS)

Vuitton, V.; Frisari, M.; Thissen, R.; Dutuit, O.; Bonnet, J.-Y.; Quirico, E.; Sciamma O'Brien, E.; Szopa, C.; Carrasco, N.; Somogyi, A.; Smith, M.; Hörst, S. M.; Yelle, R.

2010-04-01

We propose here a systematic ultra-high resolution mass spectrometry and MS/MS study in order to provide a more coherent and complete characterization of the structure of the molecules making up the soluble fraction of the Titan tholins.

Analysis of sesterterpenoids from Aspergillus terreus using ESI-QTOF and ESI-IT.

PubMed

Wu, Zhi-Jun; Fang, Dong-Mei; Han, Dan; Li, Guo-You; Chen, Xiao-Zhen; Qi, Hua-Yi; Zhang, Guo-Lin

2010-01-01

Biosynthesis of terretonin was studied due to the interesting skeleton of this series of sesterterpenoids. Very recently, López-Gresa reported two new sesterterpenoids (terretonins E and F) which are inhibitors of the mammalian mitochondrial respiratory chain. Mass spectrometry (MS), especially tandem mass spectrometry, has been one of the most important physicochemical methods for the identification of trace natural products due to it rapidity, sensitivity and low levels of sample consumption. The potential application prospect and unique skeleton prompted us to study structural characterisation using MS. To obtain sufficient information for rapid structural elucidation of this class of compounds using MS. The elemental composition of the product ions was confirmed by low-energy ESI-CID-QTOF-MS/MS analyses. The fragmentation pathways were postulated on the basis of ESI-QTOF-MS/MS/MS and ESI-IT-MS(n) spectra. Common features and major differences between ESI-QTOF-MS/MS and IT-MS(n) spectra were compared. For ESI-QTOF-MS/MS/MS experiments, capillary exit voltage was raised to induce in-source dissociation. Ammonium acetate or acetic acid were added into solutions to improve the intensity of [M + H]+. The collision energy was optimised to achieve sufficient fragmentation. Some fragmentation pathways were unambiguously proposed by the variety of abundance of fragment ions at different collision energies even without MS(n) spectra. Fragmentation pathways of five representative sesterterpenoids were elucidated using ESI-QTOF-MS/MS/MS and ESI-IT-MS(n) in both positive- and negative-ion mode. The key group of characterising fragmentation profiles was ring B, and these fragmentation patterns are helpful to identify different types of sestertepenoids. Complementary information obtained from fragmentation experiments of [M + H]+ (or [M + NH4]+ and [M-H](-) precursor ions is especially valuable for rapid identification of this kind of sesterterpenoid.

Structural Dynamics of the GW182 Silencing Domain Including its RNA Recognition motif (RRM) Revealed by Hydrogen-Deuterium Exchange Mass Spectrometry

NASA Astrophysics Data System (ADS)

Cieplak-Rotowska, Maja K.; Tarnowski, Krzysztof; Rubin, Marcin; Fabian, Marc R.; Sonenberg, Nahum; Dadlez, Michal; Niedzwiecka, Anna

2018-01-01

The human GW182 protein plays an essential role in micro(mi)RNA-dependent gene silencing. miRNA silencing is mediated, in part, by a GW182 C-terminal region called the silencing domain, which interacts with the poly(A) binding protein and the CCR4-NOT deadenylase complex to repress protein synthesis. Structural studies of this GW182 fragment are challenging due to its predicted intrinsically disordered character, except for its RRM domain. However, detailed insights into the properties of proteins containing disordered regions can be provided by hydrogen-deuterium exchange mass spectrometry (HDX/MS). In this work, we applied HDX/MS to define the structural state of the GW182 silencing domain. HDX/MS analysis revealed that this domain is clearly divided into a natively unstructured part, including the CCR4-NOT interacting motif 1, and a distinct RRM domain. The GW182 RRM has a very dynamic structure, since water molecules can penetrate the whole domain in 2 h. The finding of this high structural dynamics sheds new light on the RRM structure. Though this domain is one of the most frequently occurring canonical protein domains in eukaryotes, these results are - to our knowledge - the first HDX/MS characteristics of an RRM. The HDX/MS studies show also that the α2 helix of the RRM can display EX1 behavior after a freezing-thawing cycle. This means that the RRM structure is sensitive to environmental conditions and can change its conformation, which suggests that the state of the RRM containing proteins should be checked by HDX/MS in regard of the conformational uniformity. [Figure not available: see fulltext.

A pilot mixed-methods evaluation of MS INFoRm: a self-directed fatigue management resource for individuals with multiple sclerosis.

PubMed

Akbar, Nadine; Turpin, Karen; Petrin, Julie; Smyth, Penny; Finlayson, Marcia

2018-06-01

Fatigue management interventions for individuals with multiple sclerosis (MS) often feature structured programmes requiring repeated, in-person attendance that is not possible for all individuals. We sought to determine whether MS INFoRm, a self-directed fatigue management resource for individuals with MS, was worth further, more rigorous evaluation. Our indicators of worthiness were actual use of the resource by participants over 3 months, reductions in fatigue impact and increases in self-efficacy, and participant reports of changes in fatigue management knowledge and behaviours. This was a single-group, mixed-methods, before-after pilot study in individuals with MS reporting mild to moderate fatigue. Thirty-five participants were provided with MS INFoRm by a USB flash drive to use at home for 3 months, on their own volition. Twenty-three participants completed all standardized questionnaires, semi-structured interviews and study process measures. Participants reported actively using MS INFoRm over the 3-month study period (median total time spent using MS INFoRm=315 min) as well as significantly lower overall fatigue impact (Modified Fatigue Impact Scale: t=2.6, P=0.01), increased knowledge of MS fatigue (z=-2.8, P=0.01) and greater confidence in managing MS fatigue (z=-3.3, P=0.001). Individuals with significant reductions in fatigue impact also reported behavioural changes including tracking fatigue, better communication with others, greater awareness, improved quality of life and being more proactive. This study provides evidence that further rigorous evaluation of MS INFoRm, a self-directed resource for managing fatigue, is worth pursuing.

Study of the structures of photodegradation impurities and pathways of photodegradation of cilnidipine by liquid chromatography/Q-Orbitrap mass spectrometry.

PubMed

Zeng, Hongxia; Wang, Fan; Zhu, Bingqi; Zhong, Weihui; Shan, Weiguang; Wang, Jian

2016-08-15

The structures of photodegradation impurities in cilnidipine were studied by liquid chromatography/Q-Orbitrap mass spectrometry (LC/Q-Orbitrap MS) for the further improvement of the official monographs in Pharmacopoeias. The complete fragmentation patterns of impurities were investigated to obtain their structural information. Two pathways of photodegradation of cilnidipine were also explored to clarify the source of impurities in cilnidipine. Chromatographic separation was performed on a Boston Group C18 column (250 mm × 4.6 mm, 5 μm). The mobile phase consisted of acetonitrile/H2 O at a ratio of 75:25 (v/v). In order to determine the m/z values of the molecular ions and formulas of all detected impurities, full scan LC/MS in both positive and negative ion modes was firstly performed using a Thermo LC system coupled with a Q-Orbitrap high-resolution mass spectrometer. LC/MS/MS analysis was also carried out on target compounds to obtain as much structural information as possible. Five novel photodegradation impurities of cilnidipine were separated and identified based on the high-resolution MS/MS data. Impurity III was synthesized and its structure was confirmed by (1) H-NMR and (13) C-NMR data. Two photodegradation pathways to produce different photodegradation impurities were also revealed in this study. Among those impurities, impurities II and III were the main impurities which existed in the cilnidipine available on the market. Impurity II (the Z-isomer) was mainly produced when cilnidipine powder was directly exposed to daylight while impurity III (containing a piperidine ring) was mainly produced when cilnidipine was exposed to daylight in an ethanolic solution. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Abnormal functional connectivity and cortical integrity influence dominant hand motor disability in multiple sclerosis: a multimodal analysis.

PubMed

Zhong, Jidan; Nantes, Julia C; Holmes, Scott A; Gallant, Serge; Narayanan, Sridar; Koski, Lisa

2016-12-01

Functional reorganization and structural damage occur in the brains of people with multiple sclerosis (MS) throughout the disease course. However, the relationship between resting-state functional connectivity (FC) reorganization in the sensorimotor network and motor disability in MS is not well understood. This study used resting-state fMRI, T1-weighted and T2-weighted, and magnetization transfer (MT) imaging to investigate the relationship between abnormal FC in the sensorimotor network and upper limb motor disability in people with MS, as well as the impact of disease-related structural abnormalities within this network. Specifically, the differences in FC of the left hemisphere hand motor region between MS participants with preserved (n = 17) and impaired (n = 26) right hand function, compared with healthy controls (n = 20) was investigated. Differences in brain atrophy and MT ratio measured at the global and regional levels were also investigated between the three groups. Motor preserved MS participants had stronger FC in structurally intact visual information processing regions relative to motor impaired MS participants. Motor impaired MS participants showed weaker FC in the sensorimotor and somatosensory association cortices and more severe structural damage throughout the brain compared with the other groups. Logistic regression analysis showed that regional MTR predicted motor disability beyond the impact of global atrophy whereas regional grey matter volume did not. More importantly, as the first multimodal analysis combining resting-state fMRI, T1-weighted, T2-weighted and MTR images in MS, we demonstrate how a combination of structural and functional changes may contribute to motor impairment or preservation in MS. Hum Brain Mapp 37:4262-4275, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Mass spectrometry in grape and wine chemistry. Part I: polyphenols.

PubMed

Flamini, Riccardo

2003-01-01

Mass spectrometry, had and still has, a very important role for research and quality control in the viticulture and enology field, and its analytical power is relevant for structural studies on aroma and polyphenolic compounds. Polyphenols are responsible for the taste and color of wine, and confer astringency and structure to the beverage. The knowledge of the anthocyanic structure is very important to predict the aging attitude of wine, and to attempt to resolve problems about color stability. Moreover, polyphenols are the main compounds related to the benefits of wine consumption in the diet, because of their properties in the treatment of circulatory disorders such as capillary fragility, peripheral chronic venous insufficiency, and microangiopathy of the retina. Liquid Chromatography-Mass Spectrometry (LC-MS) techniques are nowadays the best analytical approach to study polyphenols in grape extracts and wine, and are the most effective tool in the study of the structure of anthocyanins. The MS/MS approach is a very powerful tool that permits anthocyanin aglycone and sugar moiety characterization. LC-MS allows the characterization of complex structures of grape polyphenols, such as procyanidins, proanthocyanidins, prodelphinidins, and tannins, and provides experimental evidence for structures that were previously only hypothesized. The matrix-assisted-laser-desorption-ionization-time-of-flight (MALDI-TOF) technique is suitable to determine the presence of molecules of higher molecular weight with high accuracy, and it has been applied with success to study procyanidin oligomers up to heptamers in the reflectron mode, and up to nonamers in the linear mode. The levels of resveratrol in wine, an important polyphenol well-known for its beneficial effects, have been determined by SPME and LC-MS, and the former approach led to the best results in terms of sensitivity. Copyright 2003 Wiley Periodicals, Inc.

Electrospray ionization tandem mass spectrometry of ammonium cationized polyethers.

PubMed

Nasioudis, Andreas; Heeren, Ron M A; van Doormalen, Irene; de Wijs-Rot, Nicolette; van den Brink, Oscar F

2011-05-01

Quaternary ammonium salts (Quats) and amines are known to facilitate the MS analysis of high molar mass polyethers by forming low charge state adduct ions. The formation, stability, and behavior upon collision-induced dissociation (CID) of adduct ions of polyethers with a variety of Quats and amines were studied by electrospray ionization quadrupole time-of-flight, quadrupole ion trap, and linear ion trap tandem mass spectrometry (MS/MS). The linear ion trap instrument was part of an Orbitrap hybrid mass spectrometer that allowed accurate mass MS/MS measurements. The Quats and amines studied were of different degree of substitution, structure, and size. The stability of the adduct ions was related to the structure of the cation, especially the amine's degree of substitution. CID of singly/doubly charged primary and tertiary ammonium cationized polymers resulted in the neutral loss of the amine followed by fragmentation of the protonated product ions. The latter reveals information about the monomer unit, polymer sequence, and endgroup structure. In addition, the detection of product ions retaining the ammonium ion was observed. The predominant process in the CID of singly charged quaternary ammonium cationized polymers was cation detachment, whereas their doubly charged adduct ions provided the same information as the primary and tertiary ammonium cationized adduct ions. This study shows the potential of specific amines as tools for the structural elucidation of high molar mass polyethers. © American Society for Mass Spectrometry, 2011

Enhancing Bottom-up and Top-down Proteomic Measurements with Ion Mobility Separations

DOE PAGES

Baker, Erin Shammel; Burnum-Johnson, Kristin E.; Ibrahim, Yehia M.; ...

2015-07-03

Proteomic measurements with greater throughput, sensitivity and additional structural information enhance the in-depth characterization of complex mixtures and targeted studies with additional information and higher confidence. While liquid chromatography separation coupled with mass spectrometry (LC-MS) measurements have provided information on thousands of proteins in different sample types, the additional of another rapid separation stage providing structural information has many benefits for analyses. Technical advances in ion funnels and multiplexing have enabled ion mobility separations to be easily and effectively coupled with LC-MS proteomics to enhance the information content of measurements. Finally, herein, we report on applications illustrating increased sensitivity, throughput,more » and structural information by utilizing IMS-MS and LC-IMS-MS measurements for both bottom-up and top-down proteomics measurements.« less

Integration of electrochemistry with ultra-performance liquid chromatography/mass spectrometry.

PubMed

Cai, Yi; Zheng, Qiuling; Liu, Yong; Helmy, Roy; Loo, Joseph A; Chen, Hao

2015-01-01

This study presents the development of ultra-performance liquid chromatography (UPLC) mass spectrometry (MS) combined with electrochemistry (EC) for the first time and its application for the structural analysis of proteins/peptides that contain disulfide bonds. In our approach, a protein/peptide mixture sample undergoes a fast UPLC separation and subsequent electrochemical reduction in an electrochemical flow cell followed by online MS and tandem mass spectrometry (MS/MS) analyses. The electrochemical cell is coupled to the mass spectrometer using our recently developed desorption electrospray ionization (DESI) interface. Using this UPLC/EC/DESI-MS method, peptides that contain disulfide bonds can be differentiated from those without disulfide bonds, as the former are electroactive and reducible. MS/MS analysis of the disulfide-reduced peptide ions provides increased information on the sequence and disulfide-linkage pattern. In a reactive DESI- MS detection experiment in which a supercharging reagent was used to dope the DESI spray solvent, increased charging was obtained for the UPLC-separated proteins. Strikingly, upon online electrolytic reduction, supercharged proteins (e.g., α-lactalbumin) showed even higher charging, which will be useful in top- down protein structure MS analysis as increased charges are known to promote protein ion dissociation. Also, the separation speed and sensitivity are enhanced by approximately 1(~)2 orders of magnitude by using UPLC for the liquid chromatography (LC)/EC/MS platform, in comparison to the previously used high- performance liquid chromatography (HPLC). This UPLC/EC/DESI-MS method combines the power of fast UPLC separation, fast electrochemical conversion, and online MS structural analysis for a potentially valuable tool for proteomics research and bioanalysis.

Integration of Electrochemistry with Ultra Performance Liquid Chromatography/Mass Spectrometry (UPLC/MS)

PubMed Central

Cai, Yi; Zheng, Qiuling; Liu, Yong; Helmy, Roy; Loo, Joseph A.; Chen, Hao

2015-01-01

This study presents the development of ultra-performance liquid chromatography/mass spectrometry (UPLC/MS) combined with electrochemistry (EC) for the first time and its application for the structural analysis of disulfide bond-containing proteins/peptides. In our approach, a protein/peptide mixture sample undergoes fast UPLC separation and subsequent electrochemical reduction in an electrochemical flow cell followed by online MS and MS/MS analyses. The electrochemical cell is coupled to MS using our recently developed desorption electrospray ionization (DESI) interface. Using this UPLC/EC/DESI-MS method, disulfide bond-containing peptides can be differentiated from those without disulfide bonds as the former are electroactive and reducible. Tandem MS analysis of the disulfide-reduced peptide ions provides increased sequence and disulfide linkage pattern information. In a reactive DESI-MS detection experiment in which a supercharging reagent was used to dope the DESI spray solvent, increased charging was obtained for the UPLC-separated proteins. Strikingly, upon online electrolytic reduction, supercharged proteins (e.g., α-lactalbumin) showed even higher charging, which would be useful in top-down protein structure analysis as increased charges are known to promote protein ion dissociation. Also, the separation speed and sensitivity are enhanced by approximately 1~2 orders of magnitude by using UPLC for the LC/EC/MS platform, in comparison to the previously used high performance liquid chromatography (HPLC). This UPLC/EC/DESI-MS method combines the power of fast UPLC separation, fast electrochemical conversion and online MS structural analysis for a potentially valuable tool for proteomics research and bioanalysis. PMID:26307715

Electrical Conductivity of Molten DyCl3-NaCl and DyCl3-KCl Systems: An Approach to Structural Interpretations of Rare Earth Chloride Melts

NASA Astrophysics Data System (ADS)

Iwadate, Yasuhiko; Ohkubo, Takahiro

2017-11-01

Electrical conductivities (κs) of molten DyCl3-NaCl and DyCl3-KCl systems were estimated by measuring the impedances of each mixture melt at any temperature and/or frequency. The molar volumes (Vms) were measured by dilatometry and represented as a polynomial empirical equation of temperature and composition. Due to both the properties, the molar conductivities (Λms) were calculated and their temperature and/or composition dependences were discussed from the standpoint of structural features as well. The κs increased curvilinearly with increasing temperature across the whole composition ranges. This trend was also applied to the Λms which was fitted by an Arrhenius-type equation. The relationship of Λms with melt composition was studied and the Λms were found to decrease with increasing composition of DyCl3. These findings were interpreted based on the results of structural science so far reported, and finally, the relationship between Λms and the structures of pure rare earth chloride melts was discussed.

Automated Assignment of MS/MS Cleavable Cross-Links in Protein 3D-Structure Analysis

NASA Astrophysics Data System (ADS)

Götze, Michael; Pettelkau, Jens; Fritzsche, Romy; Ihling, Christian H.; Schäfer, Mathias; Sinz, Andrea

2015-01-01

CID-MS/MS cleavable cross-linkers hold an enormous potential for an automated analysis of cross-linked products, which is essential for conducting structural proteomics studies. The created characteristic fragment ion patterns can easily be used for an automated assignment and discrimination of cross-linked products. To date, there are only a few software solutions available that make use of these properties, but none allows for an automated analysis of cleavable cross-linked products. The MeroX software fills this gap and presents a powerful tool for protein 3D-structure analysis in combination with MS/MS cleavable cross-linkers. We show that MeroX allows an automatic screening of characteristic fragment ions, considering static and variable peptide modifications, and effectively scores different types of cross-links. No manual input is required for a correct assignment of cross-links and false discovery rates are calculated. The self-explanatory graphical user interface of MeroX provides easy access for an automated cross-link search platform that is compatible with commonly used data file formats, enabling analysis of data originating from different instruments. The combination of an MS/MS cleavable cross-linker with a dedicated software tool for data analysis provides an automated workflow for 3D-structure analysis of proteins. MeroX is available at www.StavroX.com .

LC-MS/MS-based approach for obtaining exposure estimates of metabolites in early clinical trials using radioactive metabolites as reference standards.

PubMed

Zhang, Donglu; Raghavan, Nirmala; Chando, Theodore; Gambardella, Janice; Fu, Yunlin; Zhang, Duxi; Unger, Steve E; Humphreys, W Griffith

2007-12-01

An LC-MS/MS-based approach that employs authentic radioactive metabolites as reference standards was developed to estimate metabolite exposures in early drug development studies. This method is useful to estimate metabolite levels in studies done with non-radiolabeled compounds where metabolite standards are not available to allow standard LC-MS/MS assay development. A metabolite mixture obtained from an in vivo source treated with a radiolabeled compound was partially purified, quantified, and spiked into human plasma to provide metabolite standard curves. Metabolites were analyzed by LC-MS/MS using the specific mass transitions and an internal standard. The metabolite concentrations determined by this approach were found to be comparable to those determined by valid LC-MS/MS assays. This approach does not requires synthesis of authentic metabolites or the knowledge of exact structures of metabolites, and therefore should provide a useful method to obtain early estimates of circulating metabolites in early clinical or toxicological studies.

Changes of Metabolomic Profile in Helianthus annuus under Exposure to Chromium(VI) Studied by capHPLC-ESI-QTOF-MS and MS/MS

PubMed Central

Gonzalez Ibarra, Alan Alexander; Wrobel, Kazimierz; Yanez Barrientos, Eunice; Corrales Escobosa, Alma Rosa; Gutierrez Corona, J. Felix; Enciso Donis, Israel

2017-01-01

The application of capHPLC-ESI-QTOF-MS and MS/MS to study the impact of Cr(VI) on metabolites profile in Helianthus annuus is reported. Germinated seeds were grown hydroponically in the presence of Cr(VI) (25 mgCr/L) and root extracts of the exposed and control plants were analyzed by untargeted metabolomic approach. The main goal was to detect which metabolite groups were mostly affected by Cr(VI) stress; two data analysis tools (ProfileAnalysis, Bruker, and online XCMS) were used under criteria of intensity threshold 5 · 104 cps, fold change ≥ 5, and p ≤ 0.01, yielding precursor ions. Molecular formulas were assigned based on data processing with two computational tools (SIRIUS and MS-Finder); annotation of candidate structures was performed by database search using CSI:FingerID and MS-Finder. Even though ultimate identification has not been achieved, it was demonstrated that secondary metabolism became activated under Cr(VI) stress. Among 42 candidate compounds returned from database search for seven molecular formulas, ten structures corresponded to isocoumarin derivatives and eleven were sesquiterpenes or sesquiterpene lactones; three benzofurans and four glycoside or pyrane derivatives of phenolic compounds were also suggested. To gain further insight on the effect of Cr(VI) in sunflower, isocoumarins and sesquiterpenes were selected as the target compounds for future study. PMID:29359067

[Structure of maxillary sinus mucous membrane under normal conditions and in odontogenic perforative sinusitis].

PubMed

Baĭdik, O D; Logvinov, S V; Zubarev, S G; Sysoliatin, P G; Gurin, A A

2011-01-01

Methods of light, electron microscopy and immunohistochemistry were used to study the samples of maxillary sinus (MS) mucous membrane (MM) under normal conditions and in odontogenic sinusitis. To study the normal structure, the samples were obtained at autopsy from 26 human corpses 12-24 hours after death. Electron microscopic and immunohistochemical study was performed on biopsies of grossly morphologically unchanged MS MM, obtained during the operations for retention cysts in 6 patients. MS MM in perforative sinusitis was studied using the biopsies obtained from 43 patients. The material is broken into 4 groups depending on perforative sinusitis duration. Under normal conditions, MS MM is lined with a pseudostratified columnar ciliated epithelium. Degenerative changes of ciliated epithelial cells were already detected at short time intervals after MS perforations and become apparent due to reduction of specific volume of mitochondria and, rough endoplasmic reticulum, and increase of nuclear-cytoplasmic ratio. In the globlet cells, the reduction of nuclear-cytoplasmic ratio was associated with the disturbance of the secretory product release. At time intervals exceeding 3 months, epithelium underwent metaplasia into simple cuboidal and stratified squamous keratinized, while in MS MM lamina propria, cellular infiltration was increased. CD4+ cell content in sinus MM gradually increased, while at late periods after perforation occurrence it decreased. Low CD4+ cell count within the epithelium and the absence of muromidase on the surface of MS MM was detected. With the increase of the time interval since MS perforation, the number of CD8+ and CD20+ cells in MS MM was found to increase.

Localized atrophy of the thalamus and slowed cognitive processing speed in MS patients.

PubMed

Bergsland, Niels; Zivadinov, Robert; Dwyer, Michael G; Weinstock-Guttman, Bianca; Benedict, Ralph Hb

2016-09-01

Deep gray matter (DGM) atrophy is common in multiple sclerosis (MS), but no studies have investigated surface-based structure changes over time with respect to healthy controls (HCs). Moreover, the relationship between cognition and the spatio-temporal evolution of DGM atrophy is poorly understood. To explore DGM structural differences between MS and HCs over time in relation to neuropsychological (NP) outcomes. The participants were 44 relapsing-remitting and 20 secondary progressive MS patients and 22 HCs. All were scanned using 3T magnetic resonance imaging (MRI) at baseline and 3-year follow-up. NP examination emphasized consensus standard tests of processing speed and memory. We performed both volumetric and shape analysis of DGM structures and assessed their relationships with cognition. Compared to HCs, MS patients presented with significantly smaller DGM volumes. For the thalamus and caudate, differences in shape were mostly localized along the lateral ventricles. NP outcomes were related to both volume and shape of the DGM structures. Over 3 years, decreased cognitive processing speed was related to localized atrophy on the anterior and superior surface of the left thalamus. These findings highlight the role of atrophy in the anterior nucleus of the thalamus and its relation to cognitive decline in MS. © The Author(s), 2015.

New Potential Biomarker for Methasterone Misuse in Human Urine by Liquid Chromatography Quadrupole Time of Flight Mass Spectrometry.

PubMed

Zhang, Jianli; Lu, Jianghai; Wu, Yun; Wang, Xiaobing; Xu, Youxuan; Zhang, Yinong; Wang, Yan

2016-09-24

In this study, methasterone urinary metabolic profiles were investigated by liquid chromatography quadrupole time of flight mass spectrometry (LC-QTOF-MS) in full scan and targeted MS/MS modes with accurate mass measurement. A healthy male volunteer was asked to take the drug and liquid-liquid extraction was employed to process urine samples. Chromatographic peaks for potential metabolites were hunted out with the theoretical [M - H](-) as a target ion in a full scan experiment and actual deprotonated ions were studied in targeted MS/MS experiment. Fifteen metabolites including two new sulfates (S1 and S2), three glucuronide conjugates (G2, G6 and G7), and three free metabolites (M2, M4 and M6) were detected for methasterone. Three metabolites involving G4, G5 and M5 were obtained for the first time in human urine samples. Owing to the absence of helpful fragments to elucidate the steroid ring structure of methasterone phase II metabolites, gas chromatography mass spectrometry (GC-MS) was employed to obtain structural information of the trimethylsilylated phase I metabolite released after enzymatic hydrolysis and the potential structure was inferred using a combined MS method. Metabolite detection times were also analyzed and G2 (18-nor-17β-hydroxymethyl-2α, 17α-dimethyl-androst-13-en-3α-ol-ξ-O-glucuronide) was thought to be new potential biomarker for methasterone misuse which can be detected up to 10 days.

Tandem mass spectrometry approach for the investigation of the steroidal metabolism: structure-fragmentation relationship (SFR) in anabolic steroids and their metabolites by ESI-MS/MS analysis.

PubMed

Musharraf, Syed Ghulam; Ali, Arslan; Khan, Naik Tameem; Yousuf, Maria; Choudhary, Muhammad Iqbal; Atta-ur-Rahman

2013-02-01

Electrospray ionization tandem mass spectrometry (ESI-MS/MS) was used to investigate the effect of different substitutions introduced during metabolism on fragmentation patterns of four anabolic steroids including methyltestosterone, methandrostenolone, cis-androsterone and adrenosterone, along with their metabolites. Collision-induced dissociation (CID) analysis was performed to correlate the major product ions of 19 steroids with structural features. The analysis is done to portray metabolic alteration, such as incorporation or reduction of double bonds, hydroxylations, and/or oxidation of hydroxyl moieties to keto functional group on steroidal skeleton which leads to drastically changed product ion spectra from the respective classes of steroids, therefore, making them difficult to identify. The comparative ESI-MS/MS study also revealed some characteristic peaks to differentiate different steroidal metabolites and can be useful for the unambiguous identification of anabolic steroids in biological fluid. Moreover, LC-ESI-MS/MS analysis of fermented extract of methyltestosterone, obtained by Macrophomina phaseolina was also investigated. Copyright © 2012 Elsevier Inc. All rights reserved.

MS2Analyzer: A Software for Small Molecule Substructure Annotations from Accurate Tandem Mass Spectra

PubMed Central

2015-01-01

Systematic analysis and interpretation of the large number of tandem mass spectra (MS/MS) obtained in metabolomics experiments is a bottleneck in discovery-driven research. MS/MS mass spectral libraries are small compared to all known small molecule structures and are often not freely available. MS2Analyzer was therefore developed to enable user-defined searches of thousands of spectra for mass spectral features such as neutral losses, m/z differences, and product and precursor ions from MS/MS spectra in MSP/MGF files. The software is freely available at http://fiehnlab.ucdavis.edu/projects/MS2Analyzer/. As the reference query set, 147 literature-reported neutral losses and their corresponding substructures were collected. This set was tested for accuracy of linking neutral loss analysis to substructure annotations using 19 329 accurate mass tandem mass spectra of structurally known compounds from the NIST11 MS/MS library. Validation studies showed that 92.1 ± 6.4% of 13 typical neutral losses such as acetylations, cysteine conjugates, or glycosylations are correct annotating the associated substructures, while the absence of mass spectra features does not necessarily imply the absence of such substructures. Use of this tool has been successfully demonstrated for complex lipids in microalgae. PMID:25263576

Efficient approach for the detection and identification of new androgenic metabolites by applying SRM GC-CI-MS/MS: a methandienone case study.

PubMed

Polet, Michael; Van Gansbeke, Wim; Van Eenoo, Peter; Deventer, Koen

2016-07-01

Identification of anabolic androgenic steroids (AAS) is a vital issue in doping control and toxicology, and searching for metabolites with longer detection times remains an important task. Recently, a gas chromatography chemical ionization triple quadrupole mass spectrometry (GC-CI-MS/MS) method was introduced, and CI, in comparison with electron ionization (EI), proved to be capable of increasing the sensitivity significantly. In addition, correlations between AAS structure and fragmentation behavior could be revealed. This enables the search for previously unknown but expected metabolites by selection of their predicted transitions. The combination of both factors allows the setup of an efficient approach to search for new metabolites. The approach uses selected reaction monitoring which is inherently more sensitive than full scan or precursor ion scan. Additionally, structural information obtained from the structure specific CI fragmentation pattern facilitates metabolite identification. The procedure was demonstrated by a methandienone case study. Its metabolites have been studied extensively in the past, and this allowed an adequate evaluation of the efficiency of the approach. Thirty three metabolites were detected, including all relevant previously discovered metabolites. In our study, the previously reported long-term metabolite (18-nor-17β-hydroxymethyl,17α-methyl-androst-1,4,13-trien-3-one) could be detected up to 26 days by using GC-CI-MS/MS. The study proves the validity of the approach to search for metabolites of new synthetic AAS and new long-term metabolites of less studied AAS and illustrates the increase in sensitivity by using CI. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Separation and characterization of unknown impurities and isomers in flomoxef sodium by LC-IT-TOF MS and study of their negative-ion fragmentation regularities.

PubMed

Yu, Xu; Wang, Fan; Li, Jiani; Shan, Weiguang; Zhu, Bingqi; Wang, Jian

2017-06-05

Thirteen unknown impurities in flomoxef sodium were separated and characterized by liquid chromatography coupled with high resolution ion trap/time-of-flight mass spectrometry (LC-IT-TOF MS)with positive and negative modes of electrospray ionization method for further improvement of official monographs in pharmacopoeias. The fragmentation patterns of impurities in flomoxef in the negative ion mode were studied in detail, and new negative-ion fragmentation regularities were discovered. Chromatographic separation was performed on a Kromasil C18 column (250mm×4.6mm, 5μm). The mobile phase consisted of (A) ammonium formate aqueous solution (10mM)-methanol (84:16, v/v) and (B) ammonium formate aqueous solution (10mM)-methanol (47:53, v/v). In order to determine the m/z values of the molecular ions and formulas of all detected impurities, full scan LC-MS in both positive and negative ion modes was firstly executed to obtain the m/z value of the molecules. Then LC-MS 2 and LC-MS 3 were carried out on target compounds to obtain as much structural information as possible. Complete fragmentation patterns of impurities were studied and used to obtain information about the structures of these impurities. Structures of thirteen unknown degradation products in flomoxef sodium were deduced based on the high resolution MS n data with both positive and negative modes. The forming mechanisms of degradation products in flomoxef sodium were also studied. Copyright © 2017. Published by Elsevier B.V.

Automated software-guided identification of new buspirone metabolites using capillary LC coupled to ion trap and TOF mass spectrometry.

PubMed

Fandiño, Anabel S; Nägele, Edgar; Perkins, Patrick D

2006-02-01

The identification and structure elucidation of drug metabolites is one of the main objectives in in vitro ADME studies. Typical modern methodologies involve incubation of the drug with subcellular fractions to simulate metabolism followed by LC-MS/MS or LC-MS(n) analysis and chemometric approaches for the extraction of the metabolites. The objective of this work was the software-guided identification and structure elucidation of major and minor buspirone metabolites using capillary LC as a separation technique and ion trap MS(n) as well as electrospray ionization orthogonal acceleration time-of-flight (ESI oaTOF) mass spectrometry as detection techniques. Buspirone mainly underwent hydroxylation, dihydroxylation and N-oxidation in S9 fractions in the presence of phase I co-factors and the corresponding glucuronides were detected in the presence of phase II co-factors. The use of automated ion trap MS/MS data-dependent acquisition combined with a chemometric tool allowed the detection of five small chromatographic peaks of unexpected metabolites that co-eluted with the larger chromatographic peaks of expected metabolites. Using automatic assignment of ion trap MS/MS fragments as well as accurate mass measurements from an ESI oaTOF mass spectrometer, possible structures were postulated for these metabolites that were previously not reported in the literature. Copyright 2006 John Wiley & Sons, Ltd.

Extension of the analytical window for characterizing aromatic compounds in oils using a comprehensive suite of high-resolution mass spectrometry techniques and double bond equivalence versus carbon number plot

USGS Publications Warehouse

Cho, Yunju; Birdwell, Justin E.; Hur, Manhoi; Lee, Joonhee; Kim, Byungjoo; Kim, Sunghwan

2017-01-01

In this study, comprehensive two-dimensional (2D) gas chromatography–mass spectrometry (GC–MS), atmospheric pressure photoionization (APPI) quadrupole-Orbitrap mass spectrometry (MS), and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) were used to study the aromatic fractions of crude oil and oil shale pyrolysates (shale oils). The collected data were compared and combined in the double bond equivalence (DBE) versus carbon number plot to obtain a more complete understanding of the composition of the oil fractions. The numbers of peaks observed by each technique followed the order 2D GC–MS < Orbitrap MS < FT-ICR MS. The class distributions observed by Orbitrap MS and FT-ICR MS were similar to each other but different from that observed by 2D GC–MS. The DBE and carbon number distributions of the 2D GC–MS and Orbitrap MS data were similar for crude oil aromatics. The FT-ICR MS plots of DBE and carbon number showed an extended range of higher values relative to the other methods. For the aromatic fraction of an oil shale pyrolysate generated by the Fischer assay, only a few nitrogen-containing compounds were observed by 2D GC–MS but a large number of these compounds were detected by Orbitrap MS and FT-ICR MS. This comparison clearly shows that the data obtained from these three techniques can be combined to more completely characterize oil composition. The data obtained by Orbitrap MS and FT-ICR MS agreed well with one another, and the combined DBE versus carbon number plot provided more complete coverage of compounds present in the fractions. In addition, the chemical structure information provided by 2D GC–MS could be matched with the chemical formulas in the DBE versus carbon number plots, providing information not available in ultrahigh-resolution MS results. It was therefore concluded that the combination of 2D GC–MS, Orbitrap MS, and FT-ICR MS in the DBE versus carbon number space facilitates structural assignment of heavy oil components.

Use of ion-mobility mass spectrometry (IMS-MS) to map polyoxometalate Keplerate clusters and their supramolecular assemblies.

PubMed

Robbins, Philip J; Surman, Andrew J; Thiel, Johannes; Long, De-Liang; Cronin, Leroy

2013-03-07

We present the high-resolution (HRES-MS) and ion-mobility (IMS-MS) mass spectrometry studies of icosahedral nanoscale polyoxometalate-based {L(30)}{(Mo)Mo(5)} Keplerate clusters, and demonstrate the use of IMS-MS to resolve and map intact nanoclusters, and its potential for the discovery of new structures, in this case the first gas phase observation of 'proto-clustering' of higher order Keplerate supramolecular aggregates.

Gas chromatography/chemical ionization triple quadrupole mass spectrometry analysis of anabolic steroids: ionization and collision-induced dissociation behavior.

PubMed

Polet, Michael; Van Gansbeke, Wim; Van Eenoo, Peter; Deventer, Koen

2016-02-28

The detection of new anabolic steroid metabolites and new designer steroids is a challenging task in doping analysis. Switching from electron ionization gas chromatography triple quadrupole mass spectrometry (GC/EI-MS/MS) to chemical ionization (CI) has proven to be an efficient way to increase the sensitivity of GC/MS/MS analyses and facilitate the detection of anabolic steroids. CI also extends the possibilities of GC/MS/MS analyses as the molecular ion is retained in its protonated form due to the softer ionization. In EI it can be difficult to find previously unknown but expected metabolites due to the low abundance or absence of the molecular ion and the extensive (and to a large extent unpredictable) fragmentation. The main aim of this work was to study the CI and collision-induced dissociation (CID) behavior of a large number of anabolic androgenic steroids (AAS) as their trimethylsilyl derivatives in order to determine correlations between structures and CID fragmentation. Clarification of these correlations is needed for the elucidation of structures of unknown steroids and new metabolites. The ionization and CID behavior of 65 AAS have been studied using GC/CI-MS/MS with ammonia as the reagent gas. Glucuronidated AAS reference standards were first hydrolyzed to obtain their free forms. Afterwards, all the standards were derivatized to their trimethylsilyl forms. Full scan and product ion scan analyses were used to examine the ionization and CID behavior. Full scan and product ion scan analyses revealed clear correlations between AAS structure and the obtained mass spectra. These correlations were confirmed by analysis of multiple hydroxylated, methylated, chlorinated and deuterated analogs. AAS have been divided into three groups according to their ionization behavior and into seven groups according to their CID behavior. Correlations between fragmentation and structure were revealed and fragmentation pathways were postulated. Copyright © 2016 John Wiley & Sons, Ltd.

Whole-Genome Analysis of a Novel Fish Reovirus (MsReV) Discloses Aquareovirus Genomic Structure Relationship with Host in Saline Environments.

PubMed

Chen, Zhong-Yuan; Gao, Xiao-Chan; Zhang, Qi-Ya

2015-08-03

Aquareoviruses are serious pathogens of aquatic animals. Here, genome characterization and functional gene analysis of a novel aquareovirus, largemouth bass Micropterus salmoides reovirus (MsReV), was described. It comprises 11 dsRNA segments (S1-S11) covering 24,024 bp, and encodes 12 putative proteins including the inclusion forming-related protein NS87 and the fusion-associated small transmembrane (FAST) protein NS22. The function of NS22 was confirmed by expression in fish cells. Subsequently, MsReV was compared with two representative aquareoviruses, saltwater fish turbot Scophthalmus maximus reovirus (SMReV) and freshwater fish grass carp reovirus strain 109 (GCReV-109). MsReV NS87 and NS22 genes have the same structure and function with those of SMReV, whereas GCReV-109 is either missing the coiled-coil region in NS79 or the gene-encoding NS22. Significant similarities are also revealed among equivalent genome segments between MsReV and SMReV, but a difference is found between MsReV and GCReV-109. Furthermore, phylogenetic analysis showed that 13 aquareoviruses could be divided into freshwater and saline environments subgroups, and MsReV was closely related to SMReV in saline environments. Consequently, these viruses from hosts in saline environments have more genomic structural similarities than the viruses from hosts in freshwater. This is the first study of the relationships between aquareovirus genomic structure and their host environments.

Isotope-labeled cross-linkers and Fourier transform ion cyclotron resonance mass spectrometry for structural analysis of a protein/peptide complex.

PubMed

Ihling, Christian; Schmidt, Andreas; Kalkhof, Stefan; Schulz, Daniela M; Stingl, Christoph; Mechtler, Karl; Haack, Michael; Beck-Sickinger, Annette G; Cooper, Dermot M F; Sinz, Andrea

2006-08-01

For structural studies of proteins and their complexes, chemical cross-linking combined with mass spectrometry presents a promising strategy to obtain structural data of protein interfaces from low quantities of proteins within a short time. We explore the use of isotope-labeled cross-linkers in combination with Fourier transform ion cyclotron resonance (FTICR) mass spectrometry for a more efficient identification of cross-linker containing species. For our studies, we chose the calcium-independent complex between calmodulin and a 25-amino acid peptide from the C-terminal region of adenylyl cyclase 8 containing an "IQ-like motif." Cross-linking reactions between calmodulin and the peptide were performed in the absence of calcium using the amine-reactive, isotope-labeled (d0 and d4) cross-linkers BS3 (bis[sulfosuccinimidyl]suberate) and BS2G (bis[sulfosuccinimidyl]glutarate). Tryptic in-gel digestion of excised gel bands from covalently cross-linked complexes resulted in complicated peptide mixtures, which were analyzed by nano-HPLC/nano-ESI-FTICR mass spectrometry. In cases where more than one reactive functional group, e.g., amine groups of lysine residues, is present in a sequence stretch, MS/MS analysis is a prerequisite for unambiguously identifying the modified residues. MS/MS experiments revealed two lysine residues in the central alpha-helix of calmodulin as well as three lysine residues both in the C-terminal and N-terminal lobes of calmodulin to be cross-linked with one single lysine residue of the adenylyl cyclase 8 peptide. Further cross-linking studies will have to be conducted to propose a structural model for the calmodulin/peptide complex, which is formed in the absence of calcium. The combination of using isotope-labeled cross-linkers, determining the accurate mass of intact cross-linked products, and verifying the amino acid sequences of cross-linked species by MS/MS presents a convenient approach that offers the perspective to obtain structural data of protein assemblies within a few days.

A Novel MS-Cleavable Azo Cross-Linker for Peptide Structure Analysis by Free Radical Initiated Peptide Sequencing (FRIPS)

NASA Astrophysics Data System (ADS)

Iacobucci, Claudio; Hage, Christoph; Schäfer, Mathias; Sinz, Andrea

2017-10-01

The chemical cross-linking/mass spectrometry (MS) approach is a growing research field in structural proteomics that allows gaining insights into protein conformations. It relies on creating distance constraints between cross-linked amino acid side chains that can further be used to derive protein structures. Currently, the most urgent task for designing novel cross-linking principles is an unambiguous and automated assignment of the created cross-linked products. Here, we introduce the homobifunctional, amine-reactive, and water soluble cross-linker azobisimidoester (ABI) as a prototype of a novel class of cross-linkers. The ABI-linker possesses an innovative modular scaffold combining the benefits of collisional activation lability with open shell chemistry. This MS-cleavable cross-linker can be efficiently operated via free radical initiated peptide sequencing (FRIPS) in positive ionization mode. Our proof-of-principle study challenges the gas phase behavior of the ABI-linker for the three amino acids, lysine, leucine, and isoleucine, as well as the model peptide thymopentin. The isomeric amino acids leucine and isoleucine could be discriminated by their characteristic side chain fragments. Collisional activation experiments were conducted via positive electrospray ionization (ESI) on two Orbitrap mass spectrometers. The ABI-mediated formation of odd electron product ions in MS/MS and MS3 experiments was evaluated and compared with a previously described azo-based cross-linker. All cross-linked products were amenable to automated analysis by the MeroX software, underlining the future potential of the ABI-linker for structural proteomics studies. [Figure not available: see fulltext.

Characterization of physalins and fingerprint analysis for the quality evaluation of Physalis alkekengi L. var. franchetii by ultra-performance liquid chromatography combined with diode array detection and electrospray ionization tandem mass spectrometry.

PubMed

Zheng, Yunliang; Luan, Lianjun; Chen, Yong; Ren, Yiping; Wu, Yongjiang

2012-12-01

Physalins are important bioactive compounds from genus Physalis. They often occur as isomers, which makes the structural elucidation difficult. In the present study, the fragmentation behavior and UV characteristics of seven physalins from genus Physalis were firstly investigated using electrospray ionization tandem mass spectrometry (ESI-MS/MS) and diode array detection (DAD). Combined with ultra-performance liquid chromatography (UPLC) and DAD, the established approach to the structural identification of physalins by ESI-MS/MS was then applied to the analysis of Physalis alkekengi L. According to the UPLC retention behavior, the diagnostic UV spectra and the molecular structural information provided by MS/MS spectra, about 19 fingerprint peaks were identified, including 14 physalins and 5 other compounds. Finally, the established fingerprint method was applied to the analysis of 31 P. alkekengi L. samples collected from different locations, which reflected their similar chemical constituent properties. The proposed method provides a scientific and technical platform to the herbal industry for quality control and safety assurance of herbal preparations that contain this class of physalins. Copyright © 2012 Elsevier B.V. All rights reserved.

Specificity enhancement by electrospray ionization multistage mass spectrometry--a valuable tool for differentiation and identification of 'V'-type chemical warfare agents.

PubMed

Weissberg, Avi; Tzanani, Nitzan; Dagan, Shai

2013-12-01

The use of chemical warfare agents has become an issue of emerging concern. One of the challenges in analytical monitoring of the extremely toxic 'V'-type chemical weapons [O-alkyl S-(2-dialkylamino)ethyl alkylphosphonothiolates] is to distinguish and identify compounds of similar structure. MS analysis of these compounds reveals mostly fragment/product ions representing the amine-containing residue. Hence, isomers or derivatives with the same amine residue exhibit similar mass spectral patterns in both classical EI/MS and electrospray ionization-MS, leading to unavoidable ambiguity in the identification of the phosphonate moiety. A set of five 'V'-type agents, including O-ethyl S-(2-diisopropylamino)ethyl methylphosphonothiolate (VX), O-isobutyl S-(2-diethylamino)ethyl methylphosphonothiolate (RVX) and O-ethyl S-(2-diethylamino)ethyl methylphosphonothiolate (VM) were studied by liquid chromatography/electrospray ionization/MS, utilizing a QTRAP mass detector. MS/MS enhanced product ion scans and multistage MS(3) experiments were carried out. Based on the results, possible fragmentation pathways were proposed, and a method for the differentiation and identification of structural isomers and derivatives of 'V'-type chemical warfare agents was obtained. MS/MS enhanced product ion scans at various collision energies provided information-rich spectra, although many of the product ions obtained were at low abundance. Employing MS(3) experiments enhanced the selectivity for those low abundance product ions and provided spectra indicative of the different phosphonate groups. Study of the fragmentation pathways, revealing some less expected structures, was carried out and allowed the formulation of mechanistic rules and the determination of sets of ions typical of specific groups, for example, methylphosphonothiolates versus ethylphosphonothiolates. The new group-specific ions elucidated in this work are also useful for screening unknown 'V'-type agents and related compounds, utilizing precursor ion scan experiments. Copyright © 2013 John Wiley & Sons, Ltd.

Quantitative Protein Topography Analysis and High-Resolution Structure Prediction Using Hydroxyl Radical Labeling and Tandem-Ion Mass Spectrometry (MS)*

PubMed Central

Kaur, Parminder; Kiselar, Janna; Yang, Sichun; Chance, Mark R.

2015-01-01

Hydroxyl radical footprinting based MS for protein structure assessment has the goal of understanding ligand induced conformational changes and macromolecular interactions, for example, protein tertiary and quaternary structure, but the structural resolution provided by typical peptide-level quantification is limiting. In this work, we present experimental strategies using tandem-MS fragmentation to increase the spatial resolution of the technique to the single residue level to provide a high precision tool for molecular biophysics research. Overall, in this study we demonstrated an eightfold increase in structural resolution compared with peptide level assessments. In addition, to provide a quantitative analysis of residue based solvent accessibility and protein topography as a basis for high-resolution structure prediction; we illustrate strategies of data transformation using the relative reactivity of side chains as a normalization strategy and predict side-chain surface area from the footprinting data. We tested the methods by examination of Ca+2-calmodulin showing highly significant correlations between surface area and side-chain contact predictions for individual side chains and the crystal structure. Tandem ion based hydroxyl radical footprinting-MS provides quantitative high-resolution protein topology information in solution that can fill existing gaps in structure determination for large proteins and macromolecular complexes. PMID:25687570

Structure-based manual screening and automatic networking for systematically exploring sansanmycin analogues using high performance liquid chromatography tandem mass spectroscopy.

PubMed

Jiang, Zhi-Bo; Ren, Wei-Cong; Shi, Yuan-Yuan; Li, Xing-Xing; Lei, Xuan; Fan, Jia-Hui; Zhang, Cong; Gu, Ren-Jie; Wang, Li-Fei; Xie, Yun-Ying; Hong, Bin

2018-05-18

Sansanmycins (SS), one of several known uridyl peptide antibiotics (UPAs) possessing a unique chemical scaffold, showed a good inhibitory effect on the highly refractory pathogens Pseudomonas aeruginosa and Mycobacterium tuberculosis, especially on the multi-drug resistant M. tuberculosis. This study employed high performance liquid chromatography-mass spectrometry detector (HPLC-MSD) ion trap and LTQ orbitrap tandem mass spectrometry (MS/MS) to explore sansanmycin analogues manually and automatically by re-analysis of the Streptomyces sp. SS fermentation broth. The structure-based manual screening method, based on analysis of the fragmentation pathway of known UPAs and on comparisons of the MS/MS spectra with that of sansanmycin A (SS-A), resulted in identifying twenty sansanmycin analogues, including twelve new structures (1-12). Furthermore, to deeply explore sansanmycin analogues, we utilized a GNPS based molecular networking workflow to re-analyze the HPLC-MS/MS data automatically. As a result, eight more new sansanmycins (13-20) were discovered. Compound 1 was discovered to lose two amino acids of residue 1 (AA 1 ) and (2S, 3S)-N 3 -methyl-2,3-diamino butyric acid (DABA) from the N-terminus, and compounds 6, 11 and 12 were found to contain a 2',3'-dehydrated 4',5'-enamine-3'-deoxyuridyl moiety, which have not been reported before. Interestingly, three trace components with novel 5,6-dihydro-5'-aminouridyl group (16-18) were detected for the first time in the sansanmycin-producing strain. Their structures were primarily determined by detail analysis of the data from MS/MS. Compounds 8 and 10 were further confirmed by nuclear magnetic resonance (NMR) data, which proved the efficiency and accuracy of the method of HPLC-MS/MS for exploration of novel UPAs. Comparing to manual screening, the networking method can provide systematic visualization results. Manual screening and networking method may complement with each other to facilitate the mining of novel UPAs. Copyright © 2018 Elsevier B.V. All rights reserved.

Characterization of Glycan Structures of Chondroitin Sulfate-Glycopeptides Facilitated by Sodium Ion-Pairing and Positive Mode LC-MS/MS

NASA Astrophysics Data System (ADS)

Nilsson, Jonas; Noborn, Fredrik; Gomez Toledo, Alejandro; Nasir, Waqas; Sihlbom, Carina; Larson, Göran

2017-02-01

Purification and liquid chromatography-tandem mass spectrometry (LC-MS/MS) characterization of glycopeptides, originating from protease digests of glycoproteins, enables site-specific analysis of protein N- and O-glycosylations. We have described a protocol to enrich, hydrolyze by chondroitinase ABC, and characterize chondroitin sulfate-containing glycopeptides (CS-glycopeptides) using positive mode LC-MS/MS. The CS-glycopeptides, originating from the Bikunin proteoglycan of human urine samples, had ΔHexAGalNAcGlcAGalGalXyl- O-Ser hexasaccharide structure and were further substituted with 0-3 sulfate and 0-1 phosphate groups. However, it was not possible to exactly pinpoint sulfate attachment residues, for protonated precursors, due to extensive fragmentation of sulfate groups using high-energy collision induced dissociation (HCD). To circumvent the well-recognized sulfate instability, we now introduced Na+ ions to form sodiated precursors, which protected sulfate groups from decomposition and facilitated the assignment of sulfate modifications. Sulfate groups were pinpointed to both Gal residues and to the GalNAc of the hexasaccharide structure. The intensities of protonated and sodiated saccharide oxonium ions were very prominent in the HCD-MS2 spectra, which provided complementary structural analysis of sulfate substituents of CS-glycopeptides. We have demonstrated a considerable heterogeneity of the bikunin CS linkage region. The realization of these structural variants should be beneficial in studies aimed at investigating the importance of the CS linkage region with regards to the biosynthesis of CS and potential interactions to CS binding proteins. Also, the combined use of protonated and sodiated precursors for positive mode HCD fragmentation analysis will likely become useful for additional classes of sulfated glycopeptides.

Profiling and characterization of sialylated N-glycans by 2D-HPLC (HIAX/PGC) with online orbitrap MS/MS and offline MSn.

PubMed

Hanneman, Andrew J S; Strand, James; Huang, Chi-Ting

2014-02-01

Glycosylation is a critical parameter used to evaluate protein quality and consistency. N-linked glycan profiling is fundamental to the support of biotherapeutic protein manufacturing from early stage process development through drug product commercialization. Sialylated glycans impact the serum half-life of receptor-Fc fusion proteins (RFPs), making their quality and consistency a concern during the production of fusion proteins. Here, we describe an analytical approach providing both quantitative profiling and in-depth mass spectrometry (MS)-based structural characterization of sialylated RFP N-glycans. Aiming to efficiently link routine comparability studies with detailed structural characterization, an integrated workflow was implemented employing fluorescence detection, online positive and negative ion tandem mass spectrometry (MS/MS), and offline static nanospray ionization-sequential mass spectrometry (NSI-MS(n)). For routine use, high-performance liquid chromatography profiling employs established fluorescence detection of 2-aminobenzoic acid derivatives (2AA) and hydrophilic interaction anion-exchange chromatography (HIAX) charge class separation. Further characterization of HIAX peak fractions is achieved by online (-) ion orbitrap MS/MS, offering the advantages of high mass accuracy and data-dependent MS/MS. As required, additional characterization uses porous graphitized carbon in the second chromatographic dimension to provide orthogonal (+) ion MS/MS spectra and buffer-free liquid chromatography peak eluants that are optimum for offline (+)/(-) NSI-MS(n) investigations to characterize low-abundance species and specific moieties including O-acetylation and sulfation. © 2013 Wiley Periodicals, Inc. and the American Pharmacists Association.

Oxidation of danofloxacin by free chlorine-kinetic study, structural identification of by-products by LC-MS/MS and potential toxicity of by-products using in silico test.

PubMed

Yassine, Montaha; Rifai, Ahmad; Doumyati, Samah; Trivella, Aurélien; Mazellier, Patrick; Budzinski, Hélène; Al Iskandarani, Mohamad

2017-03-01

In this study, we aimed to investigate the kinetics and the mechanism of reaction of the fluoroquinolone antibacterial danofloxacin (DANO) by free available chlorine (FAC) during water chlorination process. Kinetic study was thus performed at pH 7.2, 20 °C in the presence of an excess of total chlorine. Under these experimental conditions, a second-order reaction rate constant (first-order relative to DANO concentration and first-order relative to FAC concentration) was evaluated to k~1446 M -1  s -1 . Five degradation products were identified at different reaction times. Their structures were investigated by using fragmentations obtained at different CID collision energies in MS/MS experiments. Moreover, the toxicity of the proposed structures was predicted by using T.E.S.T. The results indicated that all by-products may have a developmental toxicity. The oral rat LD 50 concentration was predicted to be lower than that of DANO. Furthermore, two degradation compounds presented a concentration level for fathead minnow LC 50 (96 h) lower than that of DANO and presented toxicity for the marine animals.

Analysis of a series of chlorogenic acid isomers using differential ion mobility and tandem mass spectrometry.

PubMed

Willems, Jamie L; Khamis, Mona M; Mohammed Saeid, Waleed; Purves, Randy W; Katselis, George; Low, Nicholas H; El-Aneed, Anas

2016-08-24

Chlorogenic acids are among the most abundant phenolics found in the human diet. Of these, the mono-caffeoylquinic acids are the predominant phenolics found in fruits, such as apples and pears, and products derived from them. In this research, a comprehensive study of the electrospray ionization (ESI) tandem mass spectrometric (MS/MS) dissociation behavior of the three most common mono-caffeoylquinic acids, namely 5-O-caffeoylquinic acid (5-CQA), 3-O-caffeoylquinic acid (3-CQA) and 4-O-caffeoylquinic acid (4-CQA), were determined using both positive and negative ionization. All proposed structures of the observed product ions were confirmed with second-generation MS(3) experiments. Similarities and differences between the dissociation pathways in the positive and negative ion modes are discussed, confirming the proposed structures and the established MS/MS fingerprints. MS/MS dissociation was primarily driven via the cleavage of the ester bond linking the quinic acid moiety to the caffeic acid moiety within tested molecules. Despite being structural isomers with the same m/z values and dissociation behaviors, the MS/MS data in the negative ion mode was able to differentiate the three isomers based on ion intensity for the major product ions, observed at m/z 191, 179 and 173. This differentiation was consistent among various MS instruments. In addition, ESI coupled with high-field asymmetric waveform ion mobility spectrometry-mass spectrometry (ESI-FAIMS-MS) was employed for the separation of these compounds for the first time. By combining MS/MS data and differential ion mobility, a method for the separation and identification of mono-caffeoylquinic in apple/pear juice samples was developed with a run time of less than 1 min. It is envisaged that this methodology could be used to identify pure juices based on their chlorogenic acid profile (i.e., metabolomics), and could also be used to detect juice-to-juice adulteration (e.g., apple juice addition to pear juice). Copyright © 2016 Elsevier B.V. All rights reserved.

Accurate Identification of Unknown and Known Metabolic Mixture Components by Combining 3D NMR with Fourier Transform Ion Cyclotron Resonance Tandem Mass Spectrometry.

PubMed

Wang, Cheng; He, Lidong; Li, Da-Wei; Bruschweiler-Li, Lei; Marshall, Alan G; Brüschweiler, Rafael

2017-10-06

Metabolite identification in metabolomics samples is a key step that critically impacts downstream analysis. We recently introduced the SUMMIT NMR/mass spectrometry (MS) hybrid approach for the identification of the molecular structure of unknown metabolites based on the combination of NMR, MS, and combinatorial cheminformatics. Here, we demonstrate the feasibility of the approach for an untargeted analysis of both a model mixture and E. coli cell lysate based on 2D/3D NMR experiments in combination with Fourier transform ion cyclotron resonance MS and MS/MS data. For 19 of the 25 model metabolites, SUMMIT yielded complete structures that matched those in the mixture independent of database information. Of those, seven top-ranked structures matched those in the mixture, and four of those were further validated by positive ion MS/MS. For five metabolites, not part of the 19 metabolites, correct molecular structural motifs could be identified. For E. coli, SUMMIT MS/NMR identified 20 previously known metabolites with three or more 1 H spins independent of database information. Moreover, for 15 unknown metabolites, molecular structural fragments were determined consistent with their spin systems and chemical shifts. By providing structural information for entire metabolites or molecular fragments, SUMMIT MS/NMR greatly assists the targeted or untargeted analysis of complex mixtures of unknown compounds.

Objective Sleep Structure and Cardiovascular Risk Factors in the General Population: The HypnoLaus Study

PubMed Central

Haba-Rubio, José; Marques-Vidal, Pedro; Andries, Daniela; Tobback, Nadia; Preisig, Martin; Vollenweider, Peter; Waeber, Gérard; Luca, Gianina; Tafti, Mehdi; Heinzer, Raphaël

2015-01-01

Study Objectives: To evaluate the association between objective sleep measures and metabolic syndrome (MS), hypertension, diabetes, and obesity. Design: Cross-sectional study. Setting: General population sample. Participants: There were 2,162 patients (51.2% women, mean age 58.4 ± 11.1). Interventions: Patients were evaluated for hypertension, diabetes, overweight/obesity, and MS, and underwent a full polysomnography (PSG). Measurements and Results: PSG measured variables included: total sleep time (TST), percentage and time spent in slow wave sleep (SWS) and in rapid eye movement (REM) sleep, sleep efficiency and arousal index (ArI). In univariate analyses, MS was associated with decreased TST, SWS, REM sleep, and sleep efficiency, and increased ArI. After adjustment for age, sex, smoking, alcohol, physical activity, drugs that affect sleep and depression, the ArI remained significantly higher, but the difference disappeared in patients without significant sleep disordered breathing (SDB). Differences in sleep structure were also found according to the presence or absence of hypertension, diabetes, and overweight/obesity in univariate analysis. However, these differences were attenuated after multivariate adjustment and after excluding subjects with significant SDB. Conclusions: In this population-based sample we found significant associations between sleep structure and metabolic syndrome (MS), hypertension, diabetes, and obesity. However, these associations were cancelled after multivariate adjustment. We conclude that normal variations in sleep contribute little if any to MS and associated disorders. Citation: Haba-Rubio J, Marques-Vidal P, Andries D, Tobback N, Preisig M, Vollenweider P, Waeber G, Luca G, Tafti M, Heinzer R. Objective sleep structure and cardiovascular risk factors in the general population: the HypnoLaus study. SLEEP 2015;38(3):391–400. PMID:25325467

The diverse and expanding role of mass spectrometry in structural and molecular biology.

PubMed

Lössl, Philip; van de Waterbeemd, Michiel; Heck, Albert Jr

2016-12-15

The emergence of proteomics has led to major technological advances in mass spectrometry (MS). These advancements not only benefitted MS-based high-throughput proteomics but also increased the impact of mass spectrometry on the field of structural and molecular biology. Here, we review how state-of-the-art MS methods, including native MS, top-down protein sequencing, cross-linking-MS, and hydrogen-deuterium exchange-MS, nowadays enable the characterization of biomolecular structures, functions, and interactions. In particular, we focus on the role of mass spectrometry in integrated structural and molecular biology investigations of biological macromolecular complexes and cellular machineries, highlighting work on CRISPR-Cas systems and eukaryotic transcription complexes. © 2016 The Authors. Published under the terms of the CC BY NC ND 4.0 license.

Reductive chemical release of N-glycans as 1-amino-alditols and subsequent 9-fluorenylmethyloxycarbonyl labeling for MS and LC/MS analysis.

PubMed

Wang, Chengjian; Qiang, Shan; Jin, Wanjun; Song, Xuezheng; Zhang, Ying; Huang, Linjuan; Wang, Zhongfu

2018-06-06

Glycoproteins play pivotal roles in a series of biological processes and their glycosylation patterns need to be structurally and functionally characterized. However, the lack of versatile methods to release N-glycans as functionalized forms has been undermining glycomics studies. Here a novel method is developed for dissociation of N-linked glycans from glycoproteins for analysis by MS and online LC/MS. This new method employs aqueous ammonia solution containing NaBH 3 CN as the reaction medium to release glycans from glycoproteins as 1-amino-alditol forms. The released glycans are conveniently labeled with 9-fluorenylmethyloxycarbonyl (Fmoc) and analyzed by ESI-MS and online LC/MS. Using the method, the neutral and acidic N-glycans were successfully released without peeling degradation of the core α-1,3-fucosylated structure or detectable de-N-acetylation, revealing its general applicability to various types of N-glycans. The Fmoc-derivatized N-glycans derived from chicken ovalbumin, Fagopyrum esculentum Moench Pollen and FBS were successfully analyzed by online LC/MS to distinguish isomers. The 1-amino-alditols were also permethylated to form quaternary ammonium cations at the reducing end, which enhance the MS sensitivity and are compatible with sequential multi-stage mass spectrometry (MS n ) fragmentation for glycan sequencing. The Fmoc-labeled N-glycans were further permethylated to produce methylated carbamates for determination of branches and linkages by sequential MS n fragmentation. N-Glycosylation represents one of the most common post-translational modification forms and plays pivotal roles in the structural and functional regulation of proteins in various biological activities, relating closely to human health and diseases. As a type of informational molecule, the N-glycans of glycoproteins participate directly in the molecular interactions between glycan epitopes and their corresponding protein receptors. Detailed structural and functional characterization of different types of N-glycans is essential for understanding the functional mechanisms of many biological activities and the pathologies of many diseases. Here we describe a simple, versatile method to indistinguishably release all types of N-glycans as functionalized forms without remarkable side reactions, enabling convenient, rapid analysis and preparation of released N-glycans from various complex biological samples. It is very valuable for studies on the complicated structure-function relationship of N-glycans, as well as for the search of N-glycan biomarkers of some major diseases and N-glycan related targets of some drugs. Copyright © 2018. Published by Elsevier B.V.

Mass Spectrometry as a Powerful Analytical Technique for the Structural Characterization of Synthesized and Natural Products

NASA Astrophysics Data System (ADS)

Es-Safi, Nour-Eddine; Essassi, El Mokhtar; Massoui, Mohamed; Banoub, Joseph

Mass spectrometry is an important tool for the identification and structural elucidation of natural and synthesized compounds. Its high sensitivity and the possibility of coupling liquid chromatography with mass spectrometry detection make it a technique of choice for the investigation of complex mixtures like raw natural extracts. The mass spectrometer is a universal detector that can achieve very high sensitivity and provide information on the molecular mass. More detailed information can be subsequently obtained by resorting to collision-induced dissociation tandem mass spectrometry (CID-MS/MS). In this review, the application of mass spectrometric techniques for the identification of natural and synthetic compounds is presented. The gas-phase fragmentation patterns of a series of four natural flavonoid glycosides, three synthesized benzodiazepines and two synthesized quinoxalinone derivatives were investigated using electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry techniques. Exact accurate masses were measured using a modorate resolution quadrupole orthogonal time-of-flight QqTOF-MS/MS hybrid mass spectrometer instrument. Confirmation of the molecular masses and the chemical structures of the studied compounds were achieved by exploring the gas-phase breakdown routes of the ionized molecules. This was rationalized by conducting low-energy collision CID-MS/MS analyses (product ion- and precursor ion scans) using a conventional quadrupole hexapole-quadrupole (QhQ) tandem mass spectrometer.

Mass spectrometry and renal calculi

PubMed Central

Purcarea, VL; Sisu, I; Sisu, E

2010-01-01

The present review represents a concise and complete survey of the literature covering 2004–2009, concerning the mass spectrometric techniques involved in the structural investigation of renal calculi. After a short presentation of the fundamental mass spectrometric techniques (MALDI–TOF, QTOF, MS–MS) as well as hyphenated methods (GC–MS, LC–MS, CE–MS), an extensive study of the urinary proteome analysis as well as the detection and quantification by mass spectrometry of toxins, drugs and metabolites from renal calculi is presented. PMID:20968197

Structural abnormalities and altered regional brain activity in multiple sclerosis with simple spinal cord involvement.

PubMed

Yin, Ping; Liu, Yi; Xiong, Hua; Han, Yongliang; Sah, Shambhu Kumar; Zeng, Chun; Wang, Jingjie; Li, Yongmei

2018-02-01

To assess the changes of the structural and functional abnormalities in multiple sclerosis with simple spinal cord involvement (MS-SSCI) by using resting-state functional MRI (RS-fMRI), voxel based morphology (VBM) and diffusion tensor tractography. The amplitude of low-frequency fluctuation (ALFF) of 22 patients with MS-SSCI and 22 healthy controls (HCs) matched for age, gender and education were compared by using RS-fMRI. We also compared the volume, fractional anisotropy (FA) and apparent diffusion coefficient of the brain regions in baseline brain activity by using VBM and diffusion tensor imaging. The relationships between the expanded disability states scale (EDSS) scores, changed parameters of structure and function were further explored. (1) Compared with HCs, the ALFF of the bilateral hippocampus and right middle temporal gyrus in MS-SSCI decreased significantly. However, patients exhibited increased ALFF in the left middle frontal gyrus, left posterior cingulate gyrus and right middle occipital gyrus ( two-sample t-test, after AlphaSim correction, p < 0.01, voxel size > 40). The volume of right middle frontal gyrus reduced significantly (p < 0.01). The FA and ADC of right hippocampus, the FA of left hippocampus and right middle temporal gyrus were significantly different. (2) A significant correlation between EDSS scores and ALFF was noted only in the left posterior cingulate gyrus. Our results detected structural and functional abnormalities in MS-SSCI and functional parameters were associated with clinical abnormalities. Multimodal imaging plays an important role in detecting structural and functional abnormalities in MS-SSCI. Advances in knowledge: This is the first time to apply RS-fMRI, VBM and diffusion tensor tractography to study the structural and functional abnormalities in MS-SSCI, and to explore its correlation with EDSS score.

Metabolite identification of triptolide by data-dependent accurate mass spectrometric analysis in combination with online hydrogen/deuterium exchange and multiple data-mining techniques.

PubMed

Du, Fuying; Liu, Ting; Liu, Tian; Wang, Yongwei; Wan, Yakun; Xing, Jie

2011-10-30

Triptolide (TP), the primary active component of the herbal medicine Tripterygium wilfordii Hook F, has shown promising antileukemic and anti-inflammatory activity. The pharmacokinetic profile of TP indicates an extensive metabolic elimination in vivo; however, its metabolic data is rarely available partly because of the difficulty in identifying it due to the absence of appropriate ultraviolet chromophores in the structure and the presence of endogenous interferences in biological samples. In the present study, the biotransformation of TP was investigated by improved data-dependent accurate mass spectrometric analysis, using an LTQ/Orbitrap hybrid mass spectrometer in conjunction with the online hydrogen (H)/deuterium (D) exchange technique for rapid structural characterization. Accurate full-scan MS and MS/MS data were processed with multiple post-acquisition data-mining techniques, which were complementary and effective in detecting both common and uncommon metabolites from biological matrices. As a result, 38 phase I, 9 phase II and 8 N-acetylcysteine (NAC) metabolites of TP were found in rat urine. Accurate MS/MS data were used to support assignments of metabolite structures, and online H/D exchange experiments provided additional evidence for exchangeable hydrogen atoms in the structure. The results showed the main phase I metabolic pathways of TP are hydroxylation, hydrolysis and desaturation, and the resulting metabolites subsequently undergo phase II processes. The presence of NAC conjugates indicated the capability of TP to form reactive intermediate species. This study also demonstrated the effectiveness of LC/HR-MS(n) in combination with multiple post-acquisition data-mining methods and the online H/D exchange technique for the rapid identification of drug metabolites. Copyright © 2011 John Wiley & Sons, Ltd.

Distance restraints from crosslinking mass spectrometry: mining a molecular dynamics simulation database to evaluate lysine-lysine distances.

PubMed

Merkley, Eric D; Rysavy, Steven; Kahraman, Abdullah; Hafen, Ryan P; Daggett, Valerie; Adkins, Joshua N

2014-06-01

Integrative structural biology attempts to model the structures of protein complexes that are challenging or intractable by classical structural methods (due to size, dynamics, or heterogeneity) by combining computational structural modeling with data from experimental methods. One such experimental method is chemical crosslinking mass spectrometry (XL-MS), in which protein complexes are crosslinked and characterized using liquid chromatography-mass spectrometry to pinpoint specific amino acid residues in close structural proximity. The commonly used lysine-reactive N-hydroxysuccinimide ester reagents disuccinimidylsuberate (DSS) and bis(sulfosuccinimidyl)suberate (BS(3) ) have a linker arm that is 11.4 Å long when fully extended, allowing Cα (alpha carbon of protein backbone) atoms of crosslinked lysine residues to be up to ∼24 Å apart. However, XL-MS studies on proteins of known structure frequently report crosslinks that exceed this distance. Typically, a tolerance of ∼3 Å is added to the theoretical maximum to account for this observation, with limited justification for the chosen value. We used the Dynameomics database, a repository of high-quality molecular dynamics simulations of 807 proteins representative of diverse protein folds, to investigate the relationship between lysine-lysine distances in experimental starting structures and in simulation ensembles. We conclude that for DSS/BS(3), a distance constraint of 26-30 Å between Cα atoms is appropriate. This analysis provides a theoretical basis for the widespread practice of adding a tolerance to the crosslinker length when comparing XL-MS results to structures or in modeling. We also discuss the comparison of XL-MS results to MD simulations and known structures as a means to test and validate experimental XL-MS methods. © 2014 The Protein Society.

Distance restraints from crosslinking mass spectrometry: Mining a molecular dynamics simulation database to evaluate lysine–lysine distances

PubMed Central

Merkley, Eric D; Rysavy, Steven; Kahraman, Abdullah; Hafen, Ryan P; Daggett, Valerie; Adkins, Joshua N

2014-01-01

Integrative structural biology attempts to model the structures of protein complexes that are challenging or intractable by classical structural methods (due to size, dynamics, or heterogeneity) by combining computational structural modeling with data from experimental methods. One such experimental method is chemical crosslinking mass spectrometry (XL-MS), in which protein complexes are crosslinked and characterized using liquid chromatography-mass spectrometry to pinpoint specific amino acid residues in close structural proximity. The commonly used lysine-reactive N-hydroxysuccinimide ester reagents disuccinimidylsuberate (DSS) and bis(sulfosuccinimidyl)suberate (BS3) have a linker arm that is 11.4 Å long when fully extended, allowing Cα (alpha carbon of protein backbone) atoms of crosslinked lysine residues to be up to ∼24 Å apart. However, XL-MS studies on proteins of known structure frequently report crosslinks that exceed this distance. Typically, a tolerance of ∼3 Å is added to the theoretical maximum to account for this observation, with limited justification for the chosen value. We used the Dynameomics database, a repository of high-quality molecular dynamics simulations of 807 proteins representative of diverse protein folds, to investigate the relationship between lysine–lysine distances in experimental starting structures and in simulation ensembles. We conclude that for DSS/BS3, a distance constraint of 26–30 Å between Cα atoms is appropriate. This analysis provides a theoretical basis for the widespread practice of adding a tolerance to the crosslinker length when comparing XL-MS results to structures or in modeling. We also discuss the comparison of XL-MS results to MD simulations and known structures as a means to test and validate experimental XL-MS methods. PMID:24639379

An introduction to hybrid ion trap/time-of-flight mass spectrometry coupled with liquid chromatography applied to drug metabolism studies.

PubMed

Liu, Zhao-Ying

2012-12-01

Metabolism studies play an important role at various stages of drug discovery and development. Liquid chromatography combined with mass spectrometry (LC/MS) has become a most powerful and widely used analytical tool for identifying drug metabolites. The suitability of different types of mass spectrometers for metabolite profiling differs widely, and therefore, the data quality and reliability of the results also depend on which instrumentation is used. As one of the latest LC/MS instrumentation designs, hybrid ion trap/time-of-flight MS coupled with LC (LC-IT-TOF-MS) has successfully integrated ease of operation, compatibility with LC flow rates and data-dependent MS(n) with high mass accuracy and mass resolving power. The MS(n) and accurate mass capabilities are routinely utilized to rapidly confirm the identification of expected metabolites or to elucidate the structures of uncommon or unexpected metabolites. These features make the LC-IT-TOF-MS a very powerful analytical tool for metabolite identification. This paper begins with a brief introduction to some basic principles and main properties of a hybrid IT-TOF instrument. Then, a general workflow for metabolite profiling using LC-IT-TOF-MS, starting from sample collection and preparation to final identification of the metabolite structures, is discussed in detail. The data extraction and mining techniques to find and confirm metabolites are discussed and illustrated with some examples. This paper is directed to readers with no prior experience with LC-IT-TOF-MS and will provide a broad understanding of the development and utility of this instrument for drug metabolism studies. Copyright © 2012 John Wiley & Sons, Ltd.

A new anti-MRSA antibiotic complex, WAP-8294A II. Structure characterization of minor components by ESI LCMS and MS/MS.

PubMed

Kato, Azusa; Hirata, Haruhisa; Ohashi, Yoshitami; Fujii, Kiyonaga; Mori, Kenji; Harada, Ken-ichi

2011-05-01

The anti-MRSA antibiotic, WAP-8294A, was isolated from the fermentation broth of Lysobacter sp. The major component, WAP-8294A2, is composed of 1 mol of Gly, L-Leu, L-Glu, D-Asn, D-Trp, D-threo-β-hydroxyasparagine, N-Me-D-Phe and N-Me-L-Val, and 2 mol of L-Ser, D-Orn and D-3-hydroxy-7-Me-octanoic acid. The structure of the WAP-8294A2 was mainly determined as a cyclic depsipeptide by 2D NMR experiments. However, it was difficult to use the NMR experiment to determine the minor components, A1, A4 and Ax13, isolated in small amounts. In the present study, ESI MS/MS was applied to the structure elucidation of these minor components. The structures of these minor components were determined on the basis of the fragmentation pattern of the product ions of WAP-8294A2 in the ESI MS/MS. As a result, it was confirmed that A1 and A4 had the same amino acid sequence as A2, while A1 and A4 had the 3-OH-octanoic acid and 3-OH-8-Me-nonanoic acid, respectively, in the place of the 3-OH-7-Me-octanoic acid in A2. In the structure of Ax13, it was found that Gly of A2 was changed to β-Ala of Ax13. © 2011 Japan Antibiotics Research Association All rights reserved

The challenges of healthcare delivery to people with multiple sclerosis in Iran.

PubMed

Yazdannik, Ahmadreza; Abolhassani, Shahla; Taleghani, Fariba; Zamani, Ahmadreza

2015-01-01

Multiple sclerosis (MS) is a chronic disease prevalent in young and middle-aged people. Patients with MS often have numerous complicated needs and, consequently, require a broad range of health services. Results of a number of studies indicate that patients' needs are only partially met. This study was conducted to explore the challenges of healthcare delivery to patients with MS in Iran. In this qualitative case study, 43 participants selected through purposeful sampling were interviewed using semi-structured method in the cities of Isfahan and Tehran in 2012-2013. Besides the interview, documentations relevant to healthcare delivery were collected from different sources, including websites of all Iranian universities of medical sciences, insurance organizations, patients' weblogs, news agencies, the MS Center forum for MS patients, and MS Payam bimonthly. The data were analyzed through the constant comparative analysis. The data were categorized into four main categories, including functional challenges (diagnosis problems, failure to pay attention to patient needs, failure to follow-up, and miscommunication), administrative challenges (resource allocation and supervision), policy-making challenges (lack of comprehensive services, bureaucracy, and problems in provision of medications), and structural challenges (difficult access to services, lack of comprehensive centers, space limit, and long wait). Despite all attempts of governmental and nongovernmental organizations for healthcare delivery to MS patients, these services cannot satisfy all needs of the patients. In this regard, service providers and administrators should pay more attention to the needs and expectations of patients and their families.

Satisfaction with Communicative Participation as Defined by Adults with Multiple Sclerosis: A Qualitative Study

ERIC Educational Resources Information Center

Yorkston, Kathryn M.; Baylor, Carolyn R.; Klasner, Estelle R.; Deitz, Jean; Dudgeon, Brian J.; Eadie, Tanya; Miller, Robert M.; Amtmann, Dagmar

2007-01-01

Purpose: This study examined satisfaction with communicative participation as reported by adults with multiple sclerosis (MS). Method: Eight community-dwelling adults with MS participated in semi-structured interviews. They were asked to discuss their satisfaction with their communication in a variety of situations. Interviews were analyzed using…

Structural Elucidation of Novel Saponins in the Sea Cucumber Holothuria lessoni

PubMed Central

Bahrami, Yadollah; Zhang, Wei; Chataway, Tim; Franco, Chris

2014-01-01

Sea cucumbers are prolific producers of a wide range of bioactive compounds. This study aimed to purify and characterize one class of compound, the saponins, from the viscera of the Australian sea cucumber Holothuria lessoni. The saponins were obtained by ethanolic extraction of the viscera and enriched by a liquid-liquid partition process and adsorption column chromatography. A high performance centrifugal partition chromatography (HPCPC) was applied to the saponin-enriched mixture to obtain saponins with high purity. The resultant purified saponins were profiled using MALDI-MS/MS and ESI-MS/MS which revealed the structure of isomeric saponins to contain multiple aglycones and/or sugar residues. We have elucidated the structure of five novel saponins, Holothurins D/E and Holothurinosides X/Y/Z, along with seven reported triterpene glycosides, including sulfated and non-sulfated saponins containing a range of aglycones and sugar moieties, from the viscera of H. lessoni. The abundance of novel compounds from this species holds promise for biotechnological applications. PMID:25110919

Automated software system for checking the structure and format of ACM SIG documents

NASA Astrophysics Data System (ADS)

Mirza, Arsalan Rahman; Sah, Melike

2017-04-01

Microsoft (MS) Office Word is one of the most commonly used software tools for creating documents. MS Word 2007 and above uses XML to represent the structure of MS Word documents. Metadata about the documents are automatically created using Office Open XML (OOXML) syntax. We develop a new framework, which is called ADFCS (Automated Document Format Checking System) that takes the advantage of the OOXML metadata, in order to extract semantic information from MS Office Word documents. In particular, we develop a new ontology for Association for Computing Machinery (ACM) Special Interested Group (SIG) documents for representing the structure and format of these documents by using OWL (Web Ontology Language). Then, the metadata is extracted automatically in RDF (Resource Description Framework) according to this ontology using the developed software. Finally, we generate extensive rules in order to infer whether the documents are formatted according to ACM SIG standards. This paper, introduces ACM SIG ontology, metadata extraction process, inference engine, ADFCS online user interface, system evaluation and user study evaluations.

Liquid Chromatography Electrospray Ionization Tandem Mass Spectrometric (LC/ESI-MS/MS) Study for the Identification and Characterization of In Vivo Metabolites of Cisplatin in Rat Kidney Cancer Tissues: Online Hydrogen/Deuterium (H/D) Exchange Study.

PubMed

Bandu, Raju; Ahn, Hyun Soo; Lee, Joon Won; Kim, Yong Woo; Choi, Seon Hee; Kim, Hak Jin; Kim, Kwang Pyo

2015-01-01

In vivo rat kidney tissue metabolites of an anticancer drug, cisplatin (cis-diamminedichloroplatinum [II]) (CP) which is used for the treatment of testicular, ovarian, bladder, cervical, esophageal, small cell lung, head and neck cancers, have been identified and characterized by using liquid chromatography positive ion electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) in combination with on line hydrogen/deuterium exchange (HDX) experiments. To identify in vivo metabolites, kidney tissues were collected after intravenous administration of CP to adult male Sprague-Dawley rats (n = 3 per group). The tissue samples were homogenized and extracted using newly optimized metabolite extraction procedure which involves liquid extraction with phosphate buffer containing ethyl acetate and protein precipitation with mixed solvents of methanol-water-chloroform followed by solid-phase clean-up procedure on Oasis HLB 3cc cartridges and then subjected to LC/ESI-HRMS analysis. A total of thirty one unknown in vivo metabolites have been identified and the structures of metabolites were elucidated using LC-MS/MS experiments combined with accurate mass measurements. Online HDX experiments have been used to further support the structural characterization of metabolites. The results showed that CP undergoes a series of ligand exchange biotransformation reactions with water and other nucleophiles like thio groups of methionine, cysteine, acetylcysteine, glutathione and thioether. This is the first research approach focused on the structure elucidation of biotransformation products of CP in rats, and the identification of metabolites provides essential information for further pharmacological and clinical studies of CP, and may also be useful to develop various effective new anticancer agents.

Determination of the structure and composition of Au-Ag bimetallic spherical nanoparticles using single particle ICP-MS measurements performed with normal and high temporal resolution.

PubMed

Kéri, Albert; Kálomista, Ildikó; Ungor, Ditta; Bélteki, Ádám; Csapó, Edit; Dékány, Imre; Prohaska, Thomas; Galbács, Gábor

2018-03-01

In this study, the information that can be obtained by combining normal and high resolution single particle ICP-MS (spICP-MS) measurements for spherical bimetallic nanoparticles (BNPs) was assessed. One commercial certified core-shell Au-Ag nanoparticle and three newly synthesized and fully characterized homogenous alloy Au-Ag nanoparticle batches of different composition were used in the experiments as BNP samples. By scrutinizing the high resolution spICP-MS signal time profiles, it was revealed that the width of the signal peak linearly correlates with the diameter of nanoparticles. It was also observed that the width of the peak for same-size nanoparticles is always significantly larger for Au than for Ag. It was also found that it can be reliably determined whether a BNP is of homogeneus alloy or core-shell structure and that, in the case of the latter, the core comprises of which element. We also assessed the performance of several ICP-MS based analytical methods in the analysis of the quantitative composition of bimetallic nanoparticles. Out of the three methods (normal resolution spICP-MS, direct NP nebulization with solution-mode ICP-MS, and solution-mode ICP-MS after the acid dissolution of the nanoparticles), the best accuracy and precision was achieved by spICP-MS. This method allows the determination of the composition with less than 10% relative inaccuracy and better than 3% precision. The analysis is fast and only requires the usual standard colloids for size calibration. Combining the results from both quantitative and structural analyses, the core diameter and shell thickness of core-shell particles can also be calculated. Copyright © 2017 Elsevier B.V. All rights reserved.

Comparison of HPLC/ESI-FTICR MS Versus MALDI-TOF/TOF MS for Glycopeptide Analysis of a Highly Glycosylated HIV Envelope Glycoprotein

PubMed Central

Irungu, Janet; Go, Eden P.; Zhang, Ying; Dalpathado, Dilusha S.; Liao, Hua-Xin; Haynes, Barton F.; Desaire, Heather

2013-01-01

Defining the structures and locations of the glycans attached on secreted proteins and virus envelope proteins is important in understanding how glycosylation affects their biological properties. Glycopeptide mass spectrometry (MS)-based analysis is a very powerful, emerging approach to characterize glycoproteins, in which glycosylation sites and the corresponding glycan structures are elucidated in a single MS experiment. However, to date there is not a consensus regarding which mass spectrometric platform provides the best glycosylation coverage information. Herein, we employ two of the most widely used MS approaches, online high performance liquid chromatography-electrospray ionization mass spectrometry (HPLC/ESI-MS) and offline HPLC followed by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), to determine which of the two approaches provides the best glycosylation coverage information of a complex glycoprotein, the group M consensus HIV-1 envelope, CON-S gp140ΔCFI, which has 31 potential glycosylation sites. Our results highlight differences in the informational content obtained between the two methods such as the overall number of glycosylation sites detected, the numbers of N-linked glycans present at each site, and the type of confirmatory information obtained about the glycopeptide using MS/MS experiments. The two approaches are quite complementary, both in their coverage of glycopeptides and in the information they provide in MS/MS experiments. The information in this study contributes to the field of mass spectrometry by demonstrating the strengths and limitations of two widely used MS platforms in glycoprotein analysis. PMID:18565761

Liquid chromatography-tandem mass spectrometry characterization of five new leucinostatins produced by Paecilomyces lilacinus CG-189.

PubMed

Martinez, Ana Flávia Canovas; Moraes, Luiz Alberto Beraldo

2015-03-01

The fungus Paecilomyces lilacinus produces leucinostatins—peptaibiotics that exert a range of biological activities including antimalarial, antiviral, antitumor and phytotoxicity. In this paper, we developed an analytical method employing LC-MS/MS in the precursor ion and product ion scan modes to elucidate five new leucinostatins. Direct Infusion (DI-MS) helped to identify the most abundant leucinostatins: F, D B2, S, A and K. MS/MS analysis using a triple quadrupole operating at different scan modes is a versatile tool to study natural products, especially peptaibiotics. Although DI-MS full-scan analysis is rapid and sensitive, it cannot distinguish between peptide isomers. On the other hand, LC-MS/MS operated in the precursor ion and product ion modes is time consuming, but allows identifying the structure of isomers or isobar in crude extracts.

Automated LC-HRMS(/MS) Approach for the Annotation of Fragment Ions Derived from Stable Isotope Labeling-Assisted Untargeted Metabolomics

PubMed Central

2014-01-01

Structure elucidation of biological compounds is still a major bottleneck of untargeted LC-HRMS approaches in metabolomics research. The aim of the present study was to combine stable isotope labeling and tandem mass spectrometry for the automated interpretation of the elemental composition of fragment ions and thereby facilitate the structural characterization of metabolites. The software tool FragExtract was developed and evaluated with LC-HRMS/MS spectra of both native 12C- and uniformly 13C (U-13C)-labeled analytical standards of 10 fungal substances in pure solvent and spiked into fungal culture filtrate of Fusarium graminearum respectively. Furthermore, the developed approach is exemplified with nine unknown biochemical compounds contained in F. graminearum samples derived from an untargeted metabolomics experiment. The mass difference between the corresponding fragment ions present in the MS/MS spectra of the native and U-13C-labeled compound enabled the assignment of the number of carbon atoms to each fragment signal and allowed the generation of meaningful putative molecular formulas for each fragment ion, which in turn also helped determine the elemental composition of the precursor ion. Compared to laborious manual analysis of the MS/MS spectra, the presented algorithm marks an important step toward efficient fragment signal elucidation and structure annotation of metabolites in future untargeted metabolomics studies. Moreover, as demonstrated for a fungal culture sample, FragExtract also assists the characterization of unknown metabolites, which are not contained in databases, and thus exhibits a significant contribution to untargeted metabolomics research. PMID:24965664

Content validity of the Comprehensive ICF Core Set for multiple sclerosis from the perspective of speech and language therapists.

PubMed

Renom, Marta; Conrad, Andrea; Bascuñana, Helena; Cieza, Alarcos; Galán, Ingrid; Kesselring, Jürg; Coenen, Michaela

2014-11-01

The Comprehensive International Classification of Functioning, Disability and Health (ICF) Core Set for Multiple Sclerosis (MS) is a comprehensive framework to structure the information obtained in multidisciplinary clinical settings according to the biopsychosocial perspective of the International Classification of Functioning, Disability and Health (ICF) and to guide the treatment and rehabilitation process accordingly. It is now undergoing validation from the user perspective for which it has been developed in the first place. To validate the content of the Comprehensive ICF Core Set for MS from the perspective of speech and language therapists (SLTs) involved in the treatment of persons with MS (PwMS). Within a three-round e-mail-based Delphi Study 34 SLTs were asked about PwMS' problems, resources and aspects of the environment treated by SLTs. Responses were linked to ICF categories. Identified ICF categories were compared with those included in the Comprehensive ICF Core Set for MS to examine its content validity. Thirty-four SLTs named 524 problems and resources, as well as aspects of environment. Statements were linked to 129 ICF categories (60 Body-functions categories, two Body-structures categories, 42 Activities-&-participation categories, and 25 Environmental-factors categories). SLTs confirmed 46 categories in the Comprehensive ICF Core Set. Twenty-one ICF categories were identified as not-yet-included categories. This study contributes to the content validity of the Comprehensive ICF Core Set for MS from the perspective of SLTs. Study participants agreed on a few not-yet-included categories that should be further discussed for inclusion in a revised version of the Comprehensive ICF Core Set to strengthen SLTs' perspective in PwMS' neurorehabilitation. © 2014 Royal College of Speech and Language Therapists.

Combined LC-MS/MS and Molecular Networking Approach Reveals New Cyanotoxins from the 2014 Cyanobacterial Bloom in Green Lake, Seattle.

PubMed

Teta, Roberta; Della Sala, Gerardo; Glukhov, Evgenia; Gerwick, Lena; Gerwick, William H; Mangoni, Alfonso; Costantino, Valeria

2015-12-15

Cyanotoxins obtained from a freshwater cyanobacterial collection at Green Lake, Seattle during a cyanobacterial harmful algal bloom in the summer of 2014 were studied using a new approach based on molecular networking analysis of liquid chromatography tandem mass spectrometry (LC-MS/MS) data. This MS networking approach is particularly well-suited for the detection of new cyanotoxin variants and resulted in the discovery of three new cyclic peptides, namely microcystin-MhtyR (6), which comprised about half of the total microcystin content in the bloom, and ferintoic acids C (12) and D (13). Structure elucidation of 6 was aided by a new microscale methylation procedure. Metagenomic analysis of the bloom using the 16S-ITS rRNA region identified Microcystis aeruginosa as the predominant cyanobacterium in the sample. Fragments of the putative biosynthetic genes for the new cyanotoxins were also identified, and their sequences correlated to the structure of the isolated cyanotoxins.

Applications of Mass Spectrometry to Structural Analysis of Marine Oligosaccharides

PubMed Central

Lang, Yinzhi; Zhao, Xia; Liu, Lili; Yu, Guangli

2014-01-01

Marine oligosaccharides have attracted increasing attention recently in developing potential drugs and biomaterials for their particular physical and chemical properties. However, the composition and sequence analysis of marine oligosaccharides are very challenging for their structural complexity and heterogeneity. Mass spectrometry (MS) has become an important technique for carbohydrate analysis by providing more detailed structural information, including molecular mass, sugar constituent, sequence, inter-residue linkage position and substitution pattern. This paper provides an overview of the structural analysis based on MS approaches in marine oligosaccharides, which are derived from some biologically important marine polysaccharides, including agaran, carrageenan, alginate, sulfated fucan, chitosan, glycosaminoglycan (GAG) and GAG-like polysaccharides. Applications of electrospray ionization mass spectrometry (ESI-MS) are mainly presented and the general applications of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) are also outlined. Some technical challenges in the structural analysis of marine oligosaccharides by MS have also been pointed out. PMID:24983643

In vitro biosynthesis, isolation, and identification of predominant metabolites of 2-(4-(2-hydroxyethoxy)-3,5-dimethylphenyl)-5,7-dimethoxyquinazolin-4(3H)-one (RVX-208).

PubMed

Khmelnitsky, Yuri L; Mozhaev, Vadim V; Cotterill, Ian C; Michels, Peter C; Boudjabi, Sihem; Khlebnikov, Vladimir; Madhava Reddy, M; Wagner, Gregory S; Hansen, Henrik C

2013-06-01

The structures of the two predominant metabolites (M4 and M5) of RVX-208, observed both in in vitro human and animal liver microsomal incubations, as well as in plasma from animal in vivo studies, were determined. A panel of biocatalytic systems was tested to identify biocatalysts suitable for milligram scale production of metabolite M4 from RVX-208. Rabbit liver S9 fraction was selected as the most suitable system, primarily based on pragmatic metrics such as catalyst cost and estimated yield of M4 (∼55%). Glucuronidation of RVX-208 catalyzed by rabbit liver S9 fraction was optimized to produce M4 in amounts sufficient for structural characterization. Structural studies using LC/MS/MS analysis and (1)H NMR spectroscopy showed the formation of a glycosidic bond between the primary hydroxyl group of RVX-208 and glucuronic acid. NMR results suggested that the glycosidic bond has the β-anomeric configuration. A synthetic sample of M4 confirmed the proposed structure. Metabolite M5, hypothesized to be the carboxylate of RVX-208, was prepared using human liver microsomes, purified by HPLC, and characterized by LC/MS/MS and (1)H NMR. The structure was confirmed by comparison to a synthetic sample. Both samples confirmed M5 as a product of oxidation of primary hydroxyl group of RVX-208 to carboxylic acid. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Laboratory technology and cosmochemistry

PubMed Central

Zinner, Ernst K.; Moynier, Frederic; Stroud, Rhonda M.

2011-01-01

Recent developments in analytical instrumentation have led to revolutionary discoveries in cosmochemistry. Instrumental advances have been made along two lines: (i) increase in spatial resolution and sensitivity of detection, allowing for the study of increasingly smaller samples, and (ii) increase in the precision of isotopic analysis that allows more precise dating, the study of isotopic heterogeneity in the Solar System, and other studies. A variety of instrumental techniques are discussed, and important examples of discoveries are listed. Instrumental techniques and instruments include the ion microprobe, laser ablation gas MS, Auger EM, resonance ionization MS, accelerator MS, transmission EM, focused ion-beam microscopy, atom probe tomography, X-ray absorption near-edge structure/electron loss near-edge spectroscopy, Raman microprobe, NMR spectroscopy, and inductively coupled plasma MS. PMID:21498689

Ion mobility-mass spectrometry reveals conformational flexibility in the deubiquitinating enzyme USP5.

PubMed

Scott, Daniel; Layfield, Robert; Oldham, Neil J

2015-08-01

Many proteins exhibit conformation flexibility as part of their biological function, whether through the presence of a series of well-defined states or by the existence of intrinsic disorder. Ion mobility spectrometry, in combination with MS (IM-MS), offers a rapid and sensitive means of probing ensembles of protein structures through measurement of gas-phase collisional cross sections. We have applied IM-MS analysis to the multidomain deubiquitinating enzyme ubiquitin specific protease 5 (USP5), which is believed to exhibit significant conformational flexibility. Native ESI-MS measurement of the 94-kDa USP5 revealed two distinct charge-state distributions: [M + 17H](+) to [M + 21H](+) and [M + 24H](+) to [M + 29H](+). The collisional cross sections of these ions revealed clear groupings of 52 ± 4 nm(2) for the lower charges and 66 ± 6 nm(2) for the higher charges. Molecular dynamics simulation of a compact form of USP5, based on a crystal structure, produced structures of 53-54 nm(2) following 2 ns in the gas phase, while simulation of an extended form (based on small-angle X-ray scattering data) led to structures of 64 nm(2). These data demonstrate that IM-MS is a valuable tool in studying proteins with different discrete conformational states. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The challenges of healthcare delivery to people with multiple sclerosis in Iran

PubMed Central

Yazdannik, Ahmadreza; Abolhassani, Shahla; Taleghani, Fariba; Zamani, Ahmadreza

2015-01-01

Background: Multiple sclerosis (MS) is a chronic disease prevalent in young and middle-aged people. Patients with MS often have numerous complicated needs and, consequently, require a broad range of health services. Results of a number of studies indicate that patients’ needs are only partially met. Aims: This study was conducted to explore the challenges of healthcare delivery to patients with MS in Iran. Materials and Methods: In this qualitative case study, 43 participants selected through purposeful sampling were interviewed using semi-structured method in the cities of Isfahan and Tehran in 2012–2013. Besides the interview, documentations relevant to healthcare delivery were collected from different sources, including websites of all Iranian universities of medical sciences, insurance organizations, patients’ weblogs, news agencies, the MS Center forum for MS patients, and MS Payam bimonthly. The data were analyzed through the constant comparative analysis. Results: The data were categorized into four main categories, including functional challenges (diagnosis problems, failure to pay attention to patient needs, failure to follow-up, and miscommunication), administrative challenges (resource allocation and supervision), policy-making challenges (lack of comprehensive services, bureaucracy, and problems in provision of medications), and structural challenges (difficult access to services, lack of comprehensive centers, space limit, and long wait). Conclusion: Despite all attempts of governmental and nongovernmental organizations for healthcare delivery to MS patients, these services cannot satisfy all needs of the patients. In this regard, service providers and administrators should pay more attention to the needs and expectations of patients and their families. PMID:27462625

Remodeling Functional Connectivity in Multiple Sclerosis: A Challenging Therapeutic Approach.

PubMed

Stampanoni Bassi, Mario; Gilio, Luana; Buttari, Fabio; Maffei, Pierpaolo; Marfia, Girolama A; Restivo, Domenico A; Centonze, Diego; Iezzi, Ennio

2017-01-01

Neurons in the central nervous system are organized in functional units interconnected to form complex networks. Acute and chronic brain damage disrupts brain connectivity producing neurological signs and/or symptoms. In several neurological diseases, particularly in Multiple Sclerosis (MS), structural imaging studies cannot always demonstrate a clear association between lesion site and clinical disability, originating the "clinico-radiological paradox." The discrepancy between structural damage and disability can be explained by a complex network perspective. Both brain networks architecture and synaptic plasticity may play important roles in modulating brain networks efficiency after brain damage. In particular, long-term potentiation (LTP) may occur in surviving neurons to compensate network disconnection. In MS, inflammatory cytokines dramatically interfere with synaptic transmission and plasticity. Importantly, in addition to acute and chronic structural damage, inflammation could contribute to reduce brain networks efficiency in MS leading to worse clinical recovery after a relapse and worse disease progression. These evidence suggest that removing inflammation should represent the main therapeutic target in MS; moreover, as synaptic plasticity is particularly altered by inflammation, specific strategies aimed at promoting LTP mechanisms could be effective for enhancing clinical recovery. Modulation of plasticity with different non-invasive brain stimulation (NIBS) techniques has been used to promote recovery of MS symptoms. Better knowledge of features inducing brain disconnection in MS is crucial to design specific strategies to promote recovery and use NIBS with an increasingly tailored approach.

Nanofibrous spongy microspheres enhance odontogenic differentiation of human dental pulp stem cells.

PubMed

Kuang, Rong; Zhang, Zhanpeng; Jin, Xiaobing; Hu, Jiang; Gupte, Melanie J; Ni, Longxing; Ma, Peter X

2015-09-16

Dentin regeneration is challenging due to its complicated anatomical structure and the shortage of odontoblasts. In this study, a novel injectable cell carrier, nanofibrous spongy microspheres (NF-SMS), is developed for dentin regeneration. Biodegradable and biocompatible poly(l-lactic acid)-block-poly(l-lysine) are synthesized and fabricated into NF-SMS using self-assembly and thermally induced phase separation techniques. It is hypothesized that NF-SMS with interconnected pores and nanofibers can enhance the proliferation and odontogenic differentiation of human dental pulp stem cells (hDPSCs), compared to nanofibrous microspheres (NF-MS) without pore structure and conventional solid microspheres (S-MS) with neither nanofibers nor pore structure. During the first 9 d in culture, hDPSCs proliferate significantly faster on NF-SMS than on NF-MS or S-MS (p < 0.05). Following in vitro odontogenic induction, all the examined odontogenic genes (alkaline phosphatase content, osteocalcin, bone sialoprotein, collagen 1, dentin sialophosphoprotein (DSPP)), calcium content, and DSPP protein content are found significantly higher in the NF-SMS group than in the control groups. Furthermore, 6 weeks after subcutaneous injection of hDPSCs and microspheres into nude mice, histological analysis shows that NF-SMS support superior dentin-like tissue formation compared to NF-MS or S-MS. Taken together, NF-SMS have great potential as an injectable cell carrier for dentin regeneration. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The First MS-Cleavable, Photo-Thiol-Reactive Cross-Linker for Protein Structural Studies

NASA Astrophysics Data System (ADS)

Iacobucci, Claudio; Piotrowski, Christine; Rehkamp, Anne; Ihling, Christian H.; Sinz, Andrea

2018-04-01

Cleavable cross-linkers are gaining increasing importance for chemical cross-linking/mass spectrometry (MS) as they permit a reliable and automated data analysis in structural studies of proteins and protein assemblies. Here, we introduce 1,3-diallylurea (DAU) as the first CID-MS/MS-cleavable, photo-thiol-reactive cross-linker. DAU is a commercially available, inexpensive reagent that efficiently undergoes an anti-Markovnikov hydrothiolation with cysteine residues in the presence of a radical initiator upon UV-A irradiation. Radical cysteine cross-linking proceeds via an orthogonal "click reaction" and yields stable alkyl sulfide products. DAU reacts at physiological pH and cross-linking reactions with peptides, and proteins can be performed at temperatures as low as 4 °C. The central urea bond is efficiently cleaved upon collisional activation during tandem MS experiments generating characteristic product ions. This improves the reliability of automated cross-link identification. Different radical initiators have been screened for the cross-linking reaction of DAU using the thiol-containing compounds cysteine and glutathione. Our concept has also been exemplified for the biologically relevant proteins bMunc13-2 and retinal guanylyl cyclase-activating protein-2. [Figure not available: see fulltext.

Integrated identification, qualification and quantification strategy for pharmacokinetic profile study of Guizhi Fuling capsule in healthy volunteers

PubMed Central

Zhong, Yun-Xi; Jin, Xiao-Liang; Gu, Shi-Yin; Peng, Ying; Zhang, Ke-Rong; Ou-Yang, Bing-Chen; Wang, Yu; Xiao, Wei; Wang, Zhen-Zhong; Aa, Ji-Ye; Wang, Guang-Ji; Sun, Jian-Guo

2016-01-01

Guizhi Fuling capsule (GZFL), a traditional Chinese medicine formulation, is widely used in China to relieve pain from dysmenorrhea and is now in a Phase II clinical trial in the USA. Due to the low exposure of the five main medicative ingredients (amygdalin, cinnamic acid, gallic acid, paeoniflorin and paeonol) of GZFL in human, a strategy was built to qualitatively and quantitatively identify the possible metabolites of GZFL and to describe the pharmacokinetic profiles of GZFL in human. In this strategy, LC-Q-TOF/MS was used to identify and structurally elucidate the possible metabolites of GZFL in vivo; and a time-based metabolite-confirming step (TBMCs) was used to confirm uncertain metabolites. The simultaneously quantitation results by LC-MS/MS showed low exposure of the five medicative ingredients. According to the strategy we built, a total of 36 metabolites were found and structurally elucidated. The simultaneously semi-quantitative analysis by LC-MS/MS showed that obvious time-concentration curves could be established for 12 of the metabolites, and most of them showed a relatively higher exposure. This study provides a better understanding of the metabolic processes of GZFL in human. PMID:27527657

Integrated identification, qualification and quantification strategy for pharmacokinetic profile study of Guizhi Fuling capsule in healthy volunteers.

PubMed

Zhong, Yun-Xi; Jin, Xiao-Liang; Gu, Shi-Yin; Peng, Ying; Zhang, Ke-Rong; Ou-Yang, Bing-Chen; Wang, Yu; Xiao, Wei; Wang, Zhen-Zhong; Aa, Ji-Ye; Wang, Guang-Ji; Sun, Jian-Guo

2016-08-16

Guizhi Fuling capsule (GZFL), a traditional Chinese medicine formulation, is widely used in China to relieve pain from dysmenorrhea and is now in a Phase II clinical trial in the USA. Due to the low exposure of the five main medicative ingredients (amygdalin, cinnamic acid, gallic acid, paeoniflorin and paeonol) of GZFL in human, a strategy was built to qualitatively and quantitatively identify the possible metabolites of GZFL and to describe the pharmacokinetic profiles of GZFL in human. In this strategy, LC-Q-TOF/MS was used to identify and structurally elucidate the possible metabolites of GZFL in vivo; and a time-based metabolite-confirming step (TBMCs) was used to confirm uncertain metabolites. The simultaneously quantitation results by LC-MS/MS showed low exposure of the five medicative ingredients. According to the strategy we built, a total of 36 metabolites were found and structurally elucidated. The simultaneously semi-quantitative analysis by LC-MS/MS showed that obvious time-concentration curves could be established for 12 of the metabolites, and most of them showed a relatively higher exposure. This study provides a better understanding of the metabolic processes of GZFL in human.

Thrombin-activated human platelets acutely generate oxidized docosahexaenoic-acid-containing phospholipids via 12-lipoxygenase.

PubMed

Morgan, Lloyd T; Thomas, Christopher P; Kühn, Hartmut; O'Donnell, Valerie B

2010-10-01

Arachidonate-containing oxidized phospholipids are acutely generated by 12-LOX (12-lipoxygenase) in agonist-activated platelets. In the present study, formation of structurally related lipids by oxidation of DHA (docosahexaenoic acid)-containing phospholipids is demonstrated using lipidomic approaches. Precursor scanning reverse-phase LC (liquid chromatography)-MS/MS (tandem MS) identified a new family of lipids that comprise phospholipid-esterified HDOHE (hydroxydocosahexaenoic acid). Two diacyl and two plasmalogen PEs (phosphatidylethanolamines) containing predominantly the 14-HDOHE positional isomer (18:0p/14-HDOHE-PE, 18:0a/14-HDOHE-PE, 16:0a/14-HDOHE-PE and 16:0p/14-HDOHE-PE) were structurally characterized using MS/MS and by comparison with biogenic standards. An involvement of 12-LOX was indicated as purified recombinant human 12-LOX also generated the 14-HDOHE isomer from DHA. Pharmacological studies using inhibitors and recombinant platelet 12-LOX indicate that they form via esterification of newly formed non-esterified HDOHE. HDOHE-PEs formed at significant rates (2-4 ng/4×10(7) cells) within 2-180 min of thrombin stimulation, and their formation was blocked by calcium chelation. In summary, a new family of oxidized phospholipid was identified in thrombin-activated human platelets.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weisz, Daniel A.; Gross, Michael L.; Pakrasi, Himadri B.

Photosystem II (PSII) is a photosynthetic membrane-protein complex that undergoes an intricate, tightly regulated cycle of assembly, damage, and repair. The available crystal structures of cyanobacterial PSII are an essential foundation for understanding PSII function, but nonetheless provide a snapshot only of the active complex. To study aspects of the entire PSII life-cycle, mass spectrometry (MS) has emerged as a powerful tool that can be used in conjunction with biochemical techniques. In this article, we present the MS-based approaches that are used to study PSII composition, dynamics, and structure, and review the information about the PSII life-cycle that has beenmore » gained by these methods. This information includes the composition of PSII subcomplexes, discovery of accessory PSII proteins, identification of post-translational modifications and quantification of their changes under various conditions, determination of the binding site of proteins not observed in PSII crystal structures, conformational changes that underlie PSII functions, and identification of water and oxygen channels within PSII. Lastly, we conclude with an outlook for the opportunity of future MS contributions to PSII research.« less

DESI-MS imaging and NMR spectroscopy to investigate the influence of biodiesel in the structure of commercial rubbers.

PubMed

Silva, Lorena M A; Alves Filho, Elenilson G; Simpson, André J; Monteiro, Marcos R; Cabral, Elaine; Ifa, Demian; Venâncio, Tiago

2017-10-01

Biodiesel has been introduced as an energetic matrix in several countries around the world. However, the affinity of biodiesel with the components of petrodiesel engines is a growing concern. In order to obtain information regarding the effect of biodiesel on the rubber structure, nuclear magnetic resonance technics under a new technology named as comprehensive multiphase (CMP NMR) and the imaging through desorption electrospray ionization mass spectrometry (DESI-MS imaging) were used. The 1 H CMP-DOSY NMR showed the entrapped fuel into the rubber cavities, which the higher constraint caused by the rubber structure is related to the smaller diffusion coefficient. The less affected type of rubber by biodiesel was ethylene-propylene-diene monomer (EPDM), and the most affected was synthetic rubber nitrile (NBR). The 13 C CMP MAS-SPE experiments also confirmed that the internal region of EPDM was less accessible to the biodiesel molecules (no fuels detected) while other rubbers were more susceptible to the penetration of the fuel. DESI-MS imaging revealed for the first time the topography of the rubbers exposed to fuels. The biodiesel molecules entrapped at the EPDM and NBR pores were in oxidized form, which might degrade the rubber structure at long exposure time. The employed technics enabled the study of dynamic and molecular structure of the mixing complex multiphase. The DOSY under CMP used in this study could prove helpful in assessing the interactions throughout all physical phases (liquid, solid, and gel or semi-solid) by observing swellability caused by the fuel in the rubber. In addition, the DESI-MS was especially valuable to detect the degradation products of biodiesel entangled at the rubber structure. In our knowledge, this was the first report in which chemical changes of commercial rubbers induced by biodiesel and petrodiesel were investigated by means of DESI-MS and DOSY NMR. Copyright © 2017 Elsevier B.V. All rights reserved.

Ion mobility spectrometry–mass spectrometry (IMS–MS) for on- and offline analysis of atmospheric gas and aerosol species

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krechmer, Jordan E.; Groessl, Michael; Zhang, Xuan

Measurement techniques that provide molecular-level information are needed to elucidate the multiphase processes that produce secondary organic aerosol (SOA) species in the atmosphere. Here we demonstrate the application of ion mobility spectrometry-mass spectrometry (IMS–MS) to the simultaneous characterization of the elemental composition and molecular structures of organic species in the gas and particulate phases. Molecular ions of gas-phase organic species are measured online with IMS–MS after ionization with a custom-built nitrate chemical ionization (CI) source. This CI–IMS–MS technique is used to obtain time-resolved measurements (5 min) of highly oxidized organic molecules during the 2013 Southern Oxidant and Aerosol Study (SOAS)more » ambient field campaign in the forested SE US. The ambient IMS–MS signals are consistent with laboratory IMS–MS spectra obtained from single-component carboxylic acids and multicomponent mixtures of isoprene and monoterpene oxidation products. Mass-mobility correlations in the 2-D IMS–MS space provide a means of identifying ions with similar molecular structures within complex mass spectra and are used to separate and identify monoterpene oxidation products in the ambient data that are produced from different chemical pathways. Water-soluble organic carbon (WSOC) constituents of fine aerosol particles that are not resolvable with standard analytical separation methods, such as liquid chromatography (LC), are shown to be separable with IMS–MS coupled to an electrospray ionization (ESI) source. The capability to use ion mobility to differentiate between isomers is demonstrated for organosulfates derived from the reactive uptake of isomers of isoprene epoxydiols (IEPOX) onto wet acidic sulfate aerosol. As a result, controlled fragmentation of precursor ions by collisionally induced dissociation (CID) in the transfer region between the IMS and the MS is used to validate MS peak assignments, elucidate structures of oligomers, and confirm the presence of the organosulfate functional group.« less

Ion mobility spectrometry–mass spectrometry (IMS–MS) for on- and offline analysis of atmospheric gas and aerosol species

DOE PAGES

Krechmer, Jordan E.; Groessl, Michael; Zhang, Xuan; ...

2016-07-25

Measurement techniques that provide molecular-level information are needed to elucidate the multiphase processes that produce secondary organic aerosol (SOA) species in the atmosphere. Here we demonstrate the application of ion mobility spectrometry-mass spectrometry (IMS–MS) to the simultaneous characterization of the elemental composition and molecular structures of organic species in the gas and particulate phases. Molecular ions of gas-phase organic species are measured online with IMS–MS after ionization with a custom-built nitrate chemical ionization (CI) source. This CI–IMS–MS technique is used to obtain time-resolved measurements (5 min) of highly oxidized organic molecules during the 2013 Southern Oxidant and Aerosol Study (SOAS)more » ambient field campaign in the forested SE US. The ambient IMS–MS signals are consistent with laboratory IMS–MS spectra obtained from single-component carboxylic acids and multicomponent mixtures of isoprene and monoterpene oxidation products. Mass-mobility correlations in the 2-D IMS–MS space provide a means of identifying ions with similar molecular structures within complex mass spectra and are used to separate and identify monoterpene oxidation products in the ambient data that are produced from different chemical pathways. Water-soluble organic carbon (WSOC) constituents of fine aerosol particles that are not resolvable with standard analytical separation methods, such as liquid chromatography (LC), are shown to be separable with IMS–MS coupled to an electrospray ionization (ESI) source. The capability to use ion mobility to differentiate between isomers is demonstrated for organosulfates derived from the reactive uptake of isomers of isoprene epoxydiols (IEPOX) onto wet acidic sulfate aerosol. As a result, controlled fragmentation of precursor ions by collisionally induced dissociation (CID) in the transfer region between the IMS and the MS is used to validate MS peak assignments, elucidate structures of oligomers, and confirm the presence of the organosulfate functional group.« less

Ion mobility spectrometry-mass spectrometry (IMS-MS) for on- and offline analysis of atmospheric gas and aerosol species

NASA Astrophysics Data System (ADS)

Krechmer, Jordan E.; Groessl, Michael; Zhang, Xuan; Junninen, Heikki; Massoli, Paola; Lambe, Andrew T.; Kimmel, Joel R.; Cubison, Michael J.; Graf, Stephan; Lin, Ying-Hsuan; Budisulistiorini, Sri H.; Zhang, Haofei; Surratt, Jason D.; Knochenmuss, Richard; Jayne, John T.; Worsnop, Douglas R.; Jimenez, Jose-Luis; Canagaratna, Manjula R.

2016-07-01

Measurement techniques that provide molecular-level information are needed to elucidate the multiphase processes that produce secondary organic aerosol (SOA) species in the atmosphere. Here we demonstrate the application of ion mobility spectrometry-mass spectrometry (IMS-MS) to the simultaneous characterization of the elemental composition and molecular structures of organic species in the gas and particulate phases. Molecular ions of gas-phase organic species are measured online with IMS-MS after ionization with a custom-built nitrate chemical ionization (CI) source. This CI-IMS-MS technique is used to obtain time-resolved measurements (5 min) of highly oxidized organic molecules during the 2013 Southern Oxidant and Aerosol Study (SOAS) ambient field campaign in the forested SE US. The ambient IMS-MS signals are consistent with laboratory IMS-MS spectra obtained from single-component carboxylic acids and multicomponent mixtures of isoprene and monoterpene oxidation products. Mass-mobility correlations in the 2-D IMS-MS space provide a means of identifying ions with similar molecular structures within complex mass spectra and are used to separate and identify monoterpene oxidation products in the ambient data that are produced from different chemical pathways. Water-soluble organic carbon (WSOC) constituents of fine aerosol particles that are not resolvable with standard analytical separation methods, such as liquid chromatography (LC), are shown to be separable with IMS-MS coupled to an electrospray ionization (ESI) source. The capability to use ion mobility to differentiate between isomers is demonstrated for organosulfates derived from the reactive uptake of isomers of isoprene epoxydiols (IEPOX) onto wet acidic sulfate aerosol. Controlled fragmentation of precursor ions by collisionally induced dissociation (CID) in the transfer region between the IMS and the MS is used to validate MS peak assignments, elucidate structures of oligomers, and confirm the presence of the organosulfate functional group.

Elucidation of a side reaction occurring during nitroxide-mediated polymerization of cyclic ketene acetals by tandem mass spectrometric end-group analysis of aliphatic polyesters.

PubMed

Albergaria Pereira, Bruna de Fátima; Tardy, Antoine; Monnier, Valérie; Guillaneuf, Yohann; Gigmes, Didier; Charles, Laurence

2015-12-15

In order to prevent side reactions while developing new polymerization processes, their mechanism has to be understood and one first key insight is the structure of the end-groups in polymeric by-products. The synthetic method scrutinized here is the nitroxide-mediated polymerization (NMP) of a cyclic ketene acetal, a promising alternative process to the production of polyesters. Polymer end-group characterization was performed by mass spectrometry (MS), combining elemental composition information derived from accurate mass data in the MS mode with fragmentation features recorded in the MS/MS mode. Electrospray was used as the ionization method to ensure the integrity of original chain terminations and a quadrupole time-of-flight (QTOF) instrument was employed for high-resolution mass measurements in both MS and tandem mass spectrometry (MS/MS) modes. Occurrence of side reactions in the studied polymerization method, first evidenced by an unusual increase in dispersity with conversion, was confirmed in MS with the detection of two polymeric impurities in addition to the expected species. Fragmentation rules were first established for this new polyester family in order to derive useful structural information from MS/MS data. In addition to a usual NMP by-product, the initiating group of the second polymeric impurities revealed the degradation of the nitroxide moiety. Unambiguous MS/MS identification of end-groups in by-products sampled from the polymerization medium allowed an unusual side reaction to be identified during the NMP preparation of polyesters. On-going optimization of the polymerization method aims at preventing this undesired process. Copyright © 2015 John Wiley & Sons, Ltd.

An integrated native mass spectrometry and top-down proteomics method that connects sequence to structure and function of macromolecular complexes

NASA Astrophysics Data System (ADS)

Li, Huilin; Nguyen, Hong Hanh; Ogorzalek Loo, Rachel R.; Campuzano, Iain D. G.; Loo, Joseph A.

2018-02-01

Mass spectrometry (MS) has become a crucial technique for the analysis of protein complexes. Native MS has traditionally examined protein subunit arrangements, while proteomics MS has focused on sequence identification. These two techniques are usually performed separately without taking advantage of the synergies between them. Here we describe the development of an integrated native MS and top-down proteomics method using Fourier-transform ion cyclotron resonance (FTICR) to analyse macromolecular protein complexes in a single experiment. We address previous concerns of employing FTICR MS to measure large macromolecular complexes by demonstrating the detection of complexes up to 1.8 MDa, and we demonstrate the efficacy of this technique for direct acquirement of sequence to higher-order structural information with several large complexes. We then summarize the unique functionalities of different activation/dissociation techniques. The platform expands the ability of MS to integrate proteomics and structural biology to provide insights into protein structure, function and regulation.

UPLC-MS/MS quantitative analysis and structural fragmentation study of five Parmotrema lichens from the Eastern Ghats.

PubMed

Kumar, K; Siva, Bandi; Sarma, V U M; Mohabe, Satish; Reddy, A Madhusudana; Boustie, Joel; Tiwari, Ashok K; Rao, N Rama; Babu, K Suresh

2018-07-15

Comparative phytochemical analysis of five lichen species [Parmotrema tinctorum (Delise ex Nyl.) Hale, P. andinum (Mull. Arg.) Hale, P. praesorediosum (Nyl.) Hale, P. grayanum (Hue) Hale, P. austrosinense (Zahlbr.) Hale] of Parmotrema genus were performed using two complementary UPLC-MS systems. The first system consists of high resolution UPLC-QToF-MS/MS spectrometer and the second system consisted of UPLC-MS/MS in Multiple Reaction Monitoring (MRM) mode for quantitative analysis of major constituents in the selected lichen species. The individual compounds (47 compounds) were identified using Q-ToF-MS/MS, via comparison of the exact molecular masses from their MS/MS spectra, the comparison of literature data and retention times to those of standard compounds which were isolated from crude extract of abundant lichen, P. tinctorum. The analysis also allowed us to identify unknown peaks/compounds, which were further characterized by their mass fragmentation studies. The quantitative MRM analysis was useful to have a better discrimination of species according to their chemical profile. Moreover, the determination of antioxidant activities (ABTS + inhibition) and Advance Glycation Endproducts (AGEs) inhibition carried out for the crude extracts revealed a potential antiglycaemic activity to be confirmed for P. austrosinense. Copyright © 2018 Elsevier B.V. All rights reserved.

General unknown screening procedure for the characterization of human drug metabolites in forensic toxicology: applications and constraints.

PubMed

Sauvage, François-Ludovic; Picard, Nicolas; Saint-Marcoux, Franck; Gaulier, Jean-Michel; Lachâtre, Gérard; Marquet, Pierre

2009-09-01

LC coupled to single (LC-MS) and tandem (LC-MS/MS) mass spectrometry is recognized as the most powerful analytical tools for metabolic studies in drug discovery. In this article, we describe five cases illustrating the utility of screening xenobiotic metabolites in routine analysis of forensic samples using LC-MS/MS. Analyses were performed using a previously published LC-MS/MS general unknown screening (GUS) procedure developed using a hybrid linear IT-tandem mass spectrometer. In each of the cases presented, the presence of metabolites of xenobiotics was suspected after analyzing urine samples. In two cases, the parent drug was also detected and the metabolites were merely useful to confirm drug intake, but in three other cases, metabolite detection was of actual forensic interest. The presented results indicate that: (i) the GUS procedure developed is useful to detect a large variety of drug metabolites, which would have been hardly detected using targeted methods in the context of clinical or forensic toxicology; (ii) metabolite structure can generally be inferred from their "enhanced" product ion scan spectra; and (iii) structure confirmation can be achieved through in vitro metabolic experiments or through the analysis of urine samples from individuals taking the parent drug.

A novel tandem mass spectrometry method for first-line screening of mainly beta-thalassemia from dried blood spots.

PubMed

Yu, Chaowen; Huang, Shuodan; Wang, Ming; Zhang, Juan; Liu, Hao; Yuan, Zhaojian; Wang, Xingbin; He, Xiaoyan; Wang, Jie; Zou, Lin

2017-02-10

Traditional methods for thalassemia screening are time-consuming and easily affected by cell hemolysis or hemoglobin degradation in stored blood samples. Tandem mass spectrometry (MS/MS) proved to be an effective technology for sickle cell disorders (SCD) screening. Here, we developed a novel MS/MS method for β-thalassemia screening from dried blood spots (DBS). Stable isotopic-labeled peptides were used as internal standards for quantification and calculation of the α:β-globin ratios. We used the α:β-globin ratio cutoffs to differentiate between normal individuals and patients with thalassemia. About 781 patients and 300 normal individuals were analyzed. The α:β-globin ratios showed significant difference between normal and β-thalassemia patients (P<0.01), particularly when the disease was homozygous or double heterozygous with another α- or β-thalassemia mutation. In the parallel study, all cases screened for suspected thalassemia from six hundred DBS samples by using this MS/MS method were successfully confirmed by genotyping. The intra-assay and inter-assay CVs of the ratios ranged from 2.4% to 3.9% and 4.7% to 7.1%, and there was no significant sample carryover or matrix effect for this MS/MS method. Combined with SCD screening, this MS/MS method could be used as a first-line screening assay for both structural and expression abnormalities of human hemoglobin. Traditional methods for thalassemia screening were depending on the structural integrity of tetramers and could be affected by hemolysis and degradation of whole blood samples, especially when stored. We used proteospecific peptides produced by the tryptic digestion of each globin to evaluate the production ratio between α- and β-globin chains, which turned out to be quite stable even when stored for more than two months. Though most of the peptides were specific to α-globin or β-globin, we only chose four most informative peptides and its stable isotopic-labeled peptides as internal standards for analysis, which could obtain a high accuracy. Currently, we are the first to address the application of MS/MS for thalassemia screening, when combined with SCD screening, this MS/MS method could be used as a first-line screening assay for both structural and expression abnormalities of human hemoglobin. Copyright © 2016. Published by Elsevier B.V.

Evaluating Barriers to Adherence to Dietary Recommendations in Iranian Adults with Metabolic Syndrome: A Qualitative Study Using the Theory of Reasoned Action.

PubMed

Esmaeili, Naseh; Alizadeh, Mohammad; Tarighat Esfanjani, Ali; Kheirouri, Sorayya

2016-07-01

Metabolic syndrome (MS) is defined as a pattern of metabolic disorders including central obesity, insulin resistance or hyperglycemia, high blood pressure, and dyslipidemia. Many studies show a clear relationship between diet and components of MS. The aim of the current study was to identify barriers to adherence to dietary recommendations among Iranian MS patients. The theory of reasoned action (TRA) served as the framework for this qualitative study. Data collection was conducted through six semi-structured focus group discussions, from Apr to Jun 2013. Subjects included 36 married men and women with different levels of education between the ages of 20-50 with MS diagnosed based on IDF's (International Diabetes federation) criteria. All focus group discussions were audio recorded and transcribed. The thematic content analysis method was used to analyze the study data. This study identified the most important barriers to adherence to dietary recommendations. MS patients have problems in their attitude toward MS components and their relationship to nutrition. They also had wrong attitudes toward fats and oils, salt, dairy products, cereals, and sugary drinks and sweets. Subjective norms that affects patient eating identifies too. We identified barriers to adherence to dietary recommendations in MS patients that could be used to prevent MS consequences and provide patients with nutrition education.

Evaluating Barriers to Adherence to Dietary Recommendations in Iranian Adults with Metabolic Syndrome: A Qualitative Study Using the Theory of Reasoned Action

PubMed Central

ESMAEILI, Naseh; ALIZADEH, Mohammad; TARIGHAT ESFANJANI, Ali; KHEIROURI, Sorayya

2016-01-01

Background: Metabolic syndrome (MS) is defined as a pattern of metabolic disorders including central obesity, insulin resistance or hyperglycemia, high blood pressure, and dyslipidemia. Many studies show a clear relationship between diet and components of MS. The aim of the current study was to identify barriers to adherence to dietary recommendations among Iranian MS patients. Methods: The theory of reasoned action (TRA) served as the framework for this qualitative study. Data collection was conducted through six semi-structured focus group discussions, from Apr to Jun 2013. Subjects included 36 married men and women with different levels of education between the ages of 20–50 with MS diagnosed based on IDF’s (International Diabetes federation) criteria. All focus group discussions were audio recorded and transcribed. The thematic content analysis method was used to analyze the study data. Results: This study identified the most important barriers to adherence to dietary recommendations. MS patients have problems in their attitude toward MS components and their relationship to nutrition. They also had wrong attitudes toward fats and oils, salt, dairy products, cereals, and sugary drinks and sweets. Subjective norms that affects patient eating identifies too. Conclusion: We identified barriers to adherence to dietary recommendations in MS patients that could be used to prevent MS consequences and provide patients with nutrition education. PMID:27517000

Profiling N-glycans of the egg jelly coat of the sea urchin Paracentrotus lividus by MALDI-TOF mass spectrometry and capillary liquid chromatography electrospray ionization-ion trap tandem mass spectrometry systems.

PubMed

Şahar, Umut; Deveci, Remziye

2017-05-01

Sea urchin eggs are surrounded by a carbohydrate-rich layer, termed the jelly coat, that consists of polysaccharides and glycoproteins. In the present study, we describe two mass spectrometric strategies to characterize the N-glycosylation of the Paracentrotus lividus egg jelly coat, which has an alecithal-type extracellular matrix like mammalian eggs. Egg jelly was isolated, lyophilized, and dialyzed, followed by peptide N-glycosidase F (PNGase-F) treatment to release N-glycans from their protein chain. These N-glycans were then derivatized by permethylation reaction, and analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and capillary liquid chromatography electrospray ionization-ion trap tandem mass spectroscopy (CapLC ESI-Ion trap-MS/MS). N-glycans in the egg jelly coat glycoproteins were indicated by sodiated molecules at m/z 1579.8, 1783.9, 1988.0, 2192.0, and 2397.1 for permethylated oligosaccharides on MALDI-TOF MS. Fragmentation and structural characterization of these oligosaccharides were performed by ESI-Ion trap MS/MS. Then, MALDI-TOF-MS and ESI-Ion trap-MS/MS spectra were interpreted using the GlycoWorkbench software suite, a tool for building, displaying, and profiling glycan masses, to identify the original oligosaccharide structures. The oligosaccharides of the isolated egg jelly coat were mainly of the high mannose type. © 2017 Wiley Periodicals, Inc.

Characterization of photo-transformation products of the antibiotic drug Ciprofloxacin with liquid chromatography-tandem mass spectrometry in combination with accurate mass determination using an LTQ-Orbitrap.

PubMed

Haddad, Tarek; Kümmerer, Klaus

2014-11-01

The presence of pharmaceuticals, especially antibiotics, in the aquatic environment is of growing concern. Several studies have been carried out on the occurrence and environmental risk of these compounds. Ciprofloxacin (CIP), a broad-spectrum anti-microbial second-generation fluoroquinolone, is widely used in human and veterinary medicine. In this work, photo-degradation of CIP in aqueous solution using UV and xenon lamps was studied. The transformation products (TPs), created from CIP, were initially analyzed by an ion trap in the MS, MS/MS and MS(3) modes. These data were used to clarify the structures of the degradation products. Furthermore, the proposed products were confirmed by accurate mass measurement and empirical formula calculation for the molecular ions of TPs using LTQ-Orbitrap XL mass spectrometer. The degree of mineralization, the abundance of detected TPs and degradation pathways were determined. Eleven TPs were detected in the present study. TP1, which was never detected before, was structurally characterized in this work. All TPs still retained the core quinolone structure, which is responsible for the biological activity. As mineralization of CIP and its transformation products did not happen, the formation of stable TPs can be expected in waste water treatment and in surface water with further follow-up problems. Copyright © 2014 Elsevier Ltd. All rights reserved.

One drop chemical derivatization--DESI-MS analysis for metabolite structure identification.

PubMed

Lubin, Arnaud; Cabooter, Deirdre; Augustijns, Patrick; Cuyckens, Filip

2015-07-01

Structural elucidation of metabolites is an important part during the discovery and development process of new pharmaceutical drugs. Liquid Chromatography (LC) in combination with Mass Spectrometry (MS) is usually the technique of choice for structural identification but cannot always provide precise structural identification of the studied metabolite (e.g. site of hydroxylation and site of glucuronidation). In order to identify those metabolites, different approaches are used combined with MS data including nuclear magnetic resonance, hydrogen/deuterium exchange and chemical derivatization followed by LC-MS. Those techniques are often time-consuming and/or require extra sample pre-treatment. In this paper, a fast and easy to set up tool using desorption electrospray ionization-MS for metabolite identification is presented. In the developed method, analytes in solution are simply dried on a glass plate with printed Teflon spots and then a single drop of derivatization mixture is added. Once the spot is dried, the derivatized compound is analyzed. Six classic chemical derivatizations were adjusted to work as a one drop reaction and applied on a list of compounds with relevant functional groups. Subsequently, two successive reactions on a single spot of amoxicillin were tested and the methodology described was successfully applied on an in vitro incubated alprazolam metabolite. All reactions and analyses were performed within an hour and gave useful structural information by derivatizing functional groups, making the method a time-saving and efficient tool for metabolite identification if used in addition or in some cases as an alternative to common methods. Copyright © 2015 John Wiley & Sons, Ltd.

Native Mass Spectrometry: What is in the Name?

NASA Astrophysics Data System (ADS)

Leney, Aneika C.; Heck, Albert J. R.

2017-01-01

Electrospray ionization mass spectrometry (ESI-MS) is nowadays one of the cornerstones of biomolecular mass spectrometry and proteomics. Advances in sample preparation and mass analyzers have enabled researchers to extract much more information from biological samples than just the molecular weight. In particular, relevant for structural biology, noncovalent protein-protein and protein-ligand complexes can now also be analyzed by MS. For these types of analyses, assemblies need to be retained in their native quaternary state in the gas phase. This initial small niche of biomolecular mass spectrometry, nowadays often referred to as "native MS," has come to maturation over the last two decades, with dozens of laboratories using it to study mostly protein assemblies, but also DNA and RNA-protein assemblies, with the goal to define structure-function relationships. In this perspective, we describe the origins of and (re)define the term native MS, portraying in detail what we meant by "native MS," when the term was coined and also describing what it does (according to us) not entail. Additionally, we describe a few examples highlighting what native MS is, showing its successes to date while illustrating the wide scope this technology has in solving complex biological questions.

Effects of cannabis on cognition in patients with MS: a psychometric and MRI study.

PubMed

Pavisian, Bennis; MacIntosh, Bradley J; Szilagyi, Greg; Staines, Richard W; O'Connor, Paul; Feinstein, Anthony

2014-05-27

To determine functional and structural neuroimaging correlates of cognitive dysfunction associated with cannabis use in multiple sclerosis (MS). In a cross-sectional study, 20 subjects with MS who smoked cannabis and 19 noncannabis users with MS, matched on demographic and neurologic variables, underwent fMRI while completing a test of working memory, the N-Back. Resting-state fMRI and structural MRI data (lesion and normal-appearing brain tissue volumes, diffusion tensor imaging metrics) were also collected. Neuropsychological data pertaining to verbal (Selective Reminding Test Revised) and visual (10/36 Spatial Recall Test) memory, information processing speed (Paced Auditory Serial Addition Test [2- and 3-second versions] and Symbol Digit Modalities Test), and attention (Word List Generation) were obtained. The cannabis group performed more poorly on the more demanding of the Paced Auditory Serial Addition Test tasks (i.e., 2-second version) (p < 0.02) and the 10/36 Spatial Recall Test (p < 0.03). Cannabis users had more diffuse cerebral activation across all N-Back trials and made more errors on the 2-Back task (p < 0.006), during which they displayed increased activation relative to nonusers in parietal (p < 0.007) and anterior cingulate (p < 0.001) regions implicated in working memory. No group differences in resting-state networks or structural MRI variables were found. Patients with MS who smoke cannabis are more cognitively impaired than nonusers. Cannabis further compromises cerebral compensatory mechanisms, already faulty in MS. These imaging data boost the construct validity of the neuropsychological findings and act as a cautionary note to cannabis users and prescribers. © 2014 American Academy of Neurology.

Fast transient analysis and first-stage collision-induced dissociation with the flowing atmospheric-pressure afterglow ionization source to improve analyte detection and identification.

PubMed

Shelley, Jacob T; Hieftje, Gary M

2010-04-01

The recent development of ambient desorption/ionization mass spectrometry (ADI-MS) has enabled fast, simple analysis of many different sample types. The ADI-MS sources have numerous advantages, including little or no required sample pre-treatment, simple mass spectra, and direct analysis of solids and liquids. However, problems of competitive ionization and limited fragmentation require sample-constituent separation, high mass accuracy, and/or tandem mass spectrometry (MS/MS) to detect, identify, and quantify unknown analytes. To maintain the inherent high throughput of ADI-MS, it is essential for the ion source/mass analyzer combination to measure fast transient signals and provide structural information. In the current study, the flowing atmospheric-pressure afterglow (FAPA) ionization source is coupled with a time-of-flight mass spectrometer (TOF-MS) to analyze fast transient signals (<500 ms FWHM). It was found that gas chromatography (GC) coupled with the FAPA source resulted in a reproducible (<5% RSD) and sensitive (detection limits of <6 fmol for a mixture of herbicides) system with analysis times of ca. 5 min. Introducing analytes to the FAPA in a transient was also shown to significantly reduce matrix effects caused by competitive ionization by minimizing the number and amount of constituents introduced into the ionization source. Additionally, MS/MS with FAPA-TOF-MS, enabling analyte identification, was performed via first-stage collision-induced dissociation (CID). Lastly, molecular and structural information was obtained across a fast transient peak by modulating the conditions that caused the first-stage CID.

Neutral Loss Scan - Based Strategy for Integrated Identification of Amorfrutin Derivatives, New Peroxisome Proliferator-Activated Receptor Gamma Agonists, from Amorpha Fruticosa by UPLC-QqQ-MS/MS and UPLC-Q-TOF-MS.

PubMed

Chen, Chu; Xue, Ying; Li, Qing-Miao; Wu, Yan; Liang, Jian; Qing, Lin-Sen

2018-04-01

Amorfrutins with a 2-hydroxybenzoic acid core structure are promising natural PPARγ agonists with potent antidiabetic activity. Owing to the complex matrix and low concentration in botanical material, the identification of unknown amorfrutins remains a challenge. In the present study, a combined application of UPLC-Q-TOF-MS and UPLC-QqQ-MS was developed to discover unknown amorfrutins from fruits of Amorpha fruticosa. First, reference compounds of amorfrutin A (AA), amorfrutin B (AB), and 2-carboxy-3,5-dihydroxy-4-geranylbibenzyl (AC) were analyzed using UPLC-Q-TOF-MS to reveal the characteristic fragment ions and the possible neutral loss. Second, the extract of A. fruticosa was separated and screened by UPLC-QqQ-MS using neutral loss scan to find out suspect compounds associated with the specified neutral fragment Δm/z 44. Third, the extract was re-analyzed by UPLC-Q-TOF-MS to obtain the exact mass of quasi-molecular ion and fragment ions of each suspect compound, and to subsequently calculate their corresponding molecular formulas. Finally, according to the molecular formula of suspect compound and its fragment ions and comparing with literature data, structure elucidation of four unidentified amorfrutins was achieved. The results indicated that the combination of QqQ-MS neutral loss scan and Q-TOF-MS molecular formula calculation was proven to be a powerful tool for unknown natural product identification, and this strategy provides an effective solution to discover natural products or metabolites of trace content. Graphical Abstract ᅟ.

Neutral Loss Scan - Based Strategy for Integrated Identification of Amorfrutin Derivatives, New Peroxisome Proliferator-Activated Receptor Gamma Agonists, from Amorpha Fruticosa by UPLC-QqQ-MS/MS and UPLC-Q-TOF-MS

NASA Astrophysics Data System (ADS)

Chen, Chu; Xue, Ying; Li, Qing-Miao; Wu, Yan; Liang, Jian; Qing, Lin-Sen

2018-02-01

Amorfrutins with a 2-hydroxybenzoic acid core structure are promising natural PPARγ agonists with potent antidiabetic activity. Owing to the complex matrix and low concentration in botanical material, the identification of unknown amorfrutins remains a challenge. In the present study, a combined application of UPLC-Q-TOF-MS and UPLC-QqQ-MS was developed to discover unknown amorfrutins from fruits of Amorpha fruticosa. First, reference compounds of amorfrutin A (AA), amorfrutin B (AB), and 2-carboxy-3,5-dihydroxy-4-geranylbibenzyl (AC) were analyzed using UPLC-Q-TOF-MS to reveal the characteristic fragment ions and the possible neutral loss. Second, the extract of A. fruticosa was separated and screened by UPLC-QqQ-MS using neutral loss scan to find out suspect compounds associated with the specified neutral fragment Δm/z 44. Third, the extract was re-analyzed by UPLC-Q-TOF-MS to obtain the exact mass of quasi-molecular ion and fragment ions of each suspect compound, and to subsequently calculate their corresponding molecular formulas. Finally, according to the molecular formula of suspect compound and its fragment ions and comparing with literature data, structure elucidation of four unidentified amorfrutins was achieved. The results indicated that the combination of QqQ-MS neutral loss scan and Q-TOF-MS molecular formula calculation was proven to be a powerful tool for unknown natural product identification, and this strategy provides an effective solution to discover natural products or metabolites of trace content.

Propagating annotations of molecular networks using in silico fragmentation

PubMed Central

da Silva, Ricardo R.; Wang, Mingxun; Fox, Evan; Balunas, Marcy J.; Klassen, Jonathan L.; Dorrestein, Pieter C.

2018-01-01

The annotation of small molecules is one of the most challenging and important steps in untargeted mass spectrometry analysis, as most of our biological interpretations rely on structural annotations. Molecular networking has emerged as a structured way to organize and mine data from untargeted tandem mass spectrometry (MS/MS) experiments and has been widely applied to propagate annotations. However, propagation is done through manual inspection of MS/MS spectra connected in the spectral networks and is only possible when a reference library spectrum is available. One of the alternative approaches used to annotate an unknown fragmentation mass spectrum is through the use of in silico predictions. One of the challenges of in silico annotation is the uncertainty around the correct structure among the predicted candidate lists. Here we show how molecular networking can be used to improve the accuracy of in silico predictions through propagation of structural annotations, even when there is no match to a MS/MS spectrum in spectral libraries. This is accomplished through creating a network consensus of re-ranked structural candidates using the molecular network topology and structural similarity to improve in silico annotations. The Network Annotation Propagation (NAP) tool is accessible through the GNPS web-platform https://gnps.ucsd.edu/ProteoSAFe/static/gnps-theoretical.jsp. PMID:29668671

Propagating annotations of molecular networks using in silico fragmentation.

PubMed

da Silva, Ricardo R; Wang, Mingxun; Nothias, Louis-Félix; van der Hooft, Justin J J; Caraballo-Rodríguez, Andrés Mauricio; Fox, Evan; Balunas, Marcy J; Klassen, Jonathan L; Lopes, Norberto Peporine; Dorrestein, Pieter C

2018-04-01

The annotation of small molecules is one of the most challenging and important steps in untargeted mass spectrometry analysis, as most of our biological interpretations rely on structural annotations. Molecular networking has emerged as a structured way to organize and mine data from untargeted tandem mass spectrometry (MS/MS) experiments and has been widely applied to propagate annotations. However, propagation is done through manual inspection of MS/MS spectra connected in the spectral networks and is only possible when a reference library spectrum is available. One of the alternative approaches used to annotate an unknown fragmentation mass spectrum is through the use of in silico predictions. One of the challenges of in silico annotation is the uncertainty around the correct structure among the predicted candidate lists. Here we show how molecular networking can be used to improve the accuracy of in silico predictions through propagation of structural annotations, even when there is no match to a MS/MS spectrum in spectral libraries. This is accomplished through creating a network consensus of re-ranked structural candidates using the molecular network topology and structural similarity to improve in silico annotations. The Network Annotation Propagation (NAP) tool is accessible through the GNPS web-platform https://gnps.ucsd.edu/ProteoSAFe/static/gnps-theoretical.jsp.

Molecular Simulation-Based Structural Prediction of Protein Complexes in Mass Spectrometry: The Human Insulin Dimer

PubMed Central

Li, Jinyu; Rossetti, Giulia; Dreyer, Jens; Raugei, Simone; Ippoliti, Emiliano; Lüscher, Bernhard; Carloni, Paolo

2014-01-01

Protein electrospray ionization (ESI) mass spectrometry (MS)-based techniques are widely used to provide insight into structural proteomics under the assumption that non-covalent protein complexes being transferred into the gas phase preserve basically the same intermolecular interactions as in solution. Here we investigate the applicability of this assumption by extending our previous structural prediction protocol for single proteins in ESI-MS to protein complexes. We apply our protocol to the human insulin dimer (hIns2) as a test case. Our calculations reproduce the main charge and the collision cross section (CCS) measured in ESI-MS experiments. Molecular dynamics simulations for 0.075 ms show that the complex maximizes intermolecular non-bonded interactions relative to the structure in water, without affecting the cross section. The overall gas-phase structure of hIns2 does exhibit differences with the one in aqueous solution, not inferable from a comparison with calculated CCS. Hence, care should be exerted when interpreting ESI-MS proteomics data based solely on NMR and/or X-ray structural information. PMID:25210764

Resting State Brain Entropy Alterations in Relapsing Remitting Multiple Sclerosis.

PubMed

Zhou, Fuqing; Zhuang, Ying; Gong, Honghan; Zhan, Jie; Grossman, Murray; Wang, Ze

2016-01-01

Brain entropy (BEN) mapping provides a novel approach to characterize brain temporal dynamics, a key feature of human brain. Using resting state functional magnetic resonance imaging (rsfMRI), reliable and spatially distributed BEN patterns have been identified in normal brain, suggesting a potential use in clinical populations since temporal brain dynamics and entropy may be altered in disease conditions. The purpose of this study was to characterize BEN in multiple sclerosis (MS), a neurodegenerative disease that affects millions of people. Since currently there is no cure for MS, developing treatment or medication that can slow down its progression represents a high research priority, for which validating a brain marker sensitive to disease and the related functional impairments is essential. Because MS can start long time before any measurable symptoms and structural deficits, assessing the dynamic brain activity and correspondingly BEN may provide a critical way to study MS and its progression. Because BEN is new to MS, we aimed to assess BEN alterations in the relapsing-remitting MS (RRMS) patients using a patient versus control design, to examine the correlation of BEN to clinical measurements, and to check the correlation of BEN to structural brain measures which have been more often used in MS studies. As compared to controls, RRMS patients showed increased BEN in motor areas, executive control area, spatial coordinating area, and memory system. Increased BEN was related to greater disease severity as measured by the expanded disability status scale (EDSS) and greater tissue damage as indicated by the mean diffusivity. Patients also showed decreased BEN in other places, which was associated with less disability or fatigue, indicating a disease-related BEN re-distribution. Our results suggest BEN as a novel and useful tool for characterizing RRMS.

Isoprenoid Alcohols are Susceptible to Oxidation with Singlet Oxygen and Hydroxyl Radicals.

PubMed

Komaszylo Née Siedlecka, Joanna; Kania, Magdalena; Masnyk, Marek; Cmoch, Piotr; Lozinska, Iwona; Czarnocki, Zbigniew; Skorupinska-Tudek, Karolina; Danikiewicz, Witold; Swiezewska, Ewa

2016-02-01

Isoprenoids, as common constituents of all living cells, are exposed to oxidative agents--reactive oxygen species, for example, singlet oxygen or hydroxyl radicals. Despite this fact, products of oxidation of polyisoprenoids have never been characterized. In this study, chemical oxidation of isoprenoid alcohols (Prenol-2 and -10) was performed using singlet oxygen (generated in the presence of hydrogen peroxide/molybdate or upon photochemical reaction in the presence of porphyrin), oxygen (formed upon hydrogen peroxide dismutation) or hydroxyl radical (generated by the hydrogen peroxide/sonication, UV/titanium dioxide or UV/hydrogen peroxide) systems. The structure of the obtained products, hydroxy-, peroxy- and heterocyclic derivatives, was studied with the aid of mass spectrometry (MS) and nuclear magnetic resonance (NMR) methods. Furthermore, mass spectrometry with electrospray ionization appeared to be a useful analytical tool to detect the products of oxidation of isoprenoids (ESI-MS analysis), as well as to establish their structure on the basis of the fragmentation spectra of selected ions (ESI-MS/MS analysis). Taken together, susceptibility of polyisoprenoid alcohols to various oxidizing agents was shown for the first time.

Structural elucidation of new urinary tamoxifen metabolites by liquid chromatography quadrupole time-of-flight mass spectrometry.

PubMed

Lu, Jianghai; He, Chunji; He, Genye; Wang, Xiaobing; Xu, Youxuan; Wu, Yun; Dong, Ying; Ouyang, Gangfeng

2014-07-01

In this study, tamoxifen metabolic profiles were investigated carefully. Tamoxifen was administered to two healthy male volunteers and one female patient suffering from breast cancer. Urinary extracts were analyzed by liquid chromatography quadruple time-of-flight mass spectrometry using full scan and targeted MS/MS techniques with accurate mass measurement. Chromatographic peaks for potential metabolites were selected by using the theoretical [M + H](+) as precursor ion in full-scan experiment and m/z 72, 58 or 44 as characteristic product ions for N,N-dimethyl, N-desmethyl and N,N-didesmethyl metabolites in targeted MS/MS experiment, respectively. Tamoxifen and 37 metabolites were detected in extraction study samples. Chemical structures of seven unreported metabolites were elucidated particularly on the basis of fragmentation patterns observed for these metabolites. Several metabolic pathways containing mono- and di-hydroxylation, methoxylation, N-desmethylation, N,N-didesmethylation, oxidation and combinations were suggested. All the metabolites were detected in the urine samples up to 1 week. Copyright © 2014 John Wiley & Sons, Ltd.

Reduced rich-club connectivity is related to disability in primary progressive MS

PubMed Central

Hodecker, Sibylle; Cheng, Bastian; Wanke, Nadine; Young, Kim Lea; Hilgetag, Claus; Gerloff, Christian; Heesen, Christoph; Thomalla, Götz; Siemonsen, Susanne

2017-01-01

Objective: To investigate whether the structural connectivity of the brain's rich-club organization is altered in patients with primary progressive MS and whether such changes to this fundamental network feature are associated with disability measures. Methods: We recruited 37 patients with primary progressive MS and 21 healthy controls for an observational cohort study. Structural connectomes were reconstructed based on diffusion-weighted imaging data using probabilistic tractography and analyzed with graph theory. Results: We observed the same topological organization of brain networks in patients and controls. Consistent with the originally defined rich-club regions, we identified superior frontal, precuneus, superior parietal, and insular cortex in both hemispheres as rich-club nodes. Connectivity within the rich club was significantly reduced in patients with MS (p = 0.039). The extent of reduced rich-club connectivity correlated with clinical measurements of mobility (Kendall rank correlation coefficient τ = −0.20, p = 0.047), hand function (τ = −0.26, p = 0.014), and information processing speed (τ = −0.20, p = 0.049). Conclusions: In patients with primary progressive MS, the fundamental organization of the structural connectome in rich-club and peripheral nodes was preserved and did not differ from healthy controls. The proportion of rich-club connections was altered and correlated with disability measures. Thus, the rich-club organization of the brain may be a promising network phenotype for understanding the patterns and mechanisms of neurodegeneration in MS. PMID:28804744

Liquid chromatography/mass spectrometry-based plasma metabolic profiling study of escitalopram in subjects with major depressive disorder.

PubMed

Bandu, Raju; Lee, Hyun Jeong; Lee, Hyeong Min; Ha, Tae Hyon; Lee, Heon-Jeong; Kim, Se Joo; Ha, Kyooseob; Kim, Kwang Pyo

2018-05-01

Liquid chromatography-mass spectrometry (LC-MS) method revealed the plasma metabolite profiles in major depressive disorder patients treated with escitalopram (ECTP) (n = 7). Depression severity was assessed according to the 17-item Hamilton Depression Rating Scale. Metabolic profiles were derived from major depressive disorder subject blood samples collected after ECTP treatment. Blood plasma was separated and processed in order to effectively extract metabolites, which were then analyzed using LC-MS. We identified 19 metabolites and elucidated their structures using LC-tandem MS (LC-MS/MS) combined with elemental compositions derived from accurate mass measurements. We further used online H/D exchange experiments to verify the structural elucidations of each metabolite. Identifying molecular metabolites may provide critical insights into the pharmacological and clinical effects of ECTP treatment and may also provide useful information informing the development of new antidepressant treatments. These detailed plasma metabolite analyses may also be used to identify optimal dose concentrations in psychopharmacotherapeutic treatment through drug monitoring, as well as forming the basis for response predictions in depressed subjects. Copyright © 2018 John Wiley & Sons, Ltd.

The effects of Bi4Ti3O12 interfacial ferroelectric layer on the dielectric properties of Au/n-Si structures

NASA Astrophysics Data System (ADS)

Gökçen, Muharrem; Yıldırım, Mert

2015-06-01

Au/n-Si metal-semiconductor (MS) and Au/Bi4Ti3O12/n-Si metal-ferroelectric-semiconductor (MFS) structures were fabricated and admittance measurements were held between 5 kHz and 1 MHz at room temperature so that dielectric properties of these structures could be investigated. The ferroelectric interfacial layer Bi4Ti3O12 decreased the polarization voltage by providing permanent dipoles at metal/semiconductor interface. Depending on different mechanisms, dispersion behavior was observed in dielectric constant, dielectric loss and loss tangent versus bias voltage plots of both MS and MFS structures. The real and imaginary parts of complex modulus of MFS structure take smaller values than those of MS structure, because permanent dipoles in ferroelectric layer cause a large spontaneous polarization mechanism. While the dispersion in AC conductivity versus frequency plots of MS structure was observed at high frequencies, for MFS structure it was observed at lower frequencies.

Social aspects of multiple sclerosis for Iranian individuals.

PubMed

Abolhassani, Shahla; Yazdannik, Ahmadreza; Taleghani, Fariba; Zamani, Ahmadreza

2015-01-01

This study aimed to determine the social aspects of multiple sclerosis (MS) in the Iranian individuals. A qualitative case study approach was used for this study, which is a part of a larger qualitative study about health care delivery system of MS. Participants were selected on the basis of purposive sampling method. Semi-structured interviews regarding the social aspects of MS were conducted with 18 MS patients, 6 family members and 7 health care providers. Besides interviews with the participants, documents related to the aim of the study, including weblogs, MS magazines, special websites of individuals with MS and news agencies. Data analysis was performed using the qualitative content analysis technique. Data obtained has been categorised into five main categories, including confronting stigma symbols, the outcome of stigma, walling-in due to stigma, disturbance in normal life and concern about job. There are multiple social effects of MS on the afflicted individuals, which affect various dimensions of their life. Policy makers and health care providers must also consider these effects of MS on other dimensions of the individuals' life. Implications for Rehabilitation Multiple sclerosis (MS) is a disease which restricts social life for patients, in addition to physical impacts. Individuals with MS experienced stigma as well as problems with employment and marital life, due to improper information about MS in society. We recommend that health care workers offer proper information about MS to patients and their family members to minimise the social problems faced by them. We recommend that mass media offers proper information about MS to people in society to disseminate the correct picture of MS. We recommend that the rehabilitation team offers psychological support to patients and their families for their empowerment, to facilitate dealing with the impacts of the disease. We recommend that health care providers teach the family members about patient support and communication skills.

Isomer separation and effect of the degree of polymerization on the gas-phase structure of chondroitin sulfate oligosaccharides analyzed by ion mobility and tandem mass spectrometry.

PubMed

Poyer, Salomé; Lopin-Bon, Chrystel; Jacquinet, Jean-Claude; Salpin, Jean-Yves; Daniel, Régis

2017-12-15

Chondroitin sulfate (CS) glycosaminoglycans are bioactive sulfated polysaccharides comprising repeating units of uronic acid and N-acetyl galactose sulfated at various positions. The optimal length and sulfation pattern of the CS bioactive sequences remain elusive so that structure-activity relationships cannot be easily established. Development of efficient analytical methods allowing the differentiation of the various sulfation patterns of CS sequences is therefore of particular importance to correlate their biological functions to the sulfation pattern. Discrimination of different oligomers (dp2 to dp6) of synthetic chondroitin sulfate isomers was evaluated by electrospray ionization tandem mass spectrometry (ESI-MS/MS) in the negative-ion mode from deprotonated and alkali adduct species. In addition, ion mobility mass spectrometry (IMS-MS) was used to study the influence of both the degree of polymerization and sulfate group location on the gas-phase conformation of CS oligomers. ESI-MS/MS spectra of chondroitin sulfate isomers show characteristic product ions exclusively from alkali adduct species (Li, Na, K and Cs). Whatever the alkali adducts studied, MS/MS of chondroitin oligosaccharides sulfated at position 6 yields a specific product ion at m/z 139 while CS oligosaccharides sulfated at position 4 show a specific product ion at m/z 154. Being observed for the different CS oligomers di-, tetra- and hexasaccharides, these fragment ions are considered as diagnostic ions for chondroitin 6-O-sulfate and chondroitin 4-O-sulfate, respectively. IMS-MS experiments reveal that collision cross-sections (CCS) of CS oligomers with low charge states evolved linearly with degrees of polymerization indicating a similar gas-phase conformation. This study allows the fast and unambiguous differentiation of CS isomers sulfated at position 6 or 4 for both saturated and unsaturated analogues from MS/MS experiments. In addition, the CCS linear evolution of CS oligomers in function of the degree of polymerization indicates that no folding occurs even for hexasaccharides. Copyright © 2017 John Wiley & Sons, Ltd.

Optimization and application of atmospheric pressure chemical and photoionization hydrogen-deuterium exchange mass spectrometry for speciation of oxygen-containing compounds.

PubMed

Acter, Thamina; Kim, Donghwi; Ahmed, Arif; Jin, Jang Mi; Yim, Un Hyuk; Shim, Won Joon; Kim, Young Hwan; Kim, Sunghwan

2016-05-01

This paper presents a detailed investigation of the feasibility of optimized positive and negative atmospheric pressure chemical ionization (APCI) mass spectrometry (MS) and atmospheric pressure photoionization (APPI) MS coupled to hydrogen-deuterium exchange (HDX) for structural assignment of diverse oxygen-containing compounds. The important parameters for optimization of HDX MS were characterized. The optimized techniques employed in the positive and negative modes showed satisfactory HDX product ions for the model compounds when dichloromethane and toluene were employed as a co-solvent in APCI- and APPI-HDX, respectively. The evaluation of the mass spectra obtained from 38 oxygen-containing compounds demonstrated that the extent of the HDX of the ions was structure-dependent. The combination of information provided by different ionization techniques could be used for better speciation of oxygen-containing compounds. For example, (+) APPI-HDX is sensitive to compounds with alcohol, ketone, or aldehyde substituents, while (-) APPI-HDX is sensitive to compounds with carboxylic functional groups. In addition, the compounds with alcohol can be distinguished from other compounds by the presence of exchanged peaks. The combined information was applied to study chemical compositions of degraded oils. The HDX pattern, double bond equivalent (DBE) distribution, and previously reported oxidation products were combined to predict structures of the compounds produced from oxidation of oil. Overall, this study shows that APCI- and APPI-HDX MS are useful experimental techniques that can be applied for the structural analysis of oxygen-containing compounds.

Structural Studies of MS2 Bacteriophage Virus Particle Disassembly by Nuclear Magnetic Resonance Relaxation Measurements

PubMed Central

Anobom, C. D.; Albuquerque, S. C.; Albernaz, F. P.; Oliveira, A. C.; Silva, J. L.; Peabody, D. S.; Valente, A. P.; Almeida, F. C. L.

2003-01-01

In this article we studied, by nuclear magnetic resonance relaxation measurements, the disassembly of a virus particle—the MS2 bacteriophage. MS2 is one of the single-stranded RNA bacteriophages that infect Escherichia coli. At pH 4.5, the phage turns to a metastable state, as is indicated by an increase in the observed nuclear magnetic resonance signal intensity upon decreasing the pH from 7.0 to 4.5. Steady-state fluorescence and circular dichroism spectra at pH 4.5 show that the difference in conformation and secondary structure is not pronounced if compared with the phage at pH 7.0. At pH 4.5, two-dimensional 15N-1H heteronuclear multiple quantum coherence (HMQC) spectrum shows ∼40 crosspeaks, corresponding to the most mobile residues of MS2 coat protein at pH 4.5. The 15N linewidth is ∼30 Hz, which is consistent with an intermediate with a rotational relaxation time of 100 ns. The average spin lattice relaxation time (T1) of the mobile residues was measured at different temperatures, clearly distinguishing between the dimer and the equilibrium intermediate. The results show, for the first time, the presence of intermediates in the process of dissociation of the MS2 bacteriophage. PMID:12770895

Differential Cationization of Fatty Acids with Monovalent Cations Studied by ESI-MS/MS and Computational Approach.

PubMed

Sudarshana Reddy, B; Pavankumar, P; Sridhar, L; Saha, Soumen; Narahari Sastry, G; Prabhakar, S

2018-04-24

The intercellular and intracellular transport of charged species (Na + /K + ) entail interaction of the ions with neutral organic molecules and formation of adduct ions. The rate of transport of the ions across the cell membrane(s) may depend on the stability of the adduct ions, which in turn rely on structural aspects of the organic molecules that interact with the ions. Positive ion ESI mass spectra were recorded for the solutions containing fatty acids (FAs) and monovalent cations (X=Li + , Na + , K + , Rb + and Cs + ). Product ion spectra of the [FA+X] + ions were recorded at different collision energies. Theoretical studies were exploited under both gas phase and solvent phase to investigate the structural effects of the fatty acids during cationization. Stability of [FA+X] + adduct ions were further estimated by means of AIM topological analyses and interaction energy (IE) values. Positive ion ESI-MS analyses of the solution of FAs and X + ions showed preferential binding of the K + ions to FAs. The K + ion binding increased with the increase in number of double bonds of FAs, while decreased with increase in the number of carbons of FAs. Dissociation curves of [FA+X] + ions indicated the relative stability order of the [FA+X] + ions and it was in line with the observed trends in ESI-MS. The solvent phase computational studies divulged the mode of binding and the binding efficiencies of different FAs with monovalent cations. Among the studied monovalent cations, the cationization of FAs follow the order K + >Na + >Li + >Rb + >Cs + . The docosahexaenoic acid showed high efficiency in binding with K + ion. The K + ion binding efficiency of FAs depends on the number of double bonds in unsaturated FAs and the carbon chain length in saturated FAs. The cationization trends of FAs obtained from the ESI-MS, ESI-MS/MS analyses were in good agreement with solvent phase computational studies. This article is protected by copyright. All rights reserved.

Identification and Affinity-Quantification of ß-Amyloid and α-Synuclein Polypeptides Using On-Line SAW-Biosensor-Mass Spectrometry

NASA Astrophysics Data System (ADS)

Slamnoiu, Stefan; Vlad, Camelia; Stumbaum, Mihaela; Moise, Adrian; Lindner, Kathrin; Engel, Nicole; Vilanova, Mar; Diaz, Mireia; Karreman, Christiaan; Leist, Marcel; Ciossek, Thomas; Hengerer, Bastian; Vilaseca, Marta; Przybylski, Michael

2014-08-01

Bioaffinity analysis using a variety of biosensors has become an established tool for detection and quantification of biomolecular interactions. Biosensors, however, are generally limited by the lack of chemical structure information of affinity-bound ligands. On-line bioaffinity-mass spectrometry using a surface-acoustic wave biosensor (SAW-MS) is a new combination providing the simultaneous affinity detection, quantification, and mass spectrometric structural characterization of ligands. We describe here an on-line SAW-MS combination for direct identification and affinity determination, using a new interface for MS of the affinity-isolated ligand eluate. Key element of the SAW-MS combination is a microfluidic interface that integrates affinity-isolation on a gold chip, in-situ sample concentration, and desalting with a microcolumn for MS of the ligand eluate from the biosensor. Suitable MS- acquisition software has been developed that provides coupling of the SAW-MS interface to a Bruker Daltonics ion trap-MS, FTICR-MS, and Waters Synapt-QTOF- MS systems. Applications are presented for mass spectrometric identifications and affinity (KD) determinations of the neurodegenerative polypeptides, ß-amyloid (Aß), and pathophysiological and physiological synucleins (α- and ß-synucleins), two key polypeptide systems for Alzheimer's disease and Parkinson's disease, respectively. Moreover, first in vivo applications of αSyn polypeptides from brain homogenate show the feasibility of on-line affinity-MS to the direct analysis of biological material. These results demonstrate on-line SAW-bioaffinity-MS as a powerful tool for structural and quantitative analysis of biopolymer interactions.

Simple setup for gas-phase H/D exchange mass spectrometry coupled to electron transfer dissociation and ion mobility for analysis of polypeptide structure on a liquid chromatographic time scale.

PubMed

Mistarz, Ulrik H; Brown, Jeffery M; Haselmann, Kim F; Rand, Kasper D

2014-12-02

Gas-phase hydrogen/deuterium exchange (HDX) is a fast and sensitive, yet unharnessed analytical approach for providing information on the structural properties of biomolecules, in a complementary manner to mass analysis. Here, we describe a simple setup for ND3-mediated millisecond gas-phase HDX inside a mass spectrometer immediately after ESI (gas-phase HDX-MS) and show utility for studying the primary and higher-order structure of peptides and proteins. HDX was achieved by passing N2-gas through a container filled with aqueous deuterated ammonia reagent (ND3/D2O) and admitting the saturated gas immediately upstream or downstream of the primary skimmer cone. The approach was implemented on three commercially available mass spectrometers and required no or minor fully reversible reconfiguration of gas-inlets of the ion source. Results from gas-phase HDX-MS of peptides using the aqueous ND3/D2O as HDX reagent indicate that labeling is facilitated exclusively through gaseous ND3, yielding similar results to the infusion of purified ND3-gas, while circumventing the complications associated with the use of hazardous purified gases. Comparison of the solution-phase- and gas-phase deuterium uptake of Leu-Enkephalin and Glu-Fibrinopeptide B, confirmed that this gas-phase HDX-MS approach allows for labeling of sites (heteroatom-bound non-amide hydrogens located on side-chains, N-terminus and C-terminus) not accessed by classical solution-phase HDX-MS. The simple setup is compatible with liquid chromatography and a chip-based automated nanoESI interface, allowing for online gas-phase HDX-MS analysis of peptides and proteins separated on a liquid chromatographic time scale at increased throughput. Furthermore, online gas-phase HDX-MS could be performed in tandem with ion mobility separation or electron transfer dissociation, thus enabling multiple orthogonal analyses of the structural properties of peptides and proteins in a single automated LC-MS workflow.

The structure investigations of dehydroacetic acid and 1,8-diaminonaphthalene condensation product by NMR, MS, and X-ray measurements

NASA Astrophysics Data System (ADS)

Kołodziej, B.; Morawiak, M.; Kamieński, B.; Schilf, W.

2016-05-01

A new unexpected product of condensation reaction of 1,8-diaminonaphthalene (DAN) and carbonyl compound (here: dehydroacetic acid (dha)) was synthesized. Discussion about the molecular structure of possible products of this reaction was done on the base of NMR studies. The structure of the titled product in both DMSO solution and in the solid state was resolved by analysis of its spectral data (X-ray structure analysis, multinuclear NMR in solution and solid state spectra) and MS measurements. The presented studies provided clear evidence that the titled product exists in diluted DMSO solution as the mixture of two kinetic free ionic species whereas in concentrated DMSO solution as well as in the solid state this system forms associated ionic pairs bonded together by hydrogen bonds.

Identification and characterization of stress degradants of lacosamide by LC-MS and ESI-Q-TOF-MS/MS: development and validation of a stability indicating RP-HPLC method.

PubMed

Ramisetti, Nageswara Rao; Kuntamukkala, Ramakrishna; Lakshetti, Sridhar; Sripadi, Prabhakar

2014-07-01

The current study dealt with the degradation behavior of lacosamide (LAC) under ICH prescribed stress conditions. LAC was found to be labile under acid and base hydrolytic stress conditions, while it was stable to neutral hydrolytic, oxidative, photolytic and thermal stress. In total, seven degradation products (DPs) were formed, which were separated on a C18 column using a stability-indicating method. LC-MS analyses indicated that one of the DPs had the same molecular mass as that of the drug. Structural characterization of DPs was carried out using ESI-Q-TOF-MS/MS technique. The degradation pathways and mechanisms of degradation of the drug were delineated by carrying out the degradation in different co-solvents viz. methanol, deuterated methanol, ethanol, 1-propanol and acetonitrile. The developed LC method was validated for the determination of related substances and assay of LAC as per ICH guidelines. This study demonstrates a comprehensive approach of LAC degradation studies during its development phase. Copyright © 2014. Published by Elsevier B.V.

Applications of Structural Mass Spectrometry to Metabolomics: Clarifying Bond Specific Spectral Signatures with Isotope Edited Spectroscopy

NASA Astrophysics Data System (ADS)

Gorlova, Olga; Wolke, Conrad T.; Fournier, Joseph; Colvin, Sean; Johnson, Mark; Miller, Scott

2015-06-01

Comprehensive FTIR, MS/MS and NMR of pharmaceuticals are generally readily available but characterization of their metabolites has been an obstacle. Atorvastatin is a statin drug responsible for the maintenance of cholesterol in the body. Diovan is an angiostensin receptor antagonist used to treat high blood pressure and congestive heart failure. The field of metabolomics, however, is struggling to obtain the identity of their structures. We implement mass spectrometry with cryogenic ion spectroscopy to study gaseous ions of the desired metabolites which, in combination, not only identify the mass of the metabolite but also elucidate their structures through isotope-specific infrared spectroscopy.

Complete LC/MS analysis of a Tinnevelli senna pod extract and subsequent isolation and identification of two new benzophenone glucosides.

PubMed

Terreaux, Christian; Wang, Qi; Ioset, Jean-Robert; Ndjoko, Karine; Grimminger, Wolf; Hostettmann, Kurt

2002-04-01

The hydroalcoholic extract of Tinnevelli senna is widely used as a laxative phytomedicine. In order to improve the knowledge of the chemical composition of this extract, LC/MS and LC/MS(n) studies were performed, allowing the on-line identification of most of the known constituents, i. e., flavonoids, anthraquinones and the typical dianthronic sennosides. However, the identity of four compounds could not be ascertained on-line under the given LC/MS conditions. These substances were isolated and their structures elucidated as kaempferol, the naphthalene derivative tinnevellin 8-glucoside and two new carboxylated benzophenone glucosides.

The use of advanced mass spectrometry to dissect the life-cycle of photosystem II

DOE PAGES

Weisz, Daniel A.; Gross, Michael L.; Pakrasi, Himadri B.

2016-05-10

Photosystem II (PSII) is a photosynthetic membrane-protein complex that undergoes an intricate, tightly regulated cycle of assembly, damage, and repair. The available crystal structures of cyanobacterial PSII are an essential foundation for understanding PSII function, but nonetheless provide a snapshot only of the active complex. To study aspects of the entire PSII life-cycle, mass spectrometry (MS) has emerged as a powerful tool that can be used in conjunction with biochemical techniques. In this article, we present the MS-based approaches that are used to study PSII composition, dynamics, and structure, and review the information about the PSII life-cycle that has beenmore » gained by these methods. This information includes the composition of PSII subcomplexes, discovery of accessory PSII proteins, identification of post-translational modifications and quantification of their changes under various conditions, determination of the binding site of proteins not observed in PSII crystal structures, conformational changes that underlie PSII functions, and identification of water and oxygen channels within PSII. Lastly, we conclude with an outlook for the opportunity of future MS contributions to PSII research.« less

New drostanolone metabolites in human urine by liquid chromatography time-of-flight tandem mass spectrometry and their application for doping control.

PubMed

Liu, Yang; Lu, Jianghai; Yang, Sheng; Zhang, Qingying; Xu, Youxuan

2016-04-01

Drostanolone is one of the most frequently detected anabolic androgenic steroids in doping control analysis. Here, we studied drostanolone urinary metabolic profiles using liquid chromatography quadruple time of flight mass spectrometry (LC-QTOF-MS) in full scan and targeted MS/MS modes with accurate mass measurement. The drug was administered to one healthy male volunteer and liquid-liquid extraction along with direct-injection were used to analyze urine samples. Chromatographic peaks for potential metabolites were identified with the theoretical [M-H](-) as a target ion in a full scan experiment and actual deprotonated ions were analyzed in targeted MS/MS mode. Eleven metabolites including five new sulfates, five glucuronide conjugates, and one free metabolite were confirmed for drostanolone. Due to the absence of useful fragment ions to illustrate the steroid ring structure of drostanolone phase II metabolites, gas chromatography mass spectrometry (GC-MS) was used to obtain structural details of the trimethylsilylated phase I metabolite released after enzymatic hydrolysis and a potential structure was proposed using a combined MS approach. Metabolite detection times were recorded and S4 (2α-methyl-5α-androstan-17-one-6β-ol-3α-sulfate) and G1 (2α-methyl-5α-androstan-17-one-3α-glucuronide) were thought to be new potential biomarkers for drostanolone misuse which can be detected up to 24days by liquid-liquid extraction and 7days by direct-injection analysis after intramuscular injection. S4 and G1 were also detected in two drostanolone-positive routine urine samples. Copyright © 2016 Elsevier Inc. All rights reserved.

NMR and mass spectrometric characterization of vinblastine, vincristine and some new related impurities - part I.

PubMed

Dubrovay, Zsófia; Háda, Viktor; Béni, Zoltán; Szántay, Csaba

2013-10-01

In the course of exploring the possibilities of developing a new, improved process at Gedeon Richter for the production of the "bisindole" alkaloids vinblastine (VLB) and vincristine (VCR), some novel VLB/VCR-related trace impurities were detected by analytical HPLC. Following isolation by preparative HPLC, a combination of 1D and 2D ultra high-field NMR and high-resolution (HR) (LC-)MS/MS studies allowed the structural identification and complete spectral characterization of several hitherto unpublished VLB/VCR-analogue impurities. Since the impurities could not be isolated in entirely pure forms and were available only in minute, mass-limited quantities, accessing the spectral information needed for their ab initio structure determination was met with various practical difficulties. Successful structure determination therefore relied heavily on the availability and use of detailed and definitive spectral data for both VLB and VCR. In particular, the utilization of detailed (1)H, (13)C, and (15)N NMR assignments as well as (1)H-(1)H, (1)H-(13)C and (1)H-(15)N spin-spin connectivities pertaining to different solvents for VLB/VCR base and sulphate salt was required. Although NMR studies on VLB base and other bisindoles were reported earlier in the literature, an NMR characterization of VLB and VCR under the above-mentioned circumstances and using ultra-high field instrumentation is either scarcely available or entirely lacking, therefore the necessary data had to be obtained in-house. Likewise, a modern tandem HR-ESI-MS/MS(n) fragmentation study of VLB and VCR has not been published yet. In the present paper we therefore give a thorough NMR and MS characterization of VLB and VCR specifically with a view to filling this void and to provide sufficiently extensive and solid reference data for the structural investigation of the aforementioned VLB/VCR impurities. Besides being scientifically relevant in its own right, the disclosed data should be useful for anyone interested in VLB/VCR-related molecules at a structural level. Copyright © 2012 Elsevier B.V. All rights reserved.

The Dopamine Imbalance Hypothesis of Fatigue in Multiple Sclerosis and Other Neurological Disorders

PubMed Central

Dobryakova, Ekaterina; Genova, Helen M.; DeLuca, John; Wylie, Glenn R.

2015-01-01

Fatigue is one of the most pervasive symptoms of multiple sclerosis (MS), and has engendered hundreds of investigations on the topic. While there is a growing literature using various methods to study fatigue, a unified theory of fatigue in MS is yet to emerge. In the current review, we synthesize findings from neuroimaging, pharmacological, neuropsychological, and immunological studies of fatigue in MS, which point to a specific hypothesis of fatigue in MS: the dopamine imbalance hypothesis. The communication between the striatum and prefrontal cortex is reliant on dopamine, a modulatory neurotransmitter. Neuroimaging findings suggest that fatigue results from the disruption of communication between these regions. Supporting the dopamine imbalance hypothesis, structural and functional neuroimaging studies show abnormalities in the frontal and striatal regions that are heavily innervated by dopamine neurons. Further, dopaminergic psychostimulant medication has been shown to alleviate fatigue in individuals with traumatic brain injury, chronic fatigue syndrome, and in cancer patients, also indicating that dopamine might play an important role in fatigue perception. This paper reviews the structural and functional neuroimaging evidence as well as pharmacological studies that suggest that dopamine plays a critical role in the phenomenon of fatigue. We conclude with how specific aspects of the dopamine imbalance hypothesis can be tested in future research. PMID:25814977

Risk factors for progressive axonal degeneration of the retinal nerve fibre layer in multiple sclerosis patients.

PubMed

Garcia-Martin, Elena; Pueyo, Victoria; Almarcegui, Carmen; Martin, Jesus; Ara, Jose R; Sancho, Eva; Pablo, Luis E; Dolz, Isabel; Fernandez, Javier

2011-11-01

To quantify structural and functional degeneration in the retinal nerve fibre layer (RNFL) of patients with multiple sclerosis (MS) over a 2-year time period, and to analyse the effect of prior optic neuritis (ON) as well as the duration and incidence of MS relapses. 166 MS patients and 120 healthy controls underwent assessment of visual acuity and colour vision, visual field examination, optical coherence tomography, scanning laser polarimetry and visual evoked potentials (VEPs). All subjects were re-evaluated after a period of 12 and 24 months. Changes in the optic nerve were detected by structural measurements but not by functional assessments. Changes registered in MS patients were greater than changes in healthy controls (p<0.05). Eyes with previous ON showed a greater reduction of parameters in the baseline evaluation, but RNFL atrophy was not significantly greater in the longitudinal study. Patients with MS relapses showed a greater reduction of RNFL thickness and VEP amplitude compared with non-relapsing cases. Patients with and without treatment showed similar measurement reduction, but the non-treated group had a significantly higher increase in Expanded Disability Status Scale (p=0.029). MS causes progressive axonal loss in the optic nerve, regardless of a history of ON. This ganglion cell atrophy occurs in all eyes but is more marked in MS eyes than in healthy eyes.

Structural dynamics of ribosome subunit association studied by mixing-spraying time-resolved cryo-EM

PubMed Central

Chen, Bo; Kaledhonkar, Sandip; Sun, Ming; Shen, Bingxin; Lu, Zonghuan; Barnard, David; Lu, Toh-Ming; Gonzalez, Ruben L.; Frank, Joachim

2015-01-01

Ribosomal subunit association is a key checkpoint in translation initiation, but its structural dynamics are poorly understood. Here, we used a recently developed mixing-spraying, time-resolved, cryogenic electron microscopy (cryo-EM) method to study ribosomal subunit association in the sub-second time range. We have improved this method and increased the cryo-EM data yield by tenfold. Pre-equilibrium states of the association reaction were captured by reacting the mixture of ribosomal subunits for 60 ms and 140 ms. We also identified three distinct ribosome conformations in the associated ribosomes. The observed proportions of these conformations are the same in these two time points, suggesting that ribosomes equilibrate among the three conformations within less than 60 ms upon formation. Our results demonstrate that the mixing-spraying method can capture multiple states of macromolecules during a sub-second reaction. Other fast processes, such as translation initiation, decoding and ribosome recycling, are amenable to study with this method. PMID:26004440

Study of cobalt mononitride thin films prepared using DC and high power impulse magnetron sputtering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gupta, Rachana, E-mail: dr.rachana.gupta@gmail.com; Pandey, Nidhi; Behera, Layanta

2016-05-23

In this work we studied cobalt mononitride (CoN) thin films deposited using dc magnetron sputtering (dcMS) and high power impulse magnetron sputtering (HiPIMS). A Co target was sputtered using pure N{sub 2} gas alone as the sputtering medium. Obtained long-range structural ordering was studies using x-ray diffraction (XRD), short-range structure using Co L{sub 2,3} and N K absorption edges using soft x-ray absorption spectroscopy (XAS) and the surface morphology using atomic force microscopy (AFM). It was found that HiPIMS deposited films have better long-range ordering, better stoichiometric ratio for mononitride composition and smoother texture as compared to dcMS deposited films.more » In addition, the thermal stability of HiPIMS deposited CoN film seems to be better. On the basis of different type of plasma conditions generated in HiPIMS and dcMS process, obtained results are presented and discussed.« less

Hierarchical Coarse-Graining Via a Generalized Yvon-Born Green Framework: Many-Body Correlations, Mappings, and Structural Accuracy

NASA Astrophysics Data System (ADS)

Rudzinski, Joseph F.

Atomically-detailed molecular dynamics simulations have emerged as one of the most powerful theoretic tools for studying complex, condensed-phase systems. Despite their ability to provide incredible molecular insight, these simulations are insufficient for investigating complex biological processes, e.g., protein folding or molecular aggregation, on relevant length and time scales. The increasing scope and sophistication of atomically-detailed models has motivated the development of "hierarchical" approaches, which parameterize a low resolution, coarse-grained (CG) model based on simulations of an atomically-detailed model. The utility of hierarchical CG models depends on their ability to accurately incorporate the correct physics of the underlying model. One approach for ensuring this "consistency" between the models is to parameterize the CG model to reproduce the structural ensemble generated by the high resolution model. The many-body potential of mean force is the proper CG energy function for reproducing all structural distributions of the atomically-detailed model, at the CG level of resolution. However, this CG potential is a configuration-dependent free energy function that is generally too complicated to represent or simulate. The multiscale coarse-graining (MS-CG) method employs a generalized Yvon-Born-Green (g-YBG) relation to directly determine a variationally optimal approximation to the many-body potential of mean force. The MS-CG/g-YBG method provides a convenient and transparent framework for investigating the equilibrium structure of the system, at the CG level of resolution. In this work, we investigate the fundamental limitations and approximations of the MS-CG/g-YBG method. Throughout the work, we propose several theoretic constructs to directly relate the MS-CG/g-YBG method to other popular structure-based CG approaches. We investigate the physical interpretation of the MS-CG/g-YBG correlation matrix, the quantity responsible for disentangling the various contributions to the average force on a CG site. We then employ an iterative extension of the MS-CG/g-YBG method that improves the accuracy of a particular set of low order correlation functions relative to the original MS-CG/g-YBG model. We demonstrate that this method provides a powerful framework for identifying the precise source of error in an MS-CG/g-YBG model. We then propose a method for identifying an optimal CG representation, prior to the development of the CG model. We employ these techniques together to demonstrate that in the cases where the MS-CG/g-YBG method fails to determine an accurate model, a fundamental problem likely exists with the chosen CG representation or interaction set. Additionally, we explicitly demonstrate that while the iterative model successfully improves the accuracy of the low order structure, it does so by distorting the higher order structural correlations relative to the underlying model. Finally, we apply these methods to investigate the utility of the MS-CG/g- YBG method for developing models for systems with complex intramolecular structure. Overall, our results demonstrate the power of the g-YBG framework for developing accurate CG models and for investigating the driving forces of equilibrium structures for complex condensed-phase systems. This work also explicitly motivates future development of bottom-up CG methods and highlights some outstanding problems in the field. iii.

MS/MS-Assisted Design of Sequence-Controlled Synthetic Polymers for Improved Reading of Encoded Information

NASA Astrophysics Data System (ADS)

Charles, Laurence; Cavallo, Gianni; Monnier, Valérie; Oswald, Laurence; Szweda, Roza; Lutz, Jean-François

2017-06-01

In order to improve their MS/MS sequencing, structure of sequence-controlled synthetic polymers can be optimized based on considerations regarding their fragmentation behavior in collision-induced dissociation conditions, as demonstrated here for two digitally encoded polymer families. In poly(triazole amide)s, the main dissociation route proceeded via cleavage of the amide bond in each monomer, hence allowing the chains to be safely sequenced. However, a competitive cleavage of an ether bond in a tri(ethylene glycol) spacer placed between each coding moiety complicated MS/MS spectra while not bringing new structural information. Changing the tri(ethylene glycol) spacer to an alkyl group of the same size allowed this unwanted fragmentation pathway to be avoided, hence greatly simplifying the MS/MS reading step for such undecyl-based poly(triazole amide)s. In poly(alkoxyamine phosphodiester)s, a single dissociation pathway was achieved with repeating units containing an alkoxyamine linkage, which, by very low dissociation energy, made any other chemical bonds MS/MS-silent. Structure of these polymers was further tailored to enhance the stability of those precursor ions with a negatively charged phosphate group per monomer in order to improve their MS/MS readability. Increasing the size of both the alkyl coding moiety and the nitroxide spacer allowed sufficient distance between phosphate groups for all of them to be deprotonated simultaneously. Because the charge state of product ions increased with their polymerization degree, MS/MS spectra typically exhibited groups of fragments at one or the other side of the precursor ion depending on the original α or ω end-group they contain, allowing sequence reconstruction in a straightforward manner. [Figure not available: see fulltext.

Recent advances in mass spectrometry-based approaches for proteomics and biologics: Great contribution for developing therapeutic antibodies.

PubMed

Iwamoto, Noriko; Shimada, Takashi

2018-05-01

Since the turn of the century, mass spectrometry (MS) technologies have continued to improve dramatically, and advanced strategies that were impossible a decade ago are increasingly becoming available. The basic characteristics behind these advancements are MS resolution, quantitative accuracy, and information science for appropriate data processing. The spectral data from MS contain various types of information. The benefits of improving the resolution of MS data include accurate molecular structural-derived information, and as a result, we can obtain a refined biomolecular structure determination in a sequential and large-scale manner. Moreover, in MS data, not only accurate structural information but also the generated ion amount plays an important rule. This progress has greatly contributed a research field that captures biological events as a system by comprehensively tracing the various changes in biomolecular dynamics. The sequential changes of proteome expression in biological pathways are very essential, and the amounts of the changes often directly become the targets of drug discovery or indicators of clinical efficacy. To take this proteomic approach, it is necessary to separate the individual MS spectra derived from each biomolecule in the complexed biological samples. MS itself is not so infinite to perform the all peak separation, and we should consider improving the methods for sample processing and purification to make them suitable for injection into MS. The above-described characteristics can only be achieved using MS with any analytical instrument. Moreover, MS is expected to be applied and expand into many fields, not only basic life sciences but also forensic medicine, plant sciences, materials, and natural products. In this review, we focus on the technical fundamentals and future aspects of the strategies for accurate structural identification, structure-indicated quantitation, and on the challenges for pharmacokinetics of high-molecular-weight protein biopharmaceuticals. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Automated Lipid A Structure Assignment from Hierarchical Tandem Mass Spectrometry Data

NASA Astrophysics Data System (ADS)

Ting, Ying S.; Shaffer, Scott A.; Jones, Jace W.; Ng, Wailap V.; Ernst, Robert K.; Goodlett, David R.

2011-05-01

Infusion-based electrospray ionization (ESI) coupled to multiple-stage tandem mass spectrometry (MS n ) is a standard methodology for investigating lipid A structural diversity (Shaffer et al. J. Am. Soc. Mass. Spectrom. 18(6), 1080-1092, 2007). Annotation of these MS n spectra, however, has remained a manual, expert-driven process. In order to keep up with the data acquisition rates of modern instruments, we devised a computational method to annotate lipid A MS n spectra rapidly and automatically, which we refer to as hierarchical tandem mass spectrometry (HiTMS) algorithm. As a first-pass tool, HiTMS aids expert interpretation of lipid A MS n data by providing the analyst with a set of candidate structures that may then be confirmed or rejected. HiTMS deciphers the signature ions (e.g., A-, Y-, and Z-type ions) and neutral losses of MS n spectra using a species-specific library based on general prior structural knowledge of the given lipid A species under investigation. Candidates are selected by calculating the correlation between theoretical and acquired MS n spectra. At a false discovery rate of less than 0.01, HiTMS correctly assigned 85% of the structures in a library of 133 manually annotated Francisella tularensis subspecies novicida lipid A structures. Additionally, HiTMS correctly assigned 85% of the structures in a smaller library of lipid A species from Yersinia pestis demonstrating that it may be used across species.

Machine-Learned Data Structures of Lipid Marker Serum Concentrations in Multiple Sclerosis Patients Differ from Those in Healthy Subjects.

PubMed

Lötsch, Jörn; Thrun, Michael; Lerch, Florian; Brunkhorst, Robert; Schiffmann, Susanne; Thomas, Dominique; Tegder, Irmgard; Geisslinger, Gerd; Ultsch, Alfred

2017-06-07

Lipid metabolism has been suggested to be a major pathophysiological mechanism of multiple sclerosis (MS). With the increasing knowledge about lipid signaling, acquired data become increasingly complex making bioinformatics necessary in lipid research. We used unsupervised machine-learning to analyze lipid marker serum concentrations, pursuing the hypothesis that for the most relevant markers the emerging data structures will coincide with the diagnosis of MS. Machine learning was implemented as emergent self-organizing feature maps (ESOM) combined with the U*-matrix visualization technique. The data space consisted of serum concentrations of three main classes of lipid markers comprising eicosanoids ( d = 11 markers), ceramides ( d = 10), and lyosophosphatidic acids ( d = 6). They were analyzed in cohorts of MS patients ( n = 102) and healthy subjects ( n = 301). Clear data structures in the high-dimensional data space were observed in eicosanoid and ceramides serum concentrations whereas no clear structure could be found in lysophosphatidic acid concentrations. With ceramide concentrations, the structures that had emerged from unsupervised machine-learning almost completely overlapped with the known grouping of MS patients versus healthy subjects. This was only partly provided by eicosanoid serum concentrations. Thus, unsupervised machine-learning identified distinct data structures of bioactive lipid serum concentrations. These structures could be superimposed with the known grouping of MS patients versus healthy subjects, which was almost completely possible with ceramides. Therefore, based on the present analysis, ceramides are first-line candidates for further exploration as drug-gable targets or biomarkers in MS.

Employment among patients with multiple sclerosis-a population study.

PubMed

Bøe Lunde, Hanne Marie; Telstad, Wenche; Grytten, Nina; Kyte, Lars; Aarseth, Jan; Myhr, Kjell-Morten; Bø, Lars

2014-01-01

To investigate demographic and clinical factors associated with employment in MS. The study included 213 (89.9%) of all MS patients in Sogn and Fjordane County, Western Norway at December 31st 2010. The patients underwent clinical evaluation, structured interviews and completed self-reported questionnaires. Demographic and clinical factors were compared between patients being employed versus patients being unemployed and according to disease course of MS. Logistic regression analysis was used to identify factors independently associated with current employment. After a mean disease duration of almost 19 years, 45% of the population was currently full-time or part- time employed. Patients with relapsing -remitting MS (RRMS) had higher employment rate than patients with secondary (SPMS) and primary progressive (PPMS). Higher educated MS patients with lower age at onset, shorter disease duration, less severe disability and less fatigue were most likely to be employed. Nearly half of all MS patients were still employed after almost two decades of having MS. Lower age at onset, shorter disease duration, higher education, less fatigue and less disability were independently associated with current employment. These key clinical and demographic factors are important to understand the reasons to work ability in MS. The findings highlight the need for environmental adjustments at the workplace to accommodate individual 's needs in order to improve working ability among MS patients.

A strategy to improve the identification reliability of the chemical constituents by high-resolution mass spectrometry-based isomer structure prediction combined with a quantitative structure retention relationship analysis: Phthalide compounds in Chuanxiong as a test case.

PubMed

Zhang, Qingqing; Huo, Mengqi; Zhang, Yanling; Qiao, Yanjiang; Gao, Xiaoyan

2018-06-01

High-resolution mass spectrometry (HRMS) provides a powerful tool for the rapid analysis and identification of compounds in herbs. However, the diversity and large differences in the content of the chemical constituents in herbal medicines, especially isomerisms, are a great challenge for mass spectrometry-based structural identification. In the current study, a new strategy for the structural characterization of potential new phthalide compounds was proposed by isomer structure predictions combined with a quantitative structure-retention relationship (QSRR) analysis using phthalide compounds in Chuanxiong as an example. This strategy consists of three steps. First, the structures of phthalide compounds were reasonably predicted on the basis of the structure features and MS/MS fragmentation patterns: (1) the collected raw HRMS data were preliminarily screened by an in-house database; (2) the MS/MS fragmentation patterns of the analogous compounds were summarized; (3) the reported phthalide compounds were identified, and the structures of the isomers were reasonably predicted. Second, the QSRR model was established and verified using representative phthalide compound standards. Finally, the retention times of the predicted isomers were calculated by the QSRR model, and the structures of these peaks were rationally characterized by matching retention times of the detected chromatographic peaks and the predicted isomers. A multiple linear regression QSRR model in which 6 physicochemical variables were screened was built using 23 phthalide standards. The retention times of the phthalide isomers in Chuanxiong were well predicted by the QSRR model combined with reasonable structure predictions (R 2 =0.955). A total of 81 peaks were detected from Chuanxiong and assigned to reasonable structures, and 26 potential new phthalide compounds were structurally characterized. This strategy can improve the identification efficiency and reliability of homologues in complex materials. Copyright © 2018 Elsevier B.V. All rights reserved.

HCV RNA traffic and association with NS5A in living cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fiches, Guillaume N.; Eyre, Nicholas S.; Aloia, Amanda L.

The spatiotemporal dynamics of Hepatitis C Virus (HCV) RNA localisation are poorly understood. To address this we engineered HCV genomes harbouring MS2 bacteriophage RNA stem-loops within the 3′-untranslated region to allow tracking of HCV RNA via specific interaction with a MS2-Coat-mCherry fusion protein. Despite the impact of these insertions on viral fitness, live imaging revealed that replication of tagged-HCV genomes induced specific redistribution of the mCherry-tagged-MS2-Coat protein to motile and static foci. Further analysis showed that HCV RNA was associated with NS5A in both static and motile structures while a subset of motile NS5A structures was devoid of HCV RNA.more » Further investigation of viral RNA traffic with respect to lipid droplets (LDs) revealed HCV RNA-positive structures in close association with LDs. These studies provide new insights into the dynamics of HCV RNA traffic with NS5A and LDs and provide a platform for future investigations of HCV replication and assembly. - Highlights: • HCV can tolerate can bacteriophage MS2 stem-loop insertions within the 3′ UTR. • MS2 stem-loop containing HCV genomes allow for real-time imaging of HCV RNA. • HCV RNA is both static and motile and associates with NS5A and lipid droplets.« less

[Preparation of scopolamine hydrobromide nanoparticles-in-microsphere system].

PubMed

Lü, Wei-ling; Hu, Jin-hong; Zhu, Quan-gang; Li, Feng-qian

2010-07-01

This study is to prepare scopolamine hydrobromide nanoparticles-in-microsphere system (SH-NiMS) and evaluate its drug release characteristics in vitro. SH nanoparticles were prepared by ionic crosslinking method with tripolyphosphate (TPP) as crosslinker and chitosan as carrier. Orthogonal design was used to optimize the formulation of SH nanoparticles, which took the property of encapsulation efficiency and drug loading as evaluation parameters. With HPMC as carrier, adjusted the parameters of spray drying technique and sprayed the SH nanoparticles in microspheres encaposulated by HPMC was formed and which is called nanoparticles-in-microsphere system (NiMS). SH-NiMS appearances were observed by SEM, structure was obsearved by FT-IR and the release characteristics in vitro were evaluated. The optimized formulation of SH nanoparticles was TPP/CS 1:3 (w/w), HPMC 0.3%, SH 0.2%. The solution peristaltic speed of the spray drying technique was adjusted to 15%, and the temperature of inlet was 110 degrees C. The encapsulation product yeild, drug loading and particle sizes of SH-NiMS were 94.2%, 20.4%, and 1256.5 nm, respectively. The appearances and the structure of SH-NiMS were good. The preparation method of SH-NiMS is stable and reliable to use, which provide a new way to develop new dosage form.

A multiple-dimension liquid chromatography coupled with mass spectrometry data strategy for the rapid discovery and identification of unknown compounds from a Chinese herbal formula (Er-xian decoction).

PubMed

Wang, Caihong; Zhang, Jinlan; Wu, Caisheng; Wang, Zhe

2017-10-06

It is very important to rapidly discover and identify the multiple components of traditional Chinese medicine (TCM) formula. High performance liquid chromatography with high resolution tandem mass spectrometry (HPLC-HRMS/MS) has been widely used to analyze TCM formula and contains multiple-dimension data including retention time (RT), high resolution mass (HRMS), multiple-stage mass spectrometric (MS n ), and isotope intensity distribution (IID) data. So it is very necessary to exploit a useful strategy to utilize multiple-dimension data to rapidly probe structural information and identify chemical compounds. In this study, a new strategy to initiatively use the multiple-dimension LC-MS data has been developed to discover and identify unknown compounds of TCM in many styles. The strategy guarantees the fast discovery of candidate structural information and provides efficient structure clues for identification. The strategy contains four steps in sequence: (1) to discover potential compounds and obtain sub-structure information by the mass spectral tree similarity filter (MTSF) technique, based on HRMS and MS n data; (2) to classify potential compounds into known chemical classes by discriminant analysis (DA) on the basis of RT and HRMS data; (3) to hit the candidate structural information of compounds by intersection sub-structure between MTSF and DA (M,D-INSS); (4) to annotate and confirm candidate structures by IID data. This strategy allowed for the high exclusion efficiency (greater than 41%) of irrelevant ions in er-xian decoction (EXD) while providing accurate structural information of 553 potential compounds and identifying 66 candidates, therefore accelerating and simplifying the discovery and identification of unknown compounds in TCM formula. Copyright © 2017 Elsevier B.V. All rights reserved.

Evaluating nanoscale ultra-thin metal films by means of lateral photovoltaic effect in metal-semiconductor structure.

PubMed

Zheng, Diyuan; Yu, Chongqi; Zhang, Qian; Wang, Hui

2017-12-15

Nanoscale metal-semiconductor (MS) structure materials occupy an important position in semiconductor and microelectronic field due to their abundant physical phenomena and effects. The thickness of metal films is a critical factor in determining characteristics of MS devices. How to detect or evaluate the metal thickness is always a key issue for realizing high performance MS devices. In this work, we propose a direct surface detection by use of the lateral photovoltaic effect (LPE) in MS structure, which can not only measure nanoscale thickness, but also detect the fluctuation of metal films. This method is based on the fact that the output of lateral photovoltaic voltage (LPV) is closely linked with the metal thickness at the laser spot. We believe this laser-based contact-free detection is a useful supplement to the traditional methods, such as AFM, SEM, TEM or step profiler. This is because these traditional methods are always incapable of directly detecting ultra-thin metal films in MS structure materials.

Evaluating nanoscale ultra-thin metal films by means of lateral photovoltaic effect in metal-semiconductor structure

NASA Astrophysics Data System (ADS)

Zheng, Diyuan; Yu, Chongqi; Zhang, Qian; Wang, Hui

2017-12-01

Nanoscale metal-semiconductor (MS) structure materials occupy an important position in semiconductor and microelectronic field due to their abundant physical phenomena and effects. The thickness of metal films is a critical factor in determining characteristics of MS devices. How to detect or evaluate the metal thickness is always a key issue for realizing high performance MS devices. In this work, we propose a direct surface detection by use of the lateral photovoltaic effect (LPE) in MS structure, which can not only measure nanoscale thickness, but also detect the fluctuation of metal films. This method is based on the fact that the output of lateral photovoltaic voltage (LPV) is closely linked with the metal thickness at the laser spot. We believe this laser-based contact-free detection is a useful supplement to the traditional methods, such as AFM, SEM, TEM or step profiler. This is because these traditional methods are always incapable of directly detecting ultra-thin metal films in MS structure materials.

The MS@Work study: a 3-year prospective observational study on factors involved with work participation in patients with relapsing-remitting Multiple Sclerosis.

PubMed

van der Hiele, Karin; van Gorp, Dennis A M; Heerings, Marco A P; van Lieshout, Irma; Jongen, Peter J; Reneman, Michiel F; van der Klink, Jac J L; Vosman, Frans; Middelkoop, Huub A M; Visser, Leo H

2015-08-12

Multiple Sclerosis (MS) is the most common cause of neurological disability in young and middle-aged adults. At this stage in life most people are in the midst of their working career. The majority of MS patients are unable to retain employment within 10 years from disease onset. Leading up to unemployment, many may experience a reduction in hours or work responsibilities and increased time missed from work. The MS@Work study examines various factors that may influence work participation in relapsing-remitting MS patients, including disease-related factors, the working environment and personal factors. The MS@Work study is a multicenter, 3-year prospective observational study on work participation in patients with relapsing-remitting MS. We aim to include 350 patients through 15-18 MS outpatient clinics in the Netherlands. Eligible participants are 18 years and older, and either currently employed or within three years since their last employment. At baseline and after 1, 2 and 3 years, the participants are asked to complete online questionnaires (including questions on work participation, work problems and accommodations, cognitive and physical ability, anxiety, depression, psychosocial stress, quality of life, fatigue, empathy, personality traits and coping strategies) and undergo cognitive and neurological examinations. After six months, patients are requested to only complete online questionnaires. Patient perspectives on maintaining and improving work participation and reasons to stop working are gathered through semi-structured interviews in a sub-group of patients. Prospective studies with long-term follow-up on work participation in MS are rare, or take into account a limited number of factors. The MS@Work study provides a 3-year follow-up on various factors that may influence work participation in patients with relapsing-remitting MS. We aim to identify factors that relate to job loss and to provide information about preventative measures for physicians, psychologists and other professionals working in the field of occupational health.

Aerodynamic profiling of terminal building using computational fluid dynamics approach

NASA Astrophysics Data System (ADS)

Vidhya, S.; Pradeep Kumar, R.; Hareesh, M.; Sekar, S. K.

2017-11-01

A case study of isolated building is studied using ANSYS CFX and SAP2000. The plan idea of 30m by 60m is chosen for terminal building. The model is subjected to different wind incidence from 0° to 90° and 45° with 30° interval for 55m/s wind speed. By using tributary area method, the forces at the each mesh node are summed up to get corresponding wind force at that joint within that area. The best effective structural system is determined by designing the structure for each wind incidence. Wind analysis and design is carried out for increasing wind speed above 55m/s to identify the collapse pattern of structure. External supporting members are suggested to withstand that maximum wind speed.

LC-MS and MS/MS in the analysis of recombinant proteins

NASA Astrophysics Data System (ADS)

Coulot, M.; Domon, B.; Grossenbacher, H.; Guenat, C.; Maerki, W.; Müller, D. R.; Richter, W. J.

1993-03-01

Applicability and performance of electrospray ionization mass spectrometry (ESIMS) is demonstrated for protein analysis. ESIMS is applied in conjunction with on-line HPLC (LC-ESlMS) and direct tandem mass spectrometry (positive and negative ion mode ESlMS/MS) to the structural characterization of a recombinant protein (r-hirudin variant 1) and a congener phosphorylated at threonine 45 (RP-1).

Annotation and Structural Analysis of Sialylated Human Milk Oligosaccharides

PubMed Central

Wu, Shuai; Grimm, Rudolf; German, J. Bruce; Lebrilla, Carlito B.

2011-01-01

Sialylated human milk oligosaccharides (SHMOs) are important components of human milk oligosaccharides. Sialic acids are typically found on the nonreducing end and are known binding sites for pathogens and aid in neonates’ brain development. Due to their negative charge and hydrophilic nature, they also help modulate cell-cell interactions. It has also been shown that sialic acids are involved in regulating the immune response and aid in brain development. In this study, the enriched SHMOs from pooled milk sample were analyzed by HPLC-Chip/QTOF MS. The instrument employs a microchip-based nano-LC column packed with porous graphitized carbon (PGC) to provide excellent isomer separation for SHMOs with highly reproducible retention time. The precursor ions were further examined with collision-induced dissociation (CID). By applying the proper collision energy, isomers can be readily differentiated by diagnostic peaks and characteristic fragmentation patterns. A set of 30 SHMO structures with retention times, accurate masses and MS/MS spectra was deduced and incorporated into an HMO library. When combined with previously determined neutral components, a library with over 70 structures is obtained allowing high-throughput oligosaccharide structure identification. PMID:21133381

Estimation of Hydrogen-Exchange Protection Factors from MD Simulation Based on Amide Hydrogen Bonding Analysis.

PubMed

Park, In-Hee; Venable, John D; Steckler, Caitlin; Cellitti, Susan E; Lesley, Scott A; Spraggon, Glen; Brock, Ansgar

2015-09-28

Hydrogen exchange (HX) studies have provided critical insight into our understanding of protein folding, structure, and dynamics. More recently, hydrogen exchange mass spectrometry (HX-MS) has become a widely applicable tool for HX studies. The interpretation of the wealth of data generated by HX-MS experiments as well as other HX methods would greatly benefit from the availability of exchange predictions derived from structures or models for comparison with experiment. Most reported computational HX modeling studies have employed solvent-accessible-surface-area based metrics in attempts to interpret HX data on the basis of structures or models. In this study, a computational HX-MS prediction method based on classification of the amide hydrogen bonding modes mimicking the local unfolding model is demonstrated. Analysis of the NH bonding configurations from molecular dynamics (MD) simulation snapshots is used to determine partitioning over bonded and nonbonded NH states and is directly mapped into a protection factor (PF) using a logistics growth function. Predicted PFs are then used for calculating deuteration values of peptides and compared with experimental data. Hydrogen exchange MS data for fatty acid synthase thioesterase (FAS-TE) collected for a range of pHs and temperatures was used for detailed evaluation of the approach. High correlation between prediction and experiment for observable fragment peptides is observed in the FAS-TE and additional benchmarking systems that included various apo/holo proteins for which literature data were available. In addition, it is shown that HX modeling can improve experimental resolution through decomposition of in-exchange curves into rate classes, which correlate with prediction from MD. Successful rate class decompositions provide further evidence that the presented approach captures the underlying physical processes correctly at the single residue level. This assessment is further strengthened in a comparison of residue resolved protection factor predictions for staphylococcal nuclease with NMR data, which was also used to compare prediction performance with other algorithms described in the literature. The demonstrated transferable and scalable MD based HX prediction approach adds significantly to the available tools for HX-MS data interpretation based on available structures and models.

Estimation of Hydrogen-Exchange Protection Factors from MD Simulation Based on Amide Hydrogen Bonding Analysis

PubMed Central

Park, In-Hee; Venable, John D.; Steckler, Caitlin; Cellitti, Susan E.; Lesley, Scott A.; Spraggon, Glen; Brock, Ansgar

2015-01-01

Hydrogen exchange (HX) studies have provided critical insight into our understanding of protein folding, structure and dynamics. More recently, Hydrogen Exchange Mass Spectrometry (HX-MS) has become a widely applicable tool for HX studies. The interpretation of the wealth of data generated by HX-MS experiments as well as other HX methods would greatly benefit from the availability of exchange predictions derived from structures or models for comparison with experiment. Most reported computational HX modeling studies have employed solvent-accessible-surface-area based metrics in attempts to interpret HX data on the basis of structures or models. In this study, a computational HX-MS prediction method based on classification of the amide hydrogen bonding modes mimicking the local unfolding model is demonstrated. Analysis of the NH bonding configurations from Molecular Dynamics (MD) simulation snapshots is used to determine partitioning over bonded and non-bonded NH states and is directly mapped into a protection factor (PF) using a logistics growth function. Predicted PFs are then used for calculating deuteration values of peptides and compared with experimental data. Hydrogen exchange MS data for Fatty acid synthase thioesterase (FAS-TE) collected for a range of pHs and temperatures was used for detailed evaluation of the approach. High correlation between prediction and experiment for observable fragment peptides is observed in the FAS-TE and additional benchmarking systems that included various apo/holo proteins for which literature data were available. In addition, it is shown that HX modeling can improve experimental resolution through decomposition of in-exchange curves into rate classes, which correlate with prediction from MD. Successful rate class decompositions provide further evidence that the presented approach captures the underlying physical processes correctly at the single residue level. This assessment is further strengthened in a comparison of residue resolved protection factor predictions for staphylococcal nuclease with NMR data, which was also used to compare prediction performance with other algorithms described in the literature. The demonstrated transferable and scalable MD based HX prediction approach adds significantly to the available tools for HX-MS data interpretation based on available structures and models. PMID:26241692

Supervised resistance training results in changes in postural control in patients with multiple sclerosis.

PubMed

Huisinga, Jessie M; Filipi, Mary L; Stergiou, Nicholas

2012-01-01

Postural disturbances are one of the first reported symptoms in patients with Multiple Sclerosis (MS). The purpose of this study was to investigate the effect of supervised resistance training on postural control in MS patients. Postural control was assessed using amount of sway variability [Root Mean Square (RMS)] and temporal structure of sway variability [Lyapunov Exponent (LyE)] from 15 MS patients. Posture was evaluated before and after completion of three months of resistance training. There were significant differences between MS patients pretraining and healthy controls for both LyE (p = .000) and RMS (p = .002), but no differences between groups after training. There was a significant decrease in RMS (p = .025) and a significant increase in LyE (p = .049) for MS patients pre- to posttraining. The findings suggested that postural control of MS patients could be affected by a supervised resistance training intervention.

Coming to Grips with Ambiguity: Ion Mobility-Mass Spectrometry for Protein Quaternary Structure Assignment

NASA Astrophysics Data System (ADS)

Eschweiler, Joseph D.; Frank, Aaron T.; Ruotolo, Brandon T.

2017-10-01

Multiprotein complexes are central to our understanding of cellular biology, as they play critical roles in nearly every biological process. Despite many impressive advances associated with structural characterization techniques, large and highly-dynamic protein complexes are too often refractory to analysis by conventional, high-resolution approaches. To fill this gap, ion mobility-mass spectrometry (IM-MS) methods have emerged as a promising approach for characterizing the structures of challenging assemblies due in large part to the ability of these methods to characterize the composition, connectivity, and topology of large, labile complexes. In this Critical Insight, we present a series of bioinformatics studies aimed at assessing the information content of IM-MS datasets for building models of multiprotein structure. Our computational data highlights the limits of current coarse-graining approaches, and compelled us to develop an improved workflow for multiprotein topology modeling, which we benchmark against a subset of the multiprotein complexes within the PDB. This improved workflow has allowed us to ascertain both the minimal experimental restraint sets required for generation of high-confidence multiprotein topologies, and quantify the ambiguity in models where insufficient IM-MS information is available. We conclude by projecting the future of IM-MS in the context of protein quaternary structure assignment, where we predict that a more complete knowledge of the ultimate information content and ambiguity within such models will undoubtedly lead to applications for a broader array of challenging biomolecular assemblies. [Figure not available: see fulltext.

Sequencing the oligosaccharide pool in the low molecular weight heparin dalteparin with offline HPLC and ESI-MS/MS.

PubMed

Wang, Zhangjie; Zhang, Tianji; Xie, Shaoshuai; Liu, Xinyue; Li, Hongmei; Linhardt, Robert J; Chi, Lianli

2018-03-01

Low molecular weight heparins (LMWHs) are widely used anticoagulant drugs. The composition and sequence of LMWH oligosaccharides determine their safety and efficacy. The short oligosaccharide pool in LMWHs undergoes more depolymerization reactions than the longer chains and is the most sensitive indicator of the manufacturing process. Electrospray ionization tandem mass spectrometry (ESI-MS/MS) has been demonstrated as a powerful tool to sequence synthetic heparin oligosaccharide but never been applied to analyze complicated mixture like LMWHs. We established an offline strong anion exchange (SAX)-high performance liquid chromatography (HPLC) and ESI-MS/MS approach to sequence the short oligosaccharides of dalteparin sodium. With the help of in-house developed MS/MS interpretation software, the sequences of 18 representative species ranging from tetrasaccharide to octasaccharide were obtained. Interestingly, we found a novel 2,3-disulfated hexauronic acid structure and reconfirmed it by complementary heparinase digestion and LC-MS/MS analysis. This approach provides straightforward and in-depth insight to the structure of LMWHs and the reaction mechanism of heparin depolymerization. Copyright © 2017 Elsevier Ltd. All rights reserved.

Investigating the Structural Compaction of Biomolecules Upon Transition to the Gas-Phase Using ESI-TWIMS-MS.

PubMed

Devine, Paul W A; Fisher, Henry C; Calabrese, Antonio N; Whelan, Fiona; Higazi, Daniel R; Potts, Jennifer R; Lowe, David C; Radford, Sheena E; Ashcroft, Alison E

2017-09-01

Collision cross-section (CCS) measurements obtained from ion mobility spectrometry-mass spectrometry (IMS-MS) analyses often provide useful information concerning a protein's size and shape and can be complemented by modeling procedures. However, there have been some concerns about the extent to which certain proteins maintain a native-like conformation during the gas-phase analysis, especially proteins with dynamic or extended regions. Here we have measured the CCSs of a range of biomolecules including non-globular proteins and RNAs of different sequence, size, and stability. Using traveling wave IMS-MS, we show that for the proteins studied, the measured CCS deviates significantly from predicted CCS values based upon currently available structures. The results presented indicate that these proteins collapse to different extents varying on their elongated structures upon transition into the gas-phase. Comparing two RNAs of similar mass but different solution structures, we show that these biomolecules may also be susceptible to gas-phase compaction. Together, the results suggest that caution is needed when predicting structural models based on CCS data for RNAs as well as proteins with non-globular folds. Graphical Abstract ᅟ.

Mass Spectrometry Imaging of Drug Related Crystal-Like Structures in Formalin-Fixed Frozen and Paraffin-Embedded Rabbit Kidney Tissue Sections

NASA Astrophysics Data System (ADS)

Bruinen, Anne L.; van Oevelen, Cateau; Eijkel, Gert B.; Van Heerden, Marjolein; Cuyckens, Filip; Heeren, Ron M. A.

2016-01-01

A multimodal mass spectrometry imaging (MSI) based approach was used to characterize the molecular content of crystal-like structures in a frozen and paraffin embedded piece of a formalin-fixed rabbit kidney. Matrix assisted laser desorption/ionization time-of-flight (MALDI-TOF) imaging and desorption electrospray ionization (DESI) mass spectrometry imaging were combined to analyze the frozen and paraffin embedded sample without further preparation steps to remove the paraffin. The investigated rabbit kidney was part of a study on a drug compound in development, in which severe renal toxicity was observed in dosed rabbits. Histological examination of the kidney showed tubular degeneration with precipitation of crystal-like structures in the cortex, which were assumed to cause the renal toxicity. The MS imaging approach was used to find out whether the crystal-like structures were composed of the drug compound, metabolites, or an endogenous compound as a reaction to the drug administration. The generated MALDI-MSI data were analyzed using principal component analysis. In combination with the MS/MS results, this way of data processing demonstrates that the crystal structures were mainly composed of metabolites and relatively little parent drug.

Utilization of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for structural studies related to biology and disease

NASA Astrophysics Data System (ADS)

Costello, Catherine E.; Helin, Jari; Ngoka, Lambert C. M.

1996-04-01

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), because of its high sensitivity and relatively straightforward requirements for sample preparation, is contributing to the solution of structural problems in biology and to the development of therapeutic approaches through increased understanding of pharmacology and enhanced capabilities for quality control of pharmaceuticals. We are using a reflectron TOF- MS for the determination of molecular weights of individual compounds and the components of mixtures that are naturally occurring or are generated through enzymic digests, and employing the post-source decay mode to elucidate structural details. To maximize the sensitivity and information content of the spectra, varied matrices, derivative, and stepwise degradation procedures are being explored. Present studies include investigations of oligosaccharides, neutral glycolipids, gangliosides, glycoproteins, neuropeptides and proteins. Rules for fragmentation are being developed with model compounds and used for the structural elucidation of unknowns. When adequate sample amounts are available, the results are compared with low- and high-energy collision-induced decomposition spectra obtained with tandem MS in order to provide a data base for the correlation of spectral features and guidance in selection of approaches for scarce biological samples. Current projects include biophysical studies of glycoplipids, glycoproteins and oligosaccharides and investigations of the substance P receptor, transthyretin genetic variants and cisplatin-DNA interactions.

Practical Methods for Including Torsional Anharmonicity in Thermochemical Calculations on Complex Molecules: The Internal-Coordinate Multi-Structural Approximation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zheng, J.; Yu, T.; Papajak, E.

2011-01-01

Many methods for correcting harmonic partition functions for the presence of torsional motions employ some form of one-dimensional torsional treatment to replace the harmonic contribution of a specific normal mode. However, torsions are often strongly coupled to other degrees of freedom, especially other torsions and low-frequency bending motions, and this coupling can make assigning torsions to specific normal modes problematic. Here, we present a new class of methods, called multi-structural (MS) methods, that circumvents the need for such assignments by instead adjusting the harmonic results by torsional correction factors that are determined using internal coordinates. We present three versions ofmore » the MS method: (i) MS-AS based on including all structures (AS), i.e., all conformers generated by internal rotations; (ii) MS-ASCB based on all structures augmented with explicit conformational barrier (CB) information, i.e., including explicit calculations of all barrier heights for internal-rotation barriers between the conformers; and (iii) MS-RS based on including all conformers generated from a reference structure (RS) by independent torsions. In the MS-AS scheme, one has two options for obtaining the local periodicity parameters, one based on consideration of the nearly separable limit and one based on strongly coupled torsions. The latter involves assigning the local periodicities on the basis of Voronoi volumes. The methods are illustrated with calculations for ethanol, 1-butanol, and 1-pentyl radical as well as two one-dimensional torsional potentials. The MS-AS method is particularly interesting because it does not require any information about conformational barriers or about the paths that connect the various structures.« less

Practical methods for including torsional anharmonicity in thermochemical calculations on complex molecules: the internal-coordinate multi-structural approximation.

PubMed

Zheng, Jingjing; Yu, Tao; Papajak, Ewa; Alecu, I M; Mielke, Steven L; Truhlar, Donald G

2011-06-21

Many methods for correcting harmonic partition functions for the presence of torsional motions employ some form of one-dimensional torsional treatment to replace the harmonic contribution of a specific normal mode. However, torsions are often strongly coupled to other degrees of freedom, especially other torsions and low-frequency bending motions, and this coupling can make assigning torsions to specific normal modes problematic. Here, we present a new class of methods, called multi-structural (MS) methods, that circumvents the need for such assignments by instead adjusting the harmonic results by torsional correction factors that are determined using internal coordinates. We present three versions of the MS method: (i) MS-AS based on including all structures (AS), i.e., all conformers generated by internal rotations; (ii) MS-ASCB based on all structures augmented with explicit conformational barrier (CB) information, i.e., including explicit calculations of all barrier heights for internal-rotation barriers between the conformers; and (iii) MS-RS based on including all conformers generated from a reference structure (RS) by independent torsions. In the MS-AS scheme, one has two options for obtaining the local periodicity parameters, one based on consideration of the nearly separable limit and one based on strongly coupled torsions. The latter involves assigning the local periodicities on the basis of Voronoi volumes. The methods are illustrated with calculations for ethanol, 1-butanol, and 1-pentyl radical as well as two one-dimensional torsional potentials. The MS-AS method is particularly interesting because it does not require any information about conformational barriers or about the paths that connect the various structures.

Atypical cleavage of protonated N-fatty acyl amino acids derived from aspartic acid evidenced by sequential MS3 experiments.

PubMed

Boukerche, Toufik Taalibi; Alves, Sandra; Le Faouder, Pauline; Warnet, Anna; Bertrand-Michel, Justine; Bouchekara, Mohamed; Belbachir, Mohammed; Tabet, Jean-Claude

2016-12-01

Lipidomics calls for information on detected lipids and conjugates whose structural elucidation by mass spectrometry requires to rationalization of their gas phase dissociations toward collision-induced dissociation (CID) processes. This study focused on activated dissociations of two lipoamino acid (LAA) systems composed of N-palmitoyl acyl coupled with aspartic and glutamic acid mono ethyl esters (as LAA (*D) and LAA (*E) ). Although in MS/MS, their CID spectra show similar trends, e.g., release of water and ethanol, the [(LAA (*D/*E) +H)-C 2 H 5 OH] + product ions dissociate via distinct pathways in sequential MS 3 experiments. The formation of all the product ions is rationalized by charge-promoted cleavages often involving stepwise processes with ion isomerization into ion-dipole prior to dissociation. The latter explains the maleic anhydride or ketene neutral losses from N-palmitoyl acyl aspartate and glutamate anhydride fragment ions, respectively. Consequently, protonated palmitoyl acid amide is generated from LAA (*D), whereas LAA (*E) leads to the [*E+H-H 2 O] + anhydride. The former releases ammonia to provide acylium, which gives the C n H (2n-1) and C n H (2n-3) carbenium series. This should offer structural information, e.g., to locate either unsaturation(s) or alkyl group branching present on the various fatty acyl moieties of lipo-aspartic acid in further studies based on MS n experiments.

Slow-freezing-induced changes of birefringent structures in human oocytes are related to responsiveness to ovulation induction.

PubMed

Molinari, Emanuela; Revelli, Alberto; Racca, Cinzia; Delle Piane, Luisa; Massobrio, Marco

2010-05-01

The slow-freezing method is widely used to freeze human oocytes, both for fertility preservation and in routine IVF programmes. Slow freezing damages some of the cell's structures, including the meiotic spindle (MS) and the zona pellucida (ZP). Polarized light microscopy was used to study the variations induced by slow freezing on the MS and the ZP of human oocytes and to analyse the relationship between slow-freezing effects on the gamete and some clinical characteristics, such as age, body mass index and ovarian responsiveness to ovulation induction (expressed as total follicle-stimulating hormone dose/retrieved oocyte). Both the MS and the ZP (particularly its inner layer) underwent significant changes during slow-freezing procedure. The MS became thinner and structurally less organized (lower retardance) (P<0.001 and P<0.05, respectively), whereas the ZP became thicker and its inner layer lost structural organization (both P<0.05). These morphological changes were unrelated to the patient's age or body mass index, but ZP variations in thickness and retardance were significantly related to ovarian responsiveness (P=0.033 and P=0.026, respectively), suggesting that patients with a higher response to gonadotrophins produce oocytes better able to preserve their characteristics after freezing-thawing. Copyright (c) 2010 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

Machine-Learned Data Structures of Lipid Marker Serum Concentrations in Multiple Sclerosis Patients Differ from Those in Healthy Subjects

PubMed Central

Lötsch, Jörn; Thrun, Michael; Lerch, Florian; Brunkhorst, Robert; Schiffmann, Susanne; Thomas, Dominique; Tegder, Irmgard; Geisslinger, Gerd; Ultsch, Alfred

2017-01-01

Lipid signaling has been suggested to be a major pathophysiological mechanism of multiple sclerosis (MS). With the increasing knowledge about lipid signaling, acquired data become increasingly complex making bioinformatics necessary in lipid research. We used unsupervised machine-learning to analyze lipid marker serum concentrations, pursuing the hypothesis that for the most relevant markers the emerging data structures will coincide with the diagnosis of MS. Machine learning was implemented as emergent self-organizing feature maps (ESOM) combined with the U*-matrix visualization technique. The data space consisted of serum concentrations of three main classes of lipid markers comprising eicosanoids (d = 11 markers), ceramides (d = 10), and lyosophosphatidic acids (d = 6). They were analyzed in cohorts of MS patients (n = 102) and healthy subjects (n = 301). Clear data structures in the high-dimensional data space were observed in eicosanoid and ceramides serum concentrations whereas no clear structure could be found in lysophosphatidic acid concentrations. With ceramide concentrations, the structures that had emerged from unsupervised machine-learning almost completely overlapped with the known grouping of MS patients versus healthy subjects. This was only partly provided by eicosanoid serum concentrations. Thus, unsupervised machine-learning identified distinct data structures of bioactive lipid serum concentrations. These structures could be superimposed with the known grouping of MS patients versus healthy subjects, which was almost completely possible with ceramides. Therefore, based on the present analysis, ceramides are first-line candidates for further exploration as drug-gable targets or biomarkers in MS. PMID:28590455

Analysis of Proteins, Protein Complexes, and Organellar Proteomes Using Sheathless Capillary Zone Electrophoresis - Native Mass Spectrometry

NASA Astrophysics Data System (ADS)

Belov, Arseniy M.; Viner, Rosa; Santos, Marcia R.; Horn, David M.; Bern, Marshall; Karger, Barry L.; Ivanov, Alexander R.

2017-12-01

Native mass spectrometry (MS) is a rapidly advancing field in the analysis of proteins, protein complexes, and macromolecular species of various types. The majority of native MS experiments reported to-date has been conducted using direct infusion of purified analytes into a mass spectrometer. In this study, capillary zone electrophoresis (CZE) was coupled online to Orbitrap mass spectrometers using a commercial sheathless interface to enable high-performance separation, identification, and structural characterization of limited amounts of purified proteins and protein complexes, the latter with preserved non-covalent associations under native conditions. The performance of both bare-fused silica and polyacrylamide-coated capillaries was assessed using mixtures of protein standards known to form non-covalent protein-protein and protein-ligand complexes. High-efficiency separation of native complexes is demonstrated using both capillary types, while the polyacrylamide neutral-coated capillary showed better reproducibility and higher efficiency for more complex samples. The platform was then evaluated for the determination of monoclonal antibody aggregation and for analysis of proteomes of limited complexity using a ribosomal isolate from E. coli. Native CZE-MS, using accurate single stage and tandem-MS measurements, enabled identification of proteoforms and non-covalent complexes at femtomole levels. This study demonstrates that native CZE-MS can serve as an orthogonal and complementary technique to conventional native MS methodologies with the advantages of low sample consumption, minimal sample processing and losses, and high throughput and sensitivity. This study presents a novel platform for analysis of ribosomes and other macromolecular complexes and organelles, with the potential for discovery of novel structural features defining cellular phenotypes (e.g., specialized ribosomes). [Figure not available: see fulltext.

Discrimination of Isomers of Released N- and O-Glycans Using Diagnostic Product Ions in Negative Ion PGC-LC-ESI-MS/MS

NASA Astrophysics Data System (ADS)

Ashwood, Christopher; Lin, Chi-Hung; Thaysen-Andersen, Morten; Packer, Nicolle H.

2018-03-01

Profiling cellular protein glycosylation is challenging due to the presence of highly similar glycan structures that play diverse roles in cellular physiology. As the anomericity and the exact linkage type of a single glycosidic bond can influence glycan function, there is a demand for improved and automated methods to confirm detailed structural features and to discriminate between structurally similar isomers, overcoming a significant bottleneck in the analysis of data generated by glycomics experiments. We used porous graphitized carbon-LC-ESI-MS/MS to separate and detect released N- and O-glycan isomers from mammalian model glycoproteins using negative mode resonance activation CID-MS/MS. By interrogating similar fragment spectra from closely related glycan isomers that differ only in arm position and sialyl linkage, product fragment ions for discrimination between these features were discovered. Using the Skyline software, at least two diagnostic fragment ions of high specificity were validated for automated discrimination of sialylation and arm position in N-glycan structures, and sialylation in O-glycan structures, complementing existing structural diagnostic ions. These diagnostic ions were shown to be useful for isomer discrimination using both linear and 3D ion trap mass spectrometers when analyzing complex glycan mixtures from cell lysates. Skyline was found to serve as a useful tool for automated assessment of glycan isomer discrimination. This platform-independent workflow can potentially be extended to automate the characterization and quantitation of other challenging glycan isomers. [Figure not available: see fulltext.

An Uncertainty Structure Matrix for Models and Simulations

NASA Technical Reports Server (NTRS)

Green, Lawrence L.; Blattnig, Steve R.; Hemsch, Michael J.; Luckring, James M.; Tripathi, Ram K.

2008-01-01

Software that is used for aerospace flight control and to display information to pilots and crew is expected to be correct and credible at all times. This type of software is typically developed under strict management processes, which are intended to reduce defects in the software product. However, modeling and simulation (M&S) software may exhibit varying degrees of correctness and credibility, depending on a large and complex set of factors. These factors include its intended use, the known physics and numerical approximations within the M&S, and the referent data set against which the M&S correctness is compared. The correctness and credibility of an M&S effort is closely correlated to the uncertainty management (UM) practices that are applied to the M&S effort. This paper describes an uncertainty structure matrix for M&S, which provides a set of objective descriptions for the possible states of UM practices within a given M&S effort. The columns in the uncertainty structure matrix contain UM elements or practices that are common across most M&S efforts, and the rows describe the potential levels of achievement in each of the elements. A practitioner can quickly look at the matrix to determine where an M&S effort falls based on a common set of UM practices that are described in absolute terms that can be applied to virtually any M&S effort. The matrix can also be used to plan those steps and resources that would be needed to improve the UM practices for a given M&S effort.

The reliability and validity study of the Kinesthetic and Visual Imagery Questionnaire in individuals with Multiple Sclerosis

PubMed Central

Tabrizi, Yousef Moghadas; Zangiabadi, Nasser; Mazhari, Shahrzad; Zolala, Farzaneh

2013-01-01

Objective Motor imagery (MI) has been recently considered as an adjunct to physical rehabilitation in patients with multiple sclerosis (MS). It is necessary to assess MI abilities and benefits in patients with MS by using a reliable tool. The Kinesthetic and Visual Imagery Questionnaire (KVIQ) was recently developed to assess MI ability in patients with stroke and other disabilities. Considering the different underlying pathologies, the present study aimed to examine the validity and reliability of the KVIQ in MS patients. Method Fifteen MS patients were assessed using the KVIQ in 2 sessions (5-14days apart) by the same examiner. In the second session, the participants also completed a revised MI questionnaire (MIQ-R) as the gold standard. Intra-class correlation coefficients (ICCs) were measured to determine test-retest reliability. Spearman's correlation analysis was performed to assess concurrent validity with the MIQ-R. Furthermore, the internal consistency (Cronbach's alpha) and factorial structure of the KVIQ were studied. Results The test-retest reliability for the KVIQ was good (ICCs: total KVIQ=0.89, visual KVIQ=0.85, and kinesthetic KVIQ=0.93), and the concurrent validity between the KVIQ and MIQ-R was good (r=0.79). The KVIQ had good internal consistency, with high Cronbach's alpha (alpha=0.84). Factorial analysis showed the bi-factorial structure of the KVIQ, which was explained by visual=57.6% and kinesthetic=32.4%. Conclusions The results of the present study revealed that the KVIQ is a valid and reliable tool for assessing MI in MS patients. PMID:24271091

The reliability and validity study of the Kinesthetic and Visual Imagery Questionnaire in individuals with multiple sclerosis.

PubMed

Tabrizi, Yousef Moghadas; Zangiabadi, Nasser; Mazhari, Shahrzad; Zolala, Farzaneh

2013-01-01

Motor imagery (MI) has been recently considered as an adjunct to physical rehabilitation in patients with multiple sclerosis (MS). It is necessary to assess MI abilities and benefits in patients with MS by using a reliable tool. The Kinesthetic and Visual Imagery Questionnaire (KVIQ) was recently developed to assess MI ability in patients with stroke and other disabilities. Considering the different underlying pathologies, the present study aimed to examine the validity and reliability of the KVIQ in MS patients. Fifteen MS patients were assessed using the KVIQ in 2 sessions (5-14 days apart) by the same examiner. In the second session, the participants also completed a revised MI questionnaire (MIQ-R) as the gold standard. Intra-class correlation coefficients (ICCs) were measured to determine test-retest reliability. Spearman's correlation analysis was performed to assess concurrent validity with the MIQ-R. Furthermore, the internal consistency (Cronbach's alpha) and factorial structure of the KVIQ were studied. The test-retest reliability for the KVIQ was good (ICCs: total KVIQ=0.89, visual KVIQ=0.85, and kinesthetic KVIQ=0.93), and the concurrent validity between the KVIQ and MIQ-R was good (r=0.79). The KVIQ had good internal consistency, with high Cronbach's alpha (alpha=0.84). Factorial analysis showed the bi-factorial structure of the KVIQ, which was explained by visual=57.6% and kinesthetic=32.4%. The results of the present study revealed that the KVIQ is a valid and reliable tool for assessing MI in MS patients.

Multiple sclerosis (MS) in the life cycle of the family: An interpretative phenomenological analysis of the perspective of persons with recently diagnosed MS.

PubMed

de Ceuninck van Capelle, Archie; Visser, Leo H; Vosman, Frans

2016-12-01

In this study the authors explored how people with recently diagnosed multiple sclerosis (MS) experience their disease within their family lives. Ten people in various stages of the cycle of family life (leaving home, finding a partner, raising children, parenting adolescents, launching children) who had been diagnosed with MS were interviewed in half-structured conversational interviews. Transcriptions were analyzed following a phenomenological approach. Five themes were found: (a) dwindling capacity for housekeeping and childcare (b) struggling to ask for or to accept help, (c) countering awkward attitudes toward my illness, (d) suspecting family members of concealing their, and (e) watching family members wrestle with your illness. The participants described that their illness affected their ability to care for their family and home as they used to. Only a couple of studies have addressed the first person perspective of patients on family and MS. The study expands on these studies by exploring not previously examined perspectives on leaving home, finding a partner, parenting adolescents, and launching children. The findings on family and MS, approached as elements of the first person perspective of MS patients, may guide future research. Given the pivotal role of worries on family in patient experience of MS, we argue that acknowledgment of family as a constitutive element of the patient perspective should be integrated in regular MS care. The authors suggest that the clinical handling of MS as a family issue needs to be done thoughtfully and with attention to the specifics of each unique family situation. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Stepwise evolution of protein native structure with electrospray into the gas phase, 10−12 to 102 s

PubMed Central

Breuker, Kathrin; McLafferty, Fred W.

2008-01-01

Mass spectrometry (MS) has been revolutionized by electrospray ionization (ESI), which is sufficiently “gentle” to introduce nonvolatile biomolecules such as proteins and nucleic acids (RNA or DNA) into the gas phase without breaking covalent bonds. Although in some cases noncovalent bonding can be maintained sufficiently for ESI/MS characterization of the solution structure of large protein complexes and native enzyme/substrate binding, the new gaseous environment can ultimately cause dramatic structural alterations. The temporal (picoseconds to minutes) evolution of native protein structure during and after transfer into the gas phase, as proposed here based on a variety of studies, can involve side-chain collapse, unfolding, and refolding into new, non-native structures. Control of individual experimental factors allows optimization for specific research objectives. PMID:19033474

Hepatoprotective effect against CCl4-induced acute liver damage in mice and High-performance liquid chromatography mass spectrometric method for analysis of the constituents of extract of Rubus crataegifolius.

PubMed

Sun, Yongjiao; Jia, Lingyun; Huang, Zhanbo; Wang, Jing; Lu, Jincai; Li, Jing

2017-11-01

This study is an attempt to evaluate the hepatoprotective activity of Rubus Crataegifolius against carbon tetrachloride-induced liver injury in mice. 70% ethanolic, ethyl acetate and n-BuOH extract of R. crataegifolius were administered daily for 14 days in experimental animals before they were treated with CCl 4 . The hepatoprotective activity of the extracts in this study was compared with the reference drug silymarin. A high-performance liquid chromatography mass spectrometric (HPLC-EIS-MS/MS) method was developed for the determination of the constituents of the extracts. According to the data of HPLC-EIS-MS/MS, the chemical structures of the largely 14 constituents of R. crataegifolius were identified online without time-consuming isolation. Ethyl acetate extracts of R. crataegifolius showed strong antioxidant activities and significant protective effect against acute hepatotoxicity induced by CCl 4 . According to the data of HPLC-EIS-MS/MS, Oleanic acid, Phlorizin dehydrate and Quercetin-3-rhamnoside are considered as the main hepatoprotective factor in ethyl acetate extract.

Rock Burst Monitoring by Integrated Microseismic and Electromagnetic Radiation Methods

NASA Astrophysics Data System (ADS)

Li, Xuelong; Wang, Enyuan; Li, Zhonghui; Liu, Zhentang; Song, Dazhao; Qiu, Liming

2016-11-01

For this study, microseismic (MS) and electromagnetic radiation (EMR) monitoring systems were installed in a coal mine to monitor rock bursts. The MS system monitors coal or rock mass ruptures in the whole mine, whereas the EMR equipment monitors the coal or rock stress in a small area. By analysing the MS energy, number of MS events, and EMR intensity with respect to rock bursts, it has been shown that the energy and number of MS events present a "quiet period" 1-3 days before the rock burst. The data also show that the EMR intensity reaches a peak before the rock burst and this EMR intensity peak generally corresponds to the MS "quiet period". There is a positive correlation between stress and EMR intensity. Buckling failure of coal or rock depends on the rheological properties and occurs after the peak stress in the high-stress concentration areas in deep mines. The MS "quiet period" before the rock burst is caused by the heterogeneity of the coal and rock structures, the transfer of high stress into internal areas, locked patches, and self-organized criticality near the stress peak. This study increases our understanding of coal and rock instability in deep mines. Combining MS and EMR to monitor rock burst could improve prediction accuracy.

Comparative Study of Three Methods for Affinity Measurements: Capillary Electrophoresis Coupled with UV Detection and Mass Spectrometry, and Direct Infusion Mass Spectrometry

NASA Astrophysics Data System (ADS)

Mironov, Gleb G.; Logie, Jennifer; Okhonin, Victor; Renaud, Justin B.; Mayer, Paul M.; Berezovski, Maxim V.

2012-07-01

We present affinity capillary electrophoresis and mass spectrometry (ACE-MS) as a comprehensive separation technique for label-free solution-based affinity analysis. The application of ACE-MS for measuring affinity constants between eight small molecule drugs [ibuprofen, s-flurbiprofen, diclofenac, phenylbutazone, naproxen, folic acid, resveratrol, and 4,4'-(propane-1,3-diyl) dibenzoic acid] and β-cyclodextrin is described. We couple on-line ACE with MS to combine the separation and kinetic capability of ACE together with the molecular weight and structural elucidation of MS in one system. To understand the full potential of ACE-MS, we compare it with two other methods: Direct infusion mass spectrometry (DIMS) and ACE with UV detection (ACE-UV). After the evaluation, DIMS provides less reliable equilibrium dissociation constants than separation-based ACE-UV and ACE-MS, and cannot be used solely for the study of noncovalent interactions. ACE-MS determines apparent dissociation constants for all reacting small molecules in a mixture, even in cases when drugs overlap with each other during separation. The ability of ACE-MS to interact, separate, and rapidly scan through m/z can facilitate the simultaneous affinity analysis of multiple interacting pairs, potentially leading to the high-throughput screening of drug candidates.

Brain activation patterns and cognitive processing speed in patients with pediatric-onset multiple sclerosis.

PubMed

Akbar, Nadine; Banwell, Brenda; Sled, John G; Binns, Malcolm A; Doesburg, Sam M; Rypma, Bart; Lysenko, Magdalena; Till, Christine

2016-01-01

This study aimed to determine the extent and pattern of brain activation elicited by a functional magnetic resonance imaging version of the Symbol Digit Modalities Test (fMRI-SDMT), a task of information processing speed, in pediatric-onset multiple sclerosis (MS) patients as compared to sex- and age-matched non-MS self-reported healthy individuals. Participants included 20 right-handed individuals aged 13-24 years with pediatric-onset MS (mean age = 19 years, 15 female) and 16 non-MS self-reported healthy individuals. All participants underwent a 3.0-tesla MRI scan with structural (T1; T2; proton density, PD; fluid-attenuated inversion recovery, FLAIR) and fMRI-SDMT acquisition. Participants were instructed to indicate with a button press whether a single pairing of a symbol to a number matched any of those shown in a key that displays nine possible pairings. Response time (p = .909) and accuracy (p = .832) on the fMRI-SDMT did not differ between groups. However, the MS group demonstrated lower overall activation than the non-MS group in the right middle frontal gyrus (p = .003). Within the MS group, faster response time was associated with greater activation of the right inferior occipital, anterior cingulate, right superior parietal, thalamus, and left superior occipital cortices (all p < .05). A significant interaction effect was demonstrated, indicating that faster response time was associated with greater activation of the left superior occipital region in the pediatric MS group than in the non-MS group (p = .002). Attenuated activation of frontal regions was observed in this cohort of pediatric-onset MS patients when performing the fMRI-SDMT, even in the absence of behaviorally detectable deficits. Within the MS group only, faster response time elicited greater activation, suggesting this to be an adaptive mechanism that may contribute to limiting the impact of disease-related structural pathology.

Quantitative evaluation of protein conformation in pharmaceuticals using cross-linking reactions coupled with LC-MS/MS analysis.

PubMed

Yamaguchi, Hideto; Hirakura, Yutaka; Shirai, Hiroki; Mimura, Hisashi; Toyo'oka, Toshimasa

2011-06-01

The need for a simple and high-throughput method for identifying the tertiary structure of protein pharmaceuticals has increased. In this study, a simple method for mapping the protein fold is proposed for use as a complementary quality test. This method is based on cross-linking a protein using a [bis(sulfosuccinimidyl)suberate (BS(3))], followed by peptide mapping by LC-MS. Consensus interferon (CIFN) was used as the model protein. The tryptic map obtained via liquid chromatography tandem mass spectroscopy (LC-MS/MS) and the mass mapping obtained via matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy were used to identify cross-linked peptides. While LC-MS/MS analyses found that BS(3) formed cross-links in the loop region of the protein, which was regarded as the biologically active site, sodium dodecyl-sulfate polyacrylamide gel electrophoresis demonstrated that cross-linking occurred within a protein molecule, but not between protein molecules. The occurrence of cross-links at the active site depends greatly on the conformation of the protein, which is determined by the denaturing conditions. Quantitative evaluation of the tertiary structure of CIFN was thus possible by monitoring the amounts of cross-linked peptides generated. Assuming that background information is available at the development stage, this method may be applicable to process development as a complementary test for quality control. Copyright © 2011 Elsevier B.V. All rights reserved.

Structural Characterization of the Degradation Products of a Minor Natural Sweet Diterpene Glycoside Rebaudioside M under Acidic Conditions

PubMed Central

Prakash, Indra; Chaturvedula, Venkata Sai Prakash; Markosyan, Avetik

2014-01-01

Degradation of rebaudioside M, a minor sweet component of Stevia rebaudiana Bertoni, under conditions that simulated extreme pH and temperature conditions has been studied. Thus, rebaudioside M was treated with 0.1 M phosphoric acid solution (pH 2.0) and 80 °C temperature for 24 h. Experimental results indicated that rebaudioside M under low pH and higher temperature yielded three minor degradation compounds, whose structural characterization was performed on the basis of 1D (1H-, 13C-) & 2D (COSY, HSQC, HMBC) NMR, HRMS, MS/MS spectral data as well as enzymatic and acid hydrolysis studies. PMID:24424316

Structure-performance relationships of phenyl cinnamic acid derivatives as MALDI-MS matrices for sulfatide detection.

PubMed

Tambe, Suparna; Blott, Henning; Fülöp, Annabelle; Spang, Nils; Flottmann, Dirk; Bräse, Stefan; Hopf, Carsten; Junker, Hans-Dieter

2017-02-01

A key aspect for the further development of matrix-assisted laser desorption ionization (MALDI)-mass spectrometry (MS) is a better understanding of the working principles of MALDI matrices. To address this issue, a chemical compound library of 59 structurally related cinnamic acid derivatives was synthesized. Potential MALDI matrices were evaluated with sulfatides, a class of anionic lipids which are abundant in complex brain lipid mixtures. For each matrix relative mean S/N ratios of sulfatides were determined against 9-aminoacridine as a reference matrix using negative ion mass spectrometry with 355 and 337 nm laser systems. The comparison of matrix features with their corresponding relative mean S/N ratios for sulfatide detection identified correlations between matrix substitution patterns, their chemical functionality, and their MALDI-MS performance. Crystal structures of six selected matrices provided structural insight in hydrogen bond interactions in the solid state. Principal component analysis allowed the additional identification of correlation trends between structural and physical matrix properties like number of exchangeable protons at the head group, MW, logP, UV-Vis, and sulfatide detection sensitivity. Graphical abstract Design, synthesis and mass spectrometric evaluation of MALDI-MS matrix compound libraries allows the identification of matrix structure - MALDI-MS performance relationships using multivariate statistics as a tool.

Sizing and Discovery of Nanosized Polyoxometalate Clusters by Mass Spectrometry

PubMed Central

2016-01-01

Ion mobility-mass spectrometry (IM-MS) is a powerful technique for structural characterization, e.g., sizing and conformation, particularly when combined with quantitative modeling and comparison to theoretical values. Traveling wave IM-MS (TW-IM-MS) has recently become commercially available to nonspecialist groups and has been exploited in the structural study of large biomolecules, however reliable calibrants for large anions have not been available. Polyoxometalate (POM) species—nanoscale inorganic anions—share many of the facets of large biomolecules, however, the full potential of IM-MS in their study has yet to be realized due to a lack of suitable calibration data or validated theoretical models. Herein we address these limitations by reporting DT-IM (drift tube) data for a set of POM clusters {M12} Keggin 1, {M18} Dawson 2, and two {M7} Anderson derivatives 3 and 4 which demonstrate their use as a TW-IM-MS calibrant set to facilitate characterization of very large (ca. 1–4 nm) anionic species. The data was also used to assess the validity of standard techniques to model the collision cross sections of large inorganic anions using the nanoscale family of compounds based upon the {Se2W29} unit including the trimer, {Se8W86O299} A, tetramer, {Se8W116O408} B, and hexamer {Se12W174O612} C, including their relative sizing in solution. Furthermore, using this data set, we demonstrated how IM-MS can be used to conveniently characterize and identify the synthesis of two new, i.e., previously unreported POM species, {P8W116}, unknown D, and {Te8W116}, unknown E, which are not amenable to analysis by other means with the approximate formulation of [H34W118X8M2O416]44–, where X = P and M = Co for D and X = Te and M = Mn for E. This work establishes a new type of inorganic calibrant for IM-MS allowing sizing, structural analysis, and discovery of molecular nanostructures directly from solution. PMID:26906879

Employment among Patients with Multiple Sclerosis-A Population Study

PubMed Central

Bøe Lunde, Hanne Marie; Telstad, Wenche; Grytten, Nina; Kyte, Lars; Aarseth, Jan; Myhr, Kjell-Morten; Bø, Lars

2014-01-01

Objective To investigate demographic and clinical factors associated with employment in MS. Methods The study included 213 (89.9%) of all MS patients in Sogn and Fjordane County, Western Norway at December 31st 2010. The patients underwent clinical evaluation, structured interviews and completed self-reported questionnaires. Demographic and clinical factors were compared between patients being employed versus patients being unemployed and according to disease course of MS. Logistic regression analysis was used to identify factors independently associated with current employment. Results After a mean disease duration of almost 19 years, 45% of the population was currently full-time or part- time employed. Patients with relapsing –remitting MS (RRMS) had higher employment rate than patients with secondary (SPMS) and primary progressive (PPMS). Higher educated MS patients with lower age at onset, shorter disease duration, less severe disability and less fatigue were most likely to be employed. Conclusions Nearly half of all MS patients were still employed after almost two decades of having MS. Lower age at onset, shorter disease duration, higher education, less fatigue and less disability were independently associated with current employment. These key clinical and demographic factors are important to understand the reasons to work ability in MS. The findings highlight the need for environmental adjustments at the workplace to accommodate individual ’s needs in order to improve working ability among MS patients. PMID:25054972

Identification of pesticide transformation products in agricultural soils using liquid chromatography/quadrupole-time-of-flight mass spectrometry.

PubMed

Padilla-Sánchez, Juan A; Michael Thurman, E; Plaza-Bolaños, Patricia; Ferrer, Imma

2012-05-15

A study of pesticide transformation products (TPs) was carried out in soils of agricultural areas working under integrated pest management programs (IPMs). Bupirimate and cyromazine were the pesticides detected in soils after an initial pre-screening. The aim of this work was the identification of relevant TPs of these two pesticides. Soil samples were extracted by pressurized liquid extraction (PLE), using a mixture of ethyl acetate/methanol (3:1, v/v), and analyzed by ultra-high-pressure liquid chromatography coupled to hybrid quadrupole-time-of-flight mass spectrometry (UHPLC-QTOF-MS). For confirmation purposes, tandem mass spectrometry (MS(2) ) experiments were carried out using QTOF-MS, obtaining specific fragment structures of the pesticides and their degradates. Retention times and exact masses of the protonated molecules were used for the identification of the pesticides bupirimate (m/z 317.1642) and cyromazine (m/z 167.1040) and their respective TPs, namely ethirimol (m/z 210.1601) and melamine (m/z 127.0727). A novel strategy using pseudo-MS(3) experiments was developed to confirm the structure of bupirimate TP (ethirimol). This strategy consists of generating the particular TP in the ion source, via collision-induced fragmentation, and then performing MS/MS to the fragment ion formed in-source. Ethirimol and melamine were identified as degradation products of bupirimate and cyromazine, respectively. The study was applied to the analysis of 15 agricultural soil samples finding bupirimate and ethirimol in seven samples, cyromazine in one sample and melamine in four samples. Copyright © 2012 John Wiley & Sons, Ltd.

"Putting one foot in front of the other": a qualitative study of emotional experiences and help-seeking in women with multiple sclerosis.

PubMed

Blundell Jones, Joanna; Walsh, Sue; Isaac, Claire

2014-12-01

Treatments for depression and anxiety in multiple sclerosis (MS) are effective but evidence suggests that individuals do not always seek help for emotional difficulties. This study explored how ten women with MS (aged 30-64), recruited via a hospital based MS clinic, coped with and understood their emotions. The semi-structured interviews were analysed using interpretative phenomenological analysis. Eight participants discussed the analytic process and themes. Four overarching themes emerged: Disclosure stress, Uncomfortable dependence, Facing deterioration and One step at a time. The women struggled emotionally with many aspects of living with MS yet coping alone provided a way of defying MS and maintaining independence and control. The women needed emotional support but reported thinking others either did not notice or understand; their emotions often felt invisible. More holistic care from services was desired. Non help-seeking for distress was partially influenced by a desire to keep things "normal" and a lack of knowledge regarding service provision.

New Features in the Lipid A Structure of Brucella suis and Brucella abortus Lipopolysaccharide

NASA Astrophysics Data System (ADS)

Casabuono, Adriana C.; Czibener, Cecilia; Del Giudice, Mariela G.; Valguarnera, Ezequiel; Ugalde, Juan E.; Couto, Alicia S.

2017-12-01

Brucellaceae are Gram-negative bacteria that cause brucellosis, one of the most distributed worldwide zoonosis, transmitted to humans by contact with either infected animals or their products. The lipopolysaccharide exposed on the cell surface has been intensively studied and is considered a major virulence factor of Brucella. In the last years, structural studies allowed the determination of new structures in the core oligosaccharide and the O-antigen of this lipopolysaccharide. In this work, we have reinvestigated the lipid A structure isolated from B. suis and B. abortus lipopolysaccharides. A detailed study by MALDI-TOF mass spectrometry in the positive and negative ion modes of the lipid A moieties purified from both species was performed. Interestingly, a new feature was detected: the presence of a pyrophosphorylethanolamine residue substituting the backbone. LID-MS/MS analysis of some of the detected ions allowed assurance that the Lipid A structure composed by the diGlcN3N disaccharide, mainly hexa-acylated and penta-acylated, bearing one phosphate and one pyrophosphorylethanolamine residue. [Figure not available: see fulltext.

New Features in the Lipid A Structure of Brucella suis and Brucella abortus Lipopolysaccharide.

PubMed

Casabuono, Adriana C; Czibener, Cecilia; Del Giudice, Mariela G; Valguarnera, Ezequiel; Ugalde, Juan E; Couto, Alicia S

2017-12-01

Brucellaceae are Gram-negative bacteria that cause brucellosis, one of the most distributed worldwide zoonosis, transmitted to humans by contact with either infected animals or their products. The lipopolysaccharide exposed on the cell surface has been intensively studied and is considered a major virulence factor of Brucella. In the last years, structural studies allowed the determination of new structures in the core oligosaccharide and the O-antigen of this lipopolysaccharide. In this work, we have reinvestigated the lipid A structure isolated from B. suis and B. abortus lipopolysaccharides. A detailed study by MALDI-TOF mass spectrometry in the positive and negative ion modes of the lipid A moieties purified from both species was performed. Interestingly, a new feature was detected: the presence of a pyrophosphorylethanolamine residue substituting the backbone. LID-MS/MS analysis of some of the detected ions allowed assurance that the Lipid A structure composed by the diGlcN3N disaccharide, mainly hexa-acylated and penta-acylated, bearing one phosphate and one pyrophosphorylethanolamine residue. Graphical abstract ᅟ.

Study on the application of shear-wave elastography to thin-layered media and tubular structure: Finite-element analysis and experiment verification

NASA Astrophysics Data System (ADS)

Jang, Jun-keun; Kondo, Kengo; Namita, Takeshi; Yamakawa, Makoto; Shiina, Tsuyoshi

2016-07-01

Shear-wave elastography (SWE) enables the noninvasive and quantitative evaluation of the mechanical properties of human soft tissue. Generally, shear-wave velocity (C S) can be estimated using the time-of-flight (TOF) method. Young’s modulus is then calculated directly from the estimated C S. However, because shear waves in thin-layered media propagate as guided waves, C S cannot be accurately estimated using the conventional TOF method. Leaky Lamb dispersion analysis (LLDA) has recently been proposed to overcome this problem. In this study, we performed both experimental and finite-element (FE) analyses to evaluate the advantages of LLDA over TOF. In FE analysis, we investigated why the conventional TOF is ineffective for thin-layered media. In phantom experiments, C S results estimated using the two methods were compared for 1.5 and 2% agar plates and tube phantoms. Furthermore, it was shown that Lamb waves can be applied to tubular structures by extracting lateral waves traveling in the long axis direction of the tube using a two-dimensional window. Also, the effects of the inner radius and stiffness (or shear wavelength) of the tube on the estimation performance of LLDA were experimentally discussed. In phantom experiments, the results indicated good agreement between LLDA (plate phantoms of 2 mm thickness: 5.0 m/s for 1.5% agar and 7.2 m/s for 2% agar; tube phantoms with 2 mm thickness and 2 mm inner radius: 5.1 m/s for 1.5% agar and 7.0 m/s for 2% agar; tube phantoms with 2 mm thickness and 4 mm inner radius: 5.3 m/s for 1.5% agar and 7.3 m/s for 2% agar) and SWE measurements (bulk phantoms: 5.3 m/s ± 0.27 for 1.5% agar and 7.3 m/s ± 0.54 for 2% agar).

Analysis of phytochemical variations in dioecious Tinospora cordifolia stems using HPLC/QTOF MS/MS and UPLC/QqQLIT -MS/MS.

PubMed

Bajpai, Vikas; Singh, Awantika; Chandra, Preeti; Negi, M P S; Kumar, Nikhil; Kumar, Brijesh

2016-01-01

The stem of dioecious Tinospora cordifolia (Menispermaceae) is a commonly used traditional Ayurvedic medicine in India having several therapeutic properties. To develop and validate LC-MS methods for the identification and simultaneous quantitation of various secondary metabolites and to study metabolomic variations in the stem of male and female plants. Ethanolic extract of stems were analysed by HPLC/ESI-QTOF-MS/MS for rapid screening of bioactive phytochemicals. High resolution MS and MS/MS in positive ESI mode were used for structural investigation of secondary metabolites. An UPLC/ESI-QqQ(LIT) -MS/MS method in MRM mode was developed and validated for the simultaneous quantitation of five bioactive alkaloids. Identification and characterisation of 36 metabolites including alkaloids, sesquiterpenes and phytoecdysteroids were performed using LC-MS and MS/MS techniques. The bioactive alkaloids such as jatrorrhizine, magnoflorine, isocorydine, palmatine and tetrahydropalmatine were successfully quantified in male and female plants. The mean abundances of magnoflorine jatrorrhizine, and oblongine were significantly (P < 0.05) higher in male plants while mean abundances of tetrahydropalmatine, norcoclaurine, and reticuline were significantly (P < 0.05) higher in female plants. Phytochemicals in the stem of male and female Tinospora cordifolia showed significant qualitative and quantitative variations. LC-MS and MS/MS methods can be used to differentiate between male and female plants based on their chemical profiles and quantities of the marker bioactive alkaloids. This chemical composition difference was also evident during vegetative stage when there were no male and female flowers. Copyright © 2015 John Wiley & Sons, Ltd.

Virucidal Influence of Ionic Liquids on Phages P100 and MS2

PubMed Central

Fister, Susanne; Mester, Patrick; Sommer, Julia; Witte, Anna K.; Kalb, Roland; Wagner, Martin; Rossmanith, Peter

2017-01-01

An increasing number of publications describe the potential of ionic liquids (ILs) as novel antimicrobials, antibacterial coatings and even as active pharmaceutical ingredients. Nevertheless, a major research area, notably their impact on viruses, has so far been neglected. Consequently the aim of this study was to examine the effects of ILs on the infectivity of viruses. A systematic analysis to investigate the effects of defined structural elements of ILs on virus activity was performed using 55 ILs. All structure activity relationships (SARs) were tested on the human norovirus surrogate phage MS2 and phage P100 representing non-enveloped DNA viruses. Results demonstrate that IL SAR conclusions, established for prokaryotes and eukaryotes, are not readily applicable to the examined phages. A virus-type-dependent IL influence was also apparent. Overall, four ILs, covering different structural elements, were found to reduce phage P100 infectivity by ≥4 log10 units, indicating a virucidal effect, whereas the highest reduction for phage MS2 was about 3 log10 units. Results indicate that future applications of ILs as virucidal agents will require development of novel SARs and the obtained results serve as a good starting point for future studies. PMID:28883814

Identification of a new sulfonic acid metabolite of metolachlor in soil

USGS Publications Warehouse

Aga, D.S.; Thurman, E.M.; Yockel, M.E.; Zimmerman, L.R.; Williams, T.D.

1996-01-01

An ethanesulfonic acid metabolite of metolachlor (metolachlor ESA) was identified in soil-sample extracts by negative-ion, fast-atom bombardment mass spectrometry (FAB-MS) and FAB tandem mass spectrometry (FAB-MS/MS). Production fragments from MS/MS analysis of the deprotonated molecular ion of metolachlor ESA in the soil extract can be reconciled with the structure of the synthesized standard. The elemental compositions of the (M - H)- ions of the metolachlor ESA standard and the soil-sample extracts were confirmed by high-resolution mass spectrometry. A dissipation study revealed that metolachlor ESA is formed in soil under field conditions corresponding to a decrease in the concentration of the parent herbicide, metolachlor. The identification of the sulfonated metabolite of metolachlor suggests that the glutathione conjugation pathway is a common detoxification pathway shared by chloroacetanilide herbicides.

Causes, effects and connectivity changes in MS-related cognitive decline.

PubMed

Rimkus, Carolina de Medeiros; Steenwijk, Martijn D; Barkhof, Frederik

2016-01-01

Cognitive decline is a frequent but undervalued aspect of multiple sclerosis (MS). Currently, it remains unclear what the strongest determinants of cognitive dysfunction are, with grey matter damage most directly related to cognitive impairment. Multi-parametric studies seem to indicate that individual factors of MS-pathology are highly interdependent causes of grey matter atrophy and permanent brain damage. They are associated with intermediate functional effects (e.g. in functional MRI) representing a balance between disconnection and (mal) adaptive connectivity changes. Therefore, a more comprehensive MRI approach is warranted, aiming to link structural changes with functional brain organization. To better understand the disconnection syndromes and cognitive decline in MS, this paper reviews the associations between MRI metrics and cognitive performance, by discussing the interactions between multiple facets of MS pathology as determinants of brain damage and how they affect network efficiency.

Development of a UHPLC-MS/MS method for the measurement of chlortetracycline degradation in swine manure

USDA-ARS?s Scientific Manuscript database

An ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method was developed capable of simultaneously measuring chlortetracycline (CTC), epi-chlortetracycline (epi-CTC) and isochlortetracycline (ICTC), as well as other structurally related tetracyclines in swine manur...

Identification of Crosslinked Peptides after Click-based Enrichment Using Sequential CID and ETD Tandem Mass Spectrometry

PubMed Central

Chowdhury, Saiful M.; Du, Xiuxia; Tolić, Nikola; Wu, Si; Moore, Ronald J.; Mayer, M. Uljana; Smith, Richard D.; Adkins, Joshua N.

2010-01-01

Chemical crosslinking combined with mass spectrometry can be a powerful approach for the identification of protein-protein interactions and for providing constraints on protein structures. However, enrichment of crosslinked peptides is crucial to reduce sample complexity before mass spectrometric analysis. In addition compact crosslinkers are often preferred to provide short spacer lengths, surface accessibility to the protein complexes, and must have reasonable solubility under condition where the native complex structure is stable. In this study, we present a novel compact crosslinker that contains two distinct features: 1) an alkyne tag and 2) a small molecule detection tag (NO2-) to maintain reasonable solubility in water. The alkyne tag enables enrichment of the crosslinked peptide after proteolytic cleavage after coupling of an affinity tag using alkyne-azido click chemistry. Neutral loss of the small NO2- moiety provides a secondary means of detecting crosslinked peptides in MS/MS analyses, providing additional confidence in peptide identifications. We show the labeling efficiency of this crosslinker, which we termed CLIP (Click-enabled Linker for Interacting Proteins) using ubiquitin. The enrichment capability of CLIP is demonstrated for crosslinked ubiquitin in highly complex E. coli cell lysates. Sequential CID-MS/MS and ETD-MS/MS of inter-crosslinked peptides (two peptides connected with a crosslinker) are also demonstrated for improved automated identification of crosslinked peptides. PMID:19496583

A fragmentation study of dihydroquercetin using triple quadrupole mass spectrometry and its application for identification of dihydroflavonols in Citrus juices.

PubMed

Abad-García, Beatriz; Garmón-Lobato, Sergio; Berrueta, Luis A; Gallo, Blanca; Vicente, Francisca

2009-09-01

A mass spectrometric method using electrospray ionization with triple quadrupole and quadrupole time-of-flight hybrid (Q-Tof) mass spectrometry has been applied to the structural characterization of dihydroflavonols. This family of compounds has been studied by liquid chromatography/tandem mass spectrometry (LC/MS/MS) for the first time in this work. A comprehensive study of the product ion MS spectra of the [M+H](+) ion of a commercially available standard has been performed. The most useful fragmentations in terms of structural identification are those that involve cleavage of the C-ring, resulting in diagnostic ions of dihydroflavonol family: (1,3)A(0) (+), (1,2)B(0) (+), (1,2)B(0) (+)-CO, (0,2)A(0) (+), (0,2)A(0) (+)-H(2)O, (0,2)A(0) (+)-CO, and (0,2)A(0) (+)-H(2)O-CO, that allow the characterization of the substituents in the A- and B-rings. In addition to those ions, other product ions due to losses of H(2)O and CO molecules from the Y(0) (+) ion were observed. Their fragmentation mechanisms and ion structures have been proposed. The established fragmentation patterns have been used to successfully identity three dihydroflavonols found in tangerine juices for the first time. Copyright (c) 2009 John Wiley & Sons, Ltd.

Structure Determination of an Inter-strand-type cis-anti Cyclobutane Thymine Dimer Produced in High Yield by UVB Light in an Oligodeoxynucleotide at Acidic pH

PubMed Central

Su, Dian G. T.; Kao, Jeffrey L.-F.; Gross, Michael L.; Taylor, John-Stephen A.

2009-01-01

UVB irradiation of DNA produces photodimers in adjacent DNA bases and on rare occasions in non-adjacent bases. UVB irradiation (312 nm) of d(GTATCATGAGGTGC) gave rise to an unknown DNA photoproduct in approximately 40% yield at acidic pH of about 5. This product has a much shorter retention time in reverse phase HPLC compared to known dipyrimidine photoproducts of this sequence. A large upfield shift of two thymine H6 NMR signals and photoreversion to the parent ODN upon irradiation with 254 nm light indicates that the photoproduct is a cyclobutane thymine dimer. Exonuclease-coupled MS assay establishes that the photodimer forms between T2 and T7, which was confirmed by tandem mass spectrometric MS/MS identification of the endonuclease P1 digestion product d(T2[A3])=pd(T7[G8]). Acidic hydrolysis of the photoproduct gave a product with the same retention time on reverse phase HPLC and the same MS/MS fragmentation pattern as authentic Thy[c,a]Thy. 2D NOE NMR data are consistent with a cis-anti cyclobutane dimer between the 3′-sides of T2 and T7 in anti glycosyl conformations that had to have arisen from an inter-stand type reaction. In addition to pH-dependent, the photoproduct yield is highly sequence specific and concentration dependent, indicating that it results from a higher order folded structure. The efficient formation of this inter-strand-type photoproduct suggests the existence of a new type of folding motif and the possibility that this type of photoproduct might also form in other folded structures, such as G-quadruplexes and i-motif structures which can be now studied by the methods described. PMID:18680367

Relationships between trunk performance, gait and postural control in persons with multiple sclerosis.

PubMed

Freund, Jane E; Stetts, Deborah M; Vallabhajosula, Srikant

2016-06-30

Multiple sclerosis (MS) is a chronic progressive disease of the central nervous system. Compared to healthy individuals, persons with multiple sclerosis (PwMS) have increased postural sway in quiet stance, decreased gait speed and increased fall incidence. Trunk performance has been implicated in postural control, gait dysfunction, and fall prevention in older adults. However, the relationship of trunk performance to postural control and gait has not been adequately studied in PwMS. To compare trunk muscle structure and performance in PwMS to healthy age and gendered-matched controls (HC); to determine the effects of isometric trunk endurance testing on postural control in both populations; and to determine the relationship of trunk performance with postural control, gait and step activity in PwMS. Fifteen PwMS and HC completed ultrasound imaging of trunk muscles, 10 m walk test, isometric trunk endurance tests, and postural sway test. Participants wore a step activity monitor for 7 days. PwMS had worse isometric trunk endurance compared to HC. PwMS trunk flexion endurance negatively correlated to several postural control measures and positively correlated to gait speed and step activity. Clinicians should consider evaluation and interventions directed at impaired trunk endurance in PwMS.

Neural correlates of gait variability in people with multiple sclerosis with fall history.

PubMed

Kalron, Alon; Allali, Gilles; Achiron, Anat

2018-05-28

Investigate the association between step time variability and related brain structures in accordance with fall status in people with multiple sclerosis (PwMS). The study included 225 PwMS. A whole-brain MRI was performed by a high-resolution 3.0-Telsa MR scanner in addition to volumetric analysis based on 3D T1-weighted images using the FreeSurfer image analysis suite. Step time variability was measured by an electronic walkway. Participants were defined as "fallers" (at least two falls during the previous year) and "non-fallers". One hundred and five PwMS were defined as fallers and had a greater step time variability compared to non-fallers (5.6% (S.D.=3.4) vs. 3.4% (S.D.=1.5); p=0.001). MS fallers exhibited a reduced volume in the left caudate and both cerebellum hemispheres compared to non-fallers. By using a linear regression analysis no association was found between gait variability and related brain structures in the total cohort and non-fallers group. However, the analysis found an association between the left hippocampus and left putamen volumes with step time variability in the faller group; p=0.031, 0.048, respectively, controlling for total cranial volume, walking speed, disability, age and gender. Nevertheless, according to the hierarchical regression model, the contribution of these brain measures to predict gait variability was relatively small compared to walking speed. An association between low left hippocampal, putamen volumes and step time variability was found in PwMS with a history of falls, suggesting brain structural characteristics may be related to falls and increased gait variability in PwMS. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

LC-MS/MS analysis of permethylated free oligosaccharides and N-glycans derived from human, bovine, and goat milk samples.

PubMed

Dong, Xue; Zhou, Shiyue; Mechref, Yehia

2016-06-01

Oligosaccharides in milk not only provide nutrition to the infants but also have significant immune biofunctions such as inhibition of pathogen binding to the host cell. The main component in milk oligosaccharides is free oligosaccharides. Since the proteins in milk are highly glycosylated, N-glycans in milk also play an import role. In this study, we investigated the permethylated free oligosaccharides and N-glycans extracted from bovine, goat, and human milks using LC-MS/MS. Quantitation profiles of free oligosaccharides and N-glycans were reported. The number of free oligosaccharides observed in bovine, goat, and human milk samples (without isomeric consideration) were 11, 8, and 11, respectively. Human milk had more complex free oligosaccharides structures than the other two milk samples. Totally 58, 21, and 43 N-glycan structures (without isomeric consideration) were associated with whey proteins extracted from bovine, goat, and human milk samples, respectively. Bovine milk free oligosaccharides and N-glycans from whey proteins were highly sialylated and to a lesser extend fucosylated. Goat and human milk free oligosaccharides and N-glycans from whey proteins were both highly fucosylated. Also, the isomeric glycans in milk samples were determined by porous graphitic carbon LC at elevated temperatures. For example, separation of human milk free oligosaccharide Gal-GlcNAc-(Fuc)-Gal-Glc and Gal-GlcNAc-Gal-Glc-Fuc isomers was achieved using porous graphitic carbon column. Permethylation of the glycan structures facilitated the interpretation of MS/MS. For example, internal cleavage and glycosidic bond cleavage are readily distinguished in the tandem mass spectra of permethylated glycans. This feature resulted in the identification of several isomers. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Coupling Flash LC with MS for enrichment and isolation of milk oligosaccharides for functional studies

PubMed Central

Strum, John S.; Aldredge, Danielle; Barile, Daniela; Lebrilla, Carlito B.

2013-01-01

Mass spectrometry has been coupled with flash liquid chromatography to yield new capabilities for isolating non-chromophoric material from complicated biological mixtures. A flash LC/MS/MS method enabled fraction collection of milk oligosaccharides from biological mixtures based on composition and structure. The method is compatible with traditional gas-pressure driven flow flash chromatography, widely employed in organic chemistry laboratories. The on-line mass detector enabled real-time optimization of chromatographic parameters to favor separation of oligosaccharides that would otherwise be indistinguishable from co-eluting components with a non-specific detector. Unlike previously described preparative LC/MS techniques, we have employed a dynamic flow connection that permits any flow rate from the flash system to be delivered from 1–200 mL/min without affecting the ionization conditions of the mass spectrometer. A new way of packing large amounts of graphitized carbon allowed the enrichment and separation of milligram quantities of structurally heterogeneous mixtures of human milk oligosaccharides (HMOs) and bovine milk oligosaccharides (BMOs). Abundant saccharide components in milk, such as lactose and lacto-N-tetraose, were separated from the rarer and less abundant oligosaccharides that have greater structural diversity and biological functionality. Neutral and acidic HMOs and BMOs were largely separated and enriched with a dual binary solvent system. PMID:22370281

MS5 Mediates Early Meiotic Progression and Its Natural Variants May Have Applications for Hybrid Production in Brassica napus

PubMed Central

Xin, Qiang; Shen, Yi; Li, Xi; Lu, Wei; Wang, Xiang; Han, Xue; Dong, Faming; Wan, Lili; Yang, Guangsheng; Cheng, Zhukuan

2016-01-01

During meiotic prophase I, chromatin undergoes dynamic changes to establish a structural basis for essential meiotic events. However, the mechanism that coordinates chromosome structure and meiotic progression remains poorly understood in plants. Here, we characterized a spontaneous sterile mutant MS5bMS5b in oilseed rape (Brassica napus) and found its meiotic chromosomes were arrested at leptotene. MS5 is preferentially expressed in reproductive organs and encodes a Brassica-specific protein carrying conserved coiled-coil and DUF626 domains with unknown function. MS5 is essential for pairing of homologs in meiosis, but not necessary for the initiation of DNA double-strand breaks. The distribution of the axis element-associated protein ASY1 occurs independently of MS5, but localization of the meiotic cohesion subunit SYN1 requires functional MS5. Furthermore, both the central element of the synaptonemal complex and the recombination element do not properly form in MS5bMS5b mutants. Our results demonstrate that MS5 participates in progression of meiosis during early prophase I and its allelic variants lead to differences in fertility, which may provide a promising strategy for pollination control for heterosis breeding. PMID:27194707

Epitope Structure of the Carbohydrate Recognition Domain of Asialoglycoprotein Receptor to a Monoclonal Antibody Revealed by High-Resolution Proteolytic Excision Mass Spectrometry

NASA Astrophysics Data System (ADS)

Stefanescu, Raluca; Born, Rita; Moise, Adrian; Ernst, Beat; Przybylski, Michael

2011-01-01

Recent studies suggest that the H1 subunit of the carbohydrate recognition domain (H1CRD) of the asialoglycoprotein receptor is used as an entry site into hepatocytes by hepatitis A and B viruses and Marburg virus. Thus, molecules binding specifically to the CRD might exert inhibition towards these diseases by blocking the virus entry site. We report here the identification of the epitope structure of H1CRD to a monoclonal antibody by proteolytic epitope excision of the immune complex and high-resolution MALDI-FTICR mass spectrometry. As a prerequisite of the epitope determination, the primary structure of the H1CRD antigen was characterised by ESI-FTICR-MS of the intact protein and by LC-MS/MS of tryptic digest mixtures. Molecular mass determination and proteolytic fragments provided the identification of two intramolecular disulfide bridges (seven Cys residues), and a Cys-mercaptoethanol adduct formed by treatment with β-mercaptoethanol during protein extraction. The H1CRD antigen binds to the monoclonal antibody in both native and Cys-alkylated form. For identification of the epitope, the antibody was immobilized on N-hydroxysuccinimide (NHS)-activated Sepharose. Epitope excision and epitope extraction with trypsin and FTICR-MS of affinity-bound peptides provided the identification of two specific epitope peptides (5-16) and (17-23) that showed high affinity to the antibody. Affinity studies of the synthetic epitope peptides revealed independent binding of each peptide to the antibody.

[Effectivity of screening, concepts and attitudes towards metabolic síndrome: a study in bipolar patients followed in Hospital Santa Maria psychiatric consultation].

PubMed

Guerreiro, Diogo Frasquilho; Navarro, Rita; Telles-Correia, Diogo; Martins, Paulo; Trigo, Elsa; Silva, Manuela; Neves, António; Góis, Carlos; Figueira, Maria Luísa

2010-01-01

The Metabolic Syndrome (MS) is constituted by a set of specific metabolic alterations being postulated that the main dysfunction is insulin resistance, associated with abdominal type obesity, hypertension, hyperglycemia and dyslipidemia. Epidemiological data indicates prevalence of MS of about 25%. Estimates point to higher prevalence of MS in bipolar (BP) patients, between 30 to 35%. Cost-effective screening methods, not recurring to blood test, have been researched. Test the viability of MS screening without using blood tests. Analyse knowledge and importance given to the issue of MS in Bipolar patients. Observational, cross-sectional, exploratory study. Random sample of 15 BP patients, in euthymic phase, between 18 and 65 years. Semi-structured interview, YMRS, HAMD were applied. MS diagnosis was investigated according to the International Diabetes Federation (IDF), including blood tests. Screening of MS was defined positive if blood pressure > or = to 130/85 or on anti-hypertensive medication and Abdominal Perimeter > 90 cm in males or > 80 cm in females. Afterwards a questionnaire about knowledge, attitudes and concerns on MS was applied. 14 patients completed the investigation protocol, 1 patient didn't do blood testing for unknown reasons. Five patients (36%) met IDF criteria for MS. Screening sensitivity was 80% and specificity 78% on our sample (1 false positive and 2 false negative). Twelve patients (80%) were overweight or obese. Mean IMC in patients that met IDF criteria for MS was 30 while in the other group mean IMC was 26, showing statistical significance. Only 3 (20%) have ever heard about MS, but the majority of the patients were concerned, in decreasing order, about weight gain, blood pressure cholesterol and hyperglycemia control. Although limited by small sample size, this study strengthens the idea that MS screening can be effective in clinical practice, it also indicates the need to educate BP patients about MS and to prevent overweight.

Non-enzymolytic adenosine barcode-mediated dual signal amplification strategy for ultrasensitive protein detection using LC-MS/MS.

PubMed

Yang, Wen; Li, Tengfei; Shu, Chang; Ji, Shunli; Wang, Lei; Wang, Yan; Li, Duo; Mtalimanja, Michael; Sun, Luning; Ding, Li

2018-05-10

A method is described for the determination of proteins with LC-MS/MS enabled by a small molecule (adenosine) barcode and based on a double-recognition sandwich structure. The coagulation protein thrombin was chosen as the model analyte. Magnetic nanoparticles were functionalized with aptamer29 (MNP/apt29) and used to capture thrombin from the samples. MNP/apt29 forms a sandwich with functionalized gold nanoparticles modified with (a) aptamer15 acting as thrombin-recognizing element and (b) a large number of adenosine as mass barcodes. The sandwich formed (MNP/apt29-thrombin-apt15/AuNP/adenosine) can ben magnetically separated from the sample. Mass barcodes are subsequently released from the sandwiched structure for further analysis by adding 11-mercaptoundecanoic acid. Adenosine is then detected by LC-MS/MS as it reflects the level of thrombin with impressively amplified signal. Numerous adenosines introduced into the sandwich proportional to the target concentration further amplify the signal. Under optimized conditions, the response is linearly proportional to the thrombin concentration in the range of 0.02 nM to 10 nM, with a detection limit of 9 fM. The application of this method to the determination of thrombin in spiked plasma samples gave recoveries that ranged from 92.3% to 104.7%. Graphical abstract Schematic representation of a method for the determination of thrombin with LC-MS/MS. The method is based on a double-recognition sandwiched structure. With LC-MS/MS, mass barcodes (adenosine) are detected to quantify thrombin, which amplifies the detection signal impressively.

Mass spectrometry of rhenium complexes: a comparative study by using LDI-MS, MALDI-MS, PESI-MS and ESI-MS.

PubMed

Petroselli, Gabriela; Mandal, Mridul Kanti; Chen, Lee Chuin; Ruiz, Gustavo T; Wolcan, Ezequiel; Hiraoka, Kenzo; Nonami, Hiroshi; Erra-Balsells, Rosa

2012-03-01

A group of rhenium (I) complexes including in their structure ligands such as CF(3)SO(3)-, CH(3)CO(2)-, CO, 2,2'-bipyridine, dipyridil[3,2-a:2'3'-c]phenazine, naphthalene-2-carboxylate, anthracene-9-carboxylate, pyrene-1-carboxylate and 1,10-phenanthroline have been studied for the first time by mass spectrometry. The probe electrospray ionization (PESI) is a technique based on electrospray ionization (ESI) that generates electrospray from the tip of a solid metal needle. In this work, mass spectra for organometallic complexes obtained by PESI were compared with those obtained by classical ESI and high flow rate electrospray ionization assisted by corona discharge (HF-ESI-CD), an ideal method to avoid decomposition of the complexes and to induce their oxidation to yield intact molecular cation radicals in gas state [M](+·) and to produce their reduction yielding the gas species [M](-·). It was found that both techniques showed in general the intact molecular ions of the organometallics studied and provided additional structure characteristic diagnostic fragments. As the rhenium complexes studied in the present work showed strong absorption in the UV-visible region, particularly at 355 nm, laser desorption ionization (LDI) mass spectrometry experiments could be conducted. Although intact molecular ions could be detected in a few cases, LDI mass spectra showed diagnostic fragments for characterization of the complexes structure. Furthermore, matrix-assisted laser desorption ionization (MALDI) mass spectra were obtained. Nor-harmane, a compound with basic character, was used as matrix, and the intact molecular ions were detected in two examples, in negative ion mode as the [M](-·) species. Results obtained with 2-[(2E)-3-(4-tert-buthylphenyl)-2-methylprop-2-enylidene] malononitrile (DCTB) as matrix are also described. LDI experiments provided more information about the rhenium complex structures than did the MALDI ones. Copyright © 2012 John Wiley & Sons, Ltd.

Identification and structural characterisation of triterpene saponins from the root of Ardisia mamillata Hance by HPLC-ESI-QTOF-MS/MS.

PubMed

Zhang, Er-Fei; Ling, Yun; Yin, Zi; Zhang, Qing

2018-04-01

Triterpene saponins in medicinal plants attract scientific attentions for their structural diversity and significant bioactivities. In this work, a high-performance liquid chromatography coupled to electrospray ionisation and quadrupole time-of-flight mass spectrometry (HPLC-ESI-QTOF-MS/MS) method is used to rapidly separate and identify triterpene saponins from the extract of Ardisia mamillata Hance (AMH). In the full scan mass spectrum, the accurate determination of molecular formula is obtained by the predominant ion [M + HCOO] - in negative ion mode. As a result, 30 triterpene saponins are identified or tentatively identified in the plant extract. Of these, 17 triterpene saponins are new compounds. In conclusion, the HPLC-ESI-QTOF-MS/MS is an efficient technique to separate and identify triterpene saponins in complex matrices of medicinal plant.

Cognitive rehabilitation and mindfulness in multiple sclerosis (REMIND-MS): a study protocol for a randomised controlled trial.

PubMed

Nauta, Ilse M; Speckens, Anne E M; Kessels, Roy P C; Geurts, Jeroen J G; de Groot, Vincent; Uitdehaag, Bernard M J; Fasotti, Luciano; de Jong, Brigit A

2017-11-21

Cognitive problems frequently occur in patients with multiple sclerosis (MS) and profoundly affect their quality of life. So far, the best cognitive treatment options for MS patients are a matter of debate. Therefore, this study aims to investigate the effectiveness of two promising non-pharmacological treatments: cognitive rehabilitation therapy (CRT) and mindfulness-based cognitive therapy (MBCT). Furthermore, this study aims to gain additional knowledge about the aetiology of cognitive problems among MS patients, since this may help to develop and guide effective cognitive treatments. In a dual-centre, single-blind randomised controlled trial (RCT), 120 MS patients will be randomised into one of three parallel groups: CRT, MBCT or enhanced treatment as usual (ETAU). Both CRT and MBCT consist of a structured 9-week program. ETAU consists of one appointment with an MS specialist nurse. Measurements will be performed at baseline, post-intervention and 6 months after the interventions. The primary outcome measure is the level of subjective cognitive complaints. Secondary outcome measures are objective cognitive function, functional brain network measures (using magnetoencephalography), psychological symptoms, well-being, quality of life and daily life functioning. To our knowledge, this will be the first RCT that investigates the effect of MBCT on cognitive function among MS patients. In addition, studying the effect of CRT on cognitive function may provide direction to the contradictory evidence that is currently available. This study will also provide information on changes in functional brain networks in relation to cognitive function. To conclude, this study may help to understand and treat cognitive problems among MS patients. This trial was prospectively registered at the Dutch Trial Registration (number NTR6459 , registered on 31 May 2017).

Ultrahigh-performance liquid chromatography-ion trap mass spectrometry characterization of the steroidal saponins of Dioscorea panthaica Prain et Burkill and its application for accelerating the isolation and structural elucidation of steroidal saponins.

PubMed

Wang, Weihao; Zhao, Ye; Jing, Wenguang; Zhang, Jun; Xiao, Hui; Zha, Qin; Liu, An

2015-03-01

Dioscorea panthaica is a traditional Chinese medicinal herb used in the treatment of various physiological conditions, including cardiovascular disease, gastropathy and hypertension. Steroidal saponins (SS) are the main active ingredients of this herb and have effects on myocardial ischemia and cancer. The phytochemical evaluation of SS is both time-consuming and laborious, and the isolation and structural determination steps can be especially demanding. For this reason, the development of new methods to accelerate the processes involved in the identification, isolation and structural elucidation of SS is highly desirable. In this study, a new ultrahigh performance liquid chromatography-ion trap mass spectrometry (UHPLC-IT/MS(n)) method has been developed for the identification of the SS in D. panthaica Prain et Burkill. Notably, the current method can distinguish between spirostanol and furostanol-type compounds based on the fragmentation patterns observed by electrospray ionization-ion trap mass spectrometry (ESI-IT/MS(n)) analysis. UHPLC-IT/MS(n) was used to conduct a detailed investigation of the number, structural class and order of the sugar moieties in the sugar chains of the SS present in D. panthaica. The established fragmentation features were used to analyze the compounds found in the 65% ethanol fraction of the water extracts of D. panthaica. Twenty-three SS were identified, including 11 potential new compounds and six groups of isomers. Two of these newly identified SS were selected as representative examples, and their chemical structures were confirmed by (1)H and (13)C NMR analyses. This newly developed UHPLC-IT/MS(n) method therefore allowed for the efficient identification, isolation and structural determination of the SS in D. panthaica. Copyright © 2015 Elsevier Inc. All rights reserved.

Detection and characterization of a new metabolite of 17alpha-methyltestosterone.

PubMed

Pozo, Oscar J; Van Eenoo, Peter; Deventer, Koen; Lootens, Leen; Van Thuyne, Wim; Parr, Maria K; Schänzer, Wilhelm; Sancho, Juan V; Hernández, Felix; Meuleman, Philip; Leroux-Roels, Geert; Delbeke, Frans T

2009-11-01

The misuse of the anabolic steroid methyltestosterone is currently routinely monitored in doping control laboratories by gas chromatography-mass spectrometry (GC-MS) of two of its metabolites: 17alpha-methyl-5beta-androstane-3alpha,17beta-diol and 17alpha-methyl-5alpha-androstane-3alpha,17beta-diol. Because of the absence of any easy ionizable moiety, these metabolites are poorly detectable using liquid chromatography-tandem mass spectrometry (LC-MS/MS) with electrospray ionization (ESI). In this study, the metabolism of methyltestosterone has been reinvestigated by the use of a precursor ion scan method in LC-ESI-MS/MS. Two metabolites have been detected using this method. Both compounds have been confirmed in postadministration urine samples of an urokinase plasminogen activator-severe combined immunodeficiency (uPA-SCID) mouse with humanized liver and were characterized by LC-MS/MS and GC-MS using both quadrupole and time of flight analyzers. From the detailed study of the fragmentation, these metabolites were proposed to be epimethyltestosterone and a dehydrogenated compound. Epimethyltestosterone has previously been described as a minor metabolite, whereas the occurrence of the oxidized metabolite has not been reported. Comparison with the synthesized reference revealed that the structure of the dehydrogenated metabolite is 6-ene-epimethyltestosterone. A selected reaction monitoring method including three transitions for each metabolite has been developed and applied to samples from an excretion study and to samples declared positive after GC-MS analysis. 6-Ene-epimethyltestosterone was found in all samples, showing its applicability in the detection of methyltestosterone misuse.

Structure and properties of small molecule-polymer blend semiconductors for organic thin film transistors.

PubMed

Kang, Jihoon; Shin, Nayool; Jang, Do Young; Prabhu, Vivek M; Yoon, Do Y

2008-09-17

A comprehensive structural and electrical characterization of solution-processed blend films of 6,13-bis(triisopropylsilylethynyl) pentacene (TIPS-pentacene) semiconductor and poly(alpha-methylstyrene) (PalphaMS) insulator was performed to understand and optimize the blend semiconductor films, which are very attractive as the active layer in solution-processed organic thin-film transistors (OTFTs). Our study, based on careful measurements of specular neutron reflectivity and grazing-incidence X-ray diffraction, showed that the blends with a low molecular-mass PalphaMS exhibited a strong segregation of TIPS-pentacene only at the air interface, but surprisingly the blends with a high molecular-mass PalphaMS showed a strong segregation of TIPS-pentacene at both air and bottom substrate interfaces with high crystallinity and desired orientation. This finding led to the preparation of a TIPS-pentacene/PalphaMS blend active layer with superior performance characteristics (field-effect mobility, on/off ratio, and threshold voltage) over those of neat TIPS-pentacene, as well as the solution-processability of technologically attractive bottom-gate/bottom-contact OTFT devices.

Expedient preparative isolation and tandem mass spectrometric characterization of C-seco triterpenoids from Neem oil.

PubMed

Haldar, Saikat; Mulani, Fayaj A; Aarthy, Thiagarayaselvam; Dandekar, Devdutta S; Thulasiram, Hirekodathakallu V

2014-10-31

C-seco triterpenoids are widely bioactive class of natural products with high structural complexity and diversity. The preparative isolation of these molecules with high purity is greatly desirable, although restricted due to the complexity of natural extracts. In this article we have demonstrated a Medium Pressure Liquid Chromatography (MPLC) based protocol for the isolation of eight major C-seco triterpenoids of salannin skeleton from Neem (Azadirachta indica) oil. Successive application of normal phase pre-packed silica-gel columns for the fractionation followed by reverse phase in automated MPLC system expedited the process and furnished highly pure metabolites. Furthermore, eight isolated triterpenoids along with five semi-synthesized derivatives were characterized using ultra performance liquid chromatography-electrospray ionization-quadrupole/orbitrap-MS/MS spectrometry as a rapid and sensitive identification technique. The structure-fragment relationships were established on the basis of plausible mechanistic pathway for the generation of daughter ions. The MS/MS spectral information of the triterpenoids was further utilized for the identification of studied molecules in the complex extract of stem and bark tissues from Neem. Copyright © 2014 Elsevier B.V. All rights reserved.

Identification of Isomeric N-Glycan Structures by Mass Spectrometry with 157 nm Laser-Induced Photofragmentation

PubMed Central

Devakumar, Arugadoss; Mechref, Yehia; Kang, Pilsoo; Novotny, Milos V.; Reilly, James P.

2008-01-01

Characterization of structural isomers has become increasingly important and extremely challenging in glycobiology. This communication demonstrates the capability of ion-trap mass spectrometry in conjunction with 157 nm photofragmentation to identify different structural isomers of permethylated N-glycans derived from ovalbumin without chromatographic separation. The results are compared with CID experiments. Photodissociation generates extensive cross-ring fragment ions as well as diagnostic glycosidic product ions that are not usually observed in CID MS/MS experiments. The detection of these product ions aids in characterizing indigenous glycan isomers. The ion-trap facilitates MSn experiments on the diagnostic glycosidic fragments and cross-ring product ions generated through photofragmentation, thus allowing unambiguous assignment of all of the isomeric structures associated with the model glycoprotein utilized in this study. Photofragmentation is demonstrated to be a powerful technique for the structural characterization of glycans. PMID:18487060

Structural elucidation and identification of a new derivative of phenethylamine using quadrupole time-of-flight mass spectrometry.

PubMed

Sekuła, Karolina; Zuba, Dariusz

2013-09-30

In recent years, the phenomenon of uncontrolled distribution of new psychoactive substances that were marketed without prior toxicological studies has been observed. Because many designer drugs are related in chemical structure, the potential for misidentifying them is an important problem. It is therefore essential to develop an analytical procedure for unequivocal elucidation of the structures of these compounds. The issue has been discussed in the context of 25I-NBMD [2-(4-iodo-2,5-dimethoxyphenyl)-N-[(2,3-methylenedioxyphenyl)methyl]ethanamine], a psychoactive substance first discovered on the drug market in 2012. The substance was extracted from blotter papers with methanol. Separation was achieved via liquid chromatography. Analysis was conducted by electrospray ionization quadrupole time-of-flight mass spectrometry (ESI-QTOFMS). Identification of the psychoactive component was supported by electron impact gas chromatography/mass spectrometry (GC/EI-MS). The high accuracy of the LC/ESI-QTOFMS method allowed the molecular mass of the investigated substance (M(exp) = 441.0438 Da; mass error, ∆m = 0.2 ppm) and the formulae of ions formed during fragmentation to be determined. The main ions were recorded at m/z = 135.0440, 290.9876 and 305.9981. Structures of the obtained ions were elucidated in the tandem mass spectrometry (MS/MS) experiments by comparing them to mass spectra of previously detected derivatives of phenethylamine. The performed study indicated the potential for using LC/QTOFMS method to identify new designer drugs. This technique can be used supplementary to standard GC/MS. Prior knowledge of the fragmentation mechanisms of phenethylamines allowed to predict the mass spectra of the novel substance--25I-NBMD. Copyright © 2013 John Wiley & Sons, Ltd.

Identification and accurate quantification of structurally related peptide impurities in synthetic human C-peptide by liquid chromatography-high resolution mass spectrometry.

PubMed

Li, Ming; Josephs, Ralf D; Daireaux, Adeline; Choteau, Tiphaine; Westwood, Steven; Wielgosz, Robert I; Li, Hongmei

2018-06-04

Peptides are an increasingly important group of biomarkers and pharmaceuticals. The accurate purity characterization of peptide calibrators is critical for the development of reference measurement systems for laboratory medicine and quality control of pharmaceuticals. The peptides used for these purposes are increasingly produced through peptide synthesis. Various approaches (for example mass balance, amino acid analysis, qNMR, and nitrogen determination) can be applied to accurately value assign the purity of peptide calibrators. However, all purity assessment approaches require a correction for structurally related peptide impurities in order to avoid biases. Liquid chromatography coupled to high resolution mass spectrometry (LC-hrMS) has become the key technique for the identification and accurate quantification of structurally related peptide impurities in intact peptide calibrator materials. In this study, LC-hrMS-based methods were developed and validated in-house for the identification and quantification of structurally related peptide impurities in a synthetic human C-peptide (hCP) material, which served as a study material for an international comparison looking at the competencies of laboratories to perform peptide purity mass fraction assignments. More than 65 impurities were identified, confirmed, and accurately quantified by using LC-hrMS. The total mass fraction of all structurally related peptide impurities in the hCP study material was estimated to be 83.3 mg/g with an associated expanded uncertainty of 3.0 mg/g (k = 2). The calibration hierarchy concept used for the quantification of individual impurities is described in detail. Graphical abstract ᅟ.

Indentification and Analysis of Occludin Phosphosites: A Combined Mass Spectroscoy and Bioinformatics Approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sundstrom, J.; Tash, B; Murakami, T

2009-01-01

The molecular function of occludin, an integral membrane component of tight junctions, remains unclear. VEGF-induced phosphorylation sites were mapped on occludin by combining MS data analysis with bioinformatics. In vivo phosphorylation of Ser490 was validated and protein interaction studies combined with crystal structure analysis suggest that Ser490 phosphorylation attenuates the interaction between occludin and ZO-1. This study demonstrates that combining MS data and bioinformatics can successfully identify novel phosphorylation sites from limiting samples.

Metabolic risk factors and arterial stiffness in Indian children of parents with metabolic syndrome.

PubMed

Khadilkar, Anuradha V; Chiplonkar, Shashi A; Pandit, Deepa S; Kinare, Arun S; Khadilkar, Vaman V

2012-02-01

To investigate the possible association between metabolic syndrome (MS) and arterial stiffness in Indian children with parental MS status. A cross-sectional study was conducted in 140 overweight/obese and 60 normal-weight Indian children (mean age, 11.4 ± 2.8 years) along with one of their parents during 2008-2009. Data on weight, height, blood pressure, serum lipids, zinc, insulin, and glucose were collected. Intima media thickness (CIMT) and stiffness parameters were assessed in the right carotid artery. Physical activity and diet were assessed using structured questionnaires. Body composition was measured using dual-energy x-ray absorptiometry. A gradual increase in the percentage of MS children with an increasing number of MS components in parents was observed. Mean values for arterial stiffness, pulse wave velocity, and elastic modulus were significantly higher in MS children of MS parents than in MS children of normal parents (p < 0.05). A significant correlation was observed for lifestyle, metabolic, and arterial parameters among child-parent pairs (p < 0.05). Multiple logistic regression revealed that children's CIMT and arterial stiffness were significantly associated (p < 0.01) with their serum levels of triglycerides, high-density lipoprotein, and zinc, as well as with parental MS-CIMT. Parental MS status and lifestyle factors increase the risk of MS and arterial abnormalities in children.

The Radiation Belt Electron Scattering by Magnetosonic Wave: Dependence on Key Parameters

NASA Astrophysics Data System (ADS)

Lei, Mingda; Xie, Lun; Li, Jinxing; Pu, Zuyin; Fu, Suiyan; Ni, Binbin; Hua, Man; Chen, Lunjin; Li, Wen

2017-12-01

Magnetosonic (MS) waves have been found capable of creating radiation belt electron butterfly distributions in the inner magnetosphere. To investigate the physical nature of the interactions between radiation belt electrons and MS waves, and to explore a preferential condition for MS waves to scatter electrons efficiently, we performed a comprehensive parametric study of MS wave-electron interactions using test particle simulations. The diffusion coefficients simulated by varying the MS wave frequency show that the scattering effect of MS waves is frequency insensitive at low harmonics (f < 20 fcp), which has great implications on modeling the electron scattering caused by MS waves with harmonic structures. The electron scattering caused by MS waves is very sensitive to wave normal angles, and MS waves with off 90° wave normal angles scatter electrons more efficiently. By simulating the diffusion coefficients and the electron phase space density evolution at different L shells under different plasma environment circumstances, we find that MS waves can readily produce electron butterfly distributions in the inner part of the plasmasphere where the ratio of electron plasma-to-gyrofrequency (fpe/fce) is large, while they may essentially form a two-peak distribution outside the plasmapause and in the inner radiation belt where fpe/fce is small.

"It gave me something big in my life to wonder and think about which took over the space … and not MS": managing well-being in multiple sclerosis through art-making.

PubMed

Hunt, Laura; Nikopoulou-Smyrni, Panagiota; Reynolds, Frances

2014-01-01

Individuals living with Multiple Sclerosis (MS) often face progressive loss of function, uncertainty and disruption to self-image and valued roles. Previous studies show that creative self-expression is valued by some people living with long-term illness, yet its meaning for people living with MS is unclear. This research study explored the meanings of leisure-based visual art-making for people living with MS. This qualitative study followed guidelines for Interpretative Phenomenological Analysis (IPA). Single semi-structured interviews were conducted with five adults (2 males; 3 females; 40-65 years), recruited from MS Ireland. Participants valued art-making for contributing to a more satisfying way of life; for filling occupational voids and using time well. Deep immersion offered respite from worry about illness. Creative classes offered social camaraderie and opportunities for learning and development. Art-making processes and products were highly affirmative, increasing emotional well-being and promoting self-worth. Most felt that they expressed valued aspects of self through their art. Art-making appeared to assist with identity maintenance, accommodating functional losses associated with MS whilst opening "new doors". Art-making offered a multi-faceted means of supporting identity and increasing fulfilment in lives that were restricted in many ways by MS.

Fragmentation study of iridoid glucosides through positive and negative electrospray ionization, collision-induced dissociation and tandem mass spectrometry.

PubMed

Es-Safi, Nour-Eddine; Kerhoas, Lucien; Ducrot, Paul-Henri

2007-01-01

Mass spectrometric methodology based on the combined use of positive and negative electrospray ionization, collision-induced dissociation (CID) and tandem mass spectrometry (MS/MS) has been applied to the mass spectral study of a series of six naturally occurring iridoids through in-source fragmentation of the protonated [M+H]+, deprotonated [M--H]- and sodiated [M+Na]+ ions. This led to the unambiguous determination of the molecular masses of the studied compounds and allowed CID spectra of the molecular ions to be obtained. Valuable structural information regarding the nature of both the glycoside and the aglycone moiety was thus obtained. Glycosidic cleavage and ring cleavages of both aglycone and sugar moieties were the major fragmentation pathways observed during CID, where the losses of small molecules, the cinnamoyl and the cinnamate parts were also observed. The formation of the ionized aglycones, sugars and their product ions was thus obtained giving information on their basic skeleton. The protonated, i.e. [M+H]+ and deprotonated [M--H]-, ions were found to fragment mainly by glycosidic cleavages. MS/MS spectra of the [M+Na]+ ions gave complementary information for the structural characterization of the studied compounds. Unlike the dissociation of protonated molecular ions, that of sodiated molecules also provided sodiated sugar fragments where the C0+ fragment corresponding to the glucose ion was obtained as base peak for all the studied compounds. Copyright (c) 2007 John Wiley & Sons, Ltd.

Child Behavior Checklist—Mania Scale (CBCL-MS): Development and Evaluation of a Population-Based Screening Scale for Bipolar Disorder

PubMed Central

Papachristou, Efstathios; Ormel, Johan; Oldehinkel, Albertine J.; Kyriakopoulos, Marinos; Reinares, María; Reichenberg, Abraham; Frangou, Sophia

2013-01-01

Context Early identification of Bipolar Disorder (BD) remains poor despite the high levels of disability associated with the disorder. Objective We developed and evaluated a new DSM orientated scale for the identification of young people at risk for BD based on the Child Behavior Checklist (CBCL) and compared its performance against the CBCL-Pediatric Bipolar Disorder (CBCL-PBD) and the CBCL-Externalizing Scale, the two most widely used scales. Methods The new scale, CBCL-Mania Scale (CBCL-MS), comprises 19 CBCL items that directly correspond to operational criteria for mania. We tested the reliability, longitudinal stability and diagnostic accuracy of the CBCL-MS on data from the TRacking Adolescents' Individual Lives Survey (TRAILS), a prospective epidemiological cohort study of 2230 Dutch youths assessed with the CBCL at ages 11, 13 and 16. At age 19 lifetime psychiatric diagnoses were ascertained with the Composite International Diagnostic Interview. We compared the predictive ability of the CBCL-MS against the CBCL-Externalising Scale and the CBCL-PBD in the TRAILS sample. Results The CBCL-MS had high internal consistency and satisfactory accuracy (area under the curve = 0.64) in this general population sample. Principal Component Analyses, followed by parallel analyses and confirmatory factor analyses, identified four factors corresponding to distractibility/disinhibition, psychosis, increased libido and disrupted sleep. This factor structure remained stable across all assessment ages. Logistic regression analyses showed that the CBCL-MS had significantly higher predictive ability than both the other scales. Conclusions Our data demonstrate that the CBCL-MS is a promising screening instrument for BD. The factor structure of the CBCL-MS showed remarkable temporal stability between late childhood and early adulthood suggesting that it maps on to meaningful developmental dimensions of liability to BD. PMID:23967059

On the role of the amygdala for experiencing fatigue in patients with multiple sclerosis.

PubMed

Hanken, Katrin; Francis, Yoselin; Kastrup, Andreas; Eling, Paul; Klein, Jan; Hildebrandt, Helmut

2018-02-01

Recently, we proposed a model explaining the origin of fatigue in multiple sclerosis (MS) patients. This model assumes that the feeling of fatigue results from inflammation-induced information processing within interoceptive brain areas. To investigate the association between self-reported cognitive fatigue and structural integrity of interoceptive brain areas in MS patients. 95 MS patients and 28 healthy controls participated in this study. All participants underwent diffusion tensor MRI and fractional anisotropy data were calculated for the amygdala, the stria terminalis and the corpus callosum, a non-interoceptive brain area. Based on the cognitive fatigue score of the Fatigue Scale for Motor and Cognition, patients were divided into moderately cognitively fatigued (cognitive fatigue score ≥ 28) and cognitively non-fatigued (cognitive fatigue score < 28) MS patients. Healthy controls were recruited as a third group. Repeated measures analyses of covariance, controlling for age, depression and brain atrophy, were performed to investigate whether the factor Group had a significant effect on the fractional anisotropy data. A significant effect of Group was observed for the amygdala (F = 3.389, p = 0.037). MS patients without cognitive fatigue presented lower values of the amygdala than MS patients with cognitive fatigue and healthy controls. For the stria terminalis and the corpus callosum, no main effect of Group was observed. The structural integrity of the amygdala in non-fatigued MS patients appears to be reduced. According to our model this might indicate that the absence of fatigue in non-fatigued MS patients might result from disturbed inflammation-induced information processing in the amygdala. Copyright © 2017 Elsevier B.V. All rights reserved.

Equivalence of electronic and mechanical stresses in structural phase stabilization: A case study of indium wires on Si(111)

NASA Astrophysics Data System (ADS)

Kim, Sun-Woo; Kim, Hyun-Jung; Ming, Fangfei; Jia, Yu; Zeng, Changgan; Cho, Jun-Hyung; Zhang, Zhenyu

2015-05-01

It was recently proposed that the stress state of a material can also be altered via electron or hole doping, a concept termed electronic stress (ES), which is different from the traditional mechanical stress (MS) due to lattice contraction or expansion. Here we demonstrate the equivalence of ES and MS in structural stabilization, using In wires on Si(111) as a prototypical example. Our systematic density-functional theory calculations reveal that, first, for the same degrees of carrier doping into the In wires, the ES of the high-temperature metallic 4 ×1 structure is only slightly compressive, while that of the low-temperature insulating 8 ×2 structure is much larger and highly anisotropic. As a consequence, the intrinsic energy difference between the two phases is significantly reduced towards electronically phase-separated ground states. Our calculations further demonstrate quantitatively that such intriguing phase tunabilities can be achieved equivalently via lattice-contraction induced MS in the absence of charge doping. We also validate the equivalence through our detailed scanning tunneling microscopy experiments. The present findings have important implications for understanding the underlying driving forces involved in various phase transitions of simple and complex systems alike.

Molecular resolution and fragmentation of fulvic acid by electrospray ionization/multistage tandem mass spectrometry

USGS Publications Warehouse

Leenheer, J.A.; Rostad, C.E.; Gates, Paul M.; Furlong, E.T.; Ferrer, I.

2001-01-01

Molecular weight distributions of fulvic acid from the Suwannee River, Georgia, were investigated by electrospray ionization/quadrupole mass spectrometry (ESI/QMS), and fragmentation pathways of specific fulvic acid masses were investigated by electrospray ionization/ion trap multistage tandem mass spectrometry (ESI/MST/MS). ESI/QMS studies of the free acid form of low molecular weight poly(carboxylic acid) standards in 75% methanol/25% water mobile phase found that negative ion detection gave the optimum generation of parent ions that can be used for molecular weight determinations. However, experiments with poly(acrylic acid) mixtures and specific high molecular weight standards found multiply charged negative ions that gave a low bias to molecular mass distributions. The number of negative charges on a molecule is dependent on the distance between charges. ESI/MST/MS of model compounds found characteristic water loss from alcohol dehydration and anhydride formation, as well as CO2 loss from decarboxylation, and CO loss from ester structures. Application of these fragmentation pathways to specific masses of fulvic acid isolated and fragmented by ESI/MST/MS is indicative of specific structures that can serve as a basis for future structural confirmation after these hypothesized structures are synthesized.

Joining strength performances of metal skin and CFRP core laminate structures realized by compression-curing process, with supporting experiments

NASA Astrophysics Data System (ADS)

Quagliato, Luca; Jang, Changsoon; Kim, Naksoo

2018-05-01

In the recent years, the trend of lightening vehicles and structures of every kind has become an ever-growing issue, both for university and industrial researchers. As demonstrated in previous authors' works, laminate structures made of metal skin (MS) and carbon fiber reinforced polymer (CFRP) core show high specific bending strength properties while granting considerable weight reduction but, so far, no investigations have been carried out on the hole sensitivity and joinability of these hybrid structures. In the present research work, the hole size sensitivity of MS-CFRP structure has been studied by means of uniaxial tensile test on 160mm (length), 25mm (width), 2.0mm (average thickness) specimens bored with Ø06mm, Ø9mm, and Ø12mm holes. The specimen thickness is composed of two metal skins of 0.4mm thickness each, 8×0.2mm CFRP stacked layers and two thin epoxy-based adhesive layers. The specimens have been manufactured by means of a compression-curing process in which the different materials are stacked and, thanks to die pressure and temperature, the curing process is completed in a relatively short time (15˜20 minutes). The specimens have been tested by means of simple tension test showing that, for the MS-CFRP material, the smaller the hole the smaller the maximum bearable load. Moreover, specimens with the same hole sizes have been bolted together with class 12 resistance bolts and tested by means of tensile test, allowing to determine the maximum transferable load between the two MS-CFRP plates. Aiming to prove the improvement in the specific transferable load, experiments on only-steel specimens with the same weight of the MS-CFRP ones and joined with the same method and bolts have been carried out, allowing to conclude that, for the 9mm hole bolted plates, the proposed material has a specific maximum transferable 27% higher than that of the steel composing their skins.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kyle, Jennifer E.; Zhang, Xing; Weitz, Karl K.

Understanding how biological molecules are generated, metabolized and eliminated in living systems is important for interpreting processes such as immune response and disease pathology. While genomic and proteomic studies have provided vast amounts of information over the last several decades, interest in lipidomics has also grown due to improved analytical technologies revealing altered lipid metabolism in type 2 diabetes, cancer, and lipid storage disease. Liquid chromatography and mass spectrometry (LC-MS) measurements are currently the dominant approach for characterizing the lipidome by providing detailed information on the spatial and temporal composition of lipids. However, interpreting lipids’ biological roles is challenging duemore » to the existence of numerous structural and stereoisomers (i.e. distinct acyl chain and double-bond positions), which are unresolvable using present LC-MS approaches. Here we show that combining structurally-based ion mobility spectrometry (IMS) with LC-MS measurements distinguishes lipid isomers and allows insight into biological and disease processes.« less

Structure determination of 3-O-caffeoyl-epi-gamma-quinide, an orphan bitter lactone in roasted coffee.

PubMed

Frank, Oliver; Blumberg, Simone; Krümpel, Gudrun; Hofmann, Thomas

2008-10-22

Recent investigations on the bitterness of coffee as well as 5- O-caffeoyl quinic acid roasting mixtures indicated the existence of another, yet unknown, bitter lactone besides the previously identified bitter compounds 5- O-caffeoyl- muco-gamma-quinide, 3- O-caffeoyl-gamma-quinide, 4- O-caffeoyl- muco-gamma-quinide, 5- O-caffeoyl- epi-delta-quinide, and 4- O-caffeoyl-gamma-quinide. In the present study, this orphan bitter lactone was isolated from the reaction products generated by dry heating of 5- O-caffeoylquinic acid model, and its structure was determined as the previously unreported 3- O-caffeoyl- epi-gamma-quinide by means of liquid chromatography-mass spectrometry (LC-MS) and one-/two-dimensional NMR experiments. The occurrence of this bitter lactone, exhibiting a low bitter recognition threshold of 58 micromol/L, in coffee beverages could be confirmed by LC-MS/MS (negative electrospray ionization) operating in the multiple reaction monitoring mode.

A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry.

PubMed

Chavez, Juan D; Eng, Jimmy K; Schweppe, Devin K; Cilia, Michelle; Rivera, Keith; Zhong, Xuefei; Wu, Xia; Allen, Terrence; Khurgel, Moshe; Kumar, Akhilesh; Lampropoulos, Athanasios; Larsson, Mårten; Maity, Shuvadeep; Morozov, Yaroslav; Pathmasiri, Wimal; Perez-Neut, Mathew; Pineyro-Ruiz, Coriness; Polina, Elizabeth; Post, Stephanie; Rider, Mark; Tokmina-Roszyk, Dorota; Tyson, Katherine; Vieira Parrine Sant'Ana, Debora; Bruce, James E

2016-01-01

Chemical cross-linking mass spectrometry (XL-MS) provides protein structural information by identifying covalently linked proximal amino acid residues on protein surfaces. The information gained by this technique is complementary to other structural biology methods such as x-ray crystallography, NMR and cryo-electron microscopy[1]. The extension of traditional quantitative proteomics methods with chemical cross-linking can provide information on the structural dynamics of protein structures and protein complexes. The identification and quantitation of cross-linked peptides remains challenging for the general community, requiring specialized expertise ultimately limiting more widespread adoption of the technique. We describe a general method for targeted quantitative mass spectrometric analysis of cross-linked peptide pairs. We report the adaptation of the widely used, open source software package Skyline, for the analysis of quantitative XL-MS data as a means for data analysis and sharing of methods. We demonstrate the utility and robustness of the method with a cross-laboratory study and present data that is supported by and validates previously published data on quantified cross-linked peptide pairs. This advance provides an easy to use resource so that any lab with access to a LC-MS system capable of performing targeted quantitative analysis can quickly and accurately measure dynamic changes in protein structure and protein interactions.

Ion/Neutral, Ion/Electron, Ion/Photon, and Ion/Ion Interactions in Tandem Mass Spectrometry: Do we need them all? Are they enough?

PubMed Central

McLuckey, Scott A.; Mentinova, Marija

2011-01-01

A range of strategies and tools has been developed to facilitate the determination of primary structures of analyte molecules of interest via tandem mass spectrometry (MS/MS). The two main factors that determine the primary structural information present in an MS/MS spectrum are the type of ion generated from the analyte molecule and the dissociation method. The ion-type subjected to dissociation is determined by the ionization method/conditions and ion transformation processes that might take place after initial gas-phase ion formation. Furthermore, the range of analyte-related ion types can be expanded via derivatization reactions prior to mass spectrometry. Dissociation methods include those that simply alter the population of internal states of the mass-selected ion (i.e., activation methods like collision-induced dissociation) as well as processes that rely on transformation of the ion-type prior to dissociation (e.g., electron capture dissociation). A variety of ionic interactions has been studied for the purpose of ion dissociation and ion transformation that include ion/neutral, ion/photon, ion/electron, and ion/ion interactions. A wide range of phenomena has been observed, many of which have been explored/developed as means for structural analysis. The techniques arising from these phenomena are discussed within the context of the elements of structure determination in tandem mass spectrometry, viz., ion-type definition and dissociation. Unique aspects of the various ion interactions are emphasized along with any barriers to widespread implementation. PMID:21472539

Surface Induced Dissociation Yields Quaternary Substructure of Refractory Noncovalent Phosphorylase B and Glutamate Dehydrogenase Complexes

NASA Astrophysics Data System (ADS)

Ma, Xin; Zhou, Mowei; Wysocki, Vicki H.

2014-03-01

Ion mobility (IM) and tandem mass spectrometry (MS/MS) coupled with native MS are useful for studying noncovalent protein complexes. Collision induced dissociation (CID) is the most common MS/MS dissociation method. However, some protein complexes, including glycogen phosphorylase B kinase (PHB) and L-glutamate dehydrogenase (GDH) examined in this study, are resistant to dissociation by CID at the maximum collision energy available in the instrument. Surface induced dissociation (SID) was applied to dissociate the two refractory protein complexes. Different charge state precursor ions of the two complexes were examined by CID and SID. The PHB dimer was successfully dissociated to monomers and the GDH hexamer formed trimeric subcomplexes that are informative of its quaternary structure. The unfolding of the precursor and the percentages of the distinct products suggest that the dissociation pathways vary for different charge states. The precursors at lower charge states (+21 for PHB dimer and +27 for GDH hexamer) produce a higher percentage of folded fragments and dissociate more symmetrically than the precusors at higher charge states (+29 for PHB dimer and +39 for GDH hexamer). The precursors at lower charge state may be more native-like than the higher charge state because a higher percentage of folded fragments and a lower percentage of highly charged unfolded fragments are detected. The combination of SID and charge reduction is shown to be a powerful tool for quaternary structure analysis of refractory noncovalent protein complexes, as illustrated by the data for PHB dimer and GDH hexamer.

From molecular chaperones to membrane motors: through the lens of a mass spectrometrist.

PubMed

Robinson, Carol V

2017-02-08

Twenty-five years ago, we obtained our first mass spectra of molecular chaperones in complex with protein ligands and entered a new field of gas-phase structural biology. It is perhaps now time to pause and reflect, and to ask how many of our initial structure predictions and models derived from mass spectrometry (MS) datasets were correct. With recent advances in structure determination, many of the most challenging complexes that we studied over the years have become tractable by other structural biology approaches enabling such comparisons to be made. Moreover, in the light of powerful new electron microscopy methods, what role is there now for MS? In considering these questions, I will give my personal view on progress and problems as well as my predictions for future directions. © 2017 The Author(s).

Quinone-based stable isotope probing for assessment of 13C substrate-utilizing bacteria

NASA Astrophysics Data System (ADS)

Kunihiro, Tadao; Katayama, Arata; Demachi, Toyoko; Veuger, Bart; Boschker, Henricus T. S.; van Oevelen, Dick

2015-04-01

In this study, we attempted to establish quinone-stable-isotope probing (SIP) technique to link substrate-utilizing bacterial group to chemotaxonomic group in bacterial community. To identify metabolically active bacterial group in various environments, SIP techniques combined with biomarkers have been widely utilized as an attractive method for environmental study. Quantitative approaches of the SIP technique have unique advantage to assess substrate-incorporation into bacteria. As a most major quantitative approach, SIP technique based on phospholipid-derived fatty acids (PLFA) have been applied to simultaneously assess substrate-incorporation rate into bacteria and microbial community structure. This approach is powerful to estimate the incorporation rate because of the high sensitivity due to the detection by a gas chromatograph-combustion interface-isotope ratio mass spectrometer (GC-c-IRMS). However, its phylogenetic resolution is limited by specificity of a compound-specific marker. We focused on respiratory quinone as a biomarker. Our previous study found a good correlation between concentrations of bacteria-specific PLFAs and quinones over several orders of magnitude in various marine sediments, and the quinone method has a higher resolution (bacterial phylum level) for resolving differences in bacterial community composition more than that of bacterial PLFA. Therefore, respiratory quinones are potentially good biomarkers for quantitative approaches of the SIP technique. The LC-APCI-MS method as molecular-mass based detection method for quinone was developed and provides useful structural information for identifying quinone molecular species in environmental samples. LC-MS/MS on hybrid triple quadrupole/linear ion trap, which enables to simultaneously identify and quantify compounds in a single analysis, can detect high molecular compounds with their isotope ions. Use of LC-MS/MS allows us to develop quinone-SIP based on molecular mass differences due to 13C abundance in the quinone. In this study, we verified carbon stable isotope of quinone compared with bulk carbon stable isotope of bacterial culture. Results indicated a good correlation between carbon stable isotope of quinone compared with bulk carbon stable isotope. However, our measurement conditions for detection of quinone isotope-ions incurred underestimation of 13C abundance in the quinone. The quinone-SIP technique needs further optimization for measurement conditions of LC-MS/MS.

Structural analysis of an intact monoclonal antibody by online electrochemical reduction of disulfide bonds and Fourier transform ion cyclotron resonance mass spectrometry.

PubMed

Nicolardi, Simone; Deelder, André M; Palmblad, Magnus; van der Burgt, Yuri E M

2014-06-03

Structural confirmation and quality control of recombinant monoclonal antibodies (mAbs) by top-down mass spectrometry is still challenging due to the size of the proteins, disulfide content, and post-translational modifications such as glycosylation. In this study we have applied electrochemistry (EC) to overcome disulfide bridge complexity in top-down analysis of mAbs. To this end, an electrochemical cell was coupled directly to an electrospray ionization (ESI) source and a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer (MS) equipped with a 15 T magnet. By performing online EC-assisted reduction of interchain disulfide bonds in an intact mAb, the released light chains could be selected for tandem mass spectrometry (MS/MS) analysis without interference from heavy-chain fragments. Moreover, the acquisition of full MS scans under denaturing conditions allowed profiling of all abundant mAb glycoforms. Ultrahigh-resolution FTICR-MS measurements provided fully resolved isotopic distributions of intact mAb and enabled the identification of the most abundant adducts and other interfering species. Furthermore, it was found that reduction of interchain disulfide bonds occurs in the ESI source dependent on capillary voltage and solvent composition. This phenomenon was systematically evaluated and compared with the results obtained from reduction in the electrochemical cell.

Validation of the Italian version of the HSE Indicator Tool.

PubMed

Magnavita, N

2012-06-01

An Italian version of the Health & Safety Executive's (HSE) Management Standards Revised Indicator Tool (MS-RIT) has been used to monitor the working conditions that may lead to stress. To initially examine the factor structure of the Italian version of the MS-RIT, in comparison with the original UK tool, and to investigate its validity and reliability; second, to study the association between occupational stress and psychological distress. Workers from 17 companies self-completed the MS-RIT and the General Health Questionnaire used to measure the psychological distress while they waited for their periodic examination at the workplace. Factor analysis was employed to ascertain whether the Italian version maintained the original subdivision into seven scales. Odds ratios were calculated to estimate the risk of impairment associated with exposure to stress at the workplace. In total, 748 workers participated; the response rate was 91%. The factor structure of the Italian MS-RIT corresponded partially to the original UK version. The 'demand', 'control', 'role', ' relationship' and 'colleague-support' scales were equivalent to the UK ones. A principal factor, termed ' elasticity', incorporated the UK 'management-support' and 'change' scales. Reliability analysis of the sub-scales revealed Cronbach's alpha values ranging from 0.75 to 0.86. Our findings confirmed the usefulness of the Italian version of the HSE MS-RIT in stress control.

Putative identification of new p-coumaroyl glycoside flavonoids in grape by ultra-high performance liquid chromatography/high-resolution mass spectrometry.

PubMed

Panighel, Annarita; De Rosso, Mirko; Dalla Vedova, Antonio; Flamini, Riccardo

2015-02-28

Grape polyphenols are antioxidant compounds, markers in vine chemotaxonomy, and involved in color stabilization of red wines. Sugar acylation usually confers higher stability on glycoside derivatives and this effect is enhanced by an aromatic substituent such as p-coumaric acid. Until now, only p-coumaroyl anthocyanins have been found in grape. A method of 'suspect screening analysis' by ultra-high-performance liquid chromatography/high-resolution mass spectrometry (UHPLC/QTOFMS) has recently been developed to study grape metabolomics. In the present study, this approach was used to identify new polyphenols in grape by accurate mass measurement, MS/MS fragmentation, and study of correlations between fragments observed and putative structures. Three putative p-coumaroyl flavonoids were identified in Raboso Piave grape extract: a dihydrokaempferide-3-O-p-coumaroylhexoside-like flavanone, isorhamnetin-3-O-p-coumaroylglucoside, and a chrysoeriol-p-coumaroylhexoside-like flavone. Accurate MS provided structural characterization of functional groups, and literature data indicates their probable position in the molecule. A fragmentation scheme is proposed for each compound. Compounds were identified by overlapping various analytical methods according to recommendations in the MS-based metabolomics literature. Stereochemistry and the definitive position of substituents in the molecule can only be confirmed by isolation and characterization or synthesis of each compound. These findings suggest addressing research of acylated polyphenol glycosides to other grape varieties. Copyright © 2015 John Wiley & Sons, Ltd.

Dissociation Behavior of a TEMPO-Active Ester Cross-Linker for Peptide Structure Analysis by Free Radical Initiated Peptide Sequencing (FRIPS) in Negative ESI-MS.

PubMed

Hage, Christoph; Ihling, Christian H; Götze, Michael; Schäfer, Mathias; Sinz, Andrea

2017-01-01

We have synthesized a homobifunctional amine-reactive cross-linking reagent, containing a TEMPO (2,2,6,6-tetramethylpiperidine-1-oxy) and a benzyl group (Bz), termed TEMPO-Bz-linker, to derive three-dimensional structural information of proteins. The aim for designing this novel cross-linker was to facilitate the mass spectrometric analysis of cross-linked products by free radical initiated peptide sequencing (FRIPS). In an initial study, we had investigated the fragmentation behavior of TEMPO-Bz-derivatized peptides upon collision activation in (+)-electrospray ionization collision-induced dissociation tandem mass spectrometry (ESI-CID-MS/MS) experiments. In addition to the homolytic NO-C bond cleavage FRIPS pathway delivering the desired odd-electron product ions, an alternative heterolytic NO-C bond cleavage, resulting in even-electron product ions mechanism was found to be relevant. The latter fragmentation route clearly depends on the protonation of the TEMPO-Bz-moiety itself, which motivated us to conduct (-)-ESI-MS, CID-MS/MS, and MS 3 experiments of TEMPO-Bz-cross-linked peptides to further clarify the fragmentation behavior of TEMPO-Bz-peptide molecular ions. We show that the TEMPO-Bz-linker is highly beneficial for conducting FRIPS in negative ionization mode as the desired homolytic cleavage of the NO-C bond is the major fragmentation pathway. Based on characteristic fragments, the isomeric amino acids leucine and isoleucine could be discriminated. Interestingly, we observed pronounced amino acid side chain losses in cross-linked peptides if the cross-linked peptides contain a high number of acidic amino acids. Graphical Abstract ᅟ.

Comparing depression screening tools in persons with multiple sclerosis (MS).

PubMed

Hanna, Joshua; Santo, Jonathan B; Blair, Mervin; Smolewska, Kathy; Warriner, Erin; Morrow, Sarah A

2017-02-01

Depression is more common among persons with multiple sclerosis (MS) than the general population. Depression in MS is associated with reduced quality of life, transition to unemployment, and cognitive impairment. Two proposed screening measures for depression in MS populations are the Hospital Anxiety and Depression Scale (HADS) and the Beck Depression Inventory-Fast Screen (BDI-FS). Our objective was to compared the associations of the BDI-FS and the HADS-D scores with history of depressive symptoms, fatigue, and functional outcomes to determine the differential clinical utility of these screening measures among persons with MS. We reviewed charts of 133 persons with MS for demographic information; scores on the HADS, BDI-FS, a fatigue measure, and a processing speed measure; and employment status. Structural equation modeling results indicated the HADS-D predicted employment status, disability status, and processing speed more effectively than did the BDI-FS, whereas both measures predicted fatigue. This study suggests the HADS-D is more effective than the BDI-FS in predicting functional outcomes known to be associated with depression among persons with MS. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Identification and Characterization of Reaction Products of 5-Hydroxytryptamine with Methylglyoxal and Glyoxal by LC/MS/MS.

PubMed

Sai Sachin, L; Nagarjuna Chary, R; Pavankumar, P; Prabhakar, S

2018-06-06

The methylglyoxal (MGO) and glyoxal (GO) are known to be at high levels in the diabetic humans. They react with amine containing proteins and amino acids to form advanced glycation end products, however, the reactivity with the other amine containing metabolites, such as neurotransmitters are not explored. In this study, we aimed at studying the reactivity of 5-hydroxytryptamine (5-HT) with MGO or GO, which may alter the metabolic function of 5-HT. The stock solutions of 5-HT, MGO and GO were made in PBS buffer at pH 7.4 and incubated 5-HT with MGO or GO at difference concentrations. The reactions were also performed at physiological concentrations. The reaction mixtures collected at different incubation times were analyzed by direct ESI-HRMS, LC/MS and LC/MS/MS conditions to detect/characterize the products. Agilent 6545 Q-TOF and Agilent 6420 triple quadrupole mass spectrometer were used for the study, and LC separations were performed on a C18 column. The direct ESI-HRMS data of the reaction mixtures showed formation of three and four reaction products when 5-HT reacted with MGO and GO, respectively. All the products showed dominant [M+H] + ions. The products were characterized by HRMS, LC/MS/MS and the literature reports on similar compounds. The products can easily be identified by LC/MS based on the accurate mass values together with retention time information. The MS/MS of the reaction products showed structure indicative fragment ions. 5-HT reacts with one or two MGO/GO to form a set of reaction products. The reaction between 5-HT and MGO or GO was faster at higher concentrations of MGO/GO (<10 min), and the same products were found even at physiological concentrations (<48 hrs). The LC-MS/MS (SRM) method can be used to screen the reaction products when present at low level. This article is protected by copyright. All rights reserved.

A qualitative study of cognitive behavioural therapy in multiple sclerosis: experiences of psychotherapists

PubMed Central

Ytterberg, Charlotte; Chruzander, Charlotte; Backenroth, Gunnel; Kierkegaard, Marie; Ahlström, Gerd; Gottberg, Kristina

2017-01-01

ABSTRACT Purpose: To investigate how psychotherapists experience using individual, face-to-face cognitive behavioural therapy (CBT) aimed at alleviating depressive symptoms in persons with multiple sclerosis (MS). Method: Semi-structured interviews with three psychotherapists were conducted after CBT with 12 participants with MS, and analysed using qualitative content analysis. Results: Two main themes emerged: Trusting their expertise as psychotherapists whilst lacking MS-specific knowledge, and The process of exploring the participants’ readiness for CBT with modifications of content and delivery. The psychotherapists perceived it difficult to know whether a symptom was attributable to depression or to MS, and for some participants the CBT needed to be adapted to a more concrete content. Conclusions: Psychotherapists may need more MS-specific knowledge and an insight into the individual’s functioning. The content of CBT in terms of concrete home assignments and behavioural activation needs to be individualised. PMID:28540774

A qualitative study of cognitive behavioural therapy in multiple sclerosis: experiences of psychotherapists.

PubMed

Ytterberg, Charlotte; Chruzander, Charlotte; Backenroth, Gunnel; Kierkegaard, Marie; Ahlström, Gerd; Gottberg, Kristina

2017-12-01

To investigate how psychotherapists experience using individual, face-to-face cognitive behavioural therapy (CBT) aimed at alleviating depressive symptoms in persons with multiple sclerosis (MS). Semi-structured interviews with three psychotherapists were conducted after CBT with 12 participants with MS, and analysed using qualitative content analysis. Two main themes emerged: Trusting their expertise as psychotherapists whilst lacking MS-specific knowledge, and The process of exploring the participants' readiness for CBT with modifications of content and delivery. The psychotherapists perceived it difficult to know whether a symptom was attributable to depression or to MS, and for some participants the CBT needed to be adapted to a more concrete content. Psychotherapists may need more MS-specific knowledge and an insight into the individual's functioning. The content of CBT in terms of concrete home assignments and behavioural activation needs to be individualised.

Metabolism studies of benzbromarone in rats by high performance liquid chromatography-quadrupole time of flight mass spectrometry.

PubMed

Wu, Haiqing; Peng, Ying; Wang, Shaojie; Wang, Kai; Zhao, Xunchen; Jiang, Fan

2012-12-12

A high performance liquid chromatography-quadrupole time of flight mass spectrometry (HPLC-QTOF-MS) method was employed in investigation of benzbromarone metabolites in rat plasma, urine, feces and bile samples. Meanwhile, the metabolic pathways of benzbromarone in rats were discussed. The identification was achieved on a reversed-phase C(18) column with mobile phase gradient method. The QTOF-MS was operated under full scan of MS or MS/MS in negative mode. The fragments were acquired by raising collision induced dissociation (CID) energy for speculating the structures of parent ions. According to the information from the chromatograms and mass spectra, 17 metabolites were obtained. Among them, the deoxidized phase I metabolites and an array of phase II metabolites-sulfate conjugates detected in the biological samples made the work more significant. Copyright © 2012 Elsevier B.V. All rights reserved.

Chemical analysis applied to the radiation sterilization of solid ketoprofen

NASA Astrophysics Data System (ADS)

Colak, S.; Maquille, A.; Tilquin, B.

2006-01-01

The aim of this work is to investigate the feasibility of radiation sterilization of ketoprofen from a chemical point of view. Although irradiated ketoprofen has already been studied in the literature [Katusin-Razem et al., Radiat. Phys. Chem. 73 111-116 (2005)], new results, on the basis of electron spin resonance (ESR) measurements and the use of hyphenated techniques (GC-MS and LC-MS), are obtained. The ESR spectra of irradiated ketoprofen consists of four unresolved resonance peaks and the mean G-value of ketoprofen is found to be 4 +/- 0.9 nmoles/J, which is very small. HPLC-UV analyses indicate that no significant loss of ketoprofen is detected after irradiation. LC-MS-MS analyses show that the structures of the non-volatile final products are similar to ketoprofen. Benzaldehyde is detected in the irradiated samples after dynamic-extraction GC-MS. The analyses show that ketoprofen is radioresistant and therefore might be radiosterilized.

Probing Protein Structure by Amino Acid-Specific Covalent Labeling and Mass Spectrometry

PubMed Central

Mendoza, Vanessa Leah; Vachet, Richard W.

2009-01-01

For many years, amino acid-specific covalent labeling has been a valuable tool to study protein structure and protein interactions, especially for systems that are difficult to study by other means. These covalent labeling methods typically map protein structure and interactions by measuring the differential reactivity of amino acid side chains. The reactivity of amino acids in proteins generally depends on the accessibility of the side chain to the reagent, the inherent reactivity of the label and the reactivity of the amino acid side chain. Peptide mass mapping with ESI- or MALDI-MS and peptide sequencing with tandem MS are typically employed to identify modification sites to provide site-specific structural information. In this review, we describe the reagents that are most commonly used in these residue-specific modification reactions, details about the proper use of these covalent labeling reagents, and information about the specific biochemical problems that have been addressed with covalent labeling strategies. PMID:19016300

Physical activity and cognitive function in adults with multiple sclerosis: an integrative review.

PubMed

Morrison, Janet D; Mayer, Lori

2017-09-01

To identify and synthesize the research evidence concerning (1) the relationship between physical activity and cognitive performance in persons with multiple sclerosis (MS) and (2) to review the reported effects of physical activity interventions on neurocognitive performance conducted in this population. Relevant peer-reviewed journal articles were identified by searching PubMed, PsychINFO, and SPORTDiscus through May 2016. Full-text articles meeting the inclusion criteria were evaluated for quality using tools developed by the National Institutes of Health. Studies deemed to be of poor quality were excluded from the review. Nineteen studies meeting the inclusion/exclusion criteria were analyzed. Nine studies reported significant relationships between higher levels of physical activity or cardiorespiratory fitness and measures of cognitive function. Data extracted from 10 physical activity intervention studies reported mixed results on the effectiveness of physical activity to improve selected domains of cognitive function in persons with MS. Although correlational studies provide evidence to support a linkage between physical activity and cognitive function in persons with MS, this linkage is confounded by factors that may have influenced the studies' results. Evidence derived from intervention studies that could support a positive effect of physical activity on cognition in persons with MS is equivocal. Implications for Rehabilitation Physical activity has numerous benefits for persons with multiple sclerosis (MS) including improvements in balance, ambulation, depression, fatigue, and quality of life. Structured physical activity programs may contribute to cognitive function stability or improvement in persons with MS.

Therapy optimization in multiple sclerosis: a prospective observational study of therapy compliance and outcomes

PubMed Central

2014-01-01

Background Data sources for MS research are numerous but rarely provide an objective measure of drug therapy compliance coupled with patient-reported health outcomes. The objective of this paper is to describe the methods and baseline characteristics of the Therapy Optimization in MS (TOP MS) study designed to investigate the relationship between disease-modifying therapy compliance and health outcomes. Methods TOP MS was designed as a prospective, observational, nationwide patient-focused study using an internet portal for data entry. The protocol was reviewed and approved by Sterling IRB. The study was registered with ClinicalTrials.gov. It captured structured survey data monthly from MS patients recruited by specialty pharmacies. Data collection included the clinical characteristics of MS such as MS relapses. Disability, quality of life and work productivity and activity impairment were assessed quarterly with well-validated scales. When events like severe fatigue or new or worsening depression were reported, feedback was provided to treating physicians. The therapy compliance measure was derived from pharmacy drug shipment records uploaded to the study database. The data presented in this paper use descriptive statistics. Results The TOP MS Study enrolled 2966 participants receiving their disease-modifying therapy (DMT) from specialty pharmacies. The mean age of the sample was 49 years, 80.4% were female, 89.9% were Caucasian and 55.7% were employed full or part time. Mean time since first symptoms was 11.5 years; mean duration since diagnosis was 9.5 years. Patient-reported EDSS was 3.5; 72.2% had a relapsing-remitting disease course. The most commonly reported symptoms at the time of enrollment were fatigue (74.7%), impaired coordination or balance (61.8%) and numbness and tingling (61.2%). Half of the sample was using glatiramer acetate and half was using beta-interferons. Conclusion Demographic and clinical characteristics of the TOP MS sample at enrollment are consistent with other community-based MS samples, and the sample appears to be representative of DMT users in the US. TOP MS data can be used to explore the associations between disease-modifying therapy compliance and health outcomes. Trial registration ClinicalTrials.gov (NCT00819000) PMID:24624979

Therapy optimization in multiple sclerosis: a prospective observational study of therapy compliance and outcomes.

PubMed

Coyle, Patricia K; Cohen, Bruce A; Leist, Thomas; Markowitz, Clyde; Oleen-Burkey, MerriKay; Schwartz, Marc; Tullman, Mark J; Zwibel, Howard

2014-03-13

Data sources for MS research are numerous but rarely provide an objective measure of drug therapy compliance coupled with patient-reported health outcomes. The objective of this paper is to describe the methods and baseline characteristics of the Therapy Optimization in MS (TOP MS) study designed to investigate the relationship between disease-modifying therapy compliance and health outcomes. TOP MS was designed as a prospective, observational, nationwide patient-focused study using an internet portal for data entry. The protocol was reviewed and approved by Sterling IRB. The study was registered with ClinicalTrials.gov. It captured structured survey data monthly from MS patients recruited by specialty pharmacies. Data collection included the clinical characteristics of MS such as MS relapses. Disability, quality of life and work productivity and activity impairment were assessed quarterly with well-validated scales. When events like severe fatigue or new or worsening depression were reported, feedback was provided to treating physicians. The therapy compliance measure was derived from pharmacy drug shipment records uploaded to the study database. The data presented in this paper use descriptive statistics. The TOP MS Study enrolled 2966 participants receiving their disease-modifying therapy (DMT) from specialty pharmacies. The mean age of the sample was 49 years, 80.4% were female, 89.9% were Caucasian and 55.7% were employed full or part time. Mean time since first symptoms was 11.5 years; mean duration since diagnosis was 9.5 years. Patient-reported EDSS was 3.5; 72.2% had a relapsing-remitting disease course. The most commonly reported symptoms at the time of enrollment were fatigue (74.7%), impaired coordination or balance (61.8%) and numbness and tingling (61.2%). Half of the sample was using glatiramer acetate and half was using beta-interferons. Demographic and clinical characteristics of the TOP MS sample at enrollment are consistent with other community-based MS samples, and the sample appears to be representative of DMT users in the US. TOP MS data can be used to explore the associations between disease-modifying therapy compliance and health outcomes. ClinicalTrials.gov (NCT00819000).

Accelerating the design of molecularly imprinted nanocomposite membranes modified by Au@polyaniline for selective enrichment and separation of ibuprofen

NASA Astrophysics Data System (ADS)

Wu, Xiuling; Wu, Yilin; Dong, Hongjun; Zhao, Juan; Wang, Chen; Zhou, Shi; Lu, Jian; Yan, Yongsheng; Li, He

2018-01-01

A novel system for harvesting molecularly imprinted nanocomposite membranes (MINcMs) with Au-modified polyaniline (Au@polyaniline) nanocomposite structure was developed for selective enrichment and separation of ibuprofen. This unique nanocomposite structure obviously enhanced the adsorption capacity, perm-selectivity performance, and regeneration ability of MINcMs. The as-prepared MINcMs showed outstanding adsorption capacity (22.02 mg g-1) of ibuprofen, which was four times higher than that of non-imprinted nanocomposite membranes (NINcMs). Furthermore, the selectivity factor of MINcMs for ibuprofen reached up to 4.67 and the perm-selectivity factor β was about 8.74, which indicated MINcMs had a good selective separation performance of ibuprofen. We envision that this novel synthesis method will open a new direction to manipulation of molecularly imprinted membrane materials and provide a simple yet convenient way to selective separation of ibuprofen.

Thalamic and hippocampal volume associated with memory functions in multiple sclerosis.

PubMed

Tremblay, Alexandra; Jobin, Céline; Demers, Mélanie; Dagenais, Emmanuelle; Narayanan, Sridar; Araújo, David; Douglas, Arnold L; Roger, Elaine; Chamelian, Laury; Duquette, Pierre; Rouleau, Isabelle

2018-06-08

Although multiple sclerosis (MS) has long been considered to primarily affect white matter, it is now recognized that cognitive deficits in MS are also related to neocortical, thalamic and hippocampal damage. However, the association between damage to these structures and memory deficits in MS is unclear. This study examines whether MS patients with cognitive impairment have a reduction of hippocampal and/or thalamic volumes compared to cognitively intact patients, and whether these volume reductions correlate with various aspects of memory function. Volumetric MRI measures of thalamus and hippocampus of forty-one patients with MS were performed. The patients were divided in two groups depending on the presence or absence of cognitive impairment, based on their neuropsychological tests scores. Right hippocampal volume was found to be associated with learning, and the left thalamic volume was found to predict performance in verbal memory. Cognitively impaired patients had a tendency to have a reduced left thalamic volume compared to cognitively intact patients. This study does not support a direct relationship between hippocampal atrophy and verbal memory. These results add to the growing evidence of the involvement of thalamus in cognitive impairment in MS and its association with verbal memory deficits. Copyright © 2018. Published by Elsevier Inc.

Characterization of phenolic compounds and antinociceptive activity of Sempervivum tectorum L. leaf juice.

PubMed

Alberti, Ágnes; Béni, Szabolcs; Lackó, Erzsébet; Riba, Pál; Al-Khrasani, Mahmoud; Kéry, Ágnes

2012-11-01

Sempervivum tectorum L. (houseleek) leaf juice has been known as a traditional herbal remedy. The aim of the present study was the chemical characterization of its phenolic compounds and to develop quantitation methods for its main flavonol glycoside, as well as to evaluate its antinociceptive activity. Lyophilized houseleek leaf juice was studied by HPLC-DAD coupled to electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) to identify flavonol glycosides, hydroxy-benzoic and hydroxy-cinnamic acids. Ten flavonol glycosides and sixteen phenolic acid compounds were identified or tentatively characterized. Structure of the main flavonol compound was identified by nuclear magnetic resonance spectroscopy. Three characteristic kaempferol glycosides were isolated and determined by LC-ESI-MS/MS with external calibration method, using the isolated compounds as standard. The main flavonol glycoside was also determined by HPLC-DAD. Validated HPLC-DAD and LC-ESI-MS/MS methods were developed to quantify kaempferol-3-O-rhamnosyl-glucoside-7-O-rhamnoside and two other kaempferol glycosides. Antinociceptive activity of houseleek leaf juice was investigated by writhing test of mice. Sempervivum extract significantly reduced pain in the mouse writhing test. Copyright © 2012 Elsevier B.V. All rights reserved.

MS Based Metabonomics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Want, Elizabeth J.; Metz, Thomas O.

Metabonomics is the latest and least mature of the systems biology triad, which also includes genomics and proteomics, and has its origins in the early orthomolecular medicine work pioneered by Linus Pauling and Arthur Robinson. It was defined by Nicholson and colleagues in 1999 as the quantitative measurement of perturbations in the metabolite complement of an integrated biological system in response to internal or external stimuli, and is often used today to describe many non-global types of metabolite analyses. Applications of metabonomics are extensive and include toxicology, nutrition, pharmaceutical research and development, physiological monitoring and disease diagnosis. For example, bloodmore » samples from millions of neonates are tested routinely by mass spectrometry (MS) as a diagnostic tool for inborn errors of metabolism. The metabonome encompasses a wide range of structurally diverse metabolites; therefore, no single analytical platform will be sufficient. Specialized sample preparation and detection techniques are required, and advances in NMR and MS technologies have led to enhanced metabonome coverage, which in turn demands improved data analysis approaches. The role of MS in metabonomics is still evolving as instrumentation and software becomes more sophisticated and as researchers realize the strengths and limitations of current technology. MS offers a wide dynamic range, high sensitivity, and reproducible, quantitative analysis. These attributes are essential for addressing the challenges of metabonomics, as the range of metabolite concentrations easily exceeds nine orders of magnitude in biofluids, and the diversity of molecular species ranges from simple amino and organic acids to lipids and complex carbohydrates. Additional challenges arise in generating a comprehensive metabolite profile, downstream data processing and analysis, and structural characterization of important metabolites. A typical workflow of MS-based metabonomics is shown in Figure 1. Gas chromatography-(GC)-MS was the most commonly used MS-based method for small molecule analysis in the 1970s and 1980s. It is still used today for the detection of many metabolic disorders and plays a strong role in plant metabonomics. Liquid chromatography (LC)-MS approaches have grown in popularity for metabolite studies, due to simpler sample preparation, reduced analysis times through the introduction of ultra-high performance liquid chromatography (UPLC)-MS and the ability to observe a wider range of metabolites. This chapter will discuss the role of MS in metabonomics, the techniques involved in this exciting area, and the current and future applications of the field. The various bioinformatics tools and multivariate analysis techniques used to maximize information recovery and to aid in the interpretation of the very large data sets typically obtained in metabonomics studies will also be discussed. While there are many different MS-based approaches utilized in metabonomics studies, emphasis will be placed on more established methods.« less

A comparative analysis of human plasma and serum proteins by combining native PAGE, whole-gel slicing and quantitative LC-MS/MS: Utilizing native MS-electropherograms in proteomic analysis for discovering structure and interaction-correlated differences.

PubMed

Wen, Meiling; Jin, Ya; Manabe, Takashi; Chen, Shumin; Tan, Wen

2017-12-01

MS identification has long been used for PAGE-separated protein bands, but global and systematic quantitation utilizing MS after PAGE has remained rare and not been reported for native PAGE. Here we reported on a new method combining native PAGE, whole-gel slicing and quantitative LC-MS/MS, aiming at comparative analysis on not only abundance, but also structures and interactions of proteins. A pair of human plasma and serum samples were used as test samples and separated on a native PAGE gel. Six lanes of each sample were cut, each lane was further sliced into thirty-five 1.1 mm × 1.1 mm squares and all the squares were subjected to standardized procedures of in-gel digestion and quantitative LC-MS/MS. The results comprised 958 data rows that each contained abundance values of a protein detected in one square in eleven gel lanes (one plasma lane excluded). The data were evaluated to have satisfactory reproducibility of assignment and quantitation. Totally 315 proteins were assigned, with each protein assigned in 1-28 squares. The abundance distributions in the plasma and serum gel lanes were reconstructed for each protein, named as "native MS-electropherograms". Comparison of the electropherograms revealed significant plasma-versus-serum differences on 33 proteins in 87 squares (fold difference > 2 or < 0.5, p < 0.05). Many of the differences matched with accumulated knowledge on protein interactions and proteolysis involved in blood coagulation, complement and wound healing processes. We expect this method would be useful to provide more comprehensive information in comparative proteomic analysis, on both quantities and structures/interactions. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Agreement Between the JCDCG, Revised NCEP-ATPIII, and IDF Definitions of Metabolic Syndrome in a Northwestern Chinese Population.

PubMed

Sun, Fei; Gao, Bin; Wang, Li; Xing, Ying; Ming, Jie; Zhou, Jie; Fu, Jianfang; Li, Xiaomiao; Xu, Shaoyong; Liu, Guocai; Ji, Qiuhe

2018-05-28

The Joint Committee for Developing Chinese Guidelines (JCDCG) introduced the Chinese definition for metabolic syndrome (MS), which has been verified in southern Chinese people but not in northwestern Chinese people. We evaluated the MS definition proposed by the JCDCG in a northwestern Chinese population, in comparison with those of the revised National Cholesterol Education Program Adult Treatment Panel III (NCEP-ATPIII) and the International Diabetes Federation (IDF). This population-based cross-sectional study was a part of the China National Diabetes and Metabolic Disorders Study conducted in Shaanxi province. We included 3243 participants aged ≥ 20 years. The age-adjusted MS prevalence was assessed per the 2007 Chinese population structure. The agreement between different definitions was assessed by the kappa statistic. The standardized prevalence of JCDCG-MS, revised ATPIII-MS, and IDF-MS was 22.4%, 29.4%, and 24.9%, respectively. Among women, the agreement of the JCDCG definition with the revised ATPIII and the IDF definition was not good (κ = 0.599 and 0.601, respectively); 54.6% of the revised ATPIII-MS and 56% of the IDF-MS were defined as MS according to the JCDCG definition. Among men, the agreement of JCDCG definition with the revised ATPIII and IDF definitions was very good (κ = 0.863) and substantial (κ = 0.741), respectively. The agreement of the JCDCG definition with the revised ATPIII and IDF definitions was insufficient in women. Compared with the other two definitions, the JCDCG definition underestimates MS prevalence in northwestern women.

Profiling of acarviostatin family secondary metabolites secreted by Streptomyces coelicoflavus ZG0656 using ultraperformance liquid chromatography coupled with electrospray ionization mass spectrometry.

PubMed

Geng, Peng; Meng, Xiansheng; Bai, Gang; Luo, Guoan

2008-10-01

Profiling of acarviostatin family secondary metabolites secreted by Streptomyces coelicoflavus ZG0656 was performed by means of a rapid and facile procedure using ultraperformance liquid chromatography coupled with electrospray ionization mass spectrometry (UPLC/ESI-MS). The acarviostatins were separated on a C18 UPLC column with a series of acetonitrile-aqueous ammonia gradients. The target homologues were detected using the multiple reaction monitoring mode, and the chemical structures were confirmed by analyzing the diagnostic fragment ions in their MS/MS spectra. All six known reference acarviostatins (I03, II03, II13, II23, III03, IV03) were thus identified. In addition, at least 74 acarviostatin homologues, including 65 novel compounds, were characterized. Some of the features of the novel structures included having up to five acarviosine moieties, an acarviosine moiety at the reducing terminus, or an incomplete acarviosine moiety at the nonreducing terminus. This type of investigation may be useful for researchers who study secondary metabolomics in microorganisms and plants, especially those who perform metabolic profiling of aminooligosaccharides and other natural products with similar structures.

Sequence Analysis and Domain Motifs in the Porcine Skin Decorin Glycosaminoglycan Chain*

PubMed Central

Zhao, Xue; Yang, Bo; Solakylidirim, Kemal; Joo, Eun Ji; Toida, Toshihiko; Higashi, Kyohei; Linhardt, Robert J.; Li, Lingyun

2013-01-01

Decorin proteoglycan is comprised of a core protein containing a single O-linked dermatan sulfate/chondroitin sulfate glycosaminoglycan (GAG) chain. Although the sequence of the decorin core protein is determined by the gene encoding its structure, the structure of its GAG chain is determined in the Golgi. The recent application of modern MS to bikunin, a far simpler chondroitin sulfate proteoglycans, suggests that it has a single or small number of defined sequences. On this basis, a similar approach to sequence the decorin of porcine skin much larger and more structurally complex dermatan sulfate/chondroitin sulfate GAG chain was undertaken. This approach resulted in information on the consistency/variability of its linkage region at the reducing end of the GAG chain, its iduronic acid-rich domain, glucuronic acid-rich domain, and non-reducing end. A general motif for the porcine skin decorin GAG chain was established. A single small decorin GAG chain was sequenced using MS/MS analysis. The data obtained in the study suggest that the decorin GAG chain has a small or a limited number of sequences. PMID:23423381

Structure and dynamics of protein waters revealed by radiolysis and mass spectrometry

PubMed Central

Gupta, Sayan; D’Mello, Rhijuta; Chance, Mark R.

2012-01-01

Water is critical for the structure, stability, and functions of macromolecules. Diffraction and NMR studies have revealed structure and dynamics of bound waters at atomic resolution. However, localizing the sites and measuring the dynamics of bound waters, particularly on timescales relevant to catalysis and macromolecular assembly, is quite challenging. Here we demonstrate two techniques: first, temperature-dependent radiolytic hydroxyl radical labeling with a mass spectrometry (MS)-based readout to identify sites of bulk and bound water interactions with surface and internal residue side chains, and second, H218O radiolytic exchange coupled MS to measure the millisecond dynamics of bound water interactions with various internal residue side chains. Through an application of the methods to cytochrome c and ubiquitin, we identify sites of water binding and measure the millisecond dynamics of bound waters in protein crevices. As these MS-based techniques are very sensitive and not protein size limited, they promise to provide unique insights into protein–water interactions and water dynamics for both small and large proteins and their complexes. PMID:22927377

Internal iron biomineralization in Imperata cylindrica, a perennial grass: chemical composition, speciation and plant localization.

PubMed

Rodríguez, N; Menéndez, N; Tornero, J; Amils, R; de la Fuente, V

2005-03-01

* The analysis of metal distribution in Imperata cylindrica, a perennial grass isolated from the banks of Tinto River (Iberian Pyritic Belt), an extreme acidic environment with high content in metals, has shown a remarkable accumulation of iron. This property has been used to study iron speciation and its distribution among different tissues and structures of the plant. * Mossbauer (MS) and X-ray diffraction (XRD) were used to determine the iron species, scanning electron microscopy (SEM) to locate iron biominerals among plant tissue structures, and energy-dispersive X-ray microanalysis (EDAX), X-ray fluorescence (TXRF) and inductively coupled plasma emission spectroscopy (ICP-MS) to confirm their elemental composition. * The MS spectral analysis indicated that iron accumulated in this plant mainly as jarosite and ferritin. The presence of jarosite was confirmed by XRD and the distribution of both minerals in structures of different tissues was ascertained by SEM-EDAX analysis. * The convergent results obtained by complementary techniques suggest a complex iron management system in I. cylindrica, probably as a consequence of the environmental conditions of its habitat.

LC-MS n Analysis of Isomeric Chondroitin Sulfate Oligosaccharides Using a Chemical Derivatization Strategy

NASA Astrophysics Data System (ADS)

Huang, Rongrong; Pomin, Vitor H.; Sharp, Joshua S.

2011-09-01

Improved methods for structural analyses of glycosaminoglycans (GAGs) are required to understand their functional roles in various biological processes. Major challenges in structural characterization of complex GAG oligosaccharides using liquid chromatography-mass spectrometry (LC-MS) include the accurate determination of the patterns of sulfation due to gas-phase losses of the sulfate groups upon collisional activation and inefficient on-line separation of positional sulfation isomers prior to MS/MS analyses. Here, a sequential chemical derivatization procedure including permethylation, desulfation, and acetylation was demonstrated to enable both on-line LC separation of isomeric mixtures of chondroitin sulfate (CS) oligosaccharides and accurate determination of sites of sulfation by MS n . The derivatized oligosaccharides have sulfate groups replaced with acetyl groups, which are sufficiently stable to survive MS n fragmentation and reflect the original sulfation patterns. A standard reversed-phase LC-MS system with a capillary C18 column was used for separation, and MS n experiments using collision-induced dissociation (CID) were performed. Our results indicate that the combination of this derivatization strategy and MS n methodology enables accurate identification of the sulfation isomers of CS hexasaccharides with either saturated or unsaturated nonreducing ends. Moreover, derivatized CS hexasaccharide isomer mixtures become separable by LC-MS method due to different positions of acetyl modifications.

Factors that Affect Mathematics-Science (MS) Scores in the Secondary Education Institutional Exam: An Application of Structural Equation Modeling

ERIC Educational Resources Information Center

Yavuz, Mustafa

2009-01-01

Discovering what determines students' success in the Secondary Education Institutional Exam is very important to parents and it is also critical for students, teachers, directors, and researchers. Research was carried out by studying the related literature and structural equation modeling techniques. A structural model was created that consisted…

Structural analysis and profiling of phenolic secondary metabolites of Mexican lupine species using LC-MS techniques.

PubMed

Wojakowska, Anna; Piasecka, Anna; García-López, Pedro M; Zamora-Natera, Francisco; Krajewski, Paweł; Marczak, Łukasz; Kachlicki, Piotr; Stobiecki, Maciej

2013-08-01

Flavonoid glycoconjugates from roots and leaves of eight North America lupine species (Lupinus elegans, Lupinus exaltatus, Lupinus hintonii, Lupinus mexicanus, Lupinus montanus, Lupinus rotundiflorus, Lupinus stipulatus, Lupinus sp.), three Mediterranean species (Lupinus albus, Lupinus angustifolius, Lupinus luteus) and one species from South America domesticated in Europe (Lupinus mutabilis) were analyzed using two LC/MS systems: low-resolution ion trap instrument and high-resolution quadrupole-time-of-flight spectrometer. As a result of the LC/MS profiling using the CID/MS(n) experiments structures of 175 flavonoid glycoconjugates found in 12 lupine species were identified at three confidence levels according to the Metabolomic Standard Initiative, mainly at level 2 and 3, some of them were classified to the level 1. Among the flavonoid derivatives recognized in the plant extracts were isomeric or isobaric compounds, differing in the degree of hydroxylation of the aglycones and the presence of glycosidic, acyl or alkyl groups in the molecules. The elemental composition of the glycoconjugate molecules was established from the exact m/z values of the protonated/deprotonated molecules ([M+H](+)/[M-H](-)) measured with the accuracy better than 5 ppm. Information concerning structures of the aglycones, the type of sugar moieties (hexose, deoxyhexose or pentose) and, in some cases, their placement on the aglycones as well as the acyl substituents of the flavonoid glycoconjugates was achieved in experiments, in which collision-induced dissociation was applied. Flavonoid aglycones present in the studied O-glycoconjugates were unambiguously identified after the comparison of the pseudo-MS(3) spectra with the spectra registered for the standards. Isomers of flavonoid glycoconjugates, in which one or two sugar moieties were attached to 4'- or 7-hydroxyl groups or directly to the C-6 or C-8 of the aglycones, could be distinguished on the basis of the MS(2) spectra. However, the collision energy applied in the CID experiments had to be optimized for each group of the compounds and there were no universal settings that allowed the acquisition of structural information for all the compounds present in the sample. Information obtained from the flavonoid conjugate profiling was used for the chemotaxonomic comparison of the studied lupine species. A clear-cut discrimination of the Mediterranean and North American lupines was obtained as a result of this analysis. Copyright © 2013 Elsevier Ltd. All rights reserved.

Probing structures of large protein complexes using zero-length cross-linking.

PubMed

Rivera-Santiago, Roland F; Sriswasdi, Sira; Harper, Sandra L; Speicher, David W

2015-11-01

Structural mass spectrometry (MS) is a field with growing applicability for addressing complex biophysical questions regarding proteins and protein complexes. One of the major structural MS approaches involves the use of chemical cross-linking coupled with MS analysis (CX-MS) to identify proximal sites within macromolecules. Identified cross-linked sites can be used to probe novel protein-protein interactions or the derived distance constraints can be used to verify and refine molecular models. This review focuses on recent advances of "zero-length" cross-linking. Zero-length cross-linking reagents do not add any atoms to the cross-linked species due to the lack of a spacer arm. This provides a major advantage in the form of providing more precise distance constraints as the cross-linkable groups must be within salt bridge distances in order to react. However, identification of cross-linked peptides using these reagents presents unique challenges. We discuss recent efforts by our group to minimize these challenges by using multiple cycles of LC-MS/MS analysis and software specifically developed and optimized for identification of zero-length cross-linked peptides. Representative data utilizing our current protocol are presented and discussed. Copyright © 2015 Elsevier Inc. All rights reserved.

[Facial emotion recognition, theory of mind and empathy in multiple sclerosis].

PubMed

Ayache, Samar S; Chalah, Moussa A; Kuempfel, Tania; Padberg, Frank; Lefaucheur, Jean-Pascal; Palm, Ulrich

2017-11-01

Multiple sclerosis (MS), a chronic progressive inflammatory disease of the central nervous system, causes frequent disability, mood disorders, fatigue, and cognitive dysfunction. As a part of the last, social cognition is frequently disturbed in MS patients. It comprises empathy and social perception of emotions from facial, bodily and vocal cues. Social cognitive deficits worsen affect decoding, interpersonal relationship, and quality of life. Despite the impact of these deficits on global functioning, only a small number of studies have investigated its correlations and overlaps with MS symptoms. This review focuses on the definition and anatomy of social cognition and draws attention to findings of neuropsychological and neuroimaging studies on social cognitive performance in MS.Results of the available studies show that social cognitive deficits are already measurable in early stages of MS. Over time course of the disease, neuropsychological and neuroimaging studies show an increase of disease burden and social and non-social cognitive impairment following the hypothesis of a disconnection syndrome resulting from gray and white matters lesions. These structural changes might exceed a threshold of compensatory restorative and neuroplasticity mechanisms and finally lead to deficits in social cognition. Considering this burden in social functioning, a further assessment of sociocognitive deficits in MS is urgently needed to provide specific therapeutic approaches and to improve quality of life. Georg Thieme Verlag KG Stuttgart · New York.

MICELLAR ELECTROKINETIC CHROMATOGRAPHY-MASS SPECTROMETRY (R823292)

EPA Science Inventory

The combination of micellar electrokinetic chromatography (MEKC) with mass spectrometry (MS) is very attractive for the direct identification of analyte molecules, for the possibility of selectivity enhancement, and for the structure confirmation and analysis in a MS-MS mode. The...

Structural and biochemical changes induced by pulsed electric field treatments on Cabernet Sauvignon grape berry skins: impact on cell wall total tannins and polysaccharides.

PubMed

Cholet, Céline; Delsart, Cristèle; Petrel, Mélina; Gontier, Etienne; Grimi, Nabil; L'hyvernay, Annie; Ghidossi, Remy; Vorobiev, Eugène; Mietton-Peuchot, Martine; Gény, Laurence

2014-04-02

Pulsed electric field (PEF) treatment is an emerging technology that is arousing increasing interest in vinification processes for its ability to enhance polyphenol extraction performance. The aim of this study was to investigate the effects of PEF treatment on grape skin histocytological structures and on the organization of skin cell wall polysaccharides and tannins, which, until now, have been little investigated. This study relates to the effects of two PEF treatments on harvested Cabernet Sauvignon berries: PEF1 (medium strength (4 kV/cm); short duration (1 ms)) and PEF2 (low intensity (0.7 kV/cm); longer duration (200 ms)). Histocytological observations and the study of levels of polysaccharidic fractions and total amounts of tannins allowed differentiation between the two treatments. Whereas PEF1 had little effect on the polyphenol structure and pectic fraction, PEF2 profoundly modified the organization of skin cell walls. Depending on the PEF parameters, cell wall structure was differently affected, providing variable performance in terms of polyphenol extraction and wine quality.

The study of dynamic force acted on water strider leg departing from water surface

NASA Astrophysics Data System (ADS)

Sun, Peiyuan; Zhao, Meirong; Jiang, Jile; Zheng, Yelong

2018-01-01

Water-walking insects such as water striders can skate on the water surface easily with the help of the hierarchical structure on legs. Numerous theoretical and experimental studies show that the hierarchical structure would help water strider in quasi-static case such as load-bearing capacity. However, the advantage of the hierarchical structure in the dynamic stage has not been reported yet. In this paper, the function of super hydrophobicity and the hierarchical structure was investigated by measuring the adhesion force of legs departing from the water surface at different lifting speed by a dynamic force sensor. The results show that the adhesion force decreased with the increase of lifting speed from 0.02 m/s to 0.4 m/s, whose mechanic is investigated by Energy analysis. In addition, it can be found that the needle shape setae on water strider leg can help them depart from water surface easily. Thus, it can serve as a starting point to understand how the hierarchical structure on the legs help water-walking insects to jump upward rapidly to avoid preying by other insects.

[Comparison of chemical composition between fresh and processed Bufonis Venenum by UPLC-TQ-MS].

PubMed

Wang, Zi-yue; Wang, Hong-lan; Zhou, Jing; Ma, Hong-yue; Gong, Yan; Yan, Wen-li; Qian, Da-wei

2015-10-01

Toad venom is the Bufo bufo gargarizans or B. melanostictus after the ears of the gland secretion, used in the treatment of various cancers in recent years. Research shows that the main anti-tumor components in bufadienolide. Bufadienolide have free type structure and conjunct type structure. To identify and clarify the difference between bufogenin and bufotoxin contained in Bufonis Venenum, which was from B. bufo gargarizans, an UPLC-TQ-MS method has been established. UPLC-TQ-MS method was used to identify and quantify the major bufadienolides in Bufonis Venenum. UPLC-TQ-MS assay with positive ion mode was performed on a Waters ACQUITY UPLC BEH C, (2.1 mm x 100 mm, 1.7 µm) with the mobile phase consisting of 0. 1% aqueous formic and acidacetonitrile in gradient elution at a flow rate of 0.4 mL · min⁻¹ and the column temperature was set at 35 °C. By comparing their retention time and high resolution mass data of Bufonis Venenum extracts, 37 effective components were primarily identified by MS/MS analysis in positive ion mode. Twenty-six of them were free-type bufadienolides (bufogenin), 11 of them were conjugated bufadienolides. There were significant differences in the main composition between fresh and processed Bufonis Venenum. The study found that the chemical composition of toad venom through great changes after processing, conjunct type content is much less, free type content as well change.

Liquid chromatography with high resolution mass spectrometry for identification of organic contaminants in fish fillet: screening and quantification assessment using two scan modes for data acquisition.

PubMed

Munaretto, Juliana S; May, Marília M; Saibt, Nathália; Zanella, Renato

2016-07-22

This study proposed a strategy to identify and quantify 182 organic contaminants from different chemical classes, as for instance pesticides, veterinary drug and personal care products, in fish fillet using liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (LC-QToF/MS). For this purpose, two different scan methods (full scan and all ions MS/MS) were evaluated to assess the best option for screening analysis in spiked fish fillet samples. In general, full scan acquisition was found to be more reliable (84%) in the automatic identification and quantification when compared to all ions MS/MS with 72% of the compounds detected. Additionally, a qualitative automatic search showed a mass accuracy error below 5ppm for 77% of the compounds in full scan mode compared to only 52% in all ions MS/MS scan. However, all ions MS/MS provides fragmentation information of the target compounds. Undoubtedly, structural information of a wide number of compounds can be obtained using high resolution mass spectrometry (HRMS), but it is necessary thoroughly assess it, in order to choose the best scan mode. Copyright © 2016 Elsevier B.V. All rights reserved.

Structural and functional diversity in Listeria cell wall teichoic acids.

PubMed

Shen, Yang; Boulos, Samy; Sumrall, Eric; Gerber, Benjamin; Julian-Rodero, Alicia; Eugster, Marcel R; Fieseler, Lars; Nyström, Laura; Ebert, Marc-Olivier; Loessner, Martin J

2017-10-27

Wall teichoic acids (WTAs) are the most abundant glycopolymers found on the cell wall of many Gram-positive bacteria, whose diverse surface structures play key roles in multiple biological processes. Despite recent technological advances in glycan analysis, structural elucidation of WTAs remains challenging due to their complex nature. Here, we employed a combination of ultra-performance liquid chromatography-coupled electrospray ionization tandem-MS/MS and NMR to determine the structural complexity of WTAs from Listeria species. We unveiled more than 10 different types of WTA polymers that vary in their linkage and repeating units. Disparity in GlcNAc to ribitol connectivity, as well as variable O -acetylation and glycosylation of GlcNAc contribute to the structural diversity of WTAs. Notably, SPR analysis indicated that constitution of WTA determines the recognition by bacteriophage endolysins. Collectively, these findings provide detailed insight into Listeria cell wall-associated carbohydrates, and will guide further studies on the structure-function relationship of WTAs. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Evaluation of the effects of tricaine methanesulfonate on retinal structure and function in koi carp (Cyprinus carpio).

PubMed

Bailey, Kate M; Hempstead, Julie E; Tobias, Jeremy R; Borst, Luke B; Clode, Alison B; Posner, Lysa P

2013-06-01

To determine whether repeated exposure to clinically relevant concentrations of tricaine methanesulfonate (MS-222) would alter retinal function or induce histologically detectable retinal lesions in koi carp (Cyprinus carpio). Prospective, controlled, experimental study. 18 healthy koi carp. 2 fish were euthanized at the start of the study, and eyes were submitted for histologic evaluation as untreated controls. Anesthesia was induced in the remaining fish with 200 mg of MS-222/L and maintained with concentrations of 125 to 150 mg/L for a total exposure time of 20 minutes daily on 1 to 13 consecutive days. On days 1, 7, and 13, electroretinography of both eyes was performed in all fish remaining in the study, and 2 fish were euthanized immediately after each procedure for histologic evaluation of the eyes. Median b-wave amplitudes were compared among study days for right eyes and for left eyes via 1-way repeated-measures ANOVA with a Bonferroni correction for multiple comparisons. Median b-wave amplitudes on days 1, 7, and 13 were 17.7, 20.9, and 17.6 μV, respectively, for right eyes and 15.1, 16.9, and 14.3 μV, respectively, for left eyes. No significant differences in b-wave amplitudes were detected among study days. No histopathologic abnormalities were identified in the retinas of any fish treated with MS-222 or in control fish. Short-term exposure of koi carp to clinically relevant concentrations of MS-222 daily for up to 13 days was not associated with changes in retinal structure or function as measured in this study.

Strategies for dereplication of natural compounds using high-resolution tandem mass spectrometry.

PubMed

Kind, Tobias; Fiehn, Oliver

2017-09-01

Complete structural elucidation of natural products is commonly performed by nuclear magnetic resonance spectroscopy (NMR), but annotating compounds to most likely structures using high-resolution tandem mass spectrometry is a faster and feasible first step. The CASMI contest 2016 (Critical Assessment of Small Molecule Identification) provided spectra of eighteen compounds for the best manual structure identification in the natural products category. High resolution precursor and tandem mass spectra (MS/MS) were available to characterize the compounds. We used the Seven Golden Rules, Sirius2 and MS-FINDER software for determination of molecular formulas, and then we queried the formulas in different natural product databases including DNP, UNPD, ChemSpider and REAXYS to obtain molecular structures. We used different in-silico fragmentation tools including CFM-ID, CSI:FingerID and MS-FINDER to rank these compounds. Additional neutral losses and product ion peaks were manually investigated. This manual and time consuming approach allowed for the correct dereplication of thirteen of the eighteen natural products.

Structural Mass Spectrometry of Proteins Using Hydroxyl Radical Based Protein Footprinting

PubMed Central

Wang, Liwen; Chance, Mark R.

2011-01-01

Structural MS is a rapidly growing field with many applications in basic research and pharmaceutical drug development. In this feature article the overall technology is described and several examples of how hydroxyl radical based footprinting MS can be used to map interfaces, evaluate protein structure, and identify ligand dependent conformational changes in proteins are described. PMID:21770468

Seven perspectives on GPCR H/D-exchange proteomics methods

PubMed Central

Zhang, Xi

2017-01-01

Recent research shows surging interest to visualize human G protein-coupled receptor (GPCR) dynamic structures using the bottom-up H/D-exchange (HDX) proteomics technology. This opinion article clarifies critical technical nuances and logical thinking behind the GPCR HDX proteomics method, to help scientists overcome cross-discipline pitfalls, and understand and reproduce the protocol at high quality. The 2010 89% HDX structural coverage of GPCR was achieved with both structural and analytical rigor. This article emphasizes systematically considering membrane protein structure stability and compatibility with chromatography and mass spectrometry (MS) throughout the pipeline, including the effects of metal ions, zero-detergent shock, and freeze-thaws on HDX result rigor. This article proposes to view bottom-up HDX as two steps to guide choices of detergent buffers and chromatography settings: (I) protein HDX labeling in native buffers, and (II) peptide-centric analysis of HDX labels, which applies (a) bottom-up MS/MS to construct peptide matrix and (b) HDX MS to locate and quantify H/D labels. The detergent-low-TCEP digestion method demystified the challenge of HDX-grade GPCR digestion. GPCR HDX proteomics is a structural approach, thus its choice of experimental conditions should let structure lead and digestion follow, not the opposite. PMID:28529698

Structure elucidation and in vitro cytotoxicity of ochratoxin α amide, a new degradation product of ochratoxin A.

PubMed

Bittner, Andrea; Cramer, Benedikt; Harrer, Henning; Humpf, Hans-Ulrich

2015-05-01

The mycotoxin ochratoxin A is a secondary metabolite occurring in a wide range of commodities. During the exposure of ochratoxin A to white and blue light, a cleavage between the carbon atom C-14 and the nitrogen atom was described. As a reaction product, the new compound ochratoxin α amide has been proposed based on mass spectrometry (MS) experiments. In the following study, we observed that this compound is also formed at high temperatures such as used for example during coffee roasting and therefore represents a further thermal ochratoxin A degradation product. To confirm the structure of ochratoxin α amide, the compound was prepared in large scale and complete structure elucidation via nuclear magnetic resonance (NMR) and MS was performed. Additionally, first studies on the toxicity of ochratoxin α amide were performed using immortalized human kidney epithelial (IHKE) cells, a cell line known to be sensitive against ochratoxin A with an IC50 value of 0.5 μM. Using this system, ochratoxin α amide revealed no cytotoxicity up to concentrations of 50 μM. Thus, these results propose that the thermal degradation of ochratoxin A to ochratoxin α amide might be a detoxification process. Finally, we present a sample preparation and a HPLC-tandem mass spectrometry (HPLC-MS/MS) method for the analysis of ochratoxin α amide in extrudates and checked its formation during the extrusion of artificially contaminated wheat grits at 150 and 180 °C, whereas no ochratoxin α amide was detectable under these conditions.

Zwitterionic-hydrophilic interaction capillary liquid chromatography coupled to tandem mass spectrometry for the characterization of human alpha-acid-glycoprotein N-glycan isomers.

PubMed

Mancera-Arteu, Montserrat; Giménez, Estela; Barbosa, José; Peracaula, Rosa; Sanz-Nebot, Victòria

2017-10-23

In this work, a μZIC-HILIC-MS/MS methodology was established in negative ion mode for the characterization of glycan isomers. The possibility to separate the glycan isomers by the μZIC-HILIC strategy coupled to a high resolution tandem mass spectrometry detection permitted us to obtain valuable information about each glycan structure. The most important diagnostic ion fragments previously described to characterize structural features of glycans, were evaluated in this study using hAGP as model glycoprotein. The assignation of hAGP glycan isomers performed in our previous work using the GRIL strategy in combination with exoglycosidase digestion [1] was used in this paper to confirm or discard some ion fragments reported in the literature and delve into the structural characterization of glycan isomers. Sialic acid as well as fucose linkage-type glycan isomers were assigned using this approach and daughter ions with higher diagnostic value were determined. The location of α2-3/α2-6 sialic acids on antennas and a deeper characterization of several highly sialylated tri- and tetraantennary glycans was also possible using the established MS/MS method. Moreover, relying on the characterization performed in Ref. [1], core and antenna fucosylation were differentiated in this work using specific ion fragments obtained in the tandem mass spectra. This methodology was also applied to hAGP purified from control and pathological serum samples, which corroborated its robustness and its potential for finding novel glycan-based biomarkers in patho-glycomic studies. Copyright © 2017 Elsevier B.V. All rights reserved.

Application of ion mobility-mass spectrometry to microRNA analysis.

PubMed

Takebayashi, Kosuke; Hirose, Kenji; Izumi, Yoshihiro; Bamba, Takeshi; Fukusaki, Eiichiro

2013-03-01

Liquid chromatography/mass spectrometry is widely used for studying sequence determination and modification analysis of small RNAs. However, the efficiency of liquid chromatography-based separation of intact small RNA species is insufficient, since the physiochemical properties among small RNAs are very similar. In this study, we focused on ion mobility-mass spectrometry (IM-MS), which is a gas-phase separation technique coupled with mass spectrometry; we have evaluated the utility of IM-MS for microRNA (miRNA) analysis. A multiply charged deprotonated ion derived from an 18-24-nt-long miRNA was formed by electrospray ionization, and then the time, called the "drift time", taken by each ion to migrate through a buffer gas was measured. Each multivalent ion was temporally separated on the basis of the charge state and structural formation; 3 types of unique mass-mobility correlation patterns (i.e., chainlike-form, hairpin-form, and dimer-form) were present on the two-dimensional mobility-mass spectrum. Moreover, we found that the ion size (sequence length) and the secondary structures of the small RNAs strongly contributed to the IM-MS-based separation, although solvent conditions such as pH had no effect. Therefore, sequence isomers could also be discerned by the selection of each specific charged ion, i.e., the 6(-) charged ion reflected a majority among chainlike-, hairpin-, and other structures. We concluded that the IM-MS provides additional capability for separation; thus, this analytical method will be a powerful tool for comprehensive small RNA analysis. Copyright © 2012. Published by Elsevier B.V.

Target-guided separation of Bougainvillea glabra betacyanins by direct coupling of preparative ion-pair high-speed countercurrent chromatography and electrospray ionization mass-spectrometry.

PubMed

Jerz, Gerold; Wybraniec, Sławomir; Gebers, Nadine; Winterhalter, Peter

2010-07-02

In this study, preparative ion-pair high-speed countercurrent chromatography was directly coupled to an electrospray ionization mass-spectrometry device (IP-HSCCC/ESI-MS-MS) for target-guided fractionation of high molecular weight acyl-oligosaccharide linked betacyanins from purple bracts of Bougainvillea glabra (Nyctaginaceae). The direct identification of six principal acyl-oligosaccharide linked betacyanins in the mass range between m/z 859 and m/z 1359 was achieved by positive ESI-MS ionization and gave access to the genuine pigment profile already during the proceeding of the preparative separation. Inclusively, all MS/MS-fragmentation data were provided during the chromatographic run for a complete analysis of substitution pattern. On-line purity evaluation of the recovered fractions is of high value in target-guided screening procedures and for immediate decisions about suitable fractions used for further structural analysis. The applied preparative hyphenation was shown to be a versatile screening method for on-line monitoring of countercurrent chromatographic separations of polar crude pigment extracts and also traced some minor concentrated compounds. For the separation of 760mg crude pigment extract the biphasic solvent system tert.-butylmethylether/n-butanol/acetonitrile/water 2:2:1:5 (v/v/v/v) was used with addition of ion-pair forming reagent trifluoroacetic acid. The preparative HSCCC-eluate had to be modified by post-column addition of a make-up solvent stream containing formic acid to reduce ion-suppression caused by trifluoroacetic acid and later significantly maximized response of ESI-MS/MS detection of target substances. A variable low-pressure split-unit guided a micro-eluate to the ESI-MS-interface for sensitive and direct on-line detection, and the major volume of the effluent stream was directed to the fraction collector for preparative sample recovery. The applied make-up solvent mixture significantly improved smoothness of the continuously measured IP-HSCCC-ESI-MS base peak ion trace in the experimental range of m/z 50-2200 by masking stationary phase bleeding and generating a stable single solvent phase for ESI-MS/MS detection. Immediate structural data were retrieved throughout the countercurrent chromatography run containing complete MS/MS-fragmentation pattern of the separated acyl-substituted betanidin oligoglycosides. Single ion monitoring indicated clearly the base-line separation of higher concentrated acylated betacyanin components. Copyright 2010 Elsevier B.V. All rights reserved.

Headache: an important factor associated with muscle soreness/pain at the two-year follow-up point among patients with major depressive disorder.

PubMed

Hung, Ching-I; Liu, Chia-Yih; Yang, Ching-Hui; Wang, Shuu-Jiun

2016-01-01

No study has compared the associations of headache, anxiety, and depression at baseline with muscle soreness or pain (MS/P) at baseline and at the two-year follow-up point among outpatients with major depressive disorder (MDD). This study aimed to investigate the above issue. This study enrolled 155 outpatients with MDD at baseline, and 131 attended a two-year follow-up appointment. At baseline, migraine was diagnosed based on the International Classification of Headache Disorders, 2(nd) edition. MDD and anxiety disorders were diagnosed using the Structured Clinical Interview for DSM-IV-TR. The visual analog scale was used to evaluate the intensities of headache and MS/P in the neck, shoulder, back, upper limbs, and lower limbs. Depression and anxiety were evaluated using the Hospital Anxiety and Depression Scale. Multiple linear regressions were used to compare the associations of these factors with MS/P. Compared with anxiety disorders, migraine was more strongly associated with MS/P in all areas at baseline and in the upper and lower limbs at follow-up. Headache intensity at baseline was the factor most strongly associated with MS/P in all areas at baseline and follow-up after controlling for depression and anxiety. Headache intensity at baseline predicted MS/P at baseline and follow-up. Migraine and headache intensity are important factors related to MS/P at baseline and follow-up among patients with MDD. Integrating depression and headache treatment might be indicated to improve MS/P.

Testing isotopic labeling with [¹³C₆]glucose as a method of advanced glycation sites identification.

PubMed

Kielmas, Martyna; Kijewska, Monika; Stefanowicz, Piotr; Szewczuk, Zbigniew

2012-12-01

The Maillard reaction occurring between reducing sugars and reactive amino groups of biomolecules leads to the formation of a heterogeneous mixture of compounds: early, intermediate, and advanced glycation end products (AGEs). These compounds could be markers of certain diseases and of the premature aging process. Detection of Amadori products can be performed by various methods, including MS/MS techniques and affinity chromatography on immobilized boronic acid. However, the diversity of the structures of AGEs makes detection of these compounds more difficult. The aim of this study was to test a new method of AGE identification based on isotope (13)C labeling. The model protein (hen egg lysozyme) was modified with an equimolar mixture of [(12)C(6)]glucose and [(13)C(6)]glucose and then subjected to reduction of the disulfide bridges followed by tryptic hydrolysis. The digest obtained was analyzed by LC-MS. The glycation products were identified on the basis of characteristic isotopic patterns resulting from the use of isotopically labeled glucose. This method allowed identification of 38 early Maillard reaction products and five different structures of the end glycation products. This isotopic labeling technique combined with LC-MS is a sensitive method for identification of advanced glycation end products even if their chemical structure is unknown. Copyright © 2012 Elsevier Inc. All rights reserved.

Ultra(high)-pressure liquid chromatography-electrospray ionization-time-of-flight-ion mobility-high definition mass spectrometry for the rapid identification and structural characterization of flavonoid glycosides from cauliflower waste.

PubMed

Gonzales, Gerard Bryan; Raes, Katleen; Coelus, Sofie; Struijs, Karin; Smagghe, Guy; Van Camp, John

2014-01-03

In this paper, a strategy for the detection and structural elucidation of flavonoid glycosides from a complex matrix in a single chromatographic run using U(H)PLC-ESI-IMS-HDMS/MS(E) is presented. This system operates using alternative low and high energy voltages that is able to perform the task of conventional MS/MS in a data-independent way without re-injection of the sample, which saves analytical time. Also, ion mobility separation (IMS) was employed as an additional separation technique for compounds that are co-eluting after U(H)PLC separation. First, the fragmentation of flavonoid standards were analyzed and criteria was set for structural elucidation of flavonoids in a plant extract. Based on retention times, UV spectra, exact mass, and MS fragment characteristics, such as abundances of daughter ions and the presence of radical ions ([Y0-H](-)), a total 19 flavonoid glycosides, of which 8 non-acylated and 11 acylated, were detected and structurally characterized in a cauliflower waste extract. Kaempferol and quercetin were the main aglycones detected while sinapic and ferulic acid were the main phenolic acids. C-glycosides were also found although their structure could not be elucidated. The proposed method can be used as a rapid screening test for flavonoid identification and for routine analysis of plant extracts, such as these derived from cauliflower waste. The study also confirms that agroindustrial wastes, such as cauliflower leaves, could be seen as a valuable source of different bioactive phenolic compounds. Copyright © 2013 Elsevier B.V. All rights reserved.

Distance geometry protocol to generate conformations of natural products to structurally interpret ion mobility-mass spectrometry collision cross sections.

PubMed

Stow, Sarah M; Goodwin, Cody R; Kliman, Michal; Bachmann, Brian O; McLean, John A; Lybrand, Terry P

2014-12-04

Ion mobility-mass spectrometry (IM-MS) allows the separation of ionized molecules based on their charge-to-surface area (IM) and mass-to-charge ratio (MS), respectively. The IM drift time data that is obtained is used to calculate the ion-neutral collision cross section (CCS) of the ionized molecule with the neutral drift gas, which is directly related to the ion conformation and hence molecular size and shape. Studying the conformational landscape of these ionized molecules computationally provides interpretation to delineate the potential structures that these CCS values could represent, or conversely, structural motifs not consistent with the IM data. A challenge in the IM-MS community is the ability to rapidly compute conformations to interpret natural product data, a class of molecules exhibiting a broad range of biological activity. The diversity of biological activity is, in part, related to the unique structural characteristics often observed for natural products. Contemporary approaches to structurally interpret IM-MS data for peptides and proteins typically utilize molecular dynamics (MD) simulations to sample conformational space. However, MD calculations are computationally expensive, they require a force field that accurately describes the molecule of interest, and there is no simple metric that indicates when sufficient conformational sampling has been achieved. Distance geometry is a computationally inexpensive approach that creates conformations based on sampling different pairwise distances between the atoms within the molecule and therefore does not require a force field. Progressively larger distance bounds can be used in distance geometry calculations, providing in principle a strategy to assess when all plausible conformations have been sampled. Our results suggest that distance geometry is a computationally efficient and potentially superior strategy for conformational analysis of natural products to interpret gas-phase CCS data.

Toward a suitable structural analysis of gene delivery carrier based on polycationic carbohydrates by electron transfer dissociation tandem mass spectrometry.

PubMed

Przybylski, Cédric; Benito, Juan M; Bonnet, Véronique; Mellet, Carmen Ortiz; García Fernández, José M

2016-12-15

Polycationic carbohydrates represent an attractive class of biomolecules for several applications and particularly as non viral gene delivery vectors. In this case, the establishment of structure-biological activity relationship requires sensitive and accurate characterization tools to both control and achieve fine structural deciphering. Electrospray-tandem mass spectrometry (ESI-MS/MS) appears as a suitable approach to address these questions. In the study herein, we have investigated the usefulness of electron transfer dissociation (ETD) to get structural data about five polycationic carbohydrates demonstrated as promising gene delivery agents. A particular attention was paid to determine the influence of charge states as well as both fluoranthene reaction time and supplementary activation (SA) on production of charge reduced species, fragmentation yield, varying from 2 to 62%, as well as to obtain the most higher both diversity and intensity of fragments, according to charge states and targeted compounds. ETD fragmentation appeared to be mainly directed toward pending group rather than carbohydrate cyclic scaffold leading to a partial sequencing for building blocks when amino groups are close to carbohydrate core, but allowing to complete structural deciphering of some of them, such as those including dithioureidocysteaminyl group which was not possible with CID only. Such findings clearly highlight the potential to help the rational choice of the suitable analytical conditions, according to the nature of the gene delivery molecules exhibiting polycationic features. Moreover, our ETD-MS/MS approach open the way to a fine sequencing/identification of grafted groups carried on various sets of oligo-/polysaccharides in various fields such as glycobiology or nanomaterials, even with unknown or questionable extraction, synthesis or modification steps. Copyright © 2016 Elsevier B.V. All rights reserved.

Distance Geometry Protocol to Generate Conformations of Natural Products to Structurally Interpret Ion Mobility-Mass Spectrometry Collision Cross Sections

PubMed Central

2015-01-01

Ion mobility-mass spectrometry (IM-MS) allows the separation of ionized molecules based on their charge-to-surface area (IM) and mass-to-charge ratio (MS), respectively. The IM drift time data that is obtained is used to calculate the ion-neutral collision cross section (CCS) of the ionized molecule with the neutral drift gas, which is directly related to the ion conformation and hence molecular size and shape. Studying the conformational landscape of these ionized molecules computationally provides interpretation to delineate the potential structures that these CCS values could represent, or conversely, structural motifs not consistent with the IM data. A challenge in the IM-MS community is the ability to rapidly compute conformations to interpret natural product data, a class of molecules exhibiting a broad range of biological activity. The diversity of biological activity is, in part, related to the unique structural characteristics often observed for natural products. Contemporary approaches to structurally interpret IM-MS data for peptides and proteins typically utilize molecular dynamics (MD) simulations to sample conformational space. However, MD calculations are computationally expensive, they require a force field that accurately describes the molecule of interest, and there is no simple metric that indicates when sufficient conformational sampling has been achieved. Distance geometry is a computationally inexpensive approach that creates conformations based on sampling different pairwise distances between the atoms within the molecule and therefore does not require a force field. Progressively larger distance bounds can be used in distance geometry calculations, providing in principle a strategy to assess when all plausible conformations have been sampled. Our results suggest that distance geometry is a computationally efficient and potentially superior strategy for conformational analysis of natural products to interpret gas-phase CCS data. PMID:25360896

Comparing Laser Desorption Ionization and Atmospheric Pressure Photoionization Coupled to Fourier Transform Ion Cyclotron Resonance Mass Spectrometry To Characterize Shale Oils at the Molecular Level

USGS Publications Warehouse

Cho, Yunjo; Jin, Jang Mi; Witt, Matthias; Birdwell, Justin E.; Na, Jeong-Geol; Roh, Nam-Sun; Kim, Sunghwan

2013-01-01

Laser desorption ionization (LDI) coupled to Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) was used to analyze shale oils. Previous work showed that LDI is a sensitive ionization technique for assessing aromatic nitrogen compounds, and oils generated from Green River Formation oil shales are well-documented as being rich in nitrogen. The data presented here demonstrate that LDI is effective in ionizing high-double-bond-equivalent (DBE) compounds and, therefore, is a suitable method for characterizing compounds with condensed structures. Additionally, LDI generates radical cations and protonated ions concurrently, the distribution of which depends upon the molecular structures and elemental compositions, and the basicity of compounds is closely related to the generation of protonated ions. This study demonstrates that LDI FT-ICR MS is an effective ionization technique for use in the study of shale oils at the molecular level. To the best of our knowledge, this is the first time that LDI FT-ICR MS has been applied to shale oils.

Structural Characterization and Absolute Quantification of Microcystin Peptides Using Collision-Induced and Ultraviolet Photo-Dissociation Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Attard, Troy J.; Carter, Melissa D.; Fang, Mengxuan; Johnson, Rudolph C.; Reid, Gavin E.

2018-05-01

Microcystin (MC) peptides produced by cyanobacteria pose a hepatotoxic threat to human health upon ingestion from contaminated drinking water. While rapid MC identification and quantification in contaminated body fluids or tissue samples is important for patient treatment and outcomes, conventional immunoassay-based measurement strategies typically lack the specificity required for unambiguous determination of specific MC variants, whose toxicity can significantly vary depending on their structures. Furthermore, the unambiguous identification and accurate quantitation of MC variants using tandem mass spectrometry (MS/MS)-based methods can be limited due to a current lack of appropriate stable isotope-labeled internal standards. To address these limitations, we have systematically examined here the sequence and charge state dependence to the formation and absolute abundance of both "global" and "variant-specific" product ions from representative MC-LR, MC-YR, MC-RR, and MC-LA peptides, using higher-energy collisional dissociation (HCD)-MS/MS, ion-trap collision-induced dissociation (CID)-MS/MS and CID-MS3, and 193 nm ultraviolet photodissociation (UPVD)-MS/MS. HCD-MS/MS was found to provide the greatest detection sensitivity for both global and variant-specific product ions in each of the MC variants, except for MC-YR where a variant-specific product uniquely formed via UPVD-MS/MS was observed with the greatest absolute abundance. A simple methodology for the preparation and characterization of 18O-stable isotope-labeled MC reference materials for use as internal standards was also developed. Finally, we have demonstrated the applicability of the methods developed herein for absolute quantification of MC-LR present in human urine samples, using capillary scale liquid chromatography coupled with ultra-high resolution / accurate mass spectrometry and HCD-MS/MS.

Rapid qualitative and quantitative analysis of proanthocyanidin oligomers and polymers by UPLC-MS/MS

USDA-ARS?s Scientific Manuscript database

Proanthocyanidins (PAs) are a structurally complex and bioactive group of tannins. Detailed analysis of PA concentration, composition, and structure typically requires the use of one or more time-consuming analytical methods. For example, the commonly employed thiolysis and phloroglucinolysis method...

ANALYSIS OF GLYCANS DERIVED FROM GLYCOCONJUGATES BY CAPILLARY ELECTROPHORESIS-MASS SPECTROMETRY

PubMed Central

Mechref, Yehia

2012-01-01

The high structural variation of glycan derived from glycoconjugates, which substantially increases with the molecular size of a protein, contributes to the complexity of glycosylation patterns commonly associated with glycoconjugates. In the case of glycoproteins, such variation originates from the multiple glycosylation sites of proteins and the number of glycan structures associated with each site (microheterogeneity). The ability to comprehensively characterize highly complex mixture of glycans has been analytically stimulating and challenging. Although the most powerful mass spectrometric (MS) and tandem MS techniques are capable of providing a wealth of structural information, they are still not able to readily identify isomeric glycan structures without high order tandem MS (MSn). The analysis of isomeric glycan structures has been attained using several separation methods, including high-pH anion exchange chromatography (HPAEC), hydrophilic interaction chromatography (HILIC) and gas chromatography (GC). However, capillary electrophoresis (CE) and microfluidics capillary electrophoresis (MCE) offer high separation efficiency and resolutions, allowing the separation of closely related glycan structures. Therefore, interfacing CE and MCE to MS is a powerful analytical approach, allowing potentially comprehensive and sensitive analysis of complex glycan samples. This review describes and discusses the utility of different CE and MCE approaches in the structural characterization of glycoproteins and the feasibility of interfacing these approaches to mass spectrometry. PMID:22180203

Structure and function of seed storage proteins in faba bean (Vicia faba L.).

PubMed

Liu, Yujiao; Wu, Xuexia; Hou, Wanwei; Li, Ping; Sha, Weichao; Tian, Yingying

2017-05-01

The protein subunit is the most important basic unit of protein, and its study can unravel the structure and function of seed storage proteins in faba bean. In this study, we identified six specific protein subunits in Faba bean (cv. Qinghai 13) combining liquid chromatography (LC), liquid chromatography-electronic spray ionization mass (LC-ESI-MS/MS) and bio-information technology. The results suggested a diversity of seed storage proteins in faba bean, and a total of 16 proteins (four GroEL molecular chaperones and 12 plant-specific proteins) were identified from 97-, 96-, 64-, 47-, 42-, and 38-kD-specific protein subunits in faba bean based on the peptide sequence. We also analyzed the composition and abundance of the amino acids, the physicochemical characteristics, secondary structure, three-dimensional structure, transmembrane domain, and possible subcellular localization of these identified proteins in faba bean seed, and finally predicted function and structure. The three-dimensional structures were generated based on homologous modeling, and the protein function was analyzed based on the annotation from the non-redundant protein database (NR database, NCBI) and function analysis of optimal modeling. The objective of this study was to identify the seed storage proteins in faba bean and confirm the structure and function of these proteins. Our results can be useful for the study of protein nutrition and achieve breeding goals for optimal protein quality in faba bean.

Exploration of polyamide structure-property relationships by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

PubMed

Barrère, Caroline; Rejaibi, Majed; Curat, Aurélien; Hubert-Roux, Marie; Lavanant, Hélène; Afonso, Carlos; Kebir, Nasreddine; Desilles, Nicolas; Lecamp, Laurence; Burel, Fabrice; Loutelier-Bourhis, Corinne

2014-08-15

Polyamides (PA) are among the most used classes of polymers because of their attractive properties. Depending on the nature and proportion of the co-monomers used for their synthesis, they can exhibit a very large range of melting temperatures (Tm ). This study aims at the correlation of data from mass spectrometry (MS) with differential scanning calorimetry (DSC) and X-ray diffraction analyses to relate molecular structure to physical properties such as melting temperature, enthalpy change and crystallinity rate. Six different PA copolymers with molecular weights around 3500 g mol(-1) were synthesized with varying proportions of different co-monomers (amino-acid AB/di-amine AA/di-acid BB). Their melting temperature, enthalpy change and crystallinity rate were measured by DSC and X-ray diffraction. Their structural characterization was carried out by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Because of the poor solubility of PA, a solvent-free sample preparation strategy was used with 2,5-dihydroxybenzoic acid (2,5-DHB) as the matrix and sodium iodide as the cationizing agent. The different proportions of the repeating unit types led to the formation of PA with melting temperatures ranging from 115°C to 185°C. The structural characterization of these samples by MALDI-TOF-MS revealed a collection of different ion distributions with different sequences of repeating units (AA, BB; AB/AA, BB and AB) in different proportions according to the mixture of monomers used in the synthesis. The relative intensities of these ion distributions were related to sample complexity and structure. They were correlated to DSC and X-ray results, to explain the observed physical properties. The structural information obtained by MALDI-TOF-MS provided a better understanding of the variation of the PA melting temperature and established a structure-properties relationship. This work will allow future PA designs to be monitored. Copyright © 2014 John Wiley & Sons, Ltd.

Investigation of some biologically relevant redox reactions using electrochemical mass spectrometry interfaced by desorption electrospray ionization.

PubMed

Lu, Mei; Wolff, Chloe; Cui, Weidong; Chen, Hao

2012-04-01

Recently we have shown that, as a versatile ionization technique, desorption electrospray ionization (DESI) can serve as a useful interface to combine electrochemistry (EC) with mass spectrometry (MS). In this study, the EC/DESI-MS method has been further applied to investigate some aqueous phase redox reactions of biological significance, including the reduction of peptide disulfide bonds and nitroaromatics as well as the oxidation of phenothiazines. It was found that knotted/enclosed disulfide bonds in the peptides apamin and endothelin could be electrochemically cleaved. Subsequent tandem MS analysis of the resulting reduced peptide ions using collision-induced dissociation (CID) and electron-capture dissociation (ECD) gave rise to extensive fragment ions, providing a fast protocol for sequencing peptides with complicated disulfide bond linkages. Flunitrazepam and clonazepam, a class of nitroaromatic drugs, are known to undergo reduction into amines which was proposed to involve nitroso and N-hydroxyl intermediates. Now in this study, these corresponding intermediate ions were successfully intercepted and their structures were confirmed by CID. This provides mass spectrometric evidence for the mechanism of the nitro to amine conversion process during nitroreduction, an important redox reaction involved in carcinogenesis. In addition, the well-known oxidation reaction of chlorpromazine was also examined. The putative transient one-electron transfer product, the chlorpromazine radical cation (m/z 318), was captured by MS, for the first time, and its structure was also verified by CID. In addition to these observations, some features of the DESI-interfaced electrochemical mass spectrometry were discussed, such as simple instrumentation and the lack of background signal. These results further demonstrate the feasibility of EC/DESI-MS for the study of the biology-relevant redox chemistry and would find applications in proteomics and drug development research.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wojcik, Roza; Webb, Ian K.; Deng, Liulin

Understanding the biological mechanisms related to lipids and glycolipids is challenging due to the vast number of possible isomers. Mass spectrometry (MS) measurements are currently the dominant approach for studying and providing detailed information on lipid and glycolipid structures. However, difficulties in distinguishing many structural isomers (e.g. distinct acyl chain positions, double bond locations, as well as glycan isomers) inhibit the understanding of their biological roles. Here we utilized ultra-high resolution ion mobility spectrometry (IMS) separations based upon the use of traveling waves in a serpentine long path length multi-pass Structures for Lossless Manipulations (SLIM) to enhance isomer resolution. Themore » multi-pass arrangement allowed separations ranging from ~16 m (1 pass) to ~470 m (32 passes) to be investigated for the distinction of lipids and glycolipids with extremely small structural differences. Lastly, these ultra-high resolution SLIM IMS-MS analyses provide a foundation for exploring and better understanding isomer specific biological and disease processes.« less

Chemical cross-linking and native mass spectrometry: A fruitful combination for structural biology

PubMed Central

Sinz, Andrea; Arlt, Christian; Chorev, Dror; Sharon, Michal

2015-01-01

Mass spectrometry (MS) is becoming increasingly popular in the field of structural biology for analyzing protein three-dimensional-structures and for mapping protein–protein interactions. In this review, the specific contributions of chemical crosslinking and native MS are outlined to reveal the structural features of proteins and protein assemblies. Both strategies are illustrated based on the examples of the tetrameric tumor suppressor protein p53 and multisubunit vinculin-Arp2/3 hybrid complexes. We describe the distinct advantages and limitations of each technique and highlight synergistic effects when both techniques are combined. Integrating both methods is especially useful for characterizing large protein assemblies and for capturing transient interactions. We also point out the future directions we foresee for a combination of in vivo crosslinking and native MS for structural investigation of intact protein assemblies. PMID:25970732

Modal Frequency Detection in Composite Beams Using Fiber Optic Sensors

DTIC Science & Technology

1997-04-18

Structures 4, 270-280 (1995). [35] Chen-Jung Li and Ray Asok , "Neural Network Representation of Fatigue Damage Dynamics," Smart Materials and Structures 3...37] Roland Ray Kilcher, "Modal Analysis and Impact Damage Assessment of Composite Laminates: an Experimental Study," M.S. thesis, University of

Structural analysis of fructans from Agave americana grown in South Africa for spirit production.

PubMed

Ravenscroft, Neil; Cescutti, Paola; Hearshaw, Meredith A; Ramsout, Ronica; Rizzo, Roberto; Timme, Elizabeth M

2009-05-27

Fructans isolated from Agave americana grown in South Africa are currently used for spirit production. Structural studies on water-soluble fructans were performed to facilitate the development of other applications including its use as a prebiotic. Acid hydrolysis followed by HPAEC-PAD analysis confirmed that the fructan was composed of glucose and fructose, and size analysis by HPAEC-PAD and size exclusion chromatography indicated that the saccharides have a DP range from 6 to 50. An average DP of 14 was estimated by (1)H NMR analysis. Linkage analysis and ESI-MS studies suggest that A. americana has a neofructan structure consisting of a central sucrose to which (2 → 1)- and (2 → 6)-linked β-D-Fruf chains are attached. The (2 → 1)-linked units extend from C-1 of Fru and C-6 of glucose, whereas the (2 → 6)-linked β-D-Fruf units are attached to C-6 of the central Fru. This structure accounts for the presence of equimolar amounts of 1,6-linked Glu and 1,2,6-linked Fru found in linkage analysis and the multiplicity of the NMR signals observed. Detailed ESI-MS studies were performed on fructan fractions: native, periodate oxidized/reduced, and permethylated oligomers. These derivatizations introduced mass differences between Glc and Fru following oxidation and between 1,2-, 1,6-, 2,6-, and 1,2,6-linked units after methylation. Thus, ESI-MS showed the presence of a single Glc per fructan chain and that it is predominantly internal, rather than terminal as found in inulin. These structural features were confirmed by the use of 1D and 2D NMR experiments.

Design and development of an ethnically-diverse imaging informatics-based eFolder system for multiple sclerosis patients.

PubMed

Ma, Kevin C; Fernandez, James R; Amezcua, Lilyana; Lerner, Alex; Shiroishi, Mark S; Liu, Brent J

2015-12-01

MRI has been used to identify multiple sclerosis (MS) lesions in brain and spinal cord visually. Integrating patient information into an electronic patient record system has become key for modern patient care in medicine in recent years. Clinically, it is also necessary to track patients' progress in longitudinal studies, in order to provide comprehensive understanding of disease progression and response to treatment. As the amount of required data increases, there exists a need for an efficient systematic solution to store and analyze MS patient data, disease profiles, and disease tracking for both clinical and research purposes. An imaging informatics based system, called MS eFolder, has been developed as an integrated patient record system for data storage and analysis of MS patients. The eFolder system, with a DICOM-based database, includes a module for lesion contouring by radiologists, a MS lesion quantification tool to quantify MS lesion volume in 3D, brain parenchyma fraction analysis, and provide quantitative analysis and tracking of volume changes in longitudinal studies. Patient data, including MR images, have been collected retrospectively at University of Southern California Medical Center (USC) and Los Angeles County Hospital (LAC). The MS eFolder utilizes web-based components, such as browser-based graphical user interface (GUI) and web-based database. The eFolder database stores patient clinical data (demographics, MS disease history, family history, etc.), MR imaging-related data found in DICOM headers, and lesion quantification results. Lesion quantification results are derived from radiologists' contours on brain MRI studies and quantified into 3-dimensional volumes and locations. Quantified results of white matter lesions are integrated into a structured report based on DICOM-SR protocol and templates. The user interface displays patient clinical information, original MR images, and viewing structured reports of quantified results. The GUI also includes a data mining tool to handle unique search queries for MS. System workflow and dataflow steps has been designed based on the IHE post-processing workflow profile, including workflow process tracking, MS lesion contouring and quantification of MR images at a post-processing workstation, and storage of quantitative results as DICOM-SR in DICOM-based storage system. The web-based GUI is designed to display zero-footprint DICOM web-accessible data objects (WADO) and the SR objects. The MS eFolder system has been designed and developed as an integrated data storage and mining solution in both clinical and research environments, while providing unique features, such as quantitative lesion analysis and disease tracking over a longitudinal study. A comprehensive image and clinical data integrated database provided by MS eFolder provides a platform for treatment assessment, outcomes analysis and decision-support. The proposed system serves as a platform for future quantitative analysis derived automatically from CAD algorithms that can also be integrated within the system for individual disease tracking and future MS-related research. Ultimately the eFolder provides a decision-support infrastructure that can eventually be used as add-on value to the overall electronic medical record. Copyright © 2015 Elsevier Ltd. All rights reserved.

Design and development of an ethnically-diverse imaging informatics-based eFolder system for multiple sclerosis patients

PubMed Central

Ma, Kevin C.; Fernandez, James R.; Amezcua, Lilyana; Lerner, Alex; Shiroishi, Mark S.; Liu, Brent J.

2016-01-01

Purpose MRI has been used to identify multiple sclerosis (MS) lesions in brain and spinal cord visually. Integrating patient information into an electronic patient record system has become key for modern patient care in medicine in recent years. Clinically, it is also necessary to track patients' progress in longitudinal studies, in order to provide comprehensive understanding of disease progression and response to treatment. As the amount of required data increases, there exists a need for an efficient systematic solution to store and analyze MS patient data, disease profiles, and disease tracking for both clinical and research purposes. Method An imaging informatics based system, called MS eFolder, has been developed as an integrated patient record system for data storage and analysis of MS patients. The eFolder system, with a DICOM-based database, includes a module for lesion contouring by radiologists, a MS lesion quantification tool to quantify MS lesion volume in 3D, brain parenchyma fraction analysis, and provide quantitative analysis and tracking of volume changes in longitudinal studies. Patient data, including MR images, have been collected retrospectively at University of Southern California Medical Center (USC) and Los Angeles County Hospital (LAC). The MS eFolder utilizes web-based components, such as browser-based graphical user interface (GUI) and web-based database. The eFolder database stores patient clinical data (demographics, MS disease history, family history, etc.), MR imaging-related data found in DICOM headers, and lesion quantification results. Lesion quantification results are derived from radiologists' contours on brain MRI studies and quantified into 3-dimensional volumes and locations. Quantified results of white matter lesions are integrated into a structured report based on DICOM-SR protocol and templates. The user interface displays patient clinical information, original MR images, and viewing structured reports of quantified results. The GUI also includes a data mining tool to handle unique search queries for MS. System workflow and dataflow steps has been designed based on the IHE post-processing workflow profile, including workflow process tracking, MS lesion contouring and quantification of MR images at a post-processing workstation, and storage of quantitative results as DICOM-SR in DICOM-based storage system. The web-based GUI is designed to display zero-footprint DICOM web-accessible data objects (WADO) and the SR objects. Summary The MS eFolder system has been designed and developed as an integrated data storage and mining solution in both clinical and research environments, while providing unique features, such as quantitative lesion analysis and disease tracking over a longitudinal study. A comprehensive image and clinical data integrated database provided by MS eFolder provides a platform for treatment assessment, outcomes analysis and decision-support. The proposed system serves as a platform for future quantitative analysis derived automatically from CAD algorithms that can also be integrated within the system for individual disease tracking and future MS-related research. Ultimately the eFolder provides a decision-support infrastructure that can eventually be used as add-on value to the overall electronic medical record. PMID:26564667

A Review of the Status of Brain Structure Research in Transsexualism.

PubMed

Guillamon, Antonio; Junque, Carme; Gómez-Gil, Esther

2016-10-01

The present review focuses on the brain structure of male-to-female (MtF) and female-to-male (FtM) homosexual transsexuals before and after cross-sex hormone treatment as shown by in vivo neuroimaging techniques. Cortical thickness and diffusion tensor imaging studies suggest that the brain of MtFs presents complex mixtures of masculine, feminine, and demasculinized regions, while FtMs show feminine, masculine, and defeminized regions. Consequently, the specific brain phenotypes proposed for MtFs and FtMs differ from those of both heterosexual males and females. These phenotypes have theoretical implications for brain intersexuality, asymmetry, and body perception in transsexuals as well as for Blanchard's hypothesis on sexual orientation in homosexual MtFs. Falling within the aegis of the neurohormonal theory of sex differences, we hypothesize that cortical differences between homosexual MtFs and FtMs and male and female controls are due to differently timed cortical thinning in different regions for each group. Cross-sex hormone studies have reported marked effects of the treatment on MtF and FtM brains. Their results are used to discuss the early postmortem histological studies of the MtF brain.

Polymer architectures via mass spectrometry and hyphenated techniques: A review.

PubMed

Crotty, Sarah; Gerişlioğlu, Selim; Endres, Kevin J; Wesdemiotis, Chrys; Schubert, Ulrich S

2016-08-17

This review covers the application of mass spectrometry (MS) and its hyphenated techniques to synthetic polymers of varying architectural complexities. The synthetic polymers are discussed as according to their architectural complexity from linear homopolymers and copolymers to stars, dendrimers, cyclic copolymers and other polymers. MS and tandem MS (MS/MS) has been extensively used for the analysis of synthetic polymers. However, the increase in structural or architectural complexity can result in analytical challenges that MS or MS/MS cannot overcome alone. Hyphenation to MS with different chromatographic techniques (2D × LC, SEC, HPLC etc.), utilization of other ionization methods (APCI, DESI etc.) and various mass analyzers (FT-ICR, quadrupole, time-of-flight, ion trap etc.) are applied to overcome these challenges and achieve more detailed structural characterizations of complex polymeric systems. In addition, computational methods (software: MassChrom2D, COCONUT, 2D maps etc.) have also reached polymer science to facilitate and accelerate data interpretation. Developments in technology and the comprehension of different polymer classes with diverse architectures have significantly improved, which allow for smart polymer designs to be examined and advanced. We present specific examples covering diverse analytical aspects as well as forthcoming prospects in polymer science. Copyright © 2016 Elsevier B.V. All rights reserved.

[Rapid identification of two new isomers in bear bile powder by LC-Q-TOF-MS combined with PCC oxidation].

PubMed

Jian, Long-Hai; Hu, Chun; Yu, Hong; Wang, Ke; Ji, Shen

2013-07-01

A rapid method of Liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-Q-TOF-MS) combined with pyridinium chlorochromate (PCC) oxidation has been developed to determine chemical structures of two novel isomers in bear bile powder. Derivatives of ursodeoxycholic acid (UDCA) and chenodeoxycholic acid (CDCA) were semi-synthesized by PCC oxidation, then were analyzed by LC-Q-TOF-MS. Separation was carried out on a reverse column with the mobile phase of acetonitrile-0.1% formic acid (45:55). The data of Q-TOF-MS was acquired by MS, MS/MS, positive and negative modes. Since UDCA and CDCA were stereochemical isomeric at an alcohol position, two oxidation products were same and have been confirmed by LC-Q-TOF-MS. Other two products were also determined based on the PCC oxidation theory. Samples of bear bile powder were dissolved by methanol and measured by LC-Q-TOF-MS. Two unknown peaks were found and identified by matching their retention times and accurate mass spectra ions with PCC oxidation productS. Finally, the structures of two new bile acids in bear bile powder were confirmed as 3alpha-hydroxy-7-oxo-5beta-cholanic acid, 7alpha-hydroxy-3-oxo-5beta-cholanic acid, respectively.

Acoustic and elastic multiple scattering and radiation from cylindrical structures

NASA Astrophysics Data System (ADS)

Amirkulova, Feruza Abdukadirovna

Multiple scattering (MS) and radiation of waves by a system of scatterers is of great theoretical and practical importance and is required in a wide variety of physical contexts such as the implementation of "invisibility" cloaks, the effective parameter characterization, and the fabrication of dynamically tunable structures, etc. The dissertation develops fast, rapidly convergent iterative techniques to expedite the solution of MS problems. The formulation of MS problems reduces to a system of linear algebraic equations using Graf's theorem and separation of variables. The iterative techniques are developed using Neumann expansion and Block Toeplitz structure of the linear system; they are very general, and suitable for parallel computations and a large number of MS problems, i.e. acoustic, elastic, electromagnetic, etc., and used for the first time to solve MS problems. The theory is implemented in Matlab and FORTRAN, and the theoretical predictions are compared to computations obtained by COMSOL. To formulate the MS problem, the transition matrix is obtained by analyzing an acoustic and an elastic single scattering of incident waves by elastic isotropic and anisotropic solids. The mathematical model of wave scattering from multilayered cylindrical and spherical structures is developed by means of an exact solution of dynamic 3D elasticity theory. The recursive impedance matrix algorithm is derived for radially heterogeneous anisotropic solids. An explicit method for finding the impedance in piecewise uniform, transverse-isotropic material is proposed; the solution is compared to elasticity theory solutions involving Buchwald potentials. Furthermore, active exterior cloaking devices are modeled for acoustic and elastic media using multipole sources. A cloaking device can render an object invisible to some incident waves as seen by some external observer. The active cloak is generated by a discrete set of multipole sources that destructively interfere with an incident wave to produce zero total field over a finite spatial region. The approach precisely determines the necessary source amplitudes and enables a cloaked region to be determined using Graf's theorem. To apply the approach, the infinite series of multipole expansions are truncated, and the accuracy of cloaking is studied by modifying the truncation parameter.

Combinatorial Approach for Large-scale Identification of Linked Peptides from Tandem Mass Spectrometry Spectra*

PubMed Central

Wang, Jian; Anania, Veronica G.; Knott, Jeff; Rush, John; Lill, Jennie R.; Bourne, Philip E.; Bandeira, Nuno

2014-01-01

The combination of chemical cross-linking and mass spectrometry has recently been shown to constitute a powerful tool for studying protein–protein interactions and elucidating the structure of large protein complexes. However, computational methods for interpreting the complex MS/MS spectra from linked peptides are still in their infancy, making the high-throughput application of this approach largely impractical. Because of the lack of large annotated datasets, most current approaches do not capture the specific fragmentation patterns of linked peptides and therefore are not optimal for the identification of cross-linked peptides. Here we propose a generic approach to address this problem and demonstrate it using disulfide-bridged peptide libraries to (i) efficiently generate large mass spectral reference data for linked peptides at a low cost and (ii) automatically train an algorithm that can efficiently and accurately identify linked peptides from MS/MS spectra. We show that using this approach we were able to identify thousands of MS/MS spectra from disulfide-bridged peptides through comparison with proteome-scale sequence databases and significantly improve the sensitivity of cross-linked peptide identification. This allowed us to identify 60% more direct pairwise interactions between the protein subunits in the 20S proteasome complex than existing tools on cross-linking studies of the proteasome complexes. The basic framework of this approach and the MS/MS reference dataset generated should be valuable resources for the future development of new tools for the identification of linked peptides. PMID:24493012

Characterisation of phenolic compounds by UPLC-QTOF-MS/MS of geopropolis from the stingless bee Melipona subnitida (jandaíra).

PubMed

de Souza, Silvana Alves; da Silva, Telma Maria Guedes; da Silva, Eva Monica Sarmento; Camara, Celso Amorim; Silva, Tania Maria Sarmento

2018-05-17

Melipona subnitida Ducke (jandaíra) is a stingless bee native to north-eastern Brazil, which produces geopropolis, a mixture of beeswax, plant resins, pollens and earth that is used for sealing beehives. To extend the knowledge on phenolic compounds in fractions obtained by C18-solid phase extraction (SPE) of nine geopropolis samples from Melipona subnitida collected at different times. Chromatographic profiles of nine samples of geopropolis from jandaíra were analysed by ultra-performance liquid chromatography coupled with a diode array detector and quadrupole time-of-flight mass spectrometry (UPLC-DAD-QTOF-MS/MS) and combined with the use of data-independent acquisition (MSE) for the profiling and structural characterisation of the phenolic compounds. The isolated compound was identified by nuclear magnetic resonance of hydrogen and carbon ( 1 H- and 13 C-NMR). The present study with geopropolis of jandaíra resulted in the characterisation of 51 phenolics by UPLC-DAD-QTOF-MS/MS: four galloyl glucosides, one ellagic acid, 11 acyl-hexosides, 23 acyl-galloyl-hexosides and 12 flavonoids. The structures of two compounds (1,6-di-O-(E)-coumaroyl-2-O-galloyl-β-d-glucopyranoside and 1-O-cinnamoyl-6-O-(E)-coumaroyl-2-O-galloyl-β-d-glucopyranoside) were established by 1 H and the attached proton test (APT) experiments as well as high-resolution electrospray ionisation mass spectroscopy (HR-ESI-MS) analysis. The geopropolis of jandaíra showed phenolic compounds galloyl hexosides, ellagic acid, acyl-(cinnamoyl/coumaroyl)-hexosides, acyl-(cinnamoyl/coumaroyl)-galloyl-hexosides and flavonoids (aglycones and acylated-O-glycosides). Copyright © 2018 John Wiley & Sons, Ltd.

Automated Solid Phase Extraction (SPE) LC/NMR Applied to the Structural Analysis of Extractable Compounds from a Pharmaceutical Packaging Material of Construction.

PubMed

Norwood, Daniel L; Mullis, James O; Davis, Mark; Pennino, Scott; Egert, Thomas; Gonnella, Nina C

2013-01-01

The structural analysis (i.e., identification) of organic chemical entities leached into drug product formulations has traditionally been accomplished with techniques involving the combination of chromatography with mass spectrometry. These include gas chromatography/mass spectrometry (GC/MS) for volatile and semi-volatile compounds, and various forms of liquid chromatography/mass spectrometry (LC/MS or HPLC/MS) for semi-volatile and relatively non-volatile compounds. GC/MS and LC/MS techniques are complementary for structural analysis of leachables and potentially leachable organic compounds produced via laboratory extraction of pharmaceutical container closure/delivery system components and corresponding materials of construction. Both hyphenated analytical techniques possess the separating capability, compound specific detection attributes, and sensitivity required to effectively analyze complex mixtures of trace level organic compounds. However, hyphenated techniques based on mass spectrometry are limited by the inability to determine complete bond connectivity, the inability to distinguish between many types of structural isomers, and the inability to unambiguously determine aromatic substitution patterns. Nuclear magnetic resonance spectroscopy (NMR) does not have these limitations; hence it can serve as a complement to mass spectrometry. However, NMR technology is inherently insensitive and its ability to interface with chromatography has been historically challenging. This article describes the application of NMR coupled with liquid chromatography and automated solid phase extraction (SPE-LC/NMR) to the structural analysis of extractable organic compounds from a pharmaceutical packaging material of construction. The SPE-LC/NMR technology combined with micro-cryoprobe technology afforded the sensitivity and sample mass required for full structure elucidation. Optimization of the SPE-LC/NMR analytical method was achieved using a series of model compounds representing the chemical diversity of extractables. This study demonstrates the complementary nature of SPE-LC/NMR with LC/MS for this particular pharmaceutical application. The identification of impurities leached into drugs from the components and materials associated with pharmaceutical containers, packaging components, and materials has historically been done using laboratory techniques based on the combination of chromatography with mass spectrometry. Such analytical techniques are widely recognized as having the selectivity and sensitivity required to separate the complex mixtures of impurities often encountered in such identification studies, including both the identification of leachable impurities as well as potential leachable impurities produced by laboratory extraction of packaging components and materials. However, while mass spectrometry-based analytical techniques have limitations for this application, newer analytical techniques based on the combination of chromatography with nuclear magnetic resonance spectroscopy provide an added dimension of structural definition. This article describes the development, optimization, and application of an analytical technique based on the combination of chromatography and nuclear magnetic resonance spectroscopy to the identification of potential leachable impurities from a pharmaceutical packaging material. The complementary nature of the analytical techniques for this particular pharmaceutical application is demonstrated.

Structural elucidation of 4-(cystein-S-yl)butyl glucosinolate from the leaves of Eruca sativa.

PubMed

Kim, Sun-Ju; Kawaharada, Chiami; Jin, Shigeki; Hashimoto, Makoto; Ishii, Gensho; Yamauchi, Hiroaki

2007-01-01

The structurally unique glucosinolate (GSL), 4-(cystein-S-yl)butyl GSL, was identified in the leaves of hydroponically-grown rocket salad (Eruca sativa Mill.). Its electrospray ionization mass spectrometry (ESI-MS)/MS spectrum indicated that this unusual GSL had a molecular weight of 414 as a desulfo (DS)-GSL, and a molecular formula of C(14)H(25)N(2)O(8)S(2) based on its negative ion matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) spectrum. For further confirmation, the 4-(cystein-S-yl)butyl DS-GSL was prepared with authentic L-Ser and purified dimeric 4-mercaptobutyl DS-GSL, and its chemical structure then confirmed by ESI-MS/MS data. It is named "glucorucolamine" as a trivial name from its ammonia sensitivity. This unique GSL was found to the greatest extent when rocket salad was grown in a 100% NH4+-N nutrient solution. Despite it clearly seems to reduce the detoxification of excess NH4+ in the leaves of rocket salad, present knowledge about the unique GSL is still far from being sufficient.

Mass spectrometric techniques for characterizing low-molecular-weight resins used as paint varnishes.

PubMed

Bonaduce, I; Colombini, M P; Degano, I; Di Girolamo, F; La Nasa, J; Modugno, F; Orsini, S

2013-01-01

The molecular structure of three low-molecular-weight resins used as paint varnishes has been characterized by use of an approach based on three different mass spectrometric techniques. We investigated the ketone resin MS2A, the aldehyde resin Laropal A81, and the hydrocarbon resin Regalrez 1094, now commonly used in restoration. To date, the molecular structures of these resins have not been completely elucidated. To improve current knowledge of the chemical composition of these materials, information obtained by gas chromatography-mass spectrometry (GC/MS), pyrolysis-gas chromatography-mass spectrometry (Py/GC/MS), and electrospray ionization mass spectrometry (ESI-Q-ToF) was combined. Analysis, in solution, of the whole polymeric fraction of the resins by flow-injection ESI-Q-ToF, and of the non-polymeric fraction by GC-MS, enabled us to identify previously unreported features of the polymer structures. In addition, the Py-GC/MS profiles that we obtained will help to enhance the databases currently available in the literature. The proposed approach can be extended to other low-molecular-weight resins used as varnishes in conservation.

Ion-pair high-speed countercurrent chromatography in fractionation of a high-molecular weight variation of acyl-oligosaccharide linked betacyanins from purple bracts of Bougainvillea glabra.

PubMed

Wybraniec, Sławomir; Jerz, Gerold; Gebers, Nadine; Winterhalter, Peter

2010-02-15

The natural pigment composition of purple bracts of Bougainvillea glabra (Nyctaginaceae) consists of a highly complex mixture of betacyanins solely differing by the substitution with a variety of acyl-oligoglycoside units. This study was focused on a two-dimensional chromatography approach, a combination of preparative high-speed countercurrent chromatography (HSCCC) and analytical C18-HPLC with ESI-DAD-MS/MS detection which finally enabled a more detailed view into the pigment profile and elucidated the existence of an overwhelming amount of varying betacyanin structures occurring in Bougainvillea bracts. The detected molecular weights of the pigments reached so far unknown high values and ranged up to maximum values of 1653 and 1683 Da for the largest molecules due to oligosaccharide linkage and multiple acyl substitutions. The preparative IP-HSCCC separation yielded 15 complex fractions containing betacyanins of enhanced polarity as well as structures with highly increased lipophilicity. Betacyanin structures extended by large oligosaccharide chains with bigger number of glycoside units and also carrying a reduced number of hydroxycinnamic acid substitutions were characteristic for polar pigments occurring mainly in the early eluting CCC fractions. IP-HSCCC was proven to be extremely effective for fractionating this complex crude betalain pigment extract into more defined 'polarity-windows'. Structural analysis by analytical LC-ESI-MS/MS in the positive ionization mode detected a total sum of 146 different betacyanin pigments in the CCC fractions of reduced complexity. Copyright 2010 Elsevier B.V. All rights reserved.

Heptameric (L12)6/L10 rather than canonical pentameric complexes are found by tandem MS of intact ribosomes from thermophilic bacteria.

PubMed

Ilag, Leopold L; Videler, Hortense; McKay, Adam R; Sobott, Frank; Fucini, Paola; Nierhaus, Knud H; Robinson, Carol V

2005-06-07

Ribosomes are universal translators of the genetic code into protein and represent macromolecular structures that are asymmetric, often heterogeneous, and contain dynamic regions. These properties pose considerable challenges for modern-day structural biology. Despite these obstacles, high-resolution x-ray structures of the 30S and 50S subunits have revealed the RNA architecture and its interactions with proteins for ribosomes from Thermus thermophilus, Deinococcus radiodurans, and Haloarcula marismortui. Some regions, however, remain inaccessible to these high-resolution approaches because of their high conformational dynamics and potential heterogeneity, specifically the so-called L7/L12 stalk complex. This region plays a vital role in protein synthesis by interacting with GTPase factors in translation. Here, we apply tandem MS, an approach widely applied to peptide sequencing for proteomic applications but not previously applied to MDa complexes. Isolation and activation of ions assigned to intact 30S and 50S subunits releases proteins S6 and L12, respectively. Importantly, this process reveals, exclusively while attached to ribosomes, a phosphorylation of L12, the protein located in multiple copies at the tip of the stalk complex. Moreover, through tandem MS we discovered a stoichiometry for the stalk protuberance on Thermus thermophilus and other thermophiles and contrast this assembly with the analogous one on ribosomes from mesophiles. Together with evidence for a potential interaction with the degradosome, these results show that important findings on ribosome structure, interactions, and modifications can be discovered by tandem MS, even on well studied ribosomes from Thermus thermophilus.

Heptameric (L12)6/L10 rather than canonical pentameric complexes are found by tandem MS of intact ribosomes from thermophilic bacteria

PubMed Central

Ilag, Leopold L.; Videler, Hortense; McKay, Adam R.; Sobott, Frank; Fucini, Paola; Nierhaus, Knud H.; Robinson, Carol V.

2005-01-01

Ribosomes are universal translators of the genetic code into protein and represent macromolecular structures that are asymmetric, often heterogeneous, and contain dynamic regions. These properties pose considerable challenges for modern-day structural biology. Despite these obstacles, high-resolution x-ray structures of the 30S and 50S subunits have revealed the RNA architecture and its interactions with proteins for ribosomes from Thermus thermophilus, Deinococcus radiodurans, and Haloarcula marismortui. Some regions, however, remain inaccessible to these high-resolution approaches because of their high conformational dynamics and potential heterogeneity, specifically the so-called L7/L12 stalk complex. This region plays a vital role in protein synthesis by interacting with GTPase factors in translation. Here, we apply tandem MS, an approach widely applied to peptide sequencing for proteomic applications but not previously applied to MDa complexes. Isolation and activation of ions assigned to intact 30S and 50S subunits releases proteins S6 and L12, respectively. Importantly, this process reveals, exclusively while attached to ribosomes, a phosphorylation of L12, the protein located in multiple copies at the tip of the stalk complex. Moreover, through tandem MS we discovered a stoichiometry for the stalk protuberance on Thermus thermophilus and other thermophiles and contrast this assembly with the analogous one on ribosomes from mesophiles. Together with evidence for a potential interaction with the degradosome, these results show that important findings on ribosome structure, interactions, and modifications can be discovered by tandem MS, even on well studied ribosomes from Thermus thermophilus. PMID:15923259

Secondary pneumatization of the maxillary sinus in callitrichid primates: insights from immunohistochemistry and bone cell distribution.

PubMed

Smith, Timothy D; Rossie, James B; Cooper, Gregory M; Mooney, Mark P; Siegel, Michael I

2005-08-01

The paranasal sinuses remain elusive both in terms of function and in the proximate mechanism of their development. The present study sought to describe the maxillary sinuses (MSs) in three species of callitrichid primates at birth, a time when secondary pneumatization occurs rapidly in humans. The MSs were examined in serially sectioned and stained slides from the heads of two Callithrix jacchus, one Leontopithecus rosalia, and two Saguinus geoffroyi. Specimens were examined microscopically regarding the distribution of osteoclasts and osteoblasts along the osseous boundaries of the MS and other parts of the maxillary bone. Selected sections were immunohistochemically evaluated for the distribution of osteopontin (OPN), which facilitates osteoclast binding. Taken together, OPN immunoreactivity and bone cell distribution suggested trends of bone resorption/deposition that were consistent among species for the superior (roof) and inferior (floor) boundaries of the MS. Expansion at the roof and floor of the MS appeared to correspond to overall vertical midfacial growth in callitrichids. Much more variability was noted for the lateral (alveolar) and medial (nasal walls) of the MS. Unlike the other species, the nasal wall of Saguinus was static and mostly composed of inferior portions of the nasal capsule that were undergoing endochondral ossification. The variation seen in the alveolar walls may relate to the presence or absence of adjacent structures, although it was noted that adjacency of deciduous molars influenced medial drift of the alveolar wall in Saguinus but not Leontopithecus. The results of this study are largely consistent with the "structural" or "architectural" hypothesis of sinus formation with respect to vertical MS enlargement, and the variable cellular/OPN distribution found along the nasal and alveolar walls was evocative of Witmer's (J Vert Paleontol 1997;17:1-73) epithelial hypothesis in revealing that most expansion occurred in regions unopposed by adjacent structures. (c) 2005 Wiley-Liss, Inc.

Task Switching in a Hierarchical Task Structure: Evidence for the Fragility of the Task Repetition Benefit

ERIC Educational Resources Information Center

Lien, Mei-Ching; Ruthruff, Eric

2004-01-01

This study examined how task switching is affected by hierarchical task organization. Traditional task-switching studies, which use a constant temporal and spatial distance between each task element (defined as a stimulus requiring a response), promote a flat task structure. Using this approach, Experiment 1 revealed a large switch cost of 238 ms.…

Gaussian and linear deconvolution of LC-MS/MS chromatograms of the eight aminobutyric acid isomers

PubMed Central

Vemula, Harika; Kitase, Yukiko; Ayon, Navid J.; Bonewald, Lynda; Gutheil, William G.

2016-01-01

Isomeric molecules present a challenge for analytical resolution and quantification, even with MS-based detection. The eight-aminobutyric acid (ABA) isomers are of interest for their various biological activities, particularly γ-aminobutyric acid (GABA) and the d- and l-isomers of β-aminoisobutyric acid (β-AIBA; BAIBA). This study aimed to investigate LC-MS/MS-based resolution of these ABA isomers as their Marfey's (Mar) reagent derivatives. HPLC was able to separate three Mar-ABA isomers l-β-ABA (l-BABA), and l- and d-α-ABA (AABA) completely, with three isomers (GABA, and d/l-BAIBA) in one chromatographic cluster, and two isomers (α-AIBA (AAIBA) and d-BABA) in a second cluster. Partially separated cluster components were deconvoluted using Gaussian peak fitting except for GABA and d-BAIBA. MS/MS detection of Marfey's derivatized ABA isomers provided six MS/MS fragments, with substantially different intensity profiles between structural isomers. This allowed linear deconvolution of ABA isomer peaks. Combining HPLC separation with linear and Gaussian deconvolution allowed resolution of all eight ABA isomers. Application to human serum found a substantial level of l-AABA (13 μM), an intermediate level of l-BAIBA (0.8 μM), and low but detectable levels (<0.2 μM) of GABA, l-BABA, AAIBA, d-BAIBA, and d-AABA. This approach should be useful for LC-MS/MS deconvolution of other challenging groups of isomeric molecules. PMID:27771391

Aquarius reveals salinity structure of tropical instability waves

NASA Astrophysics Data System (ADS)

Lee, Tong; Lagerloef, Gary; Gierach, Michelle M.; Kao, Hsun-Ying; Yueh, Simon; Dohan, Kathleen

2012-06-01

Sea surface salinity (SSS) measurements from the Aquarius/SAC-D satellite during September-December 2011 provide the first satellite observations of the salinity structure of tropical instability waves (TIWs) in the Pacific. The related SSS anomaly has a magnitude of approximately ±0.5 PSU. Different from sea surface temperature (SST) and sea surface height anomaly (SSHA) where TIW-related propagating signals are stronger a few degrees away from the equator, the SSS signature of TIWs is largest near the equator in the eastern equatorial Pacific where salty South Pacific water meets the fresher Inter-tropical Convergence Zone water. The dominant westward propagation speed of SSS near the equator is approximately 1 m/s. This is twice as fast as the 0.5 m/s TIW speed widely reported in the literature, typically from SST and SSHA away from the equator. This difference is attributed to the more dominant 17-day TIWs near the equator that have a 1 m/s dominant phase speed and the stronger 33-day TIWs away from the equator that have a 0.5 m/s dominant phase speed. The results demonstrate the important value of Aquarius in studying TIWs.

Tandem mass spectrometry characteristics of polyester anions and cations formed by electrospray ionization.

PubMed

Arnould, Mark A; Buehner, Rita W; Wesdemiotis, Chrys; Vargas, Rafael

2005-01-01

Electrospray ionization of polyesters composed of isophthalic acid and neopentyl glycol produces carboxylate anions in negative mode and mainly sodium ion adducts in positive mode. A tandem mass spectrometry (MS/MS) study of these ions in a quadrupole ion trap shows that the collisionally activated dissociation pathways of the anions are simpler than those of the corresponding cations. Charge-remote fragmentations predominate in both cases, but the spectra obtained in negative mode are devoid of the complicating cation exchange observed in positive mode. MS/MS of the Na(+) adducts gives rise to a greater number of fragments but not necessarily more structural information. In either positive or negative mode, polyester oligomers with different end groups fragment by similar mechanisms. The observed fragments are consistent with rearrangements initiated by the end groups. Single-stage ESI mass spectra also are more complex in positive mode because of extensive H/Na substitutions; this is also true for matrix-assisted laser desorption ionization (MALDI) mass spectra. Hence, formation and analysis of anions might be the method of choice for determining block length, end group structure and copolymer sequence, provided the polyester contains at least one carboxylic acid end group that is ionizable to anions.

Study on dissolution mechanism of cortisol and cortisone from hair matrix with liquid chromatography-tandem mass spectrometry.

PubMed

Xing, Xue; Chen, Zheng; Li, Jifeng; Zhang, Jing; Deng, Huihua; Lu, Zuhong

2013-06-05

Hair cortisol has been used as a biomarker of chronic stress. The detected contents of hair cortisol might depend on the incubation duration in solvents for no-milled hair samples with 3-layer structure. However, there was no research on the dissolution mechanism of hair analytes. After uniform mixture, no-milled hair samples were incubated in methanol and water for the 12 different durations and milled hair was done as comparison. Hair cortisol and cortisone were determined with high performance liquid chromatography-tandem mass spectrometry (LC-MS/MS). The measured concentrations of hair cortisol and cortisone showed ≥2 maxima during the entire incubation in methanol and water from 5 min to 72 h for no-milled hair. Hair cortisol concentration measured by LC-MS/MS was increased with the incubation duration. Conversely, it was not held when hair was powdered prior to the incubation in methanol. Hair cortisol and cortisone were dissolved from hair matrix through the 2-stage or multistage mechanism, which might depend on the hair 3-layer structure and its degree of damage. Copyright © 2013 Elsevier B.V. All rights reserved.

Reduced levels of hydroxylated, polyunsaturated ultra long-chain fatty acids in the serum of colorectal cancer patients: implications for early screening and detection

PubMed Central

2010-01-01

Background There are currently no accurate serum markers for detecting early risk of colorectal cancer (CRC). We therefore developed a non-targeted metabolomics technology to analyse the serum of pre-treatment CRC patients in order to discover putative metabolic markers associated with CRC. Using tandem-mass spectrometry (MS/MS) high throughput MS technology we evaluated the utility of selected markers and this technology for discriminating between CRC and healthy subjects. Methods Biomarker discovery was performed using Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). Comprehensive metabolic profiles of CRC patients and controls from three independent populations from different continents (USA and Japan; total n = 222) were obtained and the best inter-study biomarkers determined. The structural characterization of these and related markers was performed using liquid chromatography (LC) MS/MS and nuclear magnetic resonance technologies. Clinical utility evaluations were performed using a targeted high-throughput triple-quadrupole multiple reaction monitoring (TQ-MRM) method for three biomarkers in two further independent populations from the USA and Japan (total n = 220). Results Comprehensive metabolomic analyses revealed significantly reduced levels of 28-36 carbon-containing hydroxylated polyunsaturated ultra long-chain fatty-acids in all three independent cohorts of CRC patient samples relative to controls. Structure elucidation studies on the C28 molecules revealed two families harbouring specifically two or three hydroxyl substitutions and varying degrees of unsaturation. The TQ-MRM method successfully validated the FTICR-MS results in two further independent studies. In total, biomarkers in five independent populations across two continental regions were evaluated (three populations by FTICR-MS and two by TQ-MRM). The resultant receiver-operator characteristic curve AUCs ranged from 0.85 to 0.98 (average = 0.91 ± 0.04). Conclusions A novel comprehensive metabolomics technology was used to identify a systemic metabolic dysregulation comprising previously unknown hydroxylated polyunsaturated ultra-long chain fatty acid metabolites in CRC patients. These metabolites are easily measurable in serum and a decrease in their concentration appears to be highly sensitive and specific for the presence of CRC, regardless of ethnic or geographic background. The measurement of these metabolites may represent an additional tool for the early detection and screening of CRC. PMID:20156336

A Conformational Investigation of Propeptide Binding to the Integral Membrane Protein γ-Glutamyl Carboxylase Using Nanodisc Hydrogen Exchange Mass Spectrometry

PubMed Central

2015-01-01

Gamma (γ)-glutamyl carboxylase (GGCX) is an integral membrane protein responsible for the post-translational catalytic conversion of select glutamic acid (Glu) residues to γ-carboxy glutamic acid (Gla) in vitamin K-dependent (VKD) proteins. Understanding the mechanism of carboxylation and the role of GGCX in the vitamin K cycle is of biological interest in the development of therapeutics for blood coagulation disorders. Historically, biophysical investigations and structural characterizations of GGCX have been limited due to complexities involving the availability of an appropriate model membrane system. In previous work, a hydrogen exchange mass spectrometry (HX MS) platform was developed to study the structural configuration of GGCX in a near-native nanodisc phospholipid environment. Here we have applied the nanodisc–HX MS approach to characterize specific domains of GGCX that exhibit structural rearrangements upon binding the high-affinity consensus propeptide (pCon; AVFLSREQANQVLQRRRR). pCon binding was shown to be specific for monomeric GGCX-nanodiscs and promoted enhanced structural stability to the nanodisc-integrated complex while maintaining catalytic activity in the presence of carboxylation co-substrates. Noteworthy modifications in HX of GGCX were prominently observed in GGCX peptides 491–507 and 395–401 upon pCon association, consistent with regions previously identified as sites for propeptide and glutamate binding. Several additional protein regions exhibited minor gains in solvent protection upon propeptide incorporation, providing evidence for a structural reorientation of the GGCX complex in association with VKD carboxylation. The results herein demonstrate that nanodisc–HX MS can be utilized to study molecular interactions of membrane-bound enzymes in the absence of a complete three-dimensional structure and to map dynamic rearrangements induced upon ligand binding. PMID:24512177

Modern analytics for synthetically derived complex drug substances: NMR, AFFF-MALS, and MS tests for glatiramer acetate.

PubMed

Rogstad, Sarah; Pang, Eric; Sommers, Cynthia; Hu, Meng; Jiang, Xiaohui; Keire, David A; Boyne, Michael T

2015-11-01

Glatiramer acetate (GA) is a mixture of synthetic copolymers consisting of four amino acids (glutamic acid, lysine, alanine, and tyrosine) with a labeled molecular weight range of 5000 to 9000 Da. GA is marketed as Copaxone™ by Teva for the treatment of multiple sclerosis. Here, the agency has evaluated the structure and composition of GA and a commercially available comparator, Copolymer-1. Modern analytical technologies which can characterize these complex mixtures are desirable for analysis of their comparability and structural "sameness." In the studies herein, a molecular fingerprinting approach is taken using mass-accurate mass spectrometry (MS) analysis, nuclear magnetic resonance (NMR) (1D-(1)H-NMR, 1D-(13)C-NMR, and 2D NMR), and asymmetric field flow fractionation (AFFF) coupled with multi-angle light scattering (MALS) for an in-depth characterization of three lots of the marketplace drug and a formulated sample of the comparator. Statistical analyses were applied to the MS and AFFF-MALS data to assess these methods' ability to detect analytical differences in the mixtures. The combination of multiple orthogonal measurements by liquid chromatography coupled with MS (LC-MS), AFFF-MALS, and NMR on the same sample set was found to be fit for the intended purpose of distinguishing analytical differences between these complex mixtures of peptide chains.

Possibilities of LA-ICP-MS technique for the spatial elemental analysis of the recent fish scales: Line scan vs. depth profiling

NASA Astrophysics Data System (ADS)

Holá, Markéta; Kalvoda, Jiří; Nováková, Hana; Škoda, Radek; Kanický, Viktor

2011-01-01

LA-ICP-MS and solution based ICP-MS in combination with electron microprobe are presented as a method for the determination of the elemental spatial distribution in fish scales which represent an example of a heterogeneous layered bone structure. Two different LA-ICP-MS techniques were tested on recent common carp ( Cyprinus carpio) scales: A line scan through the whole fish scale perpendicular to the growth rings. The ablation crater of 55 μm width and 50 μm depth allowed analysis of the elemental distribution in the external layer. Suitable ablation conditions providing a deeper ablation crater gave average values from the external HAP layer and the collagen basal plate. Depth profiling using spot analysis was tested in fish scales for the first time. Spot analysis allows information to be obtained about the depth profile of the elements at the selected position on the sample. The combination of all mentioned laser ablation techniques provides complete information about the elemental distribution in the fish scale samples. The results were compared with the solution based ICP-MS and EMP analyses. The fact that the results of depth profiling are in a good agreement both with EMP and PIXE results and, with the assumed ways of incorporation of the studied elements in the HAP structure, suggests a very good potential for this method.

Electropysiologic evaluation of the visual pathway in patients with multiple sclerosis.

PubMed

Rodriguez-Mena, Diego; Almarcegui, Carmen; Dolz, Isabel; Herrero, Raquel; Bambo, Maria P; Fernandez, Javier; Pablo, Luis E; Garcia-Martin, Elena

2013-08-01

To evaluate the ability of visual evoked potentials and pattern electroretinograms (PERG) to detect subclinical axonal damage in patients during the early diagnostic stage of multiple sclerosis (MS). The authors also compared the ability of optical coherence tomography (OCT), PERG, and visual evoked potentials to detect axonal loss in MS patients and correlated the functional and structural properties of the retinal nerve fiber layer. Two hundred twenty-eight eyes of 114 subjects (57 MS patients and 57 age- and sex-matched healthy controls) were included. The visual pathway was evaluated based on functional and structural assessments. All patients underwent a complete ophthalmic examination that included assessment of visual acuity, ocular motility, intraocular pressure, visual field, papillary morphology, OCT, visual evoked potentials, and PERG. Visual evoked potentials (P100 latency and amplitude), PERG (N95 amplitude and N95/P50 ratio), and OCT parameters differed significantly between MS patients and healthy subjects. Moderate significant correlations were found between visual evoked potentials or PERG parameters and OCT measurements. Axonal damage in ganglion cells of the visual pathway can be detected based on structural measures provided by OCT in MS patients and by the N95 component and N95/P50 index of PERG, thus providing good correlation between function and structure.

Data model for the collaboration between land administration systems and agricultural land parcel identification systems.

PubMed

Inan, Halil Ibrahim; Sagris, Valentina; Devos, Wim; Milenov, Pavel; van Oosterom, Peter; Zevenbergen, Jaap

2010-12-01

The Common Agricultural Policy (CAP) of the European Union (EU) has dramatically changed after 1992, and from then on the CAP focused on the management of direct income subsidies instead of production-based subsidies. For this focus, Member States (MS) are expected to establish Integrated Administration and Control System (IACS), including a Land Parcel Identification System (LPIS) as the spatial part of IACS. Different MS have chosen different solutions for their LPIS. Currently, some MS based their IACS/LPIS on data from their Land Administration Systems (LAS), and many others use purpose built special systems for their IACS/LPIS. The issue with these different IACS/LPIS is that they do not have standardized structures; rather, each represents a unique design in each MS, both in the case of LAS based or special systems. In this study, we aim at designing a core data model for those IACS/LPIS based on LAS. For this purpose, we make use of the ongoing standardization initiatives for LAS (Land Administration Domain Model: LADM) and IACS/LPIS (LPIS Core Model: LCM). The data model we propose in this study implies the collaboration between LADM and LCM and includes some extensions. Some basic issues with the collaboration model are discussed within this study: registration of farmers, land use rights and farming limitations, geometry/topology, temporal data management etc. For further explanation of the model structure, sample instance level diagrams illustrating some typical situations are also included. Copyright © 2010 Elsevier Ltd. All rights reserved.

Comprehensive and accurate tracking of carbon origin of LC-tandem mass spectrometry collisional fragments for 13C-MFA.

PubMed

Kappelmann, Jannick; Klein, Bianca; Geilenkirchen, Petra; Noack, Stephan

2017-03-01

In recent years the benefit of measuring positionally resolved 13 C-labeling enrichment from tandem mass spectrometry (MS/MS) collisional fragments for improved precision of 13 C-Metabolic Flux Analysis ( 13 C-MFA) has become evident. However, the usage of positional labeling information for 13 C-MFA faces two challenges: (1) The mass spectrometric acquisition of a large number of potentially interfering mass transitions may hamper accuracy and sensitivity. (2) The positional identity of carbon atoms of product ions needs to be known. The present contribution addresses the latter challenge by deducing the maximal positional labeling information contained in LC-ESI-MS/MS spectra of product anions of central metabolism as well as product cations of amino acids. For this purpose, we draw on accurate mass spectrometry, selectively labeled standards, and published fragmentation pathways to structurally annotate all dominant mass peaks of a large collection of metabolites, some of which with a complete fragmentation pathway. Compiling all available information, we arrive at the most detailed map of carbon atom fate of LC-ESI-MS/MS collisional fragments yet, comprising 170 intense and structurally annotated product ions with unique carbon origin from 76 precursor ions of 72 metabolites. Our 13 C-data proof that heuristic fragmentation rules often fail to yield correct fragment structures and we expose common pitfalls in the structural annotation of product ions. We show that the positionally resolved 13 C-label information contained in the product ions that we structurally annotated allows to infer the entire isotopomer distribution of several central metabolism intermediates, which is experimentally demonstrated for malate using quadrupole-time-of-flight MS technology. Finally, the inclusion of the label information from a subset of these fragments improves flux precision in a Corynebacterium glutamicum model of the central carbon metabolism.

Coupling of Ultrafast LC with Mass Spectrometry by DESI

NASA Astrophysics Data System (ADS)

Cai, Yi; Liu, Yong; Helmy, Roy; Chen, Hao

2014-10-01

Recently we reported a desorption electrospray ionization (DESI) interface to combine liquid chromatography (LC) with mass spectrometry (MS) using a new LC eluent splitting strategy through a tiny orifice on LC capillary tube [ J. Am. Soc. Mass Spectrom. 25, 286 (2014)]. The interface introduces negligible dead volume and back pressure, thereby allowing "near real-time" MS detection, fast LC elution, and online MS-directed purification. This study further evaluates the LC/DESI-MS performance with focus of using ultra-fast LC. Using a monolithic C18 column, metabolites in urine can be separated within 1.6 min and can be online collected for subsequent structure elucidation (e.g., by NMR, UV, IR) in a recovery yield up to 99%. Using a spray solvent with alkaline pH, negative ions could be directly generated for acidic analytes (e.g., ibuprofen) in acidic LC eluent by DESI, offering a novel protocol to realize "wrong-way around" ionization for LC/MS analysis. In addition, DESI-MS is found to be compatible with ultra-performance liquid chromatography (UPLC) for the first time.

Hexose rearrangements upon fragmentation of N-glycopeptides and reductively aminated N-glycans.

PubMed

Wuhrer, Manfred; Koeleman, Carolien A M; Deelder, André M

2009-06-01

Tandem mass spectrometry of glycans and glycoconjugates in protonated form is known to result in rearrangement reactions leading to internal residue loss. Here we studied the occurrence of hexose rearrangements in tandem mass spectrometry of N-glycopeptides and reductively aminated N-glycans by MALDI-TOF/TOF-MS/MS and ESI-ion trap-MS/MS. Fragmentation of proton adducts of oligomannosidic N-glycans of ribonuclease B that were labeled with 2-aminobenzamide and 2-aminobenzoic acid resulted in transfer of one to five hexose residues to the fluorescently tagged innermost N-acetylglucosamine. Glycopeptides from various biological sources with oligomannosidic glycans were likewise shown to undergo hexose rearrangement reactions, resulting in chitobiose cleavage products that have acquired one or two hexose moieties. Tryptic immunoglobulin G Fc-glycopeptides with biantennary N-glycans likewise showed hexose rearrangements resulting in hexose transfer to the peptide moiety retaining the innermost N-acetylglucosamine. Thus, as a general phenomenon, tandem mass spectrometry of reductively aminated glycans as well as glycopeptides may result in hexose rearrangements. This characteristic of glycopeptide MS/MS has to be considered when developing tools for de novo glycopeptide structural analysis.

Set-Based Discrete Particle Swarm Optimization Based on Decomposition for Permutation-Based Multiobjective Combinatorial Optimization Problems.

PubMed

Yu, Xue; Chen, Wei-Neng; Gu, Tianlong; Zhang, Huaxiang; Yuan, Huaqiang; Kwong, Sam; Zhang, Jun

2018-07-01

This paper studies a specific class of multiobjective combinatorial optimization problems (MOCOPs), namely the permutation-based MOCOPs. Many commonly seen MOCOPs, e.g., multiobjective traveling salesman problem (MOTSP), multiobjective project scheduling problem (MOPSP), belong to this problem class and they can be very different. However, as the permutation-based MOCOPs share the inherent similarity that the structure of their search space is usually in the shape of a permutation tree, this paper proposes a generic multiobjective set-based particle swarm optimization methodology based on decomposition, termed MS-PSO/D. In order to coordinate with the property of permutation-based MOCOPs, MS-PSO/D utilizes an element-based representation and a constructive approach. Through this, feasible solutions under constraints can be generated step by step following the permutation-tree-shaped structure. And problem-related heuristic information is introduced in the constructive approach for efficiency. In order to address the multiobjective optimization issues, the decomposition strategy is employed, in which the problem is converted into multiple single-objective subproblems according to a set of weight vectors. Besides, a flexible mechanism for diversity control is provided in MS-PSO/D. Extensive experiments have been conducted to study MS-PSO/D on two permutation-based MOCOPs, namely the MOTSP and the MOPSP. Experimental results validate that the proposed methodology is promising.

XLinkDB 2.0: integrated, large-scale structural analysis of protein crosslinking data

PubMed Central

Schweppe, Devin K.; Zheng, Chunxiang; Chavez, Juan D.; Navare, Arti T.; Wu, Xia; Eng, Jimmy K.; Bruce, James E.

2016-01-01

Motivation: Large-scale chemical cross-linking with mass spectrometry (XL-MS) analyses are quickly becoming a powerful means for high-throughput determination of protein structural information and protein–protein interactions. Recent studies have garnered thousands of cross-linked interactions, yet the field lacks an effective tool to compile experimental data or access the network and structural knowledge for these large scale analyses. We present XLinkDB 2.0 which integrates tools for network analysis, Protein Databank queries, modeling of predicted protein structures and modeling of docked protein structures. The novel, integrated approach of XLinkDB 2.0 enables the holistic analysis of XL-MS protein interaction data without limitation to the cross-linker or analytical system used for the analysis. Availability and Implementation: XLinkDB 2.0 can be found here, including documentation and help: http://xlinkdb.gs.washington.edu/. Contact: jimbruce@uw.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153666

Lanthanide-organic complexes based on polyoxometalates: Solvent effect on the luminescence properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tang Qun; Liu Shuxia, E-mail: liusx@nenu.edu.cn; Liang Dadong

2012-06-15

A series of lanthanide-organic complexes based on polyoxometalates (POMs) [Ln{sub 2}(DNBA){sub 4}(DMF){sub 8}][W{sub 6}O{sub 19}] (Ln=La(1), Ce(2), Sm(3), Eu(4), Gd(5); DNBA=3,5-dinitrobenzoate; DMF=N,N-dimethylformamide) has been synthesized. These complexes consist of [W{sub 6}O{sub 19}]{sup 2-} and dimeric [Ln{sub 2}(DNBA){sub 4}(DMF){sub 8}]{sup 2+} cations. The luminescence properties of 4 are measured in solid state and different solutions, respectively. Notably, the emission intensity increases gradually with the increase of solvent permittivity, and this solvent effect can be directly observed by electrospray mass spectrometry (ESI-MS). The analyses of ESI-MS show that the eight coordinated solvent DMF units of dimeric cation are active. They can movemore » away from dimeric cations and exchange with solvent molecules. Although the POM anions escape from 3D supramolecular network, the dimeric state structure of [Ln{sub 2}(DNBA){sub 4}]{sup 2+} remains unchanged in solution. The conservation of red luminescence is attributed to the maintenance of the aggregated state structures of dimeric cations. - Graphical abstract: 3D POMs-based lanthanide-organic complexes performed the solvent effect on the luminescence property. The origin of such solvent effect can be understood and explained on the basis of the existence of coordinated active sites by the studies of ESI-MS. Highlights: Black-Right-Pointing-Pointer The solvent effect on the luminescence property of POMs-based lanthanide-organic complexes. Black-Right-Pointing-Pointer ESI-MS analyses illuminate the correlation between the structure and luminescence property. Black-Right-Pointing-Pointer The dimeric cations have eight active sites of solvent coordination. Black-Right-Pointing-Pointer The aggregated state structure of dimer cation remains unchanged in solution. Black-Right-Pointing-Pointer Luminescence associating with ESI-MS is a new method for investigating the interaction of complex and solvent.« less

Neural Plasticity in Multiple Sclerosis: The Functional and Molecular Background

PubMed Central

Glabinski, Andrzej

2015-01-01

Multiple sclerosis is an autoimmune neurodegenerative disorder resulting in motor dysfunction and cognitive decline. The inflammatory and neurodegenerative changes seen in the brains of MS patients lead to progressive disability and increasing brain atrophy. The most common type of MS is characterized by episodes of clinical exacerbations and remissions. This suggests the presence of compensating mechanisms for accumulating damage. Apart from the widely known repair mechanisms like remyelination, another important phenomenon is neuronal plasticity. Initially, neuroplasticity was connected with the developmental stages of life; however, there is now growing evidence confirming that structural and functional reorganization occurs throughout our lifetime. Several functional studies, utilizing such techniques as fMRI, TBS, or MRS, have provided valuable data about the presence of neuronal plasticity in MS patients. CNS ability to compensate for neuronal damage is most evident in RR-MS; however it has been shown that brain plasticity is also preserved in patients with substantial brain damage. Regardless of the numerous studies, the molecular background of neuronal plasticity in MS is still not well understood. Several factors, like IL-1β, BDNF, PDGF, or CB1Rs, have been implicated in functional recovery from the acute phase of MS and are thus considered as potential therapeutic targets. PMID:26229689

Lysozyme oxidation by singlet molecular oxygen: Peptide characterization using [18 O]-labeling oxygen and nLC-MS/MS.

PubMed

Marques, Emerson Finco; Medeiros, Marisa H G; Di Mascio, Paolo

2017-11-01

Singlet molecular oxygen ( 1 O 2 ) is generated in biological systems and reacts with different biomolecules. Proteins are a major target for 1 O 2 , and His, Tyr, Met, Cys, and Trp are oxidized at physiological pH. In the present study, the modification of lysozyme protein by 1 O 2 was investigated using mass spectrometry approaches. The experimental findings showed methionine, histidine, and tryptophan oxidation. The experiments were achieved using [ 18 O]-labeled 1 O 2 released from thermolabile endoperoxides in association with nano-scale liquid chromatography coupled to electrospray ionization mass spectrometry. The structural characterization by nLC-MS/MS of the amino acids in the tryptic peptides of the proteins showed addition of [ 18 O]-labeling atoms in different amino acids. Copyright © 2017 John Wiley & Sons, Ltd.

Approach to the study of flavone di-C-glycosides by high performance liquid chromatography-tandem ion trap mass spectrometry and its application to characterization of flavonoid composition in Viola yedoensis.

PubMed

Cao, Jie; Yin, Chengle; Qin, Yan; Cheng, Zhihong; Chen, Daofeng

2014-10-01

The mass spectrometric (MS) analysis of flavone di-C-glycosides has been a difficult task due to pure standards being unavailable commercially and to that the reported relative intensities of some diagnostic ions varied with MS instruments. In this study, five flavone di-C-glycoside standards from Viola yedoensis have been systematically studied by high performance liquid chromatography-electrospray ionization-tandem ion trap mass spectrometry (HPLC-ESI-IT-MS(n)) in the negative ion mode to analyze their fragmentation patterns. A new MS(2) and MS(3) hierarchical fragmentation for the identification of the sugar nature (hexoses or pentoses) at C-6 and C-8 is presented based on previously established rules of fragmentation. Here, for the first time, we report that the MS(2) and MS(3) structure-diagnostic fragments about the glycosylation types and positions are highly dependent on the configuration of the sugars at C-6 and C-8. The base peak ((0,2) X1 (0,2) X(2)(-) ion) in MS(3) spectra of di-C-glycosides could be used as a diagnostic ion for flavone aglycones. These newly proposed fragmentation behaviors have been successfully applied to the characterization of flavone di-C-glycosides found in V. yedoensis. A total of 35 flavonoid glycosides, including 1 flavone mono-C-hexoside, 2 flavone 6,8-di-C-hexosides, 11 flavone 6,8-di-C-pentosides, 13 flavone 6,8-C-hexosyl-C-pentosides, 5 acetylated flavone C-glycosides and 3 flavonol O-glycosides, were identified or tentatively identified on the base of their UV profiles, MS and MS(n) (n = 5) data, or by comparing with reference substances. Among these, the acetylated flavone C-glycosides were reported from V. yedoensis for the first time. Copyright © 2014 John Wiley & Sons, Ltd.

Functional Magnetic Resonance Imaging of Rats with Experimental Autoimmune Encephalomyelitis Reveals Brain Cortex Remodeling

PubMed Central

Tambalo, Stefano; Peruzzotti-Jametti, Luca; Rigolio, Roberta; Fiorini, Silvia; Bontempi, Pietro; Mallucci, Giulia; Balzarotti, Beatrice; Marmiroli, Paola; Sbarbati, Andrea; Cavaletti, Guido

2015-01-01

Cortical reorganization occurring in multiple sclerosis (MS) patients is thought to play a key role in limiting the effect of structural tissue damage. Conversely, its exhaustion may contribute to the irreversible disability that accumulates with disease progression. Several aspects of MS-related cortical reorganization, including the overall functional effect and likely modulation by therapies, still remain to be elucidated. The aim of this work was to assess the extent of functional cortical reorganization and its brain structural/pathological correlates in Dark Agouti rats with experimental autoimmune encephalomyelitis (EAE), a widely accepted preclinical model of chronic MS. Morphological and functional MRI (fMRI) were performed before disease induction and during the relapsing and chronic phases of EAE. During somatosensory stimulation of the right forepaw, fMRI demonstrated that cortical reorganization occurs in both relapsing and chronic phases of EAE with increased activated volume and decreased laterality index versus baseline values. Voxel-based morphometry demonstrated gray matter (GM) atrophy in the cerebral cortex, and both GM and white matter atrophy were assessed by ex vivo pathology of the sensorimotor cortex and corpus callosum. Neuroinflammation persisted in the relapsing and chronic phases, with dendritic spine density in the layer IV sensory neurons inversely correlating with the number of cluster of differentiation 45-positive inflammatory lesions. Our work provides an innovative experimental platform that may be pivotal for the comprehension of key mechanisms responsible for the accumulation of irreversible brain damage and for the development of innovative therapies to reduce disability in EAE/MS. SIGNIFICANCE STATEMENT Since the early 2000s, functional MRI (fMRI) has demonstrated profound modifications in the recruitment of cortical areas during motor, cognitive, and sensory tasks in multiple sclerosis (MS) patients. Experimental autoimmune encephalomyelitis (EAE) represents a reliable model of the chronic-progressive variant of MS. fMRI studies in EAE have not been performed extensively up to now. This paper reports fMRI studies in a rat model of MS with somatosensory stimulation of the forepaw. We demonstrated modifications in the recruitment of cortical areas consistent with data from MS patients. To the best of our knowledge, this is the first report of cortical remodeling in a preclinical in vivo model of MS. PMID:26157006

LC-MS/MS Analysis of Permethylated Free Oligosaccharides and N-glycans Derived from Human, Bovine, and Goat Milk Samples

PubMed Central

Dong, Xue; Zhou, Shiyue; Mechref, Yehia

2016-01-01

Oligosaccharides in milk not only provide nutrition to the infants, but also have significant immune biofunctions such as inhibition of pathogen binding to the host cell. The main component in milk oligosaccharides is free oligosaccharides. Since the proteins in milk are highly glycosylated, N-glycans in milk also play an import role. In this study, we investigated the permethylated free oligosaccharides and N-glycans extracted from bovine, goat and human milk using LC-MS/MS. Quantitation profiles of free oligosaccharides and N-glycans were reported. The number of free oligosaccharides observed in bovine, goat and human milk samples (without isomeric consideration) were 11, 8 and 11 respectively. Human milk had more complex free oligosaccharides structures than the other two milk samples. Totally 58, 21, and 43 N-glycan structures (without isomeric consideration) were associated with whey proteins extracted from bovine, goat and human milk samples, respectively. Bovine milk free oligosaccharides and N-glycans from whey proteins were highly sialylated and to a lesser extend fucosylated. Goat and human milk free oligosaccharides and N-glycans from whey proteins were both highly fucosylated. Also, the isomeric glycans in milk samples were determined by PGC LC at elevated temperatures. For example, separation of human milk free oligosaccharide Gal-GlcNAc-(Fuc)-Gal-Glc and Gal-GlcNAc-Gal-Glc-Fuc isomers was achieved using PGC column. Permethylation of the glycan structures facilitated the interpretation of tandem MS. For example, internal cleavage and glycosidic bond cleavage are readily distinguished in the tandem mass spectra of permethylated glycans. This feature resulted in the identification of several isomers. PMID:26959529

Mass spectrometric behavior of anabolic androgenic steroids using gas chromatography coupled to atmospheric pressure chemical ionization source. Part I: ionization.

PubMed

Raro, M; Portolés, T; Sancho, J V; Pitarch, E; Hernández, F; Marcos, J; Ventura, R; Gómez, C; Segura, J; Pozo, O J

2014-06-01

The detection of anabolic androgenic steroids (AAS) is one of the most important topics in doping control analysis. Gas chromatography coupled to (tandem) mass spectrometry (GC-MS(/MS)) with electron ionization and liquid chromatography coupled to tandem mass spectrometry have been traditionally applied for this purpose. However, both approaches still have important limitations, and, therefore, detection of all AAS is currently afforded by the combination of these strategies. Alternative ionization techniques can minimize these drawbacks and help in the implementation of a single method for the detection of AAS. In the present work, a new atmospheric pressure chemical ionization (APCI) source commercialized for gas chromatography coupled to a quadrupole time-of-flight analyzer has been tested to evaluate the ionization of 60 model AAS. Underivatized and trimethylsylil (TMS)-derivatized compounds have been investigated. The use of GC-APCI-MS allowed for the ionization of all AAS assayed irrespective of their structure. The presence of water in the source as modifier promoted the formation of protonated molecules ([M+H](+)), becoming the base peak of the spectrum for the majority of studied compounds. Under these conditions, [M+H](+), [M+H-H2O](+) and [M+H-2·H2O](+) for underivatized AAS and [M+H](+), [M+H-TMSOH](+) and [M+H-2·TMSOH](+) for TMS-derivatized AAS were observed as main ions in the spectra. The formed ions preserve the intact steroid skeleton, and, therefore, they might be used as specific precursors in MS/MS-based methods. Additionally, a relationship between the relative abundance of these ions and the AAS structure has been established. This relationship might be useful in the structural elucidation of unknown metabolites. Copyright © 2014 John Wiley & Sons, Ltd.

An innovative design for using flexible printed coils for magnetostrictive-based longitudinal guided wave sensors in steel strand inspection

NASA Astrophysics Data System (ADS)

Tse, P. W.; Liu, X. C.; Liu, Z. H.; Wu, B.; He, C. F.; Wang, X. J.

2011-05-01

Magnetostrictive sensors (MsSs) that can excite and receive guided waves are commonly used in detecting defects that may occur in cables and strands for supporting heavy structures. A conventional MsS has a hard sensing coil that is wound onto a bobbin with electric wires to generate the necessary dynamic magnetic field to excite the desired guided waves. This tailor-made hard coil is usually bulky and is not flexible enough to fit steel strands of various sizes. The conventional MsS also cannot be mounted to any steel strand that does not have a free end to allow the bobbin to pass through the structure of the tested strand. Such inflexibilities limit the use of conventional MsSs in practical situations. To solve these limitations, an innovative type of coil, called a flexible printed coil (FPC), which is made out of flexible printed film, has been designed to replace the inflexible hard coil. The flexible structure of the FPC ensures that the new MsS can be easily installed on and removed from steel strands with different diameters and without free ends. Moreover, the FPC-based MsS can be wrapped into multiple layers due to its thin and flexible design. Although multi-layer FPC creates a minor asymmetry in the dynamic magnetic field, the results of finite element analysis and experiments confirm that the longitudinal guided waves excited by a FPC-based MsS are comparable to those excited by a conventional hard coil MsS. No significant reduction in defect inspection performance was found; in fact, further advantages were identified when using the FPC-based MsS. When acting as the transmitter, the innovative FPC-based MsS can cover a longer inspection length of strand. When acting as the receiver, the FPC-based MsS is more sensitive to smaller defects that are impossible to detect using a hard coil MsS. Hence, the multi-layer FPC-based MsS has great potential for replacing the conventional hard coil MsS because of its convenient installation, and ease of fitting to different strand diameters; it is smaller, and, most importantly, performs much better in strand defect detection.

Cognitive Impairment in MS Linked to Structural and Functional Connectivity

DTIC Science & Technology

2016-10-01

AVAILABILITY STATEMENT Approved for Public Release; Distribution Unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT Multiple sclerosis (MS) is the most...9 9. Appendices……………………………………………………………9 Krupp MS130103  2  Abstract Multiple sclerosis (MS) is the most common progressive neurologic...This symptom represents a major concern for many individuals living with multiple sclerosis (MS). Unfortunately, no reliable treatments exist to

2D and 3D imaging of the gas phase close to an operating model catalyst by planar laser induced fluorescence

NASA Astrophysics Data System (ADS)

Blomberg, Sara; Zhou, Jianfeng; Gustafson, Johan; Zetterberg, Johan; Lundgren, Edvin

2016-11-01

In recent years, efforts have been made in catalysis related surface science studies to explore the possibilities to perform experiments at conditions closer to those of a technical catalyst, in particular at increased pressures. Techniques such as high pressure scanning tunneling/atomic force microscopy (HPSTM/AFM), near ambient pressure x-ray photoemission spectroscopy (NAPXPS), surface x-ray diffraction (SXRD) and polarization-modulation infrared reflection absorption spectroscopy (PM-IRAS) at semi-realistic conditions have been used to study the surface structure of model catalysts under reaction conditions, combined with simultaneous mass spectrometry (MS). These studies have provided an increased understanding of the surface dynamics and the structure of the active phase of surfaces and nano particles as a reaction occurs, providing novel information on the structure/activity relationship. However, the surface structure detected during the reaction is sensitive to the composition of the gas phase close to the catalyst surface. Therefore, the catalytic activity of the sample itself will act as a gas-source or gas-sink, and will affect the surface structure, which in turn may complicate the assignment of the active phase. For this reason, we have applied planar laser induced fluorescence (PLIF) to the gas phase in the vicinity of an active model catalysts. Our measurements demonstrate that the gas composition differs significantly close to the catalyst and at the position of the MS, which indeed should have a profound effect on the surface structure. However, PLIF applied to catalytic reactions presents several beneficial properties in addition to investigate the effect of the catalyst on the effective gas composition close to the model catalyst. The high spatial and temporal resolution of PLIF provides a unique tool to visualize the on-set of catalytic reactions and to compare different model catalysts in the same reactive environment. The technique can be applied to a large number of molecules thanks to the technical development of lasers and detectors over the last decades, and is a complementary and visual alternative to traditional MS to be used in environments difficult to asses with MS. In this article we will review general considerations when performing PLIF experiments, our experimental set-up for PLIF and discuss relevant examples of PLIF applied to catalysis.

In-depth proteomic analysis of Varroa destructor: Detection of DWV-complex, ABPV, VdMLV and honeybee proteins in the mite.

PubMed

Erban, Tomas; Harant, Karel; Hubalek, Martin; Vitamvas, Pavel; Kamler, Martin; Poltronieri, Palmiro; Tyl, Jan; Markovic, Martin; Titera, Dalibor

2015-09-11

We investigated pathogens in the parasitic honeybee mite Varroa destructor using nanoLC-MS/MS (TripleTOF) and 2D-E-MS/MS proteomics approaches supplemented with affinity-chromatography to concentrate trace target proteins. Peptides were detected from the currently uncharacterized Varroa destructor Macula-like virus (VdMLV), the deformed wing virus (DWV)-complex and the acute bee paralysis virus (ABPV). Peptide alignments revealed detection of complete structural DWV-complex block VP2-VP1-VP3, VDV-1 helicase and single-amino-acid substitution A/K/Q in VP1, the ABPV structural block VP1-VP4-VP2-VP3 including uncleaved VP4/VP2, and VdMLV coat protein. Isoforms of viral structural proteins of highest abundance were localized via 2D-E. The presence of all types of capsid/coat proteins of a particular virus suggested the presence of virions in Varroa. Also, matches between the MWs of viral structural proteins on 2D-E and their theoretical MWs indicated that viruses were not digested. The absence/scarce detection of non-structural proteins compared with high-abundance structural proteins suggest that the viruses did not replicate in the mite; hence, virions accumulate in the Varroa gut via hemolymph feeding. Hemolymph feeding also resulted in the detection of a variety of honeybee proteins. The advantages of MS-based proteomics for pathogen detection, false-positive pathogen detection, virus replication, posttranslational modifications, and the presence of honeybee proteins in Varroa are discussed.

In-depth proteomic analysis of Varroa destructor: Detection of DWV-complex, ABPV, VdMLV and honeybee proteins in the mite

PubMed Central

Erban, Tomas; Harant, Karel; Hubalek, Martin; Vitamvas, Pavel; Kamler, Martin; Poltronieri, Palmiro; Tyl, Jan; Markovic, Martin; Titera, Dalibor

2015-01-01

We investigated pathogens in the parasitic honeybee mite Varroa destructor using nanoLC-MS/MS (TripleTOF) and 2D-E-MS/MS proteomics approaches supplemented with affinity-chromatography to concentrate trace target proteins. Peptides were detected from the currently uncharacterized Varroa destructor Macula-like virus (VdMLV), the deformed wing virus (DWV)-complex and the acute bee paralysis virus (ABPV). Peptide alignments revealed detection of complete structural DWV-complex block VP2-VP1-VP3, VDV-1 helicase and single-amino-acid substitution A/K/Q in VP1, the ABPV structural block VP1-VP4-VP2-VP3 including uncleaved VP4/VP2, and VdMLV coat protein. Isoforms of viral structural proteins of highest abundance were localized via 2D-E. The presence of all types of capsid/coat proteins of a particular virus suggested the presence of virions in Varroa. Also, matches between the MWs of viral structural proteins on 2D-E and their theoretical MWs indicated that viruses were not digested. The absence/scarce detection of non-structural proteins compared with high-abundance structural proteins suggest that the viruses did not replicate in the mite; hence, virions accumulate in the Varroa gut via hemolymph feeding. Hemolymph feeding also resulted in the detection of a variety of honeybee proteins. The advantages of MS-based proteomics for pathogen detection, false-positive pathogen detection, virus replication, posttranslational modifications, and the presence of honeybee proteins in Varroa are discussed. PMID:26358842

Proanthocyanidin screening by LC-ESI-MS of Portuguese red wines made with teinturier grapes.

PubMed

Teixeira, Natércia; Azevedo, Joana; Mateus, Nuno; de Freitas, Victor

2016-01-01

Proanthocyanidins (PAs) are one of the most important polyphenolic compounds in wine. Among PAs, prodelphinidin (PD) dimers and trimers have not been widely detected in wines due to the lack of available commercial standards and the difficulty to detect and isolate them from natural sources. LC-ESI-MS (liquid chromatography-electrospray ionization-mass spectrometry) with the right chromatographic conditions has proven to be a powerful tool for PAs detection and identification in complex samples. This technique has been applied to an exhaustive study of PA composition of two Portuguese red wines made with teinturier grapes, especially for the identification of PD dimers and trimers. Tandem mass spectrometry (MS/MS) with ion trap provided additional information about the structures of these compounds through the fragmentation patterns of the pseudomolecular ions. A LC-ESI-MS method was optimized and 41 different compounds were found. Among them are included 8 PD dimers and 13 PD trimers. Copyright © 2015 Elsevier Ltd. All rights reserved.

Qualitative and quantitative analysis of branches in dextran using high-performance anion exchange chromatography coupled to quadrupole time-of-flight mass spectrometry.

PubMed

Yi, Lin; Ouyang, Yilan; Sun, Xue; Xu, Naiyu; Linhardt, Robert J; Zhang, Zhenqing

2015-12-04

Dextran, a family of natural polysaccharides, consists of an α (1→6) linked-glucose main (backbone) chain having a number of branches. The determination of the types and the quantities of branches in dextran is important in understanding its various biological roles. In this study, a hyphenated method using high-performance anion exchange chromatography (HPAEC) in parallel with pulsed amperometric detection (PAD) and mass spectrometry (MS) was applied to qualitative and quantitative analysis of dextran branches. A rotary cation-exchange cartridge array desalter was used for removal of salt from the HPAEC eluent making it MS compatible. MS and MS/MS were used to provide structural information on the enzymatically prepared dextran oligosaccharides. PAD provides quantitative data on the ratio of enzyme-resistant, branched dextran oligosaccharides. Both the types and degree of branching found in a variety of dextrans could be simultaneously determined online using this method. Copyright © 2015 Elsevier B.V. All rights reserved.

Complex Coacervate Core Micelles Containing Poly(vinyl alcohol) Inhibit Ice Recrystallization.

PubMed

Sproncken, Christian C M; Surís-Valls, Romà; Cingil, Hande E; Detrembleur, Christophe; Voets, Ilja K

2018-04-10

Complex coacervate core micelles (C3Ms) form upon complexation of oppositely charged copolymers. These co-assembled structures are widely investigated as promising building blocks for encapsulation, nanoparticle synthesis, multimodal imaging, and coating technology. Here, the impact on ice growth is investigated of C3Ms containing poly(vinyl alcohol), PVA, which is well known for its high ice recrystallization inhibition (IRI) activity. The PVA-based C3Ms are prepared upon co-assembly of poly(4-vinyl-N-methyl-pyridinium iodide) and poly(vinyl alcohol)-block-poly(acrylic acid). Their formation conditions, size, and performance as ice recrystallization inhibitors are studied. It is found that the C3Ms exhibit IRI activity at PVA monomer concentrations as low as 1 × 10 -3 m. The IRI efficacy of PVA-C3Ms is similar to that of linear PVA and PVA graft polymers, underlining the influence of vinyl alcohol monomer concentration rather than polymer architecture. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural characterization of trace stilbene glycosides in Lysidice brevicalyx Wei using liquid chromatography/diode-array detection/electrospray ionization tandem mass spectrometry.

PubMed

Hu, Youcai; Qu, Jing; Liu, Yuanyan; Yu, Shishan; Li, Jianbei; Zhang, Jinlan; Du, Dan

2010-01-01

The mass fragmentation patterns of stilbene glycosides isolated from the genus Lysidice were investigated by negative ion electrospray ionization tandem mass spectrometry, and the influence of collision energy on their fragmentation behavior is discussed. It is found that the presence of the Y(0)(-) and B(0)(-) ions in the MS(2) spectra is characteristic for 1-->6 linked diglycosyl stilbenes, while the Y(0)(-), Y(1)(-), and Z(1)(-) ions are representative ions of 1-->2 linked diglycosyl stilbenes. These results indicate that ESI-MS(n) in the negative ion mode can be used to differentiate 1-->6 and 1-->2 linked diglycosyl stilbenes. Based on the fragmentation rules, 9 new trace constituents were identified or tentatively characterized in a fraction of Lysidice brevicalyx by using HPLC/HRMS and HPLC-DAD/ESI-MS(n). The results of the present study can assist in on-line structural identification of analogous constituents and targeted isolation of novel compounds from crude plant extracts.

The use of lithiated adducts for structural analysis of acylglycerols by MS-ESI

USDA-ARS?s Scientific Manuscript database

Electrospray ionization mass spectrometry (ESI-MS) using lithium adducts is the method of choice for the analysis of acyglycerols. The method can be used for the identification of the structures of fatty acid constituents, including the number and location of double bonds and hydroxyl groups. The me...

Native Mass Spectrometry Characterizes the Photosynthetic Reaction Center Complex from the Purple Bacterium Rhodobacter sphaeroides

NASA Astrophysics Data System (ADS)

Zhang, Hao; Harrington, Lucas B.; Lu, Yue; Prado, Mindy; Saer, Rafael; Rempel, Don; Blankenship, Robert E.; Gross, Michael L.

2017-01-01

Native mass spectrometry (MS) is an emerging approach to study protein complexes in their near-native states and to elucidate their stoichiometry and topology. Here, we report a native MS study of the membrane-embedded reaction center (RC) protein complex from the purple photosynthetic bacterium Rhodobacter sphaeroides. The membrane-embedded RC protein complex is stabilized by detergent micelles in aqueous solution, directly introduced into a mass spectrometer by nano-electrospray (nESI), and freed of detergents and dissociated in the gas phase by collisional activation. As the collision energy is increased, the chlorophyll pigments are gradually released from the RC complex, suggesting that native MS introduces a near-native structure that continues to bind pigments. Two bacteriochlorophyll a pigments remain tightly bound to the RC protein at the highest collision energy. The order of pigment release and their resistance to release by gas-phase activation indicates the strength of pigment interaction in the RC complex. This investigation sets the stage for future native MS studies of membrane-embedded photosynthetic pigment-protein and related complexes.

Mass Spec Studio for Integrative Structural Biology

PubMed Central

Rey, Martial; Sarpe, Vladimir; Burns, Kyle; Buse, Joshua; Baker, Charles A.H.; van Dijk, Marc; Wordeman, Linda; Bonvin, Alexandre M.J.J.; Schriemer, David C.

2015-01-01

SUMMARY The integration of biophysical data from multiple sources is critical for developing accurate structural models of large multiprotein systems and their regulators. Mass spectrometry (MS) can be used to measure the insertion location for a wide range of topographically sensitive chemical probes, and such insertion data provide a rich, but disparate set of modeling restraints. We have developed a software platform that integrates the analysis of label-based MS data with protein modeling activities (Mass Spec Studio). Analysis packages can mine any labeling data from any mass spectrometer in a proteomics-grade manner, and link labeling methods with data-directed protein interaction modeling using HADDOCK. Support is provided for hydrogen/ deuterium exchange (HX) and covalent labeling chemistries, including novel acquisition strategies such as targeted HX-tandem MS (MS2) and data-independent HX-MS2. The latter permits the modeling of highly complex systems, which we demonstrate by the analysis of microtubule interactions. PMID:25242457

High throughput screening and antioxidant assay of dibenzo[a,c]cyclooctadiene lignans in modified-ultrasonic and supercritical fluid extracts of Schisandra chinensis Baill by liquid chromatography--mass spectrometry and a free radical-scavenging method.

PubMed

Wang, Ming-Chih; Lai, Yih-Cherng; Chang, Chia-Lin

2008-05-01

Dibenzo[a,c]cyclooctadiene lignans of Schisandra chinensis Baill are well known because of their hepatoprotective activity, antioxidant activity, and anticancer effect. For the isolation of the dibenzo[a,c]cyclooctadiene lignans of Schisandra chinensis Baill two extraction methods were used: modified-ultrasonic extraction and supercritical fluid extraction. A specific and fast analytical method for structure identification is established for quality control because structure elucidation could be accomplished by means of liquid chromatography-mass spectrometry (LC-MS) technologies. The separation and identification of the compounds were completed by: (i) a water-acetonitrile gradient system using a C18 reversed-phase column; (ii) UV detection at 225 nm; (iii) MS/MS experiments with electrospray ionization interface (ESI) ion trap mass spectrometry in the positive mode. Normalized collision energy was used to obtain fragment ions of structural relevance in the LC-MS/MS. These results provided a reliable LC-MS/MS method for the determination of the dibenzo[a,c]cyclooctadiene lignans from Schisandra chinensis Baill. Finally, we also detected 1,1-diphenyl-2-picrylhydrazyl (DPPH) scavenging effects (%) of the modified-ultrasonic and supercritical fluid extracts of Schisandra chinensis Baill compared with 6-hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic acid (Trolox). The antioxidant activities of the modified-ultrasonic and supercritical fluid extracts were lower than that of trolox.

Analysis of neem oils by LC-MS and degradation kinetics of azadirachtin-A in a controlled environment. Characterization of degradation products by HPLC-MS-MS.

PubMed

Barrek, Sami; Paisse, Olivier; Grenier-Loustalot, Marie-Florence

2004-02-01

Since it was first isolated, the oil extracted from seeds of neem (Azadirachtin indica A juss) has been extensively studied in terms of its efficacy as an insecticide. Several industrial formulations are produced as emulsifiable solutions containing a stated titer of the active ingredient azadirachtin-A (AZ-A). The work reported here is the characterization of a formulation of this insecticide marketed under the name of Neem-azal T/S and kinetic studies of the major active ingredient of this formulation. We initially performed liquid-liquid extraction to isolate the neem oil from other ingredients in the commercial mixture. This was followed by a purification using flash chromatography and semi-preparative chromatography, leading to (13)C NMR identification of structures such as azadirachtin-A, azadirachtin-B, and azadirachtin-H. The neem extract was also characterized by HPLC-MS using two ionization sources, APCI (atmospheric pressure chemical ionization) and ESI (electrospray ionization) in positive and negative ion modes of detection. This led to the identification of other compounds present in the extract-azadirachtin-D, azadirachtin-I, deacetylnimbin, deacetylsalannin, nimbin, and salannin. The comparative study of data gathered by use of the two ionization sources is discussed and shows that the ESI source enables the largest number of structures to be identified. In a second part, kinetic changes in the main product (AZ-A) were studied under precise conditions of pH (2, 4, 6, and 8), temperature (40 to 70 degrees C), and light (UV, dark room and in daylight). This enabled us to determine the degradation kinetics of the product (AZ-A) over time. The activation energy of the molecule (75+/-9 kJ mol(-1)) was determined by examining thermal stability in the range 40 to 70 degrees C. The degradation products of this compound were identified by use of HPLC-MS and HPLC-MS-MS. The results enabled proposal of a chemical degradation reaction route for AZ-A under different conditions of pH and temperature. The data show that at room temperature and pH between 4 and 5 the product degrades into two preferential forms that are hydrolyzed to a single product over time and as a function of pH change.

Crystal structure of the coat protein from the GA bacteriophage: model of the unassembled dimer.

PubMed Central

Ni, C. Z.; White, C. A.; Mitchell, R. S.; Wickersham, J.; Kodandapani, R.; Peabody, D. S.; Ely, K. R.

1996-01-01

There are four groups of RNA bacteriophages with distinct antigenic and physicochemical properties due to differences in surface residues of the viral coat proteins. Coat proteins also play a role as translational repressor during the viral life cycle, binding an RNA hairpin within the genome. In this study, the first crystal structure of the coat protein from a Group II phage GA is reported and compared to the Group I MS2 coat protein. The structure of the GA dimer was determined at 2.8 A resolution (R-factor = 0.20). The overall folding pattern of the coat protein is similar to the Group I MS2 coat protein in the intact virus (Golmohammadi R, Valegård K, Fridborg K, Liljas L. 1993, J Mol Biol 234:620-639) or as an unassembled dimer (Ni Cz, Syed R, Kodandapani R. Wickersham J, Peabody DS, Ely KR, 1995, Structure 3:255-263). The structures differ in the FG loops and in the first turn of the alpha A helix. GA and MS2 coat proteins differ in sequence at 49 of 129 amino acid residues. Sequence differences that contribute to distinct immunological and physical properties of the proteins are found at the surface of the intact virus in the AB and FG loops. There are six differences in potential RNA contact residues within the RNA-binding site located in an antiparallel beta-sheet across the dimer interface. Three differences involve residues in the center of this concave site: Lys/Arg 83, Ser/Asn 87, and Asp/Glu 89. Residue 87 was shown by molecular genetics to define RNA-binding specificity by GA or MS2 coat protein (Lim F. Spingola M, Peabody DS, 1994, J Biol Chem 269:9006-9010). This sequence difference reflects recognition of the nucleotide at position -5 in the unpaired loop of the translational operators bound by these coat proteins. In GA, the nucleotide at this position is a purine whereas in MS2, it is a pyrimidine. PMID:8976557

Crystal structure of the coat protein from the GA bacteriophage: model of the unassembled dimer.

PubMed

Ni, C Z; White, C A; Mitchell, R S; Wickersham, J; Kodandapani, R; Peabody, D S; Ely, K R

1996-12-01

There are four groups of RNA bacteriophages with distinct antigenic and physicochemical properties due to differences in surface residues of the viral coat proteins. Coat proteins also play a role as translational repressor during the viral life cycle, binding an RNA hairpin within the genome. In this study, the first crystal structure of the coat protein from a Group II phage GA is reported and compared to the Group I MS2 coat protein. The structure of the GA dimer was determined at 2.8 A resolution (R-factor = 0.20). The overall folding pattern of the coat protein is similar to the Group I MS2 coat protein in the intact virus (Golmohammadi R, Valegård K, Fridborg K, Liljas L. 1993, J Mol Biol 234:620-639) or as an unassembled dimer (Ni Cz, Syed R, Kodandapani R. Wickersham J, Peabody DS, Ely KR, 1995, Structure 3:255-263). The structures differ in the FG loops and in the first turn of the alpha A helix. GA and MS2 coat proteins differ in sequence at 49 of 129 amino acid residues. Sequence differences that contribute to distinct immunological and physical properties of the proteins are found at the surface of the intact virus in the AB and FG loops. There are six differences in potential RNA contact residues within the RNA-binding site located in an antiparallel beta-sheet across the dimer interface. Three differences involve residues in the center of this concave site: Lys/Arg 83, Ser/Asn 87, and Asp/Glu 89. Residue 87 was shown by molecular genetics to define RNA-binding specificity by GA or MS2 coat protein (Lim F. Spingola M, Peabody DS, 1994, J Biol Chem 269:9006-9010). This sequence difference reflects recognition of the nucleotide at position -5 in the unpaired loop of the translational operators bound by these coat proteins. In GA, the nucleotide at this position is a purine whereas in MS2, it is a pyrimidine.

DETECTION OF ARSENOSUGARS FROM KELP EXTRACTS VIA IC-ELECTROSPRAY IONIZATION-MS-MS AND IC MEMBRANE HYDRIDE GENERATION ICP-MS

EPA Science Inventory

The selectivity and the ability to obtain structural information from detection schemes used in arsenic speciation research are growing analytical requirements driven by the growing number of arsenicalS extracted from natural products and the need to minimize misidentification in...

Delivery of chemotherapeutics using spheres made of bioengineered spider silks derived from MaSp1 and MaSp2 proteins.

PubMed

Jastrzebska, Katarzyna; Florczak, Anna; Kucharczyk, Kamil; Lin, Yinnan; Wang, Qin; Mackiewicz, Andrzej; Kaplan, David L; Dams-Kozlowska, Hanna

2018-02-01

Analysis of the properties and chemotherapeutics delivery potential of spheres made of bioengineered spider silks MS1 and MS2. MS1 and MS2 derived from Nephila clavipes dragline silks - MaSp1 and MaSp2, respectively - formed spheres that were compared in terms of physicochemical properties, cytotoxicity and loading/release of chemotherapeutics. MS2 spheres were more dispersed, smaller, of solid core, of higher beta-sheet structure content, and of opposite (negative) charge than MS1 spheres. Preloaded MS2 showed greater applicability for mitoxantrone, while postloaded for etoposide delivery compared with MS1 spheres. However, MS1 spheres were a better choice for doxorubicin delivery than MS2. Bioengineered silks can be tailored to develop a system with optimal drug loading and release properties.

Molecular dynamics study of silicon carbide properties under external dynamic loading

NASA Astrophysics Data System (ADS)

Utkin, A. V.; Fomin, V. M.

2017-10-01

In this study, molecular dynamic simulations of high-velocity impact of a spherical 3C-SiC cluster, with a wide range of velocities (from 100 to 2600 m/s) and with a rigid wall, were performed. The analysis of the final structure shows that no structural phase transformation occurred in the material, despite the high pressure during the collision process.

Detailed Structural Characterization of Sphingolipids via 193 nm Ultraviolet Photodissociation and Ultra High Resolution Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Ryan, Eileen; Nguyen, Catherine Quynh Nhu; Shiea, Christopher; Reid, Gavin E.

2017-07-01

Sphingolipids serve not only as components of cellular membranes but also as bioactive mediators of numerous cellular functions. As the biological activities of these lipids are dependent on their structures, and due to the limitations of conventional ion activation methods employed during tandem mass spectrometry (MS/MS), there is a recognized need for the development of improved structure-specific methods for their comprehensive identification and characterization. Here, positive-ionization mode 193 nm ultraviolet photodissociation (UVPD)-MS/MS has been implemented for the detailed structural characterization of lipid species from a range of sphingolipid classes introduced to the mass spectrometer via electrospray ionization as their lithiated or protonated adducts. These include sphingosine d18:1(4E), dihydrosphingosine (sphinganine) d18:0, sphingadiene d18:2(4E,11Z), the isomeric sphingolipids ceramide d18:1(4E)/18:0 and dihydroceramide d18:0/18:1(9Z), ceramide-1-phosphate d18:1(4Z)/16:0, sphingomyelin d18:1(4E)/18:1(9Z) the glycosphingolipids galactosyl ceramide d18:1(4E)/24:1(15Z) and lactosyl ceramide d18:1(4E)/24:0, and several endogenous lipids present within a porcine brain total lipid extract. In addition to the product ions formed by higher energy collision dissociation (HCD), UVPD is shown to yield a series of novel structurally diagnostic product ions resulting from cleavage of both sphingosine carbon-carbon and acyl chain carbon-carbon double bonds for direct localization of site(s) of unsaturation, as well as via diagnostic cleavages of the sphingosine backbone and N-C amide bond linkages. With activation timescales and dissociation efficiencies similar to those found in conventional MS/MS strategies, this approach is therefore a promising new tool in the arsenal of ion activation techniques toward providing complete structural elucidation in automated, high-throughput lipid analysis workflows.

Study of subband electronic structure of Si δ-doped GaAs using magnetotransport measurements in tilted magnetic fields

NASA Astrophysics Data System (ADS)

Li, G.; Hauser, N.; Jagadish, C.; Antoszewski, J.; Xu, W.

1996-06-01

Si δ-doped GaAs grown by metal organic vapor phase epitaxy (MOVPE) is characterized using magnetotransport measurements in tilted magnetic fields. Angular dependence of the longitudinal magnetoresistance (Rxx) vs the magnetic field (B) traces in tilted magnetic fields is used to examine the existence of a quasi-two-dimensional electron gas. The subband electron densities (ni) are obtained applying fast Fourier transform (FFT) analysis to the Rxx vs B trace and using mobility spectrum (MS) analysis of the magnetic field dependent Hall data. Our results show that (1) the subband electron densities remain roughly constant when the tilted magnetic field with an angle <30° measured from the Si δ-doped plane normal is ramped up to 13 T; (2) FFT analysis of the Rxx vs B trace and MS analysis of the magnetic field dependent Hall data both give the comparable results on subband electron densities of Si δ-doped GaAs with low δ-doping concentration, however, for Si δ-doped GaAs with very high δ-doping concentration, the occupation of the lowest subbands cannot be well resolved in the MS analysis; (3) the highest subband electron mobility reported to date of 45 282 cm2/s V is observed in Si δ-doped GaAs at 77 K in the dark; and (4) the subband electron densities of Si δ-doped GaAs grown by MOVPE at 700 °C are comparable to those grown by MBE at temperatures below 600 °C. A detailed study of magnetotransport properties of Si δ-doped GaAs in the parallel magnetic fields is then carried out to further confirm the subband electronic structures revealed by FFT and MS analysis. Our results are compared to theoretical calculation previously reported in literature. In addition, influence of different cap layer structures on subband electronic structures of Si δ-doped GaAs is observed and also discussed.

Brain responses to verbal stimuli among multiple sclerosis patients with pseudobulbar affect.

PubMed

Haiman, Guy; Pratt, Hillel; Miller, Ariel

2008-08-15

To characterize the brain activity and associated cortical structures involved in pseudobulbar affect (PBA), a condition characterized by uncontrollable episodes of emotional lability in patients with multiple sclerosis (MS). Behavioral responses and event related potentials (ERP) in response to subjectively significant and neutral verbal stimuli were recorded from 33 subjects in 3 groups: 1) MS patients with PBA (MS+PBA); 2) MS patients without PBA (MS); 3) Healthy control subjects (HC). Statistical non-parametric mapping comparisons of ERP source current density distributions between groups were conducted separately for subjectively significant and for neutral stimuli. Behavioral responses showed more impulsive performance in patients with PBA. As expected, almost all ERP waveform comparisons between the MS groups and controls were significant. Source analysis indicated significantly distinct activation in MS+PBA in the vicinity of the somatosensory and motor areas in response to neutral stimuli, and at pre-motor and supplementary motor areas in response to subjectively significant stimuli. Both subjectively significant and neutral stimuli evoked higher current density in MS+PBA compared to both other groups. PBA of MS patients involves cortical structures related to sensory-motor and emotional processing, in addition to overactive involvement of motor cortical areas in response to neutral stimuli. These results may suggest that a 'disinhibition' of a "gate control"-type mechanism for emotional expression may lead to the lower emotional expression threshold of pseudobulbar affect.

DETECTION AND QUANTIFICATION OF THIO-ARSENOSUGAR IN MARINE MOLLUSKS BY IC-ICP-MS WITH AN EMPHASIS ON THE INTERACTION OF ARSENOSUGARS WITH SULFIDE AS A FUNCTION OF PH

EPA Science Inventory

The sulfar analog of As(328)(2,3-dihydroxypropyl-5-deoxy-5-dimethylarsinoyl-ß-D-riboside), abbreviated (As(328-S), was detected and quantified in five species of marine shellfish using IC-ICP-MS with structural verification via IC-ESI-MS/MS. The CAD spectra produced from the par...

Ultra-wideband polarization conversion metasurface and its application cases for antenna radiation enhancement and scattering suppression.

PubMed

Zheng, Yuejun; Zhou, Yulong; Gao, Jun; Cao, Xiangyu; Yang, Huanhuan; Li, Sijia; Xu, Liming; Lan, Junxiang; Jidi, Liaori

2017-11-23

A double-layer complementary metasurface (MS) with ultra-wideband polarization conversion is presented. Then, we propose two application cases by applying the polarization conversion structures to aperture coupling patch antenna (ACPA). Due to the existence of air-filled gap of ACPA, air substrate and dielectric substrate are used to construct the double-layer MS. The polarization conversion bandwidth is broadened toward low-frequency range. Subsequently, two application cases of antenna are proposed and investigated. The simultaneous improvement of radiation and scattering performance of antenna is normally considered as a contradiction. Gratifyingly, the contradiction is addressed in these two application cases. According to different mechanism of scattering suppression (i.e., polarization conversion and phase cancellation), the polarization conversion structures are utilized to construct uniform and orthogonal arrangement configurations. And then, the configurations are integrated into ACPA and two different kinds of metasurface-based (MS-based) ACPA are formed. Radiation properties of the two MS-based ACPAs are improved by optimizing the uniform and orthogonal arrangement configurations. The measured results suggest that ultra-wideband polarization conversion properties of the MS are achieved and radiation enhancement and scattering suppression of the two MS-based ACPAs are obtained. These results demonstrate that we provide novel approach to design high-performance polarization conversion MS and MS-based devices.

Application of characteristic ion filtering with ultra-high performance liquid chromatography quadrupole time of flight tandem mass spectrometry for rapid detection and identification of chemical profiling in Eucommia ulmoides Oliv.

PubMed

He, Mingzhen; Jia, Jia; Li, Junmao; Wu, Bei; Huang, Wenping; Liu, Mi; Li, Yan; Yang, Shilin; Ouyang, Hui; Feng, Yulin

2018-06-15

Efficient targeted identification of chemical constituents from traditional Chinese medicine is still a major challenge. In this study, we used a characteristic ion filtering strategy to characterize compounds of Eucommia ulmoides Oliv. by ultra-high performance liquid chromatography quadrupole time of flight tandem mass spectrometry (UHPLC-ESI-Q-TOF-MS/MS). By using the ion filtering approach, target constituents of Eucommia ulmoides Oliv. were easily tentatively identified from the enormous LC/MS data set. The strategy consisted of the following three steps: 1) To establishing a characteristic ion database by diagnostic product ions or neutral loss fragments; 2) To evaluate the structural information of the compounds by high-resolution diagnostic characteristic ion filtering; 3) To confirm the different classes by chemical profiling according to their MS/MS spectra. In this study, characteristic ions are summarized as five major groups of compounds in Eucommia ulmoides Oliv. In total, 113 compounds were tentatively identified, including 23 potentially novel compounds. The results form a foundation for the quality control and chemical basis of Eucommia ulmoides Oliv. Copyright © 2018 Elsevier B.V. All rights reserved.

Liquid-chromatography thermospray mass-spectrometric study of n-acylamino dilactones and 4-butyrolactones derived from Antimycin-A

USGS Publications Warehouse

Abidi, S.L.; Ha, S.C.; Rosen, R.T.

1990-01-01

Reversed-phase high-performance liquid chromatography—thermospray mass spectrometric (HPLC—MS) characteristics of four sets of lactonic complexes (one 4-butyrolactones and three dilactone complexes) derived from antimycin A were investigated. Three types of 8-hydroxy analogues were also included in the study. Pairs of a–b structures isomeric at the 8-acyloxy ester side-chains were best separated with a high-efficiency octadecylsilica column prior to analysis by HPLC—MS. Mass spectra of the a–b pairs each with identical molecular weights exhibited virtually indistinguishable fragmentation patterns, although their relative intensities were not superimposable. In some cases, HPLC—MS of the title compounds yielded mass chromatograms showing the minor components more easily recognizable than the HPLC—UV counter parts because of the apparent higher ionization efficiency of the minor isomers and increased resolution of subcomponents in the MS system. Under the mobile phase conditions employed, analyte ionization occurred with variable degrees of gas phase ammonolysis depending upon the ammonia concentration of the buffer. Potential applicability of the on-line HPLC—MS technique for the characterization of components in mixtures of antimycin analogues and isomers is demonstrated.

Analytical Strategies to Disclose Repeated Consumption of New Psychoactive Substances by Hair Analysis.

PubMed

Rotolo, Maria C; Klein, Julia; Pacifici, Roberta; Busardo, Francesco Paolo; Pichini, Simona; Marchei, Emilia

2017-01-01

New psychoactive substances (NPS) are a heterogenic group of substances with different chemical structures and psychotropic effects. Many pharmacotoxicological laboratories performing drug testing in conventional and nonconventional biological matrices for clinical and forensic purposes do not include screening procedures for NPS in their routine protocols. This is mainly due to the continued entry in the market of newly synthesized products, the low availability of reference standards, in particular of their metabolites, the low availability of immunochemical kits, etc. Moreover, many of the new compounds are very potent, and low doses ingested will lead to low concentrations in biological matrices, especially in hair. Hair analysis has become a powerful tool for detecting chronic drug use and has become a routine technique in forensic toxicology laboratories. The aim of this study was to set up analytical strategies to identify repeated consumption of NPS by hair analysis. Although UHPLC-MS/MS may represent the elective technique in studying NPS, a combination of both GC-MS and UHPLC-MS/MS techniques is useful in creating a complete toxicological image. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Validity, invariance and responsiveness of a self-report measure of functional limitations and disability in multiple sclerosis.

PubMed

Motl, Robert W; McAuley, Edward; Suh, Yoojin

2010-01-01

This study examined the structural and external aspects of score validity for the abbreviated Late Life-Function and Disability Inventory (LL-FDI) as well as its longitudinal measurement invariance and responsiveness in individuals with multiple sclerosis (MS). The sample included 292 individuals with MS who completed a battery of questionnaires on two occasions separated by 6 months. The battery included the abbreviated LL-FDI along with measures of mobility disability; neurological impairments; symptoms of fatigue, anxiety, depression and pain; health status; and quality of life. The data were analysed using Analysis of Moment Structures (AMOS) and Statistical Package for the Social Sciences (SPSS), versions 16.0. Confirmatory factor analysis supported the structural validity and longitudinal measurement invariance of the disability and functional limitations components of the abbreviated LL-FDI. MANOVA and bivariate correlations supported the external aspects of score validity based on differences in mean scores as a function of clinical MS course (relapsing vs. progressive) and level of mobility disability (mild vs. moderate mobility disability) and associations with measures of neurological impairments, symptoms, health status and QOL, respectively. ANOVA established the responsiveness (i.e., sensitivity for reflecting clinically important differences in health status across time) of the functional limitations and disability components of the abbreviated LL-FDI for detecting changes in mobility disability across 6-months. Such findings provide a new option for the measurement of functional limitations and disability using the abbreviated LL-FDI in persons with MS.

Mapping face encoding using functional MRI in multiple sclerosis across disease phenotypes.

PubMed

Rocca, Maria A; Vacchi, Laura; Rodegher, Mariaemma; Meani, Alessandro; Martinelli, Vittorio; Possa, Francesca; Comi, Giancarlo; Falini, Andrea; Filippi, Massimo

2017-10-01

Using fMRI during a face encoding (FE) task, we investigated the behavioral and fMRI correlates of FE in patients with relapse-onset multiple sclerosis (MS) at different stages of the disease and their relation with attentive-executive performance and structural MRI measures of disease-related damage. A fMRI FE task was administered to 75 MS patients (11 clinically isolated syndromes - CIS, 40 relapsing-remitting - RRMS - and 24 secondary progressive - SPMS) and 22 healthy controls (HC). fMRI activity during the face encoding condition was correlated with behavioral, clinical, neuropsychological and structural MRI variables. All study subjects activated brain regions belonging to face perception and encoding network, and deactivated areas of the default-mode network. Compared to HC, MS patients had the concomitant presence of areas of increased and decreased activations as well as increased and decreased deactivations. Compared to HC or RRMS, CIS patients experienced an increased recruitment of posterior-visual areas. Thalami, para-hippocampal gyri and right anterior cingulum were more activated in RRMS vs CIS or SPMS patients, while an increased recruitment of frontal areas was observed in SPMS vs RRMS. Areas of abnormal activations were significantly correlated with clinical, cognitive-behavioral and structural MRI measures. Abnormalities of FE network occur in MS and vary across disease clinical phenotypes. Early in the disease, an increased recruitment of areas typically devoted to face perception and encoding occurs. In SPMS patients, abnormal functional recruitment of frontal lobe areas might contribute to the severity of clinical manifestations.

Labdane diterpenes from Juniperus communis L. berries.

PubMed

Martin, Anne Marie; Queiroz, Emerson Ferreira; Marston, Andrew; Hostettmann, Kurt

2006-01-01

A phytochemical study of the methanol extract of Juniperus communis berries was undertaken. The crude extract was analysed by HPLC-UV and the isolation of the minor compounds was performed by centrifugal partition chromatography. By this means, five diterpenes were isolated, one of which was a new labdane diterpene 15,16-epoxy-12-hydroxy-8(17),13(16),14-labdatrien-19-oic acid. The structures of the isolated compounds were elucidated by spectroscopic methods, including UV, NMR, MS and HR-MS.

Nuclear Data Sheets for A = 52

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dong, Yang; Junde, Huo

2015-09-15

The nuclear structure data belonging to all nuclei with mass number A=52 have been compiled and evaluated using experimental nuclear reaction data and decay data available before July 10, 2015. This evaluaton supersedes the previous publication for this msss chain (2007Hu08, Nuclear Data Sheets 108, 773 (2007)). The data for the ε decay of {sup 52}Co (104 ms) and the ε decay of {sup 52}Ni (40.8 ms) are both incomplete, so new studies would be useful.

Characterization of a PEGylated protein therapeutic by ion exchange chromatography with on-line detection by native ESI MS and MS/MS.

PubMed

Muneeruddin, K; Bobst, C E; Frenkel, R; Houde, D; Turyan, I; Sosic, Z; Kaltashov, I A

2017-01-16

Detailed profiling of both enzymatic (e.g., glycosylation) and non-enzymatic (e.g., oxidation and deamidation) post-translational modifications (PTMs) is frequently required for the quality assessment of protein-based drugs. Challenging as it is, this task is further complicated for the so-called second-generation biopharmaceuticals, which also contain "designer PTMs" introduced to either enhance their pharmacokinetic profiles (e.g., PEGylated proteins) or endow them with therapeutic activity (e.g., protein-drug conjugates). Such modifications of protein covalent structure can dramatically increase structural heterogeneity, making the very notion of "molecular mass" meaningless, as ions representing different glycoforms of a PEGylated protein may have nearly identical distributions of ionic current as a function of m/z, making their contributions to the mass spectrum impossible to distinguish. In this work we demonstrate that a combination of ion exchange chromatography (IXC) with on-line detection by electrospray ionization mass spectrometry (ESI MS) and methods of ion manipulation in the gas phase (limited charge reduction and collision-induced dissociation) allows meaningful structural information to be obtained on a structurally heterogeneous sample of PEGylated interferon β-1a. IXC profiling of the protein sample gives rise to a convoluted chromatogram with several partially resolved peaks which can represent both deamidation and different glycosylation patterns within the protein, as well as varying extent of PEGylation. Thus, profiling the protein with on-line IXC/ESI/MS/MS allows it to be characterized by providing information on three different types of PTMs (designer, enzymatic and non-enzymatic) within a single protein therapeutic.

Finite Element Analysis of Saferooms Subjected to Tornado Impact Loads

NASA Astrophysics Data System (ADS)

Parfilko, Y.; Amaral de Arruda, F.; Varela, B.

2017-10-01

A Tornado is one of the most dreadful and unpredictable events in nature. Unfortunately, weather and geographic conditions make a large portion of the United States prone to this phenomenon. Tornado saferooms are monolithic reinforced concrete protective structures engineered to guard against these natural disasters. Saferooms must withstand impacts and wind loads from EF-5 tornadoes - where the wind speed reaches up to 150 m/s (300 mph) and airborne projectiles can reach up to 50 m/s (100 mph). The objective of this work is to evaluate the performance of a saferoom under impact from tornado-generated debris and tornado-dragged vehicles. Numerical simulations were performed to model the impact problem using explicit dynamics and energy methods. Finite element models of the saferoom, windborne debris, and vehicle models were studied using the LS-DYNA software. RHT concrete material was used to model the saferoom and vehicle models from NCAC were used to characterize damage from impacts at various speeds. Simulation results indicate good performance of the saferoom structure at vehicle impact speeds up to 25 meters per second. Damage is more significant and increases nonlinearly starting at impact velocities of 35 m/s (78 mph). Results of this study give valuable insight into the dynamic response of saferooms subjected to projectile impacts, and provide design considerations for civilian protective structures. Further work is being done to validate the models with experimental measurements.

High resolution mass spectrometric brain proteomics by MALDI-FTICR-MS combined with determination of P, S, Cu, Zn and Fe by LA-ICP-MS

NASA Astrophysics Data System (ADS)

Becker, J. Susanne; Zoriy, Miroslav; Przybylski, Michael; Becker, J. Sabine

2007-03-01

The combination of atomic and molecular mass spectrometric methods was applied for characterization and identification of several human proteins from Alzheimer's diseased brain. A brain protein mixture was separated by two-dimensional (2D) gel electrophoresis and the protein spots were fast screened by microlocal analysis using LA-ICP-MS (laser ablation inductively coupled plasma mass spectrometry) in respect to phosphorus, sulfur, copper, zinc and iron content. Five selected protein spots in 2D gel containing these elements were investigated after tryptic digestion by matrix assisted laser desorption ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FTICR-MS). Than element concentrations (P, Cu, Zn and Fe) were determined in three identified human brain proteins by LA-ICP-MS in the 2D gel. Results of structure analysis of human brain proteins by MALDI-FTICR-MS were combined with those of the direct determination of phosphorus, copper, zinc and iron concentrations in protein spots with LA-ICP-MS. From the results of atomic and molecular mass spectrometric techniques the human brain proteins were characterized in respect to their structure, sequence, phosphorylation state and metal content as well.

Pittsburgh compound-B PET white matter imaging and cognitive function in late multiple sclerosis.

PubMed

Zeydan, Burcu; Lowe, Val J; Schwarz, Christopher G; Przybelski, Scott A; Tosakulwong, Nirubol; Zuk, Samantha M; Senjem, Matthew L; Gunter, Jeffrey L; Roberts, Rosebud O; Mielke, Michelle M; Benarroch, Eduardo E; Rodriguez, Moses; Machulda, Mary M; Lesnick, Timothy G; Knopman, David S; Petersen, Ronald C; Jack, Clifford R; Kantarci, Kejal; Kantarci, Orhun H

2018-05-01

There is growing interest in white matter (WM) imaging with positron emission tomography (PET). We studied the association of cognitive function in late multiple sclerosis (MS) with cortical and WM Pittsburgh compound-B PET (PiB-PET) binding. In the population-based Mayo Clinic Study of Aging, 24 of 4869 participants had MS (12 underwent PiB-PET). Controls were age and sex matched (5:1). We used automated or semi-automated processing for quantitative image analyses and conditional logistic regression for group differences. MS patients had lower memory ( p = 0.03) and language ( p = 0.02) performance; smaller thalamic volumes ( p = 0.003); and thinner temporal ( p = 0.001) and frontal ( p = 0.045) cortices on magnetic resonance imaging (MRI) than controls. There was no difference in global cortical PiB standardized uptake value ratios between MS and controls ( p = 0.35). PiB uptake was lower in areas of WM hyperintensities compared to normal-appearing white matter (NAWM) in MS ( p = 0.0002). Reduced PiB uptake in both the areas of WM hyperintensities ( r = 0.65; p = 0.02) and NAWM ( r = 0.69; p = 0.01) was associated with decreased visuospatial performance in MS. PiB uptake in the cortex in late MS is not different from normal age-matched controls. PiB uptake in the WM in late MS may be a marker of the large network structures' integrity such as those involved in visuospatial performance.

Comprehensive and quantitative profiling of lipid species in human milk, cow milk and a phospholipid-enriched milk formula by GC and MS/MSALL.

PubMed

Sokol, Elena; Ulven, Trond; Færgeman, Nils J; Ejsing, Christer S

2015-06-01

Here we present a workflow for in-depth analysis of milk lipids that combines gas chromatography (GC) for fatty acid (FA) profiling and a shotgun lipidomics routine termed MS/MS ALL for structural characterization of molecular lipid species. To evaluate the performance of the workflow we performed a comparative lipid analysis of human milk, cow milk, and Lacprodan® PL-20, a phospholipid-enriched milk protein concentrate for infant formula. The GC analysis showed that human milk and Lacprodan have a similar FA profile with higher levels of unsaturated FAs as compared to cow milk. In-depth lipidomic analysis by MS/MS ALL revealed that each type of milk sample comprised distinct composition of molecular lipid species. Lipid class composition showed that the human and cow milk contain a higher proportion of triacylglycerols (TAGs) as compared to Lacprodan. Notably, the MS/MS ALL analysis demonstrated that the similar FA profile of human milk and Lacprodan determined by GC analysis is attributed to the composition of individual TAG species in human milk and glycerophospholipid species in Lacprodan. Moreover, the analysis of TAG molecules in Lacprodan and cow milk showed a high proportion of short-chain FAs that could not be monitored by GC analysis. The results presented here show that complementary GC and MS/MS ALL analysis is a powerful approach for characterization of molecular lipid species in milk and milk products. : Milk lipid analysis is routinely performed using gas chromatography. This method reports the total fatty acid composition of all milk lipids, but provides no structural or quantitative information about individual lipid molecules in milk or milk products. Here we present a workflow that integrates gas chromatography for fatty acid profiling and a shotgun lipidomics routine termed MS/MS ALL for structural analysis and quantification of molecular lipid species. We demonstrate the efficacy of this complementary workflow by a comparative analysis of molecular lipid species in human milk, cow milk, and a milk-based supplement used for infant formula.

Structural measurements and cell line studies of the copper-PEG-Rifampicin complex against Mycobacterium tuberculosis.

PubMed

Manning, Thomas; Mikula, Rachel; Wylie, Greg; Phillips, Dennis; Jarvis, Jackie; Zhang, Fengli

2015-02-01

The bacterium responsible for tuberculosis is increasing its resistance to antibiotics resulting in new multidrug-resistant Mycobacterium tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB). In this study, several analytical techniques including NMR, FT-ICR, MALDI-MS, LC-MS and UV/Vis are used to study the copper-Rifampicin-Polyethylene glycol (PEG-3350) complex. The copper (II) cation is a carrier for the antibiotic Rifampicin as well as nutrients for the bacterium. The NIH-NIAID cell line containing several Tb strains (including antibiotic resistant strains) is tested against seven copper-PEG-RIF complex variations. Copyright © 2014 Elsevier Ltd. All rights reserved.

Long-term structural retinal changes in patients with optic neuritis related to multiple sclerosis.

PubMed

Andersen, Maria Rene; Roar, Malte; Sejbaek, Tobias; Illes, Zsolt; Grauslund, Jakob

2017-01-01

To evaluate the long-term structural and functional outcome in patients with multiple sclerosis (MS) with and without a history of optic neuritis (ON). This was a cross-sectional study of 82 patients diagnosed with MS between 2000 and 2006 from a tertiary hospital center in Denmark. Patients gave a self-reported history of ON, and functional (visual acuity and color vision) and structural (spectra domain optical coherence tomography) markers of vision were tested. Median age and MS duration at the time of the clinical examination were 49.9 years (range 30.7-72.6 years) and 13 years (range 9-15 years), respectively. ON was not associated with impairment of visual acuity or color vision. Twenty-three patients had a history of ON in at least one eye. Compared to non-affected patients, these had a lower inferior (109 vs 113 μm, P =0.04) and temporal retinal nerve fiber layer (RNFL) thickness (56 vs 67 μm, P =0.01). In an age- and sex-adjusted logistic regression model, lower inferior and temporal RNFL were associated with a higher risk of ON (odds ratio [OR] 1.56 [95% confidence interval {CI} 1.01-2.41] and OR 1.74 [95% CI 1.10-2.77] per 10 μm decrement in RNFL thickness, respectively). Twenty patients had a history of ON in one eye. Compared to the non-affected eye, this eye had a lower RNFL (109 vs 115 μm, P =0.04) and a higher central retinal thickness/mean RNFL ratio (2.7 vs 2.4, P =0.04). Although patients with long-term MS and a previous history of ON did not have any functional loss of vision, structural neurodegeneration could be demonstrated in the affected eye.

Differentiation of isomeric N-glycan structures by normal-phase liquid chromatography-MALDI-TOF/TOF tandem mass spectrometry.

PubMed

Maslen, Sarah; Sadowski, Pawel; Adam, Alex; Lilley, Kathryn; Stephens, Elaine

2006-12-15

The detailed characterization of protein N-glycosylation is very demanding given the many different glycoforms and structural isomers that can exist on glycoproteins. Here we report a fast and sensitive method for the extensive structure elucidation of reducing-end labeled N-glycan mixtures using a combination of capillary normal-phase HPLC coupled off-line to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and TOF/TOF-MS/MS. Using this method, isobaric N-glycans released from honey bee phospholipase A2 and Arabidopsis thaliana glycoproteins were separated by normal-phase chromatography and subsequently identified by key fragment ions in the MALDI-TOF/TOF tandem mass spectra. In addition, linkage and branching information were provided by abundant cross-ring and "elimination" fragment ions in the MALDI-CID spectra that gave extensive structural information. Furthermore, the fragmentation characteristics of N-glycans reductively aminated with 2-aminobenzoic acid and 2-aminobenzamide were compared. The identification of N-glycans containing 3-linked core fucose was facilitated by distinctive ions present only in the MALDI-CID spectra of 2-aminobenzoic acid-labeled oligosaccharides. To our knowledge, this is the first MS/MS-based technique that allows confident identification of N-glycans containing 3-linked core fucose, which is a major allergenic determinant on insect and plant glycoproteins.

Discovery of Phosphodiesterase 10A (PDE10A) PET Tracer AMG 580 to Support Clinical Studies.

PubMed

Hu, Essa; Chen, Ning; Kunz, Roxanne K; Hwang, Dah-Ren; Michelsen, Klaus; Davis, Carl; Ma, Ji; Shi, Jianxia; Lester-Zeiner, Dianna; Hungate, Randall; Treanor, James; Chen, Hang; Allen, Jennifer R

2016-07-14

We report the discovery of PDE10A PET tracer AMG 580 developed to support proof of concept studies with PDE10A inhibitors in the clinic. To find a tracer with higher binding potential (BPND) in NHP than our previously reported tracer 1, we implemented a surface plasmon resonance assay to measure the binding off-rate to identify candidates with slower washout rate in vivo. Five candidates (2-6) from two structurally distinct scaffolds were identified that possessed both the in vitro characteristics that would favor central penetration and the structural features necessary for PET isotope radiolabeling. Two cinnolines (2, 3) and one keto-benzimidazole (5) exhibited PDE10A target specificity and brain uptake comparable to or better than 1 in the in vivo LC-MS/MS kinetics distribution study in SD rats. In NHP PET imaging study, [(18)F]-5 produced a significantly improved BPND of 3.1 and was nominated as PDE10A PET tracer clinical candidate for further studies.

Functionalized Ergot-alkaloids as potential dopamine D3 receptor agonists for treatment of schizophrenia

NASA Astrophysics Data System (ADS)

Ivanova, Bojidarka; Spiteller, Michael

2012-12-01

The relationship between the molecular structure and physical properties of functionalized naturally occurred Ergot-alkaloids as potential dopamine D3 receptor agonists is presented. The molecular modeling of the ergoline-skeleton is based on the comprehensive theoretical study of the binding affinity of the isolated chemicals towards the active sites of the D3 sub-type receptor (D3R) loops. The studied proton accepting ability under physiological conditions allows classifying four types of monocationics, characterizing with the different binding modes to D3R involving selected amino acid residues to the active sites. These results marked the pharmaceutical potential and clinical usage of the reported compounds as antipsychotic drugs for Schizophrenia treatment, since they allowed evaluating the highlights of the different hypothesizes of the biochemical causes the illness. The applied complex approach for theoretical and experimental elucidation, including quantum chemistry method, electrospray ionization (ESI) and matrix assisted laser desorption/ionization (MALDI) mass spectrometric (MS) methods, nuclear magnetic resonance and vibrational IR and Raman spectroscopy on the isolated fifteen novel derivatives (1)-(15) and their different protonated forms (1a)-(15a) evidenced a strong dependence of molecular conformation, physical properties and binding affinity. Thus, the semi-synthetic functionalization of the naturally occurred products (NPs), provided significant possibilities to further molecular drugs-design and development of novel derivatives with wanted biological function, using the established profile of selected classes/families of NPs. The work described chiefly the non-linear (NL) approach for the interpretation of the mass chromatograms on the performed hybrid high performance liquid chromatography (HPLC) tandem MS/MS and MS/MS/MS experiments, discussing the merits and great diversity of instrumentation flexibility, thus achieving fundamental structural information, indispensable for the analysis of Ergot-alkaloid derivatives, which under the physiological conditions easily converted to d-lysergic acid (LSD).

Global disulfide bond profiling for crude snake venom using dimethyl labeling coupled with mass spectrometry and RADAR algorithm.

PubMed

Huang, Sheng Yu; Chen, Sung Fang; Chen, Chun Hao; Huang, Hsuan Wei; Wu, Wen Guey; Sung, Wang Chou

2014-09-02

Snake venom consists of toxin proteins with multiple disulfide linkages to generate unique structures and biological functions. Determination of these cysteine connections usually requires the purification of each protein followed by structural analysis. In this study, dimethyl labeling coupled with LC-MS/MS and RADAR algorithm was developed to identify the disulfide bonds in crude snake venom. Without any protein separation, the disulfide linkages of several cytotoxins and PLA2 could be solved, including more than 20 disulfide bonds. The results show that this method is capable of analyzing protein mixture. In addition, the approach was also used to compare native cytotoxin 3 (CTX III) and its scrambled isomer, another category of protein mixture, for unknown disulfide bonds. Two disulfide-linked peptides were observed in the native CTX III, and 10 in its scrambled form, X-CTX III. This is the first study that reports a platform for the global cysteine connection analysis on a protein mixture. The proposed method is simple and automatic, offering an efficient tool for structural and functional studies of venom proteins.

Elucidating structural and molecular mechanisms of β-arrestin-biased agonism at GPCRs via MS-based proteomics.

PubMed

Xiao, Kunhong; Sun, Jinpeng

2018-01-01

The discovery of β-arrestin-dependent GPCR signaling has led to an exciting new field in GPCR pharmacology: to develop "biased agonists" that can selectively target a specific downstream signaling pathway that elicits beneficial therapeutic effects without activating other pathways that elicit negative side effects. This new trend in GPCR drug discovery requires us to understand the structural and molecular mechanisms of β-arrestin-biased agonism, which largely remain unclear. We have used cutting-edge mass spectrometry (MS)-based proteomics, combined with systems, chemical and structural biology to study protein function, macromolecular interaction, protein expression and posttranslational modifications in the β-arrestin-dependent GPCR signaling. These high-throughput proteomic studies have provided a systems view of β-arrestin-biased agonism from several perspectives: distinct receptor phosphorylation barcode, multiple receptor conformations, distinct β-arrestin conformations, and ligand-specific signaling. The information obtained from these studies offers new insights into the molecular basis of GPCR regulation by β-arrestin and provides a potential platform for developing novel therapeutic interventions through GPCRs. Copyright © 2017 Elsevier Inc. All rights reserved.

Prediction of biotransformation products of the fungicide fluopyram by electrochemistry coupled online to liquid chromatography-mass spectrometry and comparison with in vitro microsomal assays.

PubMed

Mekonnen, Tessema F; Panne, Ulrich; Koch, Matthias

2018-04-01

Biotransformation processes of fluopyram (FLP), a new succinate dehydrogenase inhibitor (SDHI) fungicide, were investigated by electrochemistry (EC) coupled online to liquid chromatography (LC) and electrospray mass spectrometry (ESI-MS). Oxidative phase I metabolite production was achieved using an electrochemical flow-through cell equipped with a boron-doped diamond (BDD) electrode. Structural elucidation and prediction of oxidative metabolism pathways were assured by retention time, isotopic patterns, fragmentation, and accurate mass measurements using EC/LC/MS, LC-MS/MS, and/or high-resolution mass spectrometry (HRMS). The results obtained by EC were compared with conventional in vitro studies by incubating FLP with rat and human liver microsomes (RLM, HLM). Known phase I metabolites of FLP (benzamide, benzoic acid, 7-hydroxyl, 8-hydroxyl, 7,8-dihydroxyl FLP, lactam FLP, pyridyl acetic acid, and Z/E-olefin FLP) were successfully simulated by EC/LC/MS. New metabolites including an imide, hydroxyl lactam, and 7-hydroxyl pyridyl acetic acid oxidative metabolites were predicted for the first time in our study using EC/LC/MS and liver microsomes. We found oxidation by dechlorination to be one of the major metabolism mechanisms of FLP. Thus, our results revealed that EC/LC/MS-based metabolic elucidation was more advantageous on time and cost of analysis and enabled matrix-free detection with valuable information about the mechanisms and intermediates of metabolism processes. Graphical abstract Oxidative metabolism of fluopyram.

Semi-Targeted Analysis of Complex Matrices by ESI FT-ICR MS or How an Experimental Bias may be Used as an Analytical Tool.

PubMed

Hertzog, Jasmine; Carré, Vincent; Dufour, Anthony; Aubriet, Frédéric

2018-03-01

Ammonia is well suited to favor deprotonation process in electrospray ionization mass spectrometry (ESI-MS) to increase the formation of [M - H] - . Nevertheless, NH 3 may react with carbonyl compounds (aldehyde, ketone) and bias the composition description of the investigated sample. This is of significant importance in the study of complex mixture such as oil or bio-oil. To assess the ability of primary amines to form imines with carbonyl compounds during the ESI-MS process, two aldehydes (vanillin and cinnamaldehyde) and two ketones (butyrophenone and trihydroxyacetophenone) have been infused in an ESI source with ammonia and two different amines (aniline and 3-chloronaniline). The (+) ESI-MS analyses have demonstrated the formation of imine whatever the considered carbonyl compound and the used primary amine, the structure of which was extensively studied by tandem mass spectrometry. Thus, it has been established that the addition of ammonia, in the solution infused in an ESI source, may alter the composition description of a complex mixture and leads to misinterpretations due to the formation of imines. Nevertheless, this experimental bias can be used to identify the carbonyl compounds in a pyrolysis bio-oil. As we demonstrated, infusion of the bio-oil with 3-chloroaniline in ESI source leads to specifically derivatized carbonyl compounds. Thanks to their chlorine isotopic pattern and the high mass measurement accuracy, (+) ESI Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) unambiguously highlighted them from the numerous C x H y O z bio-oil components. These results offer a new perspective into the detailed molecular structure of complex mixtures such as bio-oils. Graphical Abstract ᅟ.

Quantitative collision induced mass spectrometry of substituted piperazines - A correlative analysis between theory and experiment

NASA Astrophysics Data System (ADS)

Ivanova, Bojidarka; Spiteller, Michael

2017-12-01

The present paper deals with quantitative kinetics and thermodynamics of collision induced dissociation (CID) reactions of piperazines under different experimental conditions together with a systematic description of effect of counter-ions on common MS fragment reactions of piperazines; and intra-molecular effect of quaternary cyclization of substituted piperazines yielding to quaternary salts. There are discussed quantitative model equations of rate constants as well as free Gibbs energies of series of m-independent CID fragment processes in GP, which have been evidenced experimentally. Both kinetic and thermodynamic parameters are also predicted by computational density functional theory (DFT) and ab initio both static and dynamic methods. The paper examines validity of Maxwell-Boltzmann distribution to non-Boltzmann CID processes in quantitatively as well. The experiments conducted within the latter framework yield to an excellent correspondence with theoretical quantum chemical modeling. The important property of presented model equations of reaction kinetics is the applicability in predicting unknown and assigning of known mass spectrometric (MS) patterns. The nature of "GP" continuum of CID-MS coupled scheme of measurements with electrospray ionization (ESI) source is discussed, performing parallel computations in gas-phase (GP) and polar continuum at different temperatures and ionic strengths. The effect of pressure is presented. The study contributes significantly to methodological and phenomenological developments of CID-MS and its analytical implementations for quantitative and structural analyses. It also demonstrates great prospective of a complementary application of experimental CID-MS and computational quantum chemistry studying chemical reactivity, among others. To a considerable extend this work underlies the place of computational quantum chemistry to the field of experimental analytical chemistry in particular highlighting the structural analysis.

Semi-Targeted Analysis of Complex Matrices by ESI FT-ICR MS or How an Experimental Bias may be Used as an Analytical Tool

NASA Astrophysics Data System (ADS)

Hertzog, Jasmine; Carré, Vincent; Dufour, Anthony; Aubriet, Frédéric

2018-03-01

Ammonia is well suited to favor deprotonation process in electrospray ionization mass spectrometry (ESI-MS) to increase the formation of [M - H]-. Nevertheless, NH3 may react with carbonyl compounds (aldehyde, ketone) and bias the composition description of the investigated sample. This is of significant importance in the study of complex mixture such as oil or bio-oil. To assess the ability of primary amines to form imines with carbonyl compounds during the ESI-MS process, two aldehydes (vanillin and cinnamaldehyde) and two ketones (butyrophenone and trihydroxyacetophenone) have been infused in an ESI source with ammonia and two different amines (aniline and 3-chloronaniline). The (+) ESI-MS analyses have demonstrated the formation of imine whatever the considered carbonyl compound and the used primary amine, the structure of which was extensively studied by tandem mass spectrometry. Thus, it has been established that the addition of ammonia, in the solution infused in an ESI source, may alter the composition description of a complex mixture and leads to misinterpretations due to the formation of imines. Nevertheless, this experimental bias can be used to identify the carbonyl compounds in a pyrolysis bio-oil. As we demonstrated, infusion of the bio-oil with 3-chloroaniline in ESI source leads to specifically derivatized carbonyl compounds. Thanks to their chlorine isotopic pattern and the high mass measurement accuracy, (+) ESI Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) unambiguously highlighted them from the numerous CxHyOz bio-oil components. These results offer a new perspective into the detailed molecular structure of complex mixtures such as bio-oils. [Figure not available: see fulltext.

Social support network and quality of life in multiple sclerosis patients.

PubMed

Costa, David Castro; Sá, Maria José; Calheiros, José Manuel

2017-05-01

To analyse the relationship between the social support network (SSN) and health related quality of life (HRQOL) in multiple sclerosis (MS) patients. The sample comprised 150 consecutive MS patients attending our MS clinic. To assess the socio-demographic data, a specifically designed questionnaire was applied. The HRQOL dimensions were measured with the Short-Form Health Survey Questionnaire-SF36 and the SSN with the Medical Outcomes Study Social Support Survey. Spearman's correlation was used to compare the magnitude of the relationship between the SSN and HRQOL. The mean patient age was 41.7 years (± 10.4; range: 18-70 yr); the mean Expanded Disability Status Score was 2.5 (±2.4; range: 0-9). There was a statistically significant correlation between the structure of the SSN and the HRQOL. The composition of the SSN, social group membership and participation in voluntary work have an important role in the HRQOL of patients with MS.

Substitution pattern elucidation of hydroxypropyl Pinus pinaster (Ait.) bark polyflavonoid derivatives by ESI(-)-MS/MS.

PubMed

García Marrero, Danny E; Glasser, Wolfgang G; Pizzi, Antonio; Paczkowski, Sebastian; Laborie, Marie-Pierre G

2014-10-01

The structure of condensed tannins (CTs) from Pinus pinaster bark extract and their hydroxypropylated derivatives with four degrees of substitution (DS 1, 2, 3 and 4) has been characterized for the first time using negative-ion mode electrospray ionization tandem mass spectrometry (ESI(-)-MS/MS). The results showed that P. pinaster bark CTs possess structural homogeneity in terms of monomeric units (C(15), catechin). The oligomer sizes were detected to be dimers to heptamers. The derivatives showed typical phenyl-propyl ether mass fragmentation by substituent elimination (58 amu) and inherent C(15) flavonoid fissions. The relative abundance of the product ions revealed a preferential triple, tetra-/penta- and octa- hydroxypropylation substitution pattern in the monomer, dimer and trimer derivatives, respectively. A defined order of -OH reactivity towards propylene oxide was established by means of multistage experiments (A-ring ≥ B-ring > C-ring). A high structural heterogeneity of the modified oligomers was detected. Copyright © 2014 John Wiley & Sons, Ltd.

Mass spectrometric analyses of organophosphate insecticide oxon protein adducts.

PubMed

Thompson, Charles M; Prins, John M; George, Kathleen M

2010-01-01

Organophosphate (OP) insecticides continue to be used to control insect pests. Acute and chronic exposures to OP insecticides have been documented to cause adverse health effects, but few OP-adducted proteins have been correlated with these illnesses at the molecular level. Our aim was to review the literature covering the current state of the art in mass spectrometry (MS) used to identify OP protein biomarkers. We identified general and specific research reports related to OP insecticides, OP toxicity, OP structure, and protein MS by searching PubMed and Chemical Abstracts for articles published before December 2008. A number of OP-based insecticides share common structural elements that result in predictable OP-protein adducts. The resultant OP-protein adducts show an increase in molecular mass that can be identified by MS and correlated with the OP agent. Customized OP-containing probes have also been used to tag and identify protein targets that can be identified by MS. MS is a useful and emerging tool for the identification of proteins that are modified by activated organophosphate insecticides. MS can characterize the structure of the OP adduct and also the specific amino acid residue that forms the key bond with the OP. Each protein that is modified in a unique way by an OP represents a unique molecular biomarker that with further research can lead to new correlations with exposure.

Mass Spectrometric Analyses of Organophosphate Insecticide Oxon Protein Adducts

PubMed Central

Thompson, Charles M.; Prins, John M.; George, Kathleen M.

2010-01-01

Objective Organophosphate (OP) insecticides continue to be used to control insect pests. Acute and chronic exposures to OP insecticides have been documented to cause adverse health effects, but few OP-adducted proteins have been correlated with these illnesses at the molecular level. Our aim was to review the literature covering the current state of the art in mass spectrometry (MS) used to identify OP protein biomarkers. Data sources and extraction We identified general and specific research reports related to OP insecticides, OP toxicity, OP structure, and protein MS by searching PubMed and Chemical Abstracts for articles published before December 2008. Data synthesis A number of OP-based insecticides share common structural elements that result in predictable OP–protein adducts. The resultant OP–protein adducts show an increase in molecular mass that can be identified by MS and correlated with the OP agent. Customized OP-containing probes have also been used to tag and identify protein targets that can be identified by MS. Conclusions MS is a useful and emerging tool for the identification of proteins that are modified by activated organophosphate insecticides. MS can characterize the structure of the OP adduct and also the specific amino acid residue that forms the key bond with the OP. Each protein that is modified in a unique way by an OP represents a unique molecular biomarker that with further research can lead to new correlations with exposure. PMID:20056576

Equilibrium Configurations of a Fiber in a Flow

NASA Astrophysics Data System (ADS)

Guerron, Pamela; Berghout, Christopher; Nita, Bogdan; Vaidya, Ashwin

2013-11-01

The aim of this study is to understand the coupled dynamics of flexible fibers in a fluid flow. In particular, we examine the equilibrium configurations of the fiber with changing Reynolds numbers, orientations and lengths of the fiber. Our study is motivated by biological phenomena such as ciliary bending, flexing of plants and trees in winds etc. Our approach to resolving this problem has been threefold: experimental, numerical and theoretical. In our experiments we create physical models of variable length fibers inserted into a basal body structure, which is then suspended in a flow tank and positioned at different angles. The structure (fibers) are subjected to different velocities of water flow, ranging from 0m/s to 0.53 m/s in increments of 0.038 m/s. The results of the experiment were analyzed using Adobe Photoshop and the effect of the above mentioned parameters upon the shape of the fiber is analyzed. In addition, we also simulate this problem using the software Comsol and also create a simple, toy mathematical model incorporating the competing effects of tension and fluid drag on the fiber to obtain a closed form expression. Our various approaches point to consistent results.

Analytical methods in sphingolipidomics: Quantitative and profiling approaches in food analysis.

PubMed

Canela, Núria; Herrero, Pol; Mariné, Sílvia; Nadal, Pedro; Ras, Maria Rosa; Rodríguez, Miguel Ángel; Arola, Lluís

2016-01-08

In recent years, sphingolipidomics has emerged as an interesting omic science that encompasses the study of the full sphingolipidome characterization, content, structure and activity in cells, tissues or organisms. Like other omics, it has the potential to impact biomarker discovery, drug development and systems biology knowledge. Concretely, dietary food sphingolipids have gained considerable importance due to their extensively reported bioactivity. Because of the complexity of this lipid family and their diversity among foods, powerful analytical methodologies are needed for their study. The analytical tools developed in the past have been improved with the enormous advances made in recent years in mass spectrometry (MS) and chromatography, which allow the convenient and sensitive identification and quantitation of sphingolipid classes and form the basis of current sphingolipidomics methodologies. In addition, novel hyphenated nuclear magnetic resonance (NMR) strategies, new ionization strategies, and MS imaging are outlined as promising technologies to shape the future of sphingolipid analyses. This review traces the analytical methods of sphingolipidomics in food analysis concerning sample extraction, chromatographic separation, the identification and quantification of sphingolipids by MS and their structural elucidation by NMR. Copyright © 2015 Elsevier B.V. All rights reserved.

Leisure time activities of Iranian patients with multiple sclerosis: a qualitative study

PubMed Central

Hosseini, Seyed Mohammad Sadegh; Asgari, Ali; Rassafiani, Mehdi; Yazdani, Farzaneh; Mazdeh, Mehrdokht

2016-01-01

Background: Leisure time is one of the most important aspects of life, especially for people with chronic diseases. The concept and types of leisure have frequently been evaluated in different socio-cultural populations. The aim of this study was to identify the nature of leisure activities among a sample of Iranian patients with multiple sclerosis (MS) and classify the identified types of activities in the context of Iranian culture. Methods: In this qualitative study, semi-structured interview was applied to gather data from 34 MS patients that were selected through purposive sampling. The interviews were continued up to the point of saturation. Content analysis was used to explore experiences of the interviewees regarding their leisure activities. Results: Six categories of leisure activities were extracted for the studied patients with MS i.e.physical, social, individual, art/cultural, educational and spiritual/religious. Conclusion: The results represented the range and heterogeneity of leisure activities amongst the MS patients. Considering participation in spiritual/religious and social activities as leisure time undertaking might reflect cultural diversity in the perception and use of time for recreation. For mental health promotion purposes, paying special attention to the types of activities that people of different socio-cultural background choose for their refreshment could help health care providers in giving tailored advice for patients with MS and other chronic debilitating disease. PMID:27123437

ARSENIC SPECIATION IN WATER AND DIETARY SAMPLES BY IC-ICP-MS WITH STRUCTURAL VERIFICATION VIA IC-ESI-MS/MS

EPA Science Inventory

The two predominate sources of arsenic exposure are water and dietary ingestion. Dietary sources can easily exceed drinking water exposures based on "total" arsenic measurements. This can be deceiving because arsenic's toxicity is strongly dependent on its chemical form and the...

LC/MS/MS structure elucidation of reaction intermediates formed during the TiO2 photocatalysis of microcystin-LR

EPA Science Inventory

Microcystin-LR (MC-LR), a cyanotoxin and emerging drinking water contaminant, was treated with TiO(2) photocatalysts immobilized on stainless steel plates as an alternative to nanoparticles in slurry. The reaction intermediates of MC-LR were identified with mass spectrometry (MS)...

Characterization of epoxy carotenoids by fast atom bombardment collision-induced dissociation MS/MS.

PubMed

Maoka, Takashi; Fujiwara, Yasuhiro; Hashimoto, Keiji; Akimoto, Naoshige

2004-02-01

The characterization and structure of epoxy carotenoids possessing 5,6-epoxy, 5,8-epoxy and 3,6-epoxy end groups conjugated to the polyene chain were investigated using high-energy fast atom bombardment collision-induced dissociation MS/MS methods. In addition to [M - 80](+*), a characteristic fragment ion of an epoxy carotenoid, product ions resulting from the cleavage of C-C bonds in the polyene chain from the epoxy end group, such as m/z 181 (b ion) and 121 (c ion), were detected. On the other hand, diagnostic ions of m/z 286 (e-H ion) and 312 (f-H ion) were observed, not in the 5,6-epoxy or 5,8-epoxy carotenoid but in the 3,6-epoxy carotenoid. These fragmentation patterns can be used to distinguish 3,6-epoxy carotenoids from 5,6-epoxy or 5,8-epoxy carotenoids. The structure of an epoxy carotenoid, 3,6-epoxy-5,6-dihydro-7',8'-didehydro-beta,beta-carotene-5,3'-diol (8), isolated from oyster, was characterized using FAB CID-MS/MS by comparing fragmentation patterns with those of related known compounds.

Genet-specific DNA methylation probabilities detected in a spatial epigenetic analysis of a clonal plant population.

PubMed

Araki, Kiwako S; Kubo, Takuya; Kudoh, Hiroshi

2017-01-01

In sessile organisms such as plants, spatial genetic structures of populations show long-lasting patterns. These structures have been analyzed across diverse taxa to understand the processes that determine the genetic makeup of organismal populations. For many sessile organisms that mainly propagate via clonal spread, epigenetic status can vary between clonal individuals in the absence of genetic changes. However, fewer previous studies have explored the epigenetic properties in comparison to the genetic properties of natural plant populations. Here, we report the simultaneous evaluation of the spatial structure of genetic and epigenetic variation in a natural population of the clonal plant Cardamine leucantha. We applied a hierarchical Bayesian model to evaluate the effects of membership of a genet (a group of individuals clonally derived from a single seed) and vegetation cover on the epigenetic variation between ramets (clonal plants that are physiologically independent individuals). We sampled 332 ramets in a 20 m × 20 m study plot that contained 137 genets (identified using eight SSR markers). We detected epigenetic variation in DNA methylation at 24 methylation-sensitive amplified fragment length polymorphism (MS-AFLP) loci. There were significant genet effects at all 24 MS-AFLP loci in the distribution of subepiloci. Vegetation cover had no statistically significant effect on variation in the majority of MS-AFLP loci. The spatial aggregation of epigenetic variation is therefore largely explained by the aggregation of ramets that belong to the same genets. By applying hierarchical Bayesian analyses, we successfully identified a number of genet-specific changes in epigenetic status within a natural plant population in a complex context, where genotypes and environmental factors are unevenly distributed. This finding suggests that it requires further studies on the spatial epigenetic structure of natural populations of diverse organisms, particularly for sessile clonal species.

R-wave peak time at lead II in Chinese healthy adults.

PubMed

Deng, Jinhua; Chen, Tingting; Zeng, Chujuan; Lu, Nan; Zhou, Lihong; Tan, Xuerui; Yu, Min

2016-05-10

Wide QRS complex tachycardia (WCT) is a common arrhythmia. How to differentiate between WCTs is a challenge in clinical practice. Recently R-wave peak time (RWPT) at lead II was reported to be a helpful and simple tool for differentiating WCTs. However, it has remained unknown about the reference range of RWPT at lead II. In present study, we aimed to investigate the reference range of RWPT at lead II in Chinese healthy adults. A retrospective study was conducted in the First Affiliated Hospital of Shantou University Medical College in Southern China. Two thousand four hundred healthy adults aged 21-80 years with no history of structural heart diseases were included. RWPT at lead II was determined. Of 2400 healthy adults, 1200 men and 1200 women were included. The differences of age, mean heart rate and mean QRS duration at lead II between male and female were not significant. RWPT ranged from 16 to 42 ms in male while from 16 to 44 ms in female. The 95 % reference range of RWPT in normal male and female are 19.91 ~ 39.55 ms and 21.75 ~ 37.67 ms, respectively. Compared with the female, the male had a significantly longer RWPT at lead II (29.73 ± 5.01 ms vs 29.71 ± 4.06 ms in female, P = 0.000). Our study showed that RWPT at lead II is different between male and female. The male had a significantly longer RWPT at lead II than the female.

Isolation, structural elucidation, MS profiling, and evaluation of triglyceride accumulation inhibitory effects of benzophenone C-glucosides from leaves of Mangifera indica L.

PubMed

Zhang, Yi; Han, Lifeng; Ge, Dandan; Liu, Xuefeng; Liu, Erwei; Wu, Chunhua; Gao, Xiumei; Wang, Tao

2013-02-27

Seventy percent ethanol-water extract from the leaves of Mangifera indica L. (Anacardiaceae) was found to show an inhibitory effect on triglyceride (TG) accumulation in 3T3-L1 cells. From the active fraction, six new benzophenone C-glucosides, foliamangiferosides A(3) (1), A(4) (2), C(4) (3), C(5) (4), C(6) (5), and C(7) (6) together with 11 known benzophenone C-glucosides (7-17) were obtained. In this paper, isolation, structure elucidation (1-6), and MS fragment cleavage pathways of all 17 isolates were studied. 1-6 showed inhibitory effects on TG and free fatty acid accumulation in 3T3-L1 cells at 10 μM.

Tackling saponin diversity in marine animals by mass spectrometry: data acquisition and integration.

PubMed

Decroo, Corentin; Colson, Emmanuel; Demeyer, Marie; Lemaur, Vincent; Caulier, Guillaume; Eeckhaut, Igor; Cornil, Jérôme; Flammang, Patrick; Gerbaux, Pascal

2017-05-01

Saponin analysis by mass spectrometry methods is nowadays progressively supplementing other analytical methods such as nuclear magnetic resonance (NMR). Indeed, saponin extracts from plant or marine animals are often constituted by a complex mixture of (slightly) different saponin molecules that requires extensive purification and separation steps to meet the requirement for NMR spectroscopy measurements. Based on its intrinsic features, mass spectrometry represents an inescapable tool to access the structures of saponins within extracts by using LC-MS, MALDI-MS, and tandem mass spectrometry experiments. The combination of different MS methods nowadays allows for a nice description of saponin structures, without extensive purification. However, the structural characterization process is based on low kinetic energy CID which cannot afford a total structure elucidation as far as stereochemistry is concerned. Moreover, the structural difference between saponins in a same extract is often so small that coelution upon LC-MS analysis is unavoidable, rendering the isomeric distinction and characterization by CID challenging or impossible. In the present paper, we introduce ion mobility in combination with liquid chromatography to better tackle the structural complexity of saponin congeners. When analyzing saponin extracts with MS-based methods, handling the data remains problematic for the comprehensive report of the results, but also for their efficient comparison. We here introduce an original schematic representation using sector diagrams that are constructed from mass spectrometry data. We strongly believe that the proposed data integration could be useful for data interpretation since it allows for a direct and fast comparison, both in terms of composition and relative proportion of the saponin contents in different extracts. Graphical Abstract A combination of state-of-the-art mass spectrometry methods, including ion mobility spectroscopy, is developed to afford a complete description of the saponin molecules in natural extracts.

Structural Characterization of a Thrombin-Aptamer Complex by High Resolution Native Top-Down Mass Spectrometry

NASA Astrophysics Data System (ADS)

Zhang, Jiang; Loo, Rachel R. Ogorzalek; Loo, Joseph A.

2017-09-01

Native mass spectrometry (MS) with electrospray ionization (ESI) has evolved as an invaluable tool for the characterization of intact native proteins and non-covalently bound protein complexes. Here we report the structural characterization by high resolution native top-down MS of human thrombin and its complex with the Bock thrombin binding aptamer (TBA), a 15-nucleotide DNA with high specificity and affinity for thrombin. Accurate mass measurements revealed that the predominant form of native human α-thrombin contains a glycosylation mass of 2205 Da, corresponding to a sialylated symmetric biantennary oligosaccharide structure without fucosylation. Native MS showed that thrombin and TBA predominantly form a 1:1 complex under near physiological conditions (pH 6.8, 200 mM NH4OAc), but the binding stoichiometry is influenced by the solution ionic strength. In 20 mM ammonium acetate solution, up to two TBAs were bound to thrombin, whereas increasing the solution ionic strength destabilized the thrombin-TBA complex and 1 M NH4OAc nearly completely dissociated the complex. This observation is consistent with the mediation of thrombin-aptamer binding through electrostatic interactions and it is further consistent with the human thrombin structure that contains two anion binding sites on the surface. Electron capture dissociation (ECD) top-down MS of the thrombin-TBA complex performed with a high resolution 15 Tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer showed the primary binding site to be at exosite I located near the N-terminal sequence of the heavy chain, consistent with crystallographic data. High resolution native top-down MS is complementary to traditional structural biology methods for structurally characterizing native proteins and protein-DNA complexes. [Figure not available: see fulltext.

Alfalfa Mob1-like proteins are involved in cell proliferation and are localized in the cell division plane during cytokinesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Citterio, Sandra; Piatti, Simonetta; Albertini, Emidio

2006-04-15

Mps-one-binder (Mob) proteins play a crucial role in yeast cytokinesis. After cloning two Mob1-like genes, MsMob1-A and MsMob1-B from alfalfa (Medicago sativa L.) we show that, although they are constitutively expressed in roots, stems, leaves, flowers and pods, their transcripts and proteins are mostly produced in actively proliferating tissues. A polyclonal antibody specifically raised against MsMob1 proteins was used for immunolocalization studies in synchronized root tip cells. The subcellular localization of MsMob1-like proteins is demonstrated to be cell cycle-regulated. Cytoplasmic localization is faint and diffused during G{sub 1} and S. It becomes concentrated in punctuate and fibrillar structures in G{submore » 2} as well as M phase. At the stage of cytokinesis, the protein is found at the emerging cell plate marking the progressive formation of the septum. Mob1 proteins partially co-localize with microtubules structures functionally related to the spindles and important for cytokinesis in eukaryotic cells. The MsMob1 expression cannot rescue the lethality of the yeast mob1 mutant, suggesting that interaction of Mob1 proteins with their effectors may be species-specific. Localization of Mob1 proteins in the inner layer of the root cap indicates an additional function for this class of proteins in plants, which is likely related to the onset of programmed cell death.« less

Microstructural study of a nitroxide-mediated poly(ethylene oxide)/polystyrene block copolymer (PEO-b-PS) by electrospray tandem mass spectrometry.

PubMed

Girod, Marion; Phan, Trang N T; Charles, Laurence

2008-08-01

Electrospray ionization tandem mass spectrometry has been used to characterize the microstructure of a nitroxide-mediated poly(ethylene oxide)/polystyrene block copolymer, called SG1-capped PEO-b-PS. The main dissociation route of co-oligomers adducted with lithium or silver cation was observed to proceed via the homolytic cleavage of a C-ON bond, aimed at undergoing reversible homolysis during nitroxide mediated polymerization. This cleavage results in the elimination of the terminal SG1 end-group as a radical, inducing a complete depolymerization process of the PS block from the so-formed radical cation. These successive eliminations of styrene molecules allowed a straightforward determination of the PS block size. An alternative fragmentation pathway of the radical cation was shown to provide structural information on the junction group between the two blocks. Proposed dissociation mechanisms were supported by accurate mass measurements. Structural information on the SG1 end-group could be reached from weak abundance fragment ions detected in the low m/z range of the MS/MS spectrum. Amongst fragments typically expected from PS dissociation, only beta ions were produced. Moreover, specific dissociation of the PEO block was not observed to occur in MS/MS, suggesting that these rearrangement reactions do not compete effectively with dissociations of the odd-electron fragment ions. Information about the PEO block length and the initiated end-group were obtained in MS(3) experiments.

Hydrogen/deuterium exchange mass spectrometry with top-down electron capture dissociation for characterizing structural transitions of a 17 kDa protein.

PubMed

Pan, Jingxi; Han, Jun; Borchers, Christoph H; Konermann, Lars

2009-09-09

Amide H/D exchange (HDX) mass spectrometry (MS) is widely used for protein structural studies. Traditionally, this technique involves protein labeling in D(2)O, followed by acid quenching, proteolytic digestion, and analysis of peptide deuteration levels by HPLC/MS. There is great interest in the development of alternative HDX approaches involving the top-down fragmentation of electrosprayed protein ions, instead of relying on enzymatic cleavage and solution-phase separations. A number of recent studies have demonstrated that electron capture dissociation (ECD) results in fragmentation of gaseous protein ions with little or no H/D scrambling. However, the successful application of this approach for in-depth protein conformational studies has not yet been demonstrated. The current work uses horse myoglobin as a model system for assessing the suitability of HDX-MS with top-down ECD for experiments of this kind. It is found that ECD can pinpoint the locations of protected amides with an average resolution of less than two residues for this 17 kDa protein. Native holo-myoglobin (hMb) shows considerable protection from exchange in all of its helices, whereas loops are extensively deuterated. Fraying is observable at some helix termini. Removal of the prosthetic heme group from hMb produces apo-myoglobin (aMb). Both hMb and aMb share virtually the same HDX protection pattern in helices A-E, whereas helix F is unfolded in aMb. In addition, destabilization is evident for some residues close to the beginning of helix G, the end of helix H, and the C-terminus of the protein. The structural changes reported herein are largely consistent with earlier NMR data for sperm whale myoglobin, although small differences between the two systems are evident. Our findings demonstrate that the level of structural information obtainable with top-down ECD for small to medium-sized proteins considerably surpasses that of traditional HDX-MS experiments, while at the same time greatly reducing undesired amide back exchange.

Structural Limitations of Model Reference Adaptive Controllers

DTIC Science & Technology

1989-04-01

Global Uncertainty CkpVps)I4(s) kWVh(s) In [3) a design rule similar the one studied heme Dps(ms+Cs)V~)Ds = s (4) (ectly the samne when n-m--l) was...Ir represent the under the uncertainty indicated by ES and Eu. output of this structured singular value analysis, p: is an Defint 6: The Design

Novel Concepts of MS-Cleavable Cross-linkers for Improved Peptide Structure Analysis

NASA Astrophysics Data System (ADS)

Hage, Christoph; Falvo, Francesco; Schäfer, Mathias; Sinz, Andrea

2017-10-01

The chemical cross-linking/mass spectrometry (MS) approach is gaining increasing importance as an alternative method for studying protein conformation and for deciphering protein interaction networks. This study is part of our ongoing efforts to develop innovative cross-linking principles for a facile and efficient assignment of cross-linked products. We evaluate two homobifunctional, amine-reactive, and MS-cleavable cross-linkers regarding their potential for automated analysis of cross-linked products. We introduce the bromine phenylurea (BrPU) linker that possesses a unique structure yielding a distinctive fragmentation pattern on collisional activation. Moreover, BrPU delivers the characteristic bromine isotope pattern and mass defect for all cross-linker-decorated fragments. We compare the fragmentation behavior of the BrPU linker with that of our previously described MS-cleavable TEMPO-Bz linker (which consists of a 2,2,6,6-tetramethylpiperidine-1-oxy moiety connected to a benzyl group) that was developed to perform free-radical-initiated peptide sequencing. Comparative collisional activation experiments (collision-induced dissociation and higher-energy collision-induced dissociation) with both cross-linkers were conducted in negative electrospray ionization mode with an Orbitrap Fusion mass spectrometer using five model peptides. As hypothesized in a previous study, the presence of a cross-linked N-terminal aspartic acid residue seems to be the prerequisite for the loss of an intact peptide from the cross-linked products. As the BrPU linker combines a characteristic mass shift with an isotope signature, it presents a more favorable combination for automated assignment of cross-linked products compared with the TEMPO-Bz linker. [Figure not available: see fulltext.

Characterization and quantification of the chemical compositions of Scutellariae Barbatae herba and differentiation from its substitute by combining UHPLC-PDA-QTOF-MS/MS with UHPLC-MS/MS.

PubMed

Zhang, Zhifeng; He, Lili; Lu, Luyang; Liu, Yuan; Dong, Gengting; Miao, Jianhua; Luo, Pei

2015-05-10

The aim of this study was to investigate the possibility of using the non-official species Scutellaria indica L. as the substitute for the official species Scutellaria barbata D. Don. A sensitive, precise and accurate method was developed to identify their chemical compositions from the crude extracts using UHPLC-PDA-QTOF-MS/MS. 36 peaks were detected and 28 peaks have been tentatively and structurally characterized by comparing their retention times, UV spectra and HR-MS data with those of the reference substances and/or the data of the literatures. Additionally, 5 flavonoids have been quantified by multiple reaction monitoring (MRM) in the negative ionization mode. The results demonstrated that there were 23 common peaks between these two species. However, the other 13 peaks from S. barbata could not be detected in S. indica. Furthermore, the content of 5 flavonoids is significantly different. Scutellarein cannot be detected in S. indica, which was considered as the characteristic component for distinguishing the two species. Our data, therefore, clearly demonstrate that S. indica may not be used as the substitute for S. barbata and further investigation is needed to determine through investigation of their therapeutic efficacy. Copyright © 2015. Published by Elsevier B.V.

Research advances based on mass spectrometry for profiling of triacylglycerols in oils and fats and their applications.

PubMed

Xu, Shu-Ling; Wei, Fang; Xie, Ya; Lv, Xin; Dong, Xu-Yan; Chen, Hong

2018-03-23

Vegetable oils and animal fats are dietary source of lipids that play critical and multiple roles in biological function. Triacylglycerols (TAGs) are the principal component of oils and fats with significant difference in profile among different oils and fats. TAG profiling is essential for nutritional evaluation, quality control and assurance of safety in oils and fats. However, analysis of TAGs is a challenging task because of the complicated composition of TAGs and their similar physicochemical properties in oils and fats. The rapid development of mass spectrometry (MS) technology in recent years makes it possible to analyze the composition, content and structure of TAGs in the study of the physical, chemical and nutritional properties of oils, fats and related products. This review described the research advancement based on MS for profiling of TAGs in oil, fat and their applications in food. The application of MS, including direct infusion strategies, and its combination with chromatography, gas chromatography-MS (GC-MS) and liquid chromatography-MS (LC-MS), in the analysis of TAGs were reviewed. The advantages and disadvantages of these analytical methods with relevant applications for TAGs analysis in food were also described. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Attitudes, perceptions, and use of marijuana in youth with multiple sclerosis.

PubMed

Brenton, J Nicholas; Schreiner, Teri; Karoscik, Krystle; Richter, Meg; Ferrante, Samantha; Waldman, Amy; Banwell, Brenda

2018-02-01

Studies have shown a negative impact on cognition and brain volume in marijuana-using adult multiple sclerosis (MS) patients and healthy adolescents. Given that onset of MS during childhood and adolescence negatively impacts brain growth and the normal maturation of neuronal networks, the addition of marijuana exposure in these youth may be even more harmful. Determine attitudes toward and prevalence of recreational marijuana use in MS youth. We surveyed 52 consecutive pediatric-onset MS patients from three pediatric MS centers in the United States. Participants answered a structured questionnaire to capture attitudes toward marijuana and personal use habits, if present. Nearly half reported use of marijuana, with the majority beginning to use in mid-to-late adolescence. The most popular reasons for using marijuana were relaxation (72%), improvement of medical problems (64%), and stress reduction (52%). Over half (64%) of marijuana users perceived it to have negative effects on memory and focus. Cost and access were not barriers to use, despite all respondents being less than age 21. Youth with MS endorse recreational marijuana as safe, and many use marijuana frequently despite appreciating a negative impact on memory. More detailed understanding of the long-term impact of marijuana use in youth with MS is needed.

Steroids excreted in urine by neonates with 21-hydroxylase deficiency. 2. Characterization, using GC-MS and GC-MS/MS, of pregnanes and pregnenes with an oxo- group on the A- or B-ring.

PubMed

Christakoudi, Sofia; Cowan, David A; Taylor, Norman F

2012-04-01

Urine from neonates with 21-hydroxylase deficiency contains a large range of metabolites of 17-hydroxyprogesterone, 21-deoxycortisol and androgens but few have been previously described. We present the second part of a comprehensive project to characterize and identify these in order to enhance diagnosis and to further elucidate neonatal steroid metabolism. Steroids were analyzed, after extraction and enzymatic conjugate hydrolysis, as methyloxime-trimethylsilyl ether derivatives on gas-chromatographs coupled to quadrupole and ion-trap mass-spectrometers. GC-MS and GC-MS/MS spectra were used together to determine the structure of the A- and B-rings containing an oxo group. Fragmentations indicating presence of 3-, 6-, and 7-oxo groups and also 1β-, 2α-, 4β-, and 6β-hydroxyls are presented and discussed for the first time. Interpretation was aided by comparison with spectra of available relevant standards, of oxidation products of standards and urinary metabolites and of deuterated derivatives. Endogenous 1-enes and 2(3)-ene artifacts of non-hydrolyzed 3α-sulfates are also reported. D-ring and side chain structure was determined according to our previously published criteria. Likely metabolic relationships were also explored. We conclude that GC-MS combined with GC-MS/MS allows identification of the A- and B-ring structure of pregnane and pregnenes in the presence of an oxo group on one of these rings. Major oxygenations are 1β, 15β, 16α and 21-hydroxy and 6- and 7-oxo groups. Minor positions of hydroxylation are those at 2α, 4β and 6β. Three major metabolic streams exist in affected neonates in addition to the classical 3α-hydroxy-5β-pregnane pathway, i.e. these of the 3-oxo-4-enes as well as 3α- and 3β-hydroxy-5α-anes. Copyright © 2011 Elsevier Inc. All rights reserved.

Optimising magnetic resonance image quality of the ear in healthy dogs.

PubMed

Wolf, Davina; Lüpke, Matthias; Wefstaedt, Patrick; Klopmann, Thilo; Nolte, Ingo; Seifert, Hermann

2011-03-01

The aim of this study was to develop an examination protocol for magnetic resonance imaging, in order to display diagnostically important information of the canine middle and inner ear. To ensure that this protocol could also be used as a basis for determining pathological changes, the anatomical structures of the ear were presented in detail. To minimise stress through anaesthesia in live animals, preliminary examinations were carried out on four dog cadavers. During these initial examinations, three-dimensional (3D) sequences proved to be superior to two-dimensional ones. Therefore, only 3D sequences were applied for the main examinations performed on six clinically healthy Beagles. The anonymised MR images were rated by three experienced reviewers using a five-point scale. The most valuable sequence was a T2-weighted CISS sequence (TR = 16.7 ms, TE = 8.08 ms). This sequence proved to be most suitable for illustrating the inner ear structures and enabled good tissue contrasts. The sequence ranked second best was also a T2-weighted DESS sequence (TR = 19 ms, TE = 6 ms), allowing the imaging of the tympanic cavity and enabling 3D reconstruction due to its isotropic voxels. Due to low contrast and strong noise, the other sequences (TSE, FISP, MP RAGE) were not suitable for anatomical illustration of the middle and inner ear.

Structural elucidation of anti-metastatic rhamnogalacturonan II from the pectinase digest of citrus peels (Citrus unshiu).

PubMed

Park, Hye-Ryung; Park, Su Beom; Hong, Hee-Do; Suh, Hyung Joo; Shin, Kwang-Soon

2017-01-01

The aim of this study was to characterize a polysaccharide found in citrus peels with an anti-metastatic property. CPE-II was purified by the pectinase digestion of citrus peels. During in vivo lung metastasis of Colon26-M3.1, administration of 10μg of CPE-II per mouse showed 81.3% inhibition of metastasis. CPE-II consists of 15 different monosaccharides and 22 different glycosyl linkages, characteristic of rhamnogalacturonan II (RG-II). The primary structure was elucidated based on sugar composition, methylation analysis, oligosaccharide analysis, and sequencing using GC, GC-MS, LC-MS, and ESI-MS/MS analyses. Sequential degradation using partial acid hydrolysis indicated that CPE-II contained Rhap-(1→5)-Kdo, Araf-(1→5)-Dha, an AceA-containing nonasaccharide, and an uronic acid-rich oligosaccharide in addition to an α-(1→4)-galacturono-oligosaccharide main chain. The molecular weight of CPE-II was observed to decrease from 9 to 5kDa at a pH value of <2.0, as observed by HPSEC. Thus, we propose that the anti-metastatic CPE-II is primarily present as an RG-II dimer. Copyright © 2016 Elsevier B.V. All rights reserved.

Structural analysis of proanthocyanidins isolated from fruit stone of Chinese hawthorn with potent antityrosinase and antioxidant activity.

PubMed

Chai, Wei-Ming; Chen, Chih-Min; Gao, Yu-Sen; Feng, Hui-Ling; Ding, Yu-Mei; Shi, Yan; Zhou, Han-Tao; Chen, Qing-Xi

2014-01-08

Proanthocyanidins were isolated from fruit stone of Chinese hawthorn (Crataegus pinnatifida Bge. var. major N.E.Br.). Their structures were analyzed and elucidated by methods of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and high performance liquid chromatography electrospray ionization mass spectrometry (HPLC-ESI-MS). The results demonstrated that these compounds are complicated mixtures of homo- and heteropolymers consisting of procyanidin/procyanidin gallate and prodelphinidin. They possessed structural heterogeneity in monomer units, polymer length, and interflavan linkage (A-type and B-type). Their antityrosinase and antioxidant activity were then investigated. The results revealed that they can inhibit tyrosinase activities, including the monophenolase activity and the diphenolase activity. In addition, proanthocyanidins possessed potent antioxidant activity. Our studies revealed that proanthocyanidins isolated from fruit stone of Chinese hawthorn may be applied in food, agriculture, pharmaceutical, and cosmetic industries.

Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools

PubMed Central

Sud, Manish; Fahy, Eoin; Cotter, Dawn; Azam, Kenan; Vadivelu, Ilango; Burant, Charles; Edison, Arthur; Fiehn, Oliver; Higashi, Richard; Nair, K. Sreekumaran; Sumner, Susan; Subramaniam, Shankar

2016-01-01

The Metabolomics Workbench, available at www.metabolomicsworkbench.org, is a public repository for metabolomics metadata and experimental data spanning various species and experimental platforms, metabolite standards, metabolite structures, protocols, tutorials, and training material and other educational resources. It provides a computational platform to integrate, analyze, track, deposit and disseminate large volumes of heterogeneous data from a wide variety of metabolomics studies including mass spectrometry (MS) and nuclear magnetic resonance spectrometry (NMR) data spanning over 20 different species covering all the major taxonomic categories including humans and other mammals, plants, insects, invertebrates and microorganisms. Additionally, a number of protocols are provided for a range of metabolite classes, sample types, and both MS and NMR-based studies, along with a metabolite structure database. The metabolites characterized in the studies available on the Metabolomics Workbench are linked to chemical structures in the metabolite structure database to facilitate comparative analysis across studies. The Metabolomics Workbench, part of the data coordinating effort of the National Institute of Health (NIH) Common Fund's Metabolomics Program, provides data from the Common Fund's Metabolomics Resource Cores, metabolite standards, and analysis tools to the wider metabolomics community and seeks data depositions from metabolomics researchers across the world. PMID:26467476

Lipid and glycolipid isomer analyses using ultra-high resolution ion mobility spectrometry separations

DOE PAGES

Wojcik, Roza; Webb, Ian K.; Deng, Liulin; ...

2017-01-18

Understanding the biological mechanisms related to lipids and glycolipids is challenging due to the vast number of possible isomers. Mass spectrometry (MS) measurements are currently the dominant approach for studying and providing detailed information on lipid and glycolipid structures. However, difficulties in distinguishing many structural isomers (e.g. distinct acyl chain positions, double bond locations, as well as glycan isomers) inhibit the understanding of their biological roles. Here we utilized ultra-high resolution ion mobility spectrometry (IMS) separations based upon the use of traveling waves in a serpentine long path length multi-pass Structures for Lossless Manipulations (SLIM) to enhance isomer resolution. Themore » multi-pass arrangement allowed separations ranging from ~16 m (1 pass) to ~470 m (32 passes) to be investigated for the distinction of lipids and glycolipids with extremely small structural differences. Lastly, these ultra-high resolution SLIM IMS-MS analyses provide a foundation for exploring and better understanding isomer specific biological and disease processes.« less

Fragmentation studies of fulvic acids using collision induced dissociation fourier transform ion cyclotron resonance mass spectrometry.

PubMed

Witt, Matthias; Fuchser, Jens; Koch, Boris P

2009-04-01

The complex natural organic matter standard Suwannee river fulvic acid (SRFA) was analyzed by negative ion mode electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FTICR MS) using on-resonance collision induced dissociation (CID) of single ultrahigh resolved mass peaks in the ICR cell. Molecular formula assignment of precursor masses resulted in exactly one molecular formula for each of the peaks. Analyses of the corresponding fragment spectra and comparison to different standard substances revealed specific neutral losses and fragmentation patterns which result in structures consisting of a high degree of carboxyl- and fewer hydroxyl groups. The comparison of fragmented mass peaks within different pseudohomologous series (CH(2)-series, and CH(4) vs O exchange) suggested structurally based differences between these series. CID FTICR MS allowed isolating single mass peaks in a very complex natural organic matter spectrum. Subsequently, fragmentation gave structural insights into this material. Our results suggest that the structural diversity in complex humic substances is not as high as expected.

Structural Elucidation of Enzymatically Synthesized Galacto-oligosaccharides Using Ion-Mobility Spectrometry-Tandem Mass Spectrometry.

PubMed

Carević, Milica; Bezbradica, Dejan; Banjanac, Katarina; Milivojević, Ana; Fanuel, Mathieu; Rogniaux, Hélène; Ropartz, David; Veličković, Dušan

2016-05-11

Galacto-oligosaccharides (GOS) represent a diverse group of well-characterized prebiotic ingredients derived from lactose in a reaction catalyzed with β-galactosidases. Enzymatic transgalactosylation results in a mixture of compounds of various degrees of polymerization and types of linkages. Because structure plays an important role in terms of prebiotic activity, it is of crucial importance to provide an insight into the mechanism of transgalactosylation reaction and occurrence of different types of β-linkages during GOS synthesis. Our study proved that a novel one-step method, based on ion-mobility spectrometry-tandem mass spectrometry (IMS-MS/MS), enables complete elucidation of GOS structure. It has been shown that β-galactosidase from Aspergillus oryzae has the highest affinity toward formation of β-(1→3) or β-(1→6) linkages. Additionally, it was observed that the occurrence of different linkages varies during the reaction course, indicating that tailoring favorable GOS structures with improved prebiotic activity can be achieved by adequate control of enzymatic synthesis.

High Resolution Mass Spectrometry of Polyfluorinated Polyether-Based Formulation

NASA Astrophysics Data System (ADS)

Dimzon, Ian Ken; Trier, Xenia; Frömel, Tobias; Helmus, Rick; Knepper, Thomas P.; de Voogt, Pim

2016-02-01

High resolution mass spectrometry (HRMS) was successfully applied to elucidate the structure of a polyfluorinated polyether (PFPE)-based formulation. The mass spectrum generated from direct injection into the MS was examined by identifying the different repeating units manually and with the aid of an instrument data processor. Highly accurate mass spectral data enabled the calculation of higher-order mass defects. The different plots of MW and the nth-order mass defects (up to n = 3) could aid in assessing the structure of the different repeating units and estimating their absolute and relative number per molecule. The three major repeating units were -C2H4O-, -C2F4O-, and -CF2O-. Tandem MS was used to identify the end groups that appeared to be phosphates, as well as the possible distribution of the repeating units. Reversed-phase HPLC separated of the polymer molecules on the basis of number of nonpolar repeating units. The elucidated structure resembles the structure in the published manufacturer technical data. This analytical approach to the characterization of a PFPE-based formulation can serve as a guide in analyzing not just other PFPE-based formulations but also other fluorinated and non-fluorinated polymers. The information from MS is essential in studying the physico-chemical properties of PFPEs and can help in assessing the risks they pose to the environment and to human health.

High Resolution Mass Spectrometry of Polyfluorinated Polyether-Based Formulation.

PubMed

Dimzon, Ian Ken; Trier, Xenia; Frömel, Tobias; Helmus, Rick; Knepper, Thomas P; de Voogt, Pim

2016-02-01

High resolution mass spectrometry (HRMS) was successfully applied to elucidate the structure of a polyfluorinated polyether (PFPE)-based formulation. The mass spectrum generated from direct injection into the MS was examined by identifying the different repeating units manually and with the aid of an instrument data processor. Highly accurate mass spectral data enabled the calculation of higher-order mass defects. The different plots of MW and the nth-order mass defects (up to n = 3) could aid in assessing the structure of the different repeating units and estimating their absolute and relative number per molecule. The three major repeating units were -C2H4O-, -C2F4O-, and -CF2O-. Tandem MS was used to identify the end groups that appeared to be phosphates, as well as the possible distribution of the repeating units. Reversed-phase HPLC separated of the polymer molecules on the basis of number of nonpolar repeating units. The elucidated structure resembles the structure in the published manufacturer technical data. This analytical approach to the characterization of a PFPE-based formulation can serve as a guide in analyzing not just other PFPE-based formulations but also other fluorinated and non-fluorinated polymers. The information from MS is essential in studying the physico-chemical properties of PFPEs and can help in assessing the risks they pose to the environment and to human health. Graphical Abstract ᅟ.

Investigation of sliding DNA clamp dynamics by single-molecule fluorescence, mass spectrometry and structure-based modeling

PubMed Central

Gadkari, Varun V; Harvey, Sophie R; Raper, Austin T; Chu, Wen-Ting; Wang, Jin; Wysocki, Vicki H; Suo, Zucai

2018-01-01

Abstract Proliferating cell nuclear antigen (PCNA) is a trimeric ring-shaped clamp protein that encircles DNA and interacts with many proteins involved in DNA replication and repair. Despite extensive structural work to characterize the monomeric, dimeric, and trimeric forms of PCNA alone and in complex with interacting proteins, no structure of PCNA in a ring-open conformation has been published. Here, we use a multidisciplinary approach, including single-molecule Förster resonance energy transfer (smFRET), native ion mobility-mass spectrometry (IM-MS), and structure-based computational modeling, to explore the conformational dynamics of a model PCNA from Sulfolobus solfataricus (Sso), an archaeon. We found that Sso PCNA samples ring-open and ring-closed conformations even in the absence of its clamp loader complex, replication factor C, and transition to the ring-open conformation is modulated by the ionic strength of the solution. The IM-MS results corroborate the smFRET findings suggesting that PCNA dynamics are maintained in the gas phase and further establishing IM-MS as a reliable strategy to investigate macromolecular motions. Our molecular dynamic simulations agree with the experimental data and reveal that ring-open PCNA often adopts an out-of-plane left-hand geometry. Collectively, these results implore future studies to define the roles of PCNA dynamics in DNA loading and other PCNA-mediated interactions. PMID:29529283

When is Mass Spectrometry Combined with Affinity Approaches Essential? A Case Study of Tyrosine Nitration in Proteins

NASA Astrophysics Data System (ADS)

Petre, Brînduşa-Alina; Ulrich, Martina; Stumbaum, Mihaela; Bernevic, Bogdan; Moise, Adrian; Döring, Gerd; Przybylski, Michael

2012-11-01

Tyrosine nitration in proteins occurs under physiologic conditions and is increased at disease conditions associated with oxidative stress, such as inflammation and Alzheimer's disease. Identification and quantification of tyrosine-nitrations are crucial for understanding nitration mechanism(s) and their functional consequences. Mass spectrometry (MS) is best suited to identify nitration sites, but is hampered by low stabilities and modification levels and possible structural changes induced by nitration. In this insight, we discuss methods for identifying and quantifying nitration sites by proteolytic affinity extraction using nitrotyrosine (NT)-specific antibodies, in combination with electrospray-MS. The efficiency of this approach is illustrated by identification of specific nitration sites in two proteins in eosinophil granules from several biological samples, eosinophil-cationic protein (ECP) and eosinophil-derived neurotoxin (EDN). Affinity extraction combined with Edman sequencing enabled the quantification of nitration levels, which were found to be 8 % and 15 % for ECP and EDN, respectively. Structure modeling utilizing available crystal structures and affinity studies using synthetic NT-peptides suggest a tyrosine nitration sequence motif comprising positively charged residues in the vicinity of the NT- residue, located at specific surface- accessible sites of the protein structure. Affinities of Tyr-nitrated peptides from ECP and EDN to NT-antibodies, determined by online bioaffinity- MS, provided nanomolar KD values. In contrast, false-positive identifications of nitrations were obtained in proteins from cystic fibrosis patients upon using NT-specific antibodies, and were shown to be hydroxy-tyrosine modifications. These results demonstrate affinity- mass spectrometry approaches to be essential for unequivocal identification of biological tyrosine nitrations.

Quantitation of DNA adducts by stable isotope dilution mass spectrometry

PubMed Central

Tretyakova, Natalia; Goggin, Melissa; Janis, Gregory

2012-01-01

Exposure to endogenous and exogenous chemicals can lead to the formation of structurally modified DNA bases (DNA adducts). If not repaired, these nucleobase lesions can cause polymerase errors during DNA replication, leading to heritable mutations potentially contributing to the development of cancer. Due to their critical role in cancer initiation, DNA adducts represent mechanism-based biomarkers of carcinogen exposure, and their quantitation is particularly useful for cancer risk assessment. DNA adducts are also valuable in mechanistic studies linking tumorigenic effects of environmental and industrial carcinogens to specific electrophilic species generated from their metabolism. While multiple experimental methodologies have been developed for DNA adduct analysis in biological samples – including immunoassay, HPLC, and 32P-postlabeling – isotope dilution high performance liquid chromatography-electrospray ionization-tandem mass spectrometry (HPLC-ESI-MS/MS) generally has superior selectivity, sensitivity, accuracy, and reproducibility. As typical DNA adducts concentrations in biological samples are between 0.01 – 10 adducts per 108 normal nucleotides, ultrasensitive HPLC-ESI-MS/MS methodologies are required for their analysis. Recent developments in analytical separations and biological mass spectrometry – especially nanoflow HPLC, nanospray ionization MS, chip-MS, and high resolution MS – have pushed the limits of analytical HPLC-ESI-MS/MS methodologies for DNA adducts, allowing researchers to accurately measure their concentrations in biological samples from patients treated with DNA alkylating drugs and in populations exposed to carcinogens from urban air, drinking water, cooked food, alcohol, and cigarette smoke. PMID:22827593

Meeting the mental health needs of people with multiple sclerosis: a qualitative study of patients and professionals.

PubMed

Methley, Abigail; Campbell, Stephen; Cheraghi-Sohi, Sudeh; Chew-Graham, Carolyn

2017-06-01

To explore perspectives and experiences of people with multiple sclerosis (MS) and health care professionals of mental health support for MS in the UK. 24 people with MS, 13 practice nurses, 12 general practitioners (GPs) and 9 MS specialist nurses were recruited through community groups and primary care practices across North West England. Semi-structured interviews were conducted, and data analyzed thematically using constant comparative analysis within and across the data sets. The theoretical framework of candidacy was used to interrogate data. Four themes were identified: candidates for care, management choices, defining roles, and permeability and responsiveness. Candidacy for care, and symptom management, depended on the framing of symptoms through a social or medical model of depression. Normalizing symptoms could prevent help-seeking by patients. Reported referral behavior varied by professional group, based on perceived remit, competency and training needs. GPs were perceived by patients and other professionals as central for management of mental health needs in MS, but may not perceive this role themselves, suggesting a need for increased knowledge, training, and improved access to specialist care. Implications for Rehabilitation Anxiety and depression are common in people with MS. Management of mental health needs in people with MS relies on complex decisions made by both people with MS and health care professionals. General practitioners may play a key role in the ongoing management of mental health needs of people with MS.

Functional assessment of the visual pathway with multifocal visual evoked potentials, and their relationship with disability in patients with multiple sclerosis.

PubMed

Blanco, Román; Pérez-Rico, Consuelo; Puertas-Muñoz, Inmaculada; Ayuso-Peralta, Lucía; Boquete, Luciano; Arévalo-Serrano, Juan

2014-02-01

To objectively evaluate the visual function, and the relationship between disability and optic nerve dysfunction, in patients with multiple sclerosis (MS) and optic neuritis (ON), using multifocal visual evoked potentials (mfVEP). This observational, cross-sectional study assessed 28 consecutive patients with clinically definite MS, according to the McDonald criteria, and 19 age-matched healthy subjects. Disability was recorded using the Expanded Disability Status Scale (EDSS) score. The patients' mfVEP were compared to their clinical, psychophysical (Humphrey perimetry) and structural (optic coherence tomography (OCT)) diagnostic test data. We observed a significant agreement between mfVEP amplitude and Humphrey perimetry/OCT in MS-ON eyes, and between mfVEP amplitude and OCT in MS but non-ON eyes. We found significant differences in EDSS score between patients with abnormal and normal mfVEP amplitudes. Abnormal mfVEP amplitude defects (from interocular and monocular probability analysis) were found in 67.9% and 73.7% of the MS-ON and MS-non-ON group eyes, respectively. Delayed mfVEP latencies (interocular and monocular probability analysis) were seen in 70.3% and 73.7% of the MS-ON and MS-non-ON groups, respectively. We found a significant relationship between mfVEP amplitude and disease severity, as measured by EDSS score, that suggested there is a role for mfVEP amplitude as a functional biomarker of axonal loss in MS.

Visualisation of abscisic acid and 12-oxo-phytodienoic acid in immature Phaseolus vulgaris L. seeds using desorption electrospray ionisation-imaging mass spectrometry

NASA Astrophysics Data System (ADS)

Enomoto, Hirofumi; Sensu, Takuya; Sato, Kei; Sato, Futoshi; Paxton, Thanai; Yumoto, Emi; Miyamoto, Koji; Asahina, Masashi; Yokota, Takao; Yamane, Hisakazu

2017-02-01

The plant hormone abscisic acid (ABA) and the jasmonic acid related-compound 12-oxo-phytodienoic acid (OPDA) play crucial roles in seed development, dormancy, and germination. However, a lack of suitable techniques for visualising plant hormones has restricted the investigation of their biological mechanisms. In the present study, desorption electrospray ionisation-imaging mass spectrometry (DESI-IMS), a powerful tool for visualising metabolites in biological tissues, was used to visualise ABA and OPDA in immature Phaseolus vulgaris L. seed sections. The mass spectra, peak values and chemical formulae obtained from the analysis of seed sections were consistent with those determined for ABA and OPDA standards, as were the precursor and major fragment ions observed in tandem mass spectrometry (MS/MS) imaging. Furthermore, the precursor and fragment ion images showed similar distribution patterns. In addition, the localisation of ABA and OPDA using DESI-IMS was confirmed using liquid chromatography-MS/MS (LC-MS/MS). The results indicated that ABA was mainly distributed in the radical and cotyledon of the embryo, whereas OPDA was distributed exclusively in external structures, such as the hilum and seed coat. The present study is the first to report the visualisation of plant hormones using IMS, and demonstrates that DESI-IMS is a promising technique for future plant hormone research.

Genome-Wide Analyses of Calcium Sensors Reveal Their Involvement in Drought Stress Response and Storage Roots Deterioration after Harvest in Cassava.

PubMed

Hu, Wei; Yan, Yan; Tie, Weiwei; Ding, Zehong; Wu, Chunlai; Ding, Xupo; Wang, Wenquan; Xia, Zhiqiang; Guo, Jianchun; Peng, Ming

2018-04-19

Calcium (Ca 2+ ) plays a crucial role in plant development and responses to environmental stimuli. Currently, calmodulins (CaMs), calmodulin-like proteins (CMLs), and calcineurin B-like proteins (CBLs), such as Ca 2+ sensors, are not well understood in cassava ( Manihot esculenta Crantz), an important tropical crop. In the present study, 8 CaMs, 48 CMLs, and 9 CBLs were genome-wide identified in cassava, which were divided into two, four, and four groups, respectively, based on evolutionary relationship, protein motif, and gene structure analyses. Transcriptomic analysis revealed the expression diversity of cassava CaMs-CMLs-CBLs in distinct tissues and in response to drought stress in different genotypes. Generally, cassava CaMs-CMLs-CBLs showed different expression profiles between cultivated varieties (Arg7 and SC124) and wild ancestor (W14) after drought treatment. In addition, numerous CaMs-CMLs-CBLs were significantly upregulated at 6 h, 12 h, and 48 h after harvest, suggesting their possible role during storage roots (SR) deterioration. Further interaction network and co-expression analyses suggested that a CBL-mediated interaction network was widely involved in SR deterioration. Taken together, this study provides new insights into CaMs-CMLs-CBLs-mediated drought adaption and SR deterioration at the transcription level in cassava, and identifies some candidates for the genetic improvement of cassava.

Exercise barriers and preferences among women and men with multiple sclerosis.

PubMed

Asano, Miho; Duquette, Pierre; Andersen, Ross; Lapierre, Yves; Mayo, Nancy E

2013-03-01

The primary objective of this study was to estimate the extent to which women and men with MS present different exercise barriers. The secondary objective was to estimate the extent to which women and men with MS present different perceived-health, depressive symptoms, and current exercise routines or preferences. This was a cross sectional survey. 417 people with MS completed a survey of exercise barriers and current exercise routines, perceived-health and depressive symptoms. The top three exercise barriers were: too tired; impairment; and lack of time, regardless of their gender. Regardless of their gender, three times/week and 60 min/session was identified as the most common current exercise structure among physically active participants. The top three currently preferred exercise by men included walking, strengthening/weights and flexibility/stretch exercise. Women reported the same three exercises but flexibility/stretch exercise were slightly more popular than other exercise. Similarities in perceived health status and depressive symptoms were seen between women and men; expect more men were diagnosed with progressive MS (20% higher) than women, leading to a higher rate of men reporting problems with mobility. Women and men with MS differed very little on exercise barriers and current exercise routines, perceived health and depressive symptoms. Even though MS is generally considered a woman's disease, this study did not find a strong need to develop gender specific exercise or physical activity interventions for this population.

Visualisation of abscisic acid and 12-oxo-phytodienoic acid in immature Phaseolus vulgaris L. seeds using desorption electrospray ionisation-imaging mass spectrometry

PubMed Central

Enomoto, Hirofumi; Sensu, Takuya; Sato, Kei; Sato, Futoshi; Paxton, Thanai; Yumoto, Emi; Miyamoto, Koji; Asahina, Masashi; Yokota, Takao; Yamane, Hisakazu

2017-01-01

The plant hormone abscisic acid (ABA) and the jasmonic acid related-compound 12-oxo-phytodienoic acid (OPDA) play crucial roles in seed development, dormancy, and germination. However, a lack of suitable techniques for visualising plant hormones has restricted the investigation of their biological mechanisms. In the present study, desorption electrospray ionisation-imaging mass spectrometry (DESI-IMS), a powerful tool for visualising metabolites in biological tissues, was used to visualise ABA and OPDA in immature Phaseolus vulgaris L. seed sections. The mass spectra, peak values and chemical formulae obtained from the analysis of seed sections were consistent with those determined for ABA and OPDA standards, as were the precursor and major fragment ions observed in tandem mass spectrometry (MS/MS) imaging. Furthermore, the precursor and fragment ion images showed similar distribution patterns. In addition, the localisation of ABA and OPDA using DESI-IMS was confirmed using liquid chromatography-MS/MS (LC-MS/MS). The results indicated that ABA was mainly distributed in the radical and cotyledon of the embryo, whereas OPDA was distributed exclusively in external structures, such as the hilum and seed coat. The present study is the first to report the visualisation of plant hormones using IMS, and demonstrates that DESI-IMS is a promising technique for future plant hormone research. PMID:28211480

Numerical Simulation of Unsteady Turbulent Flow Induced by Two-Dimensional Elevator Car and Counter Weight System

NASA Astrophysics Data System (ADS)

Shi, Li-qun; Liu, Ying-zheng; Jin, Si-yu; Cao, Zhao-min

2007-12-01

A two-dimensional model of unsteady turbulent flow induced by high-speed elevator system was established in the present study. The research was focused on the instantaneous variation of the aerodynamic force on the car structure during traversing motion of the counter weight in the hoistway. A dynamic meshing method was employed to treat the multi-body motion system to avoid poor distortion of meshes. A comprehensive understanding of this significant aspect was obtained by varying the horizontal gap (Δ = 0.1m, 0.2m, and 0.3m) between the elevator car and the counter weight, and the moving speed ( U 0 = 2m/s, 6m/s, and 10m/s) of the elevator system. A pulsed intensification of the aerodynamic force on the elevator car and subsequent appearance of large valley with negative aerodynamic force were clearly observed in the numerical results. In parameters studied (Δ = 0.1m, U 0 = 2m/s, 6m/s, 10m/s), the peaked horizontal and vertical forces are respectively 7-11 and 4.3-5.65 times of that when the counter weight is far from the car. These results demonstrated the prominent influence of the traversing counter weight on aerodynamic force on the elevator car, which is of great significance to designers of high-speed elevator system.

Usefulness of optic nerve ultrasound to predict clinical progression in multiple sclerosis.

PubMed

Pérez Sánchez, S; Eichau Madueño, S; Rus Hidalgo, M; Domínguez Mayoral, A M; Vilches-Arenas, A; Navarro Mascarell, G; Izquierdo, G

2018-03-21

Progressive neuronal and axonal loss are considered the main causes of disability in patients with multiple sclerosis (MS). The disease frequently involves the visual system; the accessibility of the system for several functional and structural tests has made it a model for the in vivo study of MS pathogenesis. Orbital ultrasound is a non-invasive technique that enables various structures of the orbit, including the optic nerve, to be evaluated in real time. We conducted an observational, ambispective study of MS patients. Disease progression data were collected. Orbital ultrasound was performed on all patients, with power set according to the 'as low as reasonably achievable' (ALARA) principle. Optical coherence tomography (OCT) data were also collected for those patients who underwent the procedure. Statistical analysis was conducted using SPSS version 22.0. Disease progression was significantly correlated with ultrasound findings (P=.041 for the right eye and P=.037 for the left eye) and with Expanded Disability Status Scale (EDSS) score at the end of the follow-up period (P=.07 for the right eye and P=.043 for the left eye). No statistically significant differences were found with relation to relapses or other clinical variables. Ultrasound measurement of optic nerve diameter constitutes a useful, predictive factor for the evaluation of patients with MS. Smaller diameters are associated with poor clinical progression and greater disability (measured by EDSS). Copyright © 2018 Sociedad Española de Neurología. Publicado por Elsevier España, S.L.U. All rights reserved.

Brainstem dysfunction protects against syncope in multiple sclerosis.

PubMed

Habek, Mario; Krbot Skorić, Magdalena; Crnošija, Luka; Adamec, Ivan

2015-10-15

The aim of this study was to investigate the correlation between autonomic dysfunction in multiple sclerosis (MS) and brainstem dysfunction evaluated with the vestibular evoked myogenic potentials (VEMP) score and conventional MRI. Forty-five patients with the diagnosis of clinically isolated syndrome (CIS) suggestive of MS were enrolled. VEMP, heart rate, and blood pressure responses to the Valsalva maneuver, heart rate response to deep breathing, and pain provoked head-up tilt table test, as well as brain and spinal cord MRI were performed. There was no difference in the VEMP score between patients with and without signs of sympathetic or parasympathetic dysfunction. However, patients with syncope had significantly lower VEMP score compared to patients without syncope (p<0.01). Patients with orthostatic hypotension (OH) showed a trend of higher VEMP score compared to patients without OH (p=0.06). There was no difference in the presence of lesions in the brainstem or cervical spinal cord between patients with or without any of the studied autonomic parameters. The model consisting of a VEMP score of ≤5 and normal MRI of the midbrain and cervical spinal cord has sensitivity and specificity of 83% for the possibility that the patient with MS can develop syncope. Pathophysiological mechanisms underlying functional and structural disorders of autonomic nervous system in MS differ significantly. While preserved brainstem function is needed for development of syncope, structural disorders like OH could be associated with brainstem dysfunction. Copyright © 2015 Elsevier B.V. All rights reserved.

Mass Spectrometric Determination of ILPR G-quadruplex Binding Sites in Insulin and IGF-2

PubMed Central

Xiao, JunFeng

2009-01-01

The insulin-linked polymorphic region (ILPR) of the human insulin gene promoter region forms G-quadruplex structures in vitro. Previous studies show that insulin and insulin-like growth factor-2 (IGF-2) exhibit high affinity binding in vitro to 2-repeat sequences of ILPR variants a and h, but negligible binding to variant i. Two-repeat sequences of variants a and h form intramolecular G-quadruplex structures that are not evidenced for variant i. Here we report on the use of protein digestion combined with affinity capture and MALDI-MS detection to pinpoint ILPR binding sites in insulin and IGF-2. Peptides captured by ILPR variants a and h were sequenced by MALDI-MS/MS, LC-MS and in silico digestion. On-bead digestion of insulin-ILPR variant a complexes supported the conclusions. The results indicate that the sequence VCG(N)RGF is generally present in the captured peptides and is likely involved in the affinity binding interactions of the proteins with the ILPR G-quadruplexes. The significance of arginine in the interactions was studied by comparing the affinities of synthesized peptides VCGERGF and VCGEAGF with ILPR variant a. Peptides from other regions of the proteins that are connected through disulfide linkages were also detected in some capture experiments. Identification of binding sites could facilitate design of DNA binding ligands for capture and detection of insulin and IGF-2. The interactions may have biological significance as well. PMID:19747845

Structure-Specific Ribonucleases for MS-Based Elucidation of Higher-Order RNA Structure

NASA Astrophysics Data System (ADS)

Scalabrin, Matteo; Siu, Yik; Asare-Okai, Papa Nii; Fabris, Daniele

2014-07-01

Supported by high-throughput sequencing technologies, structure-specific nucleases are experiencing a renaissance as biochemical probes for genome-wide mapping of nucleic acid structure. This report explores the benefits and pitfalls of the application of Mung bean (Mb) and V1 nuclease, which attack specifically single- and double-stranded regions of nucleic acids, as possible structural probes to be employed in combination with MS detection. Both enzymes were found capable of operating in ammonium-based solutions that are preferred for high-resolution analysis by direct infusion electrospray ionization (ESI). Sequence analysis by tandem mass spectrometry (MS/MS) was performed to confirm mapping assignments and to resolve possible ambiguities arising from the concomitant formation of isobaric products with identical base composition and different sequences. The observed products grouped together into ladder-type series that facilitated their assignment to unique regions of the substrate, but revealed also a certain level of uncertainty in identifying the boundaries between paired and unpaired regions. Various experimental factors that are known to stabilize nucleic acid structure, such as higher ionic strength, presence of Mg(II), etc., increased the accuracy of cleavage information, but did not completely eliminate deviations from expected results. These observations suggest extreme caution in interpreting the results afforded by these types of reagents. Regardless of the analytical platform of choice, the results highlighted the need to repeat probing experiments under the most diverse possible conditions to recognize potential artifacts and to increase the level of confidence in the observed structural information.

Structural characterization of electrochemically and in vitro biologically generated oxidation products of atorvastatin using UHPLC/MS/MS.

PubMed

Jirásko, Robert; Mikysek, Tomáš; Chagovets, Vitaliy; Vokřál, Ivan; Holčapek, Michal

2013-09-01

Ultrahigh-performance liquid chromatography coupled with high-mass-accuracy tandem mass spectrometry (UHPLC-MS-MS) has been used for elucidation of the structures of oxidation products of atorvastatin (AT), one of the most popular commercially available drugs. The purpose of the study was identification of AT metabolites in rat hepatocytes and comparison with electrochemically generated oxidation products. AT was incubated with rat hepatocytes for 24 h. Electrochemical oxidation of AT was performed by use of a three-electrode off-line system with a glassy carbon working electrode. Three supporting electrolytes (0.1 mol L(-1) H2SO4, 0.1 mol L(-1) HCl, and 0.1 mol L(-1) NaCl) were tested, and dependence on pH was also investigated. AT undergoes oxidation by a single irreversible process at approximately +1.0 V vs. Ag/AgCl electrode. The results obtained revealed a simple and relatively fast way of determining the type of oxidation and its position, on the basis of characteristic neutral losses (NLs) and fragment ions. Unfortunately, different products were obtained by electrochemical oxidation and biotransformation of AT. High-mass-accuracy measurement combined with different UHPLC-MS-MS scans, for example reconstructed ion-current chromatograms, constant neutral loss chromatograms, or exact mass filtering, enable rapid identification of drug-related compounds. β-Oxidation, aromatic hydroxylation of the phenylaminocarbonyl group, sulfation, AT lactone and glycol formation were observed in rat biotransformation samples. In contrast, a variety of oxidation reactions on the conjugated skeleton of isopropyl substituent of AT were identified as products of electrolysis.

N-glycosylation of colorectal cancer tissues: a liquid chromatography and mass spectrometry-based investigation.

PubMed

Balog, Crina I A; Stavenhagen, Kathrin; Fung, Wesley L J; Koeleman, Carolien A; McDonnell, Liam A; Verhoeven, Aswin; Mesker, Wilma E; Tollenaar, Rob A E M; Deelder, André M; Wuhrer, Manfred

2012-09-01

Colorectal cancer is the third most common cancer worldwide with an annual incidence of ~1 million cases and an annual mortality rate of ~655,000 individuals. There is an urgent need for identifying novel targets to develop more sensitive, reliable, and specific tests for early stage detection of colon cancer. Post-translational modifications are known to play an important role in cancer progression and immune surveillance of tumors. In the present study, we compared the N-glycan profiles from 13 colorectal cancer tumor tissues and corresponding control colon tissues. The N-glycans were enzymatically released, purified, and labeled with 2-aminobenzoic acid. Aliquots were profiled by hydrophilic interaction liquid chromatography (HILIC-HPLC) with fluorescence detection and by negative mode MALDI-TOF-MS. Using partial least squares discriminant analysis to investigate the N-glycosylation changes in colorectal cancer, an excellent separation and prediction ability were observed for both HILIC-HPLC and MALDI-TOF-MS data. For structure elucidation, information from positive mode ESI-ion trap-MS/MS and negative mode MALDI-TOF/TOF-MS was combined. Among the features with a high separation power, structures containing a bisecting GlcNAc were found to be decreased in the tumor, whereas sulfated glycans, paucimannosidic glycans, and glycans containing a sialylated Lewis type epitope were shown to be increased in tumor tissues. In addition, core-fucosylated high mannose N-glycans were detected in tumor samples. In conclusion, the combination of HILIC and MALDI-TOF-MS profiling of N-glycans with multivariate statistical analysis demonstrated its potential for identifying N-glycosylation changes in colorectal cancer tissues and provided new leads that might be used as candidate biomarkers.

N-glycosylation of Colorectal Cancer Tissues

PubMed Central

Balog, Crina I. A.; Stavenhagen, Kathrin; Fung, Wesley L. J.; Koeleman, Carolien A.; McDonnell, Liam A.; Verhoeven, Aswin; Mesker, Wilma E.; Tollenaar, Rob A. E. M.; Deelder, André M.; Wuhrer, Manfred

2012-01-01

Colorectal cancer is the third most common cancer worldwide with an annual incidence of ∼1 million cases and an annual mortality rate of ∼655,000 individuals. There is an urgent need for identifying novel targets to develop more sensitive, reliable, and specific tests for early stage detection of colon cancer. Post-translational modifications are known to play an important role in cancer progression and immune surveillance of tumors. In the present study, we compared the N-glycan profiles from 13 colorectal cancer tumor tissues and corresponding control colon tissues. The N-glycans were enzymatically released, purified, and labeled with 2-aminobenzoic acid. Aliquots were profiled by hydrophilic interaction liquid chromatography (HILIC-HPLC) with fluorescence detection and by negative mode MALDI-TOF-MS. Using partial least squares discriminant analysis to investigate the N-glycosylation changes in colorectal cancer, an excellent separation and prediction ability were observed for both HILIC-HPLC and MALDI-TOF-MS data. For structure elucidation, information from positive mode ESI-ion trap-MS/MS and negative mode MALDI-TOF/TOF-MS was combined. Among the features with a high separation power, structures containing a bisecting GlcNAc were found to be decreased in the tumor, whereas sulfated glycans, paucimannosidic glycans, and glycans containing a sialylated Lewis type epitope were shown to be increased in tumor tissues. In addition, core-fucosylated high mannose N-glycans were detected in tumor samples. In conclusion, the combination of HILIC and MALDI-TOF-MS profiling of N-glycans with multivariate statistical analysis demonstrated its potential for identifying N-glycosylation changes in colorectal cancer tissues and provided new leads that might be used as candidate biomarkers. PMID:22573871

Iron accumulation in multiple sclerosis: an early pathogenic event.

PubMed

LeVine, Steven M; Bilgen, Mehmet; Lynch, Sharon G

2013-03-01

Iron has been shown to accumulate in deep gray matter structures in many forms of multiple sclerosis (MS), but detecting its presence early in the disease course (e.g., clinically isolated syndrome [CIS]) has been less clear. Here, we review a recent study where MRI scanning at 7 T together with susceptibility mapping was performed to assess iron deposition in CIS and control subjects. Susceptibility indicative of iron deposition was found to be increased in the globus pallidus, caudate, putamen and pulvinar of CIS patients compared with controls. The findings suggest that iron deposition is a pathological change that occurs early in the development of MS. Identifying the mechanisms of iron accumulation and determining whether iron promotes pathogenesis in MS are important areas of future research.

Complete structural characterization of ceramides as [M – H]− ions by multiple-stage linear ion trap mass spectrometry

PubMed Central

Hsu, Fong-Fu

2016-01-01

Ceramide is a huge lipid family consisting of diversified structures including various modifications in the fatty acyl chain and the long chain base (LCB). In this contribution, negative-ion ESI linear ion-trap multiple-stage mass spectrometric method (LIT MSn) towards complete structural determination of ceramides in ten major families characterized as the [M – H]− ions is described. Multiple sets of fragment ions reflecting the fatty acyl chain and LCB were observed in the CID MS2 spectrum, while the sequential MS3 and MS4 spectra contain structural information for locating the double bond and the functional groups, permitting realization of the fragmentation processes. Thereby, differentiation of ceramide molecules varied by chain length, the LCB (sphingosine, phytosphigosine, 6-hydroxy-sphingosine), and by the modification (α-hydroxy-, β-hydroxy-, ω-hydroxy-FA) can be achieved; and many isomeric structures in the biological specimen can be revealed in detail. PMID:27523779

High-performance liquid chromatography-mass spectrometry for mapping and sequencing glycosaminoglycan-derived oligosaccharides

PubMed Central

Volpi, Nicola; Linhardt, Robert J

2012-01-01

Glycosaminoglycans (GAGs) have proven to be very difficult to analyze and characterize because of their high negative charge density, polydispersity and sequence heterogeneity. As the specificity of the interactions between GAGs and proteins results from the structure of these polysaccharides, an understanding of GAG structure is essential for developing a structure–activity relationship. Electrospray ionization (ESI) mass spectrometry (MS) is particularly promising for the analysis of oligosaccharides chemically or enzymatically generated by GAGs because of its relatively soft ionization capacity. Furthermore, on-line high-performance liquid chromatography (HPLC)-MS greatly enhances the characterization of complex mixtures of GAG-derived oligosaccharides, providing important structural information and affording their disaccharide composition. A detailed protocol for producing oligosaccharides from various GAGs, using controlled, specific enzymatic or chemical depolymerization, is presented, together with their HPLC separation, using volatile reversed-phase ion-pairing reagents and on-line ESI-MS structural identification. This analysis provides an oligosaccharide map together with sequence information from a reading frame beginning at the nonreducing end of the GAG chains. The preparation of oligosaccharides can be carried out in 10 h, with subsequent HPLC analysis in 1–2 h and HPLC-MS analysis taking another 2 h. PMID:20448545

Sensitive and Structure-Informative N-Glycosylation Analysis by MALDI-MS; Ionization, Fragmentation, and Derivatization

PubMed Central

Nishikaze, Takashi

2017-01-01

Mass spectrometry (MS) has become an indispensable tool for analyzing post translational modifications of proteins, including N-glycosylated molecules. Because most glycosylation sites carry a multitude of glycans, referred to as “glycoforms,” the purpose of an N-glycosylation analysis is glycoform profiling and glycosylation site mapping. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has unique characteristics that are suited for the sensitive analysis of N-glycosylated products. However, the analysis is often hampered by the inherent physico-chemical properties of N-glycans. Glycans are highly hydrophilic in nature, and therefore tend to show low ion yields in both positive- and negative-ion modes. The labile nature and complicated branched structures involving various linkage isomers make structural characterization difficult. This review focuses on MALDI-MS-based approaches for enhancing analytical performance in N-glycosylation research. In particular, the following three topics are emphasized: (1) Labeling for enhancing the ion yields of glycans and glycopeptides, (2) Negative-ion fragmentation for less ambiguous elucidation of the branched structure of N-glycans, (3) Derivatization for the stabilization and linkage isomer discrimination of sialic acid residues. PMID:28794918

Investigation of epigallocatechin-3-O-caffeoate and epigallocatechin-3-O-p-coumaroate in tea leaves by LC/MS-MS analysis.

PubMed

Umehara, Masahiro; Yanae, Koji; Maruki-Uchida, Hiroko; Sai, Masahiko

2017-12-01

(-)-Epigallocatechin-3-O-gallate (EGCG), the major catechin present in green tea, exhibits potent antioxidant activity. We thereby investigated the presence of unknown components bearing the (-)-epigallocatechin (EGC) moiety in fresh tea leaf samples. Initially, liquid chromatography tandem mass spectrometry (LC-MS/MS) was employed to examine fresh tea leaves of the Yabukita, the most popular tea cultivar in Japan, which suggested the presence of the EGC phenylpropanoid derivatives, (-)-epigallocatechin-3-O-p-coumaroate (EGCpCA) and (-)-epigallocatechin-3-O-caffeoate (EGCCA). The structures of the detected EGCpCA and EGCCA were then confirmed by LC-MS/MS using synthesized EGCpCA and EGCCA as standards. In addition, EGCpCA and EGCCA were evaluated for their antioxidant activity in the ORAC (oxygen radical antioxidant capacity) and DPPH (2,2-diphenyl-1-picrylhydrazyl) radical scavenging assays, where EGCCA (8.60μmolTE/μmol, TE=Trolox equivalents) exhibited a stronger antioxidant activity than EGCG (5.52μmolTE/μmol) in the ORAC assay. Finally, EGCpCA and EGCCA were quantitated in several tea leaf samples using LC-MS/MS, and it was found that these compounds were present in lower quantities (EGCpCA, 16.8-345.8μg/g, EGCCA, 4.3-75.1μg/g in the dry tea leaves) than the major catechins. In this study, we found the potent antioxidant EGCCA using LC-MS/MS and revealed its wide existence in various tea leaves. Copyright © 2017 Elsevier Ltd. All rights reserved.

Genetic Structure of Lutzomyia longipalpis Populations in Mato Grosso Do Sul, Brazil, Based on Microsatellite Markers

PubMed Central

Santos, Mirella F. C.; Ribolla, Paulo E. M.; Alonso, Diego P.; Andrade-Filho, José D.; Casaril, Aline E.; Ferreira, Alda M. T.; Fernandes, Carlos E. S.; Brazil, Reginaldo P.; Oliveira, Alessandra G.

2013-01-01

Background Lutzomyia longipalpis (Diptera: Psychodidae) is the major vector of Leishmania (Leishmania) infantum and thus plays a crucial role in the epidemiology of American visceral leishmaniasis (AVL). This vector is the best studied species of sand fly in the Neotropical region. Many studies claim that this vector is in fact a species complex; however there is still no consensus regarding the number of species that belong into this complex or the geographical distribution of sibling species. The aim of the present study was to analyze the genetic relationships within Lu. longipalpis populations in the state of Mato Grosso do Sul (MS), Brazil. Methodology/Principal Findings We collected 30 Lu. longipalpis (15 females and 15 males) from five localities (Campo Grande, Três Lagoas, Aquidauana, Miranda and Bonito) and 30 Lu. Cruzi from Corumbá, totaling 180 sandflies from MS, and 30 Lu. longipalpis from Estrela de Alagoas, state of Alagoas (AL), Northeast Brazil. We show that eight previously described microsatellite loci were sufficient in distinguishing Lu. longipalpis from Lu. Cruzi, which is a closely related species, and in differentiating between Lu. longipalpis collected in MS versus Estrela de Alagoas. Analyses of the genotypes revealed introgression between sympatric Lu. longipalpis and Lu. Cruzi. Conclusions/Significance Our findings support the hypothesis of cryptic species within the Lu. longipalpis complex. Furthermore, our data revealed introgression between Lu. longipalpis and Lu. cruzi. This phenomenon should be further investigated to determine the level and incidence of hybridization between these two species. We also demonstrated that microsatellite markers are a powerful tool for differentiating sand fly populations and species. The present study has elucidated the population structure of Lu. longipalpis in MS and, by extension, the Neotropical Lu. longipalpis complex itself. PMID:24066129

Approach to characterization of the higher order structure of disulfide-containing proteins using hydrogen/deuterium exchange and top-down mass spectrometry.

PubMed

Wang, Guanbo; Kaltashov, Igor A

2014-08-05

Top-down hydrogen/deuterium exchange (HDX) with mass spectrometric (MS) detection has recently matured to become a potent biophysical tool capable of providing valuable information on higher order structure and conformational dynamics of proteins at an unprecedented level of structural detail. However, the scope of the proteins amenable to the analysis by top-down HDX MS still remains limited, with the protein size and the presence of disulfide bonds being the two most important limiting factors. While the limitations imposed by the physical size of the proteins gradually become more relaxed as the sensitivity, resolution and dynamic range of modern MS instrumentation continue to improve at an ever accelerating pace, the presence of the disulfide linkages remains a much less forgiving limitation even for the proteins of relatively modest size. To circumvent this problem, we introduce an online chemical reduction step following completion and quenching of the HDX reactions and prior to the top-down MS measurements of deuterium occupancy of individual backbone amides. Application of the new methodology to the top-down HDX MS characterization of a small (99 residue long) disulfide-containing protein β2-microglobulin allowed the backbone amide protection to be probed with nearly a single-residue resolution across the entire sequence. The high-resolution backbone protection pattern deduced from the top-down HDX MS measurements carried out under native conditions is in excellent agreement with the crystal structure of the protein and high-resolution NMR data, suggesting that introduction of the chemical reduction step to the top-down routine does not trigger hydrogen scrambling either during the electrospray ionization process or in the gas phase prior to the protein ion dissociation.

Before and after retrofit - response of a building during ambient and strong motions

USGS Publications Warehouse

Celebi, M.; Liu, Huaibao P.; ,

1998-01-01

This paper presents results obtained from ambient vibration and strong-motion responses of a thirteen-story, moment-resisting steel framed Santa Clara County Office Building (SCCOB) before being retrofitted by visco-elastic dampers and from ambient vibration response following the retrofit. Understanding the cumulative structural and site characteristics that affect the response of SCCOB before and after the retrofit is important in assessing earthquake hazards to other similar buildings and decision making in retrofitting them. The results emphasize the need to better evaluate structural and site characteristics in developing earthquake resisting designs that avoid resonating effects. Various studies of the strong-motion response records from the SCCOB during the 24 April 1984 (MHE) Morgan Hill (MS = 6.1), the 31 March 1986 (MLE) Mt. Lewis (MS = 6.1) and the 17 October 1989 (LPE) Loma Prieta (MS = 7.1) earthquakes show that the dynamic characteristics of the building are such that it (a) resonated (b) responded with a beating effect due to close-coupling of its translational and torsional frequencies, and (c) had a long-duration response due to low-damping. During each of these earthquakes, there was considerable contents damage and the occupants felt the rigorous vibration of the building. Ambient tests of SCCOB performed following LPE showed that both translational and torsional periods of the building are smaller than those derived from strong motions. Ambient tests performed following the retrofit of the building with visco-elastic dampers show that the structural fundamental mode frequency of the building has increased. The increased frequency implies a stiffer structure. Strong-motion response of the building during future earthquakes will ultimately validate the effectiveness of the retrofit method.This paper presents results obtained from ambient vibration and strong-motion responses of a thirteen-story, moment-resisting steel framed Santa Clara County Office Building (SCCOB) before being retrofitted by visco-elastic dampers and from ambient vibration response following the retrofit. Understanding the cumulative structural and site characteristics that affect the response of SCCOB before and after the retrofit is important in assessing earthquake hazards to other similar buildings and decision making in retrofitting them. The results emphasize the need to better evaluate structural and site characteristics in developing earthquake resisting designs that avoid resonating effects. Various studies of the strong-motion response records from the SCCOB during the 24 April 1984 (MHE) Morgan Hill (Ms = 6.1), the 31 March 1986 (MLE) Mt. Lewis (Ms = 6.1) and the 17 October 1989(LPE) Loma Prieta (Ms = 7.1) earthquakes show that the dynamic characteristics of the building are such that it (a) resonated (b) responded with a beating effect due to close-coupling of its translational and torsional frequencies, and (c) had a long-duration response due to low-damping. During each of these earthquakes, there was considerable contents damage and the occupants felt the rigorous vibration of the building. Ambient tests of SCCOB performed following LPE showed that both translational and torsional periods of the building are smaller than those derived from strong motions. Ambient tests performed following the retrofit of the building with visco-elastic dampers show that the structural fundamental mode frequency of the building has increased. The increased frequency implies a stiffer structure. Strong-motion response of the building during future earthquakes will ultimately validate the effectiveness of the retrofit method.

Advances in Analysis of Human Milk Oligosaccharides123

PubMed Central

Ruhaak, L. Renee; Lebrilla, Carlito B.

2012-01-01

Oligosaccharides in human milk strongly influence the composition of the gut microflora of neonates. Because it is now clear that the microflora play important roles in the development of the infant immune system, human milk oligosaccharides (HMO) are studied frequently. Milk samples contain complex mixtures of HMO, usually comprising several isomeric structures that can be either linear or branched. Traditionally, HMO profiling was performed using HPLC with fluorescence or UV detection. By using porous graphitic carbon liquid chromatography MS, it is now possible to separate and identify most of the isomers, facilitating linkage-specific analysis. Matrix-assisted laser desorption ionization time-of-flight analysis allows fast profiling, but does not allow isomer separation. Novel MS fragmentation techniques have facilitated structural characterization of HMO that are present at lower concentrations. These techniques now facilitate more accurate studies of HMO consumption as well as Lewis blood group determinations. PMID:22585919

Accurate recognition and feature qualify for flavonoid extracts from Liang-wai Gan Cao by liquid chromatography-high resolution-mass spectrometry and computational MS/MS fragmentation.

PubMed

He, Min; Wu, Hai; Nie, Juan; Yan, Pan; Yang, Tian-Biao; Yang, Zhi-Yu; Pei, Rui

2017-11-30

In this study, Liquid Chromatography (LC) separation combined with quadrupole-Time-Of-Flight Mass Spectrometry (qTOF-MS) detection was used to analyze the characteristic ions of the flavonoids from Liang-wai Gan Cao (Radix Glycyrrhizae uralensis). First, accurate mass measurement and isotope curve optimization could provide reliable molecular prediction after noise deduction, baseline calibration and "ghost peak recognition". Thus, some spectral features in the LC-MS data could be clearly explained. Secondly, the chemical structure of flavonoids was deduced by MS/MS fragment ions, and the in-silico spectra by MS-FINDER program provided strong support for overcoming the bottleneck of phytochemical identification. For a predicted formula and experimental MS/MS spectrum, the MS-FINDER program could sort the candidate compounds in the public database based on a comprehensive weighted score, and we took the first 20 reliable compounds to seek the target compound in an in-house database. Certainly, those fragmentation pathways could also be deduced and described as Retro-Diels-Alder (RDA) fragmentation reaction, losses of C 4 H 8 , C 5 H 8 , CH 3 , CO, CO 2 and others. Accordingly, 63 flavonoids were identified, and their in-silico bioactivity were clearly disclosed by some bioinformatics tools. In this experiment, the flavonoids obtained by the four extraction processes were tested by LC-qTOF-MS. We looked for possible Q-markers from these data matrices and then quantified them; their similarities/differences were also described. The results also indicated that the Macroporous Adsorption Resins (MARs) purification is a low cost, environmentally friendly and effective approach. Copyright © 2017 Elsevier B.V. All rights reserved.

Formation of oligomeric alkenylperoxides during the oxidation of unsaturated fatty acids: an electrospray ionization tandem mass spectrometry study.

PubMed

Villaverde, Juan José; Santos, Sónia A O; Maciel, Elisabete; Simões, Mário M Q; Pascoal Neto, Carlos; Domingues, M Rosário M; Silvestre, Armando J D

2012-02-01

This study reports the identification of oligomeric alkenylperoxides by electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry (ESI-MS(2)), during the oxidation of oleic, linoleic and linolenic acids with Fenton's (Fe(2+)/H(2)O(2)) and Fe(2+)/O(2) systems. The reactions were followed by ferrous oxidation-xylenol orange method together with GC-MS and GC-FID, allowing to observe that both oxidation systems are different in terms of hydroperoxide evolution, probably due to the presence of different intermediate reactive species: perferryl ion and OH(·) radical responsible for the decomposition of lipid hydroperoxides and formation of new compounds. The analysis of ESI-MS in the negative mode, obtained after oxidation of each fatty acid, confirmed the presence of the monomeric oxidation products together with other compounds at high mass region above m/z 550. These new ions were attributed to oligomeric structures, identified by the fragmentation pathways observed in the tandem mass spectra. Copyright © 2012 John Wiley & Sons, Ltd.

Thermal behavior of J-aggregates in a Langmuir-Blodgett film of pure merocyanine dye investigated by UV-visible and IR absorption spectroscopy.

PubMed

Hirano, Yoshiaki; Tateno, Shinsuke; Maio, Ari; Ozaki, Yukihiro

2009-03-05

We have characterized the structure of J-aggregate in a Langmuir-Blodgett film of pure merocyanine dye (MS18) fabricated under an aqueous subphase containing a cadmium ion (Cd2+) and have investigated its thermal behavior by UV-visible and IR absorption spectroscopy in the range from 25 to 250 degrees C with a continuous scan. The results of both UV-visible and IR absorption spectra indicate that temperature-dependent changes in the MS18 aggregation state in the pure MS18 system are closely and mildly linked with the MS18 intramolecular charge transfer and the behavior of the packing, orientation, conformation, and thermal mobility of MS18 hydrocarbon chain, respectively. The J-aggregate in the pure MS18 system dissociates from 25 to 150 degrees C, and the dissociation temperature at 150 degrees C is higher by 50 degrees C than that in the previous MS18- arachidic acid (C20) binary system. The lower dissociation temperature in the binary system originates from the fact that temperature-dependent structural disorder of cadmium arachidate (CdC20), being phase-separated from MS18, has an influence on the dissociation of J-aggregate. From 160 to 180 degrees C, thermally induced blue-shifted bands, caused by the oligomeric MS18 aggregation, appear at around 520 nm in the pure MS18 system by contraries, regardless of the lack of driving force by the melting phenomenon of CdC20. The temperature at which the 520 nm bands occur is in good agreement with the melting point (160 degrees C) of hydrocarbon chain in MS18 with Cd2+, whereas its chromophore part is clearly observed to melt near 205 degrees C by UV-visible spectra. Therefore, it is suggested that the driving force that induces the 520 nm band in the pure MS18 system arises from the partial melting of hydrocarbon chain in MS18 with Cd2+.

Study on Seismogenesis of 2013 Ms5.1 Badong Earthquake in the Three Gorges Reservoir Region

NASA Astrophysics Data System (ADS)

Li, X.; Zeng, Z.; Xu, S.; He, C.

2015-12-01

On 16 December, 2013, an earthquake of Ms5.1 occurred in Badong County, the Three Gorges Reservoir area, China. We collected all the 150 published focal mechanism solutions (FMS) and inversed the tectonic stress field in Badong, the Three Gorges Dam and Huangling anticline area using the software SATSI (Hardebeck and Michael, 2006). Inversion results show that the orientations of maximum principle stress axis (σ1) in Badong plunge to NNE or SSW. Detailed characteristics of the stress field indicate that the σ1 axis is almost vertical in the center of Huangling anticline and turns horizontal to the west. As to deep structures, we studied the satellite gravity anomalies of 8-638 order in this area using the EIGEN-6C2 model provided by ICGRM. Combining the seismic sounding profile through the epicenter of Badong earthquake and the petrology data, we reinterpreted the deep structure in the study area. The results show that the deep crust in Badong is unstable and the deep material's upwelling leads to Huangling anticline continued uplifting, which is consistent with the result indicated from the stress filed. Both of them provide energy for the preparation of earthquake. The FMS shows that Gaoqiao Fault is the causative fault of this Ms5.1 earthquake. Field investigations indicated that the lithology and fracture characteristic in Badong is beneficial to reservoir water infiltration. Before the earthquake, reservoir water level raised to 175m, the highest storage level, which increased the loading. Based on above researches, we believe that the Ms5.1 Badong earthquake is controlled by deep tectonic environment and stress field in shallow crust. The reservoir water infiltration and uploading increase generated by water storage of the Three Gorges area reduced the strength of Gaoqiao Fault and changed its stress state. These factors jointly promoted an abrupt movement of the fault in the critical stress state, and triggered the Ms5.1 Badong earthquake.

In situ lignocellulosic unlocking mechanism for carbohydrate hydrolysis in termites: crucial lignin modification

PubMed Central

2011-01-01

Background Termites are highly effective at degrading lignocelluloses, and thus can be used as a model for studying plant cell-wall degradation in biological systems. However, the process of lignin deconstruction and/or degradation in termites is still not well understood. Methods We investigated the associated structural modification caused by termites in the lignin biomolecular assembly in softwood tissues crucial for cell-wall degradation. We conducted comparative studies on the termite-digested (i.e. termite feces) and native (control) softwood tissues with the aid of advanced analytical techniques: 13C crosspolarization magic angle spinning and nuclear magnetic resonance (CP-MAS-NMR) spectroscopy, flash pyrolysis with gas chromatography mass spectrometry (Py-GC/MS), and Py-GC-MS in the presence of tetramethylammonium hydroxide (Py-TMAH)-GC/MS. Results The 13C CP/MAS NMR spectroscopic analysis revealed an increased level of guaiacyl-derived (G unit) polymeric framework in the termite-digested softwood (feces), while providing specific evidence of cellulose degradation. The Py-GC/MS data were in agreement with the 13C CP/MAS NMR spectroscopic studies, thus indicating dehydroxylation and modification of selective intermonomer side-chain linkages in the lignin in the termite feces. Moreover, Py-TMAH-GC/MS analysis showed significant differences in the product distribution between control and termite feces. This strongly suggests that the structural modification in lignin could be associated with the formation of additional condensed interunit linkages. Conclusion Collectively, these data further establish: 1) that the major β-O-4' (β-aryl ether) was conserved, albeit with substructure degeneracy, and 2) that the nature of the resulting polymer in termite feces retained most of its original aromatic moieties (G unit-derived). Overall, these results provide insight into lignin-unlocking mechanisms for understanding plant cell-wall deconstruction, which could be useful in development of new enzymatic pretreatment processes mimicking the termite system for biochemical conversion of lignocellulosic biomass to fuels and chemicals. PMID:21672247

An Infrared Actin Probe for Deep-Cell Electroporation-Based Single-Molecule Speckle (eSiMS) Microscopy

PubMed Central

Yamashiro, Sawako; Watanabe, Naoki

2017-01-01

Single-molecule speckle (SiMS) microscopy is a powerful method to directly elucidate biochemical reactions in live cells. However, since the signal from an individual fluorophore is extremely faint, the observation area by epi-fluorescence microscopy is restricted to the thin cell periphery to reduce autofluorescence, or only molecules near the plasma membrane are visualized by total internal reflection fluorescence (TIRF) microscopy. Here, we introduce a new actin probe labeled with near infrared (NIR) emissive CF680R dye for easy-to-use, electroporation-based SiMS microscopy (eSiMS) for deep-cell observation. CF680R-labeled actin (CF680R-actin) incorporated into actin structures and showed excellent brightness and photostability suitable for single-molecule imaging. Importantly, the intensity of autofluorescence with respect to SiMS brightness was reduced to approximately 13% compared to DyLight 550-labeled actin (DL550-actin). CF680R-actin enabled the monitoring of actin SiMS in actomyosin bundles associated with adherens junctions (AJs) located at 3.5–4 µm above the basal surfaces of epithelial monolayers. These favorable properties of CF680R-actin extend the application of eSiMS to actin turnover and flow analyses in deep cellular structures. PMID:28671584

Spinal cord atrophy in anterior-posterior direction reflects impairment in multiple sclerosis.

PubMed

Lundell, H; Svolgaard, O; Dogonowski, A-M; Romme Christensen, J; Selleberg, F; Soelberg Sørensen, P; Blinkenberg, M; Siebner, H R; Garde, E

2017-10-01

To investigate how atrophy is distributed over the cross section of the upper cervical spinal cord and how this relates to functional impairment in multiple sclerosis (MS). We analysed the structural brain MRI scans of 54 patients with relapsing-remitting MS (n=22), primary progressive MS (n=9), secondary progressive MS (n=23) and 23 age- and sex-matched healthy controls. We measured the cross-sectional area (CSA), left-right width (LRW) and anterior-posterior width (APW) of the spinal cord at the segmental level C2. We tested for a nonparametric linear relationship between these atrophy measures and clinical impairments as reflected by the Expanded Disability Status Scale (EDSS) and Multiple Sclerosis Impairment Scale (MSIS). In patients with MS, CSA and APW but not LRW were reduced compared to healthy controls (P<.02) and showed significant correlations with EDSS, MSIS and specific MSIS subscores. In patients with MS, atrophy of the upper cervical cord is most evident in the antero-posterior direction. As APW of the cervical cord can be readily derived from standard structural MRI of the brain, APW constitutes a clinically useful neuroimaging marker of disease-related neurodegeneration in MS. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Heterogeneity of ventricular repolarization in newborns with intrauterine growth restriction.

PubMed

Fouzas, Sotirios; Karatza, Ageliki A; Davlouros, Periklis A; Chrysis, Dionisios; Alexopoulos, Dimitrios; Mantagos, Stefanos; Dimitriou, Gabriel

2014-12-01

Intrauterine growth restriction (IUGR) is associated with structural and functional cardiac alterations but the electrophysiological consequences of these disturbances remain unknown. To explore the distribution of ventricular repolarization and its relation to myocardial mechanics in newborns with IUGR. STUDY DESIGN, SUBJECTS AND OUTCOME MEASUREMENTS: Conventional and tissue Doppler echocardiographic data, and electrocardiographic parameters used to describe the distribution of ventricular repolarization (dispersion of QT [QTd] and JT [JTd]), were obtained on the second (D2) and fifth (D5) postnatal day and compared between 25 IUGR newborns and 25 matched-for-gestational age controls. IUGR was associated with relative interventricular septum hypertrophy, increased left ventricular (LV) E/E' ratio and higher LV myocardial performance index (MPI). On both study days, the IUGR infants presented higher QTd and JTd compared to controls (QTd-D2: 66±20 ms vs. 36±12 ms, P<0.001; JTd-D2: 54±13 ms vs. 34±9 ms, P<0.001; QTd-D5: 61±14 ms vs. 27±12 ms, P<0.001; JTd-D5: 54±13 ms vs. 27±9 ms, P<0.001). The association between QTd and LV E/E' (D2: regression coefficient beta 0.747, R(2) 0.585; D5: beta 0.843, R(2) 0.646) and QTd and MPI (D2: beta 0.680, R(2) 0.576; D5: beta 0.698, R(2) 0.650) was also significant (P<0.001 for all analyses). Our findings suggest that IUGR is associated with electrophysiological remodeling of the neonatal heart, a process which is closely related to the underlying alterations in ventricular mechanics and might predispose to adverse electrophysiological events. Copyright © 2014 Elsevier Ltd. All rights reserved.

Metabolite profiling in Trigonella seeds via UPLC-MS and GC-MS analyzed using multivariate data analyses.

PubMed

Farag, Mohamed A; Rasheed, Dalia M; Kropf, Matthias; Heiss, Andreas G

2016-11-01

Trigonella foenum-graecum is a plant of considerable value for its nutritive composition as well as medicinal effects. This study aims to examine Trigonella seeds using a metabolome-based ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) in parallel to gas chromatography-mass spectrometry (GC-MS) coupled with multivariate data analyses. The metabolomic differences of seeds derived from three Trigonella species, i.e., T. caerulea, T. corniculata, and T. foenum-graecum, were assessed. Under specified conditions, we were able to identify 93 metabolites including 5 peptides, 2 phenolic acids, 22 C/O-flavonoid conjugates, 26 saponins, and 9 fatty acids using UPLC-MS. Several novel dipeptides, saponins, and flavonoids were found in Trigonella herein for the first time. Samples were classified via unsupervised principal component analysis (PCA) followed by supervised orthogonal projection to latent structures-discriminant analysis (OPLS-DA). A distinct separation among the investigated Trigonella species was revealed, with T. foenum-graecum samples found most enriched in apigenin-C-glycosides, viz. vicenins 1/3 and 2, compared to the other two species. In contrast to UPLC-MS, GC-MS was less efficient to classify specimens, with differences among specimens mostly attributed to fatty acyl esters. GC-MS analysis of Trigonella seed extracts led to the identification of 91 metabolites belonging mostly to fatty acyl esters, free fatty acids followed by organic acids, sugars, and amino acids. This study presents the first report on primary and secondary metabolite compositional differences among Trigonella seeds via a metabolomics approach and reveals that, among the species examined, the official T. foenum-graecum presents a better source of Trigonella secondary bioactive metabolites.

Determination and identification of hydrophilic and hydrophobic arsenic species in methanol extract of fresh cod liver by RP-HPLC with simultaneous ICP-MS and ESI-Q-TOF-MS detection.

PubMed

Arroyo-Abad, Uriel; Lischka, Susanne; Piechotta, Christian; Mattusch, Jürgen; Reemtsma, Thorsten

2013-12-01

The present study was focused on the determination and identification of arsenic species in methanolic extracts of cod liver. Arsenic species were fractionated and the fractions analysed by RP-HPLC-ICP-MS coupled with ESI-Q-TOF-MS. The total concentration of arsenic in the fresh cod liver was analysed by ICP-MS to be 1.53±0.02 mg As kg(-1)w.w. and the extraction recovery was ca. 100% and the column recovery >93%. Besides polar inorganic and methylated arsenic species (>70%) more hydrophobic arsenic-containing fatty acids and hydrocarbons occurred. Based on the mass spectrometric data proposals for molecular structures were elaborated for 20 of the organic As species included 10 arsenic-containing fatty acids (AsFA) and an arsenic-containing hydrocarbon (AsHC) mentioned for the first time in fresh cod liver. Arsenobetaine was found as main water-soluble arsenic compound in cod liver followed by higher molecular mass arsenic-containing fatty acids and hydrocarbons. Copyright © 2013 Elsevier Ltd. All rights reserved.

Use of a deuterated internal standard with pyrolysis-GC/MS dimeric marker analysis to quantify tire tread particles in the environment.

PubMed

Unice, Kenneth M; Kreider, Marisa L; Panko, Julie M

2012-11-08

Pyrolysis(pyr)-GC/MS analysis of characteristic thermal decomposition fragments has been previously used for qualitative fingerprinting of organic sources in environmental samples. A quantitative pyr-GC/MS method based on characteristic tire polymer pyrolysis products was developed for tread particle quantification in environmental matrices including soil, sediment, and air. The feasibility of quantitative pyr-GC/MS analysis of tread was confirmed in a method evaluation study using artificial soil spiked with known amounts of cryogenically generated tread. Tread concentration determined by blinded analyses was highly correlated (r2 ≥ 0.88) with the known tread spike concentration. Two critical refinements to the initial pyrolysis protocol were identified including use of an internal standard and quantification by the dimeric markers vinylcyclohexene and dipentene, which have good specificity for rubber polymer with no other appreciable environmental sources. A novel use of deuterated internal standards of similar polymeric structure was developed to correct the variable analyte recovery caused by sample size, matrix effects, and ion source variability. The resultant quantitative pyr-GC/MS protocol is reliable and transferable between laboratories.

Lipid and protein composition as driving force for multiple sclerosis

NASA Astrophysics Data System (ADS)

Beck, Roy; Shaharabani, Rona

Physical models and experiments often reduce the number of components aiming to address the fundamental mechanisms. Nevertheless, the inherent heterogeneity is an essential ingredient in the biological context. We present our recent efforts to model and understand the development of multiple sclerosis (MS) from a biophysical perspective. Myelin sheath is a multilamellar complex of various lipids and proteins that surround axons and acts as an insulating layer for proper nerve conduction. In MS the myelin structure is disrupted impairing its function. Previous studies showed that MS is correlated with small lipid composition variation and reduction in the adhesive myelin basic protein. We found that such alterations result in pathological phase transition from a lamellar to inverted hexagonal that involve enhanced local curvature. Similar curvatures are also found in vivo in diseased myelin sheaths. Since the etiology and recovery pathways of MS are currently unclear, these findings delineate novel functional roles to dominant constituents in cytoplasmic myelin sheaths, shed new light on mechanisms disrupting lipid-protein complexes, and suggest new courses for diagnosis and treatment for MS.

Study of the rice straw biodegradation in mixed culture of Trichoderma viride and Aspergillus niger by GC-MS and FTIR.

PubMed

Chen, Yaoning; Huang, Jingxia; Li, Yuanping; Zeng, Guangming; Zhang, Jiachao; Huang, Aizhi; Zhang, Jie; Ma, Shuang; Tan, Xuebin; Xu, Wei; Zhou, Wei

2015-07-01

This study was conducted to investigate the biodegradation ability of the mixed culture of Trichoderma viride and Aspergillus niger through the study of the organic matter extracted from rice straw and the lignocellulose structure by using gas chromatography-mass spectrometer (GC-MS) and Fourier transform infrared spectroscopy (FTIR). The results of the GC-MS showed that the mixed culture possessed shorter alkane (heptane) at the end of the incubation and more kinds of organic matter (except the alkanes, 29 kinds of organic matter were detected) than the pure cultures. It could be deduced that the organic matter could indicate the degradation degree of the lignocellulose to some extent. Moreover, pinene was detected in the mixed culture on days 5 and 10, which might represent the antagonistic relationship between T. viride and A. niger. The analysis of FTIR spectrums which indirectly verified the GC-MS results showed that the mixed culture possessed a better degradation of rice straw compared with the pure culture. Therefore, the methods used in this research could be considered as effective ones to investigate the lignocellulose degradation mechanism in mixed culture.

A Comparison of Supervised Machine Learning Algorithms and Feature Vectors for MS Lesion Segmentation Using Multimodal Structural MRI

PubMed Central

Sweeney, Elizabeth M.; Vogelstein, Joshua T.; Cuzzocreo, Jennifer L.; Calabresi, Peter A.; Reich, Daniel S.; Crainiceanu, Ciprian M.; Shinohara, Russell T.

2014-01-01

Machine learning is a popular method for mining and analyzing large collections of medical data. We focus on a particular problem from medical research, supervised multiple sclerosis (MS) lesion segmentation in structural magnetic resonance imaging (MRI). We examine the extent to which the choice of machine learning or classification algorithm and feature extraction function impacts the performance of lesion segmentation methods. As quantitative measures derived from structural MRI are important clinical tools for research into the pathophysiology and natural history of MS, the development of automated lesion segmentation methods is an active research field. Yet, little is known about what drives performance of these methods. We evaluate the performance of automated MS lesion segmentation methods, which consist of a supervised classification algorithm composed with a feature extraction function. These feature extraction functions act on the observed T1-weighted (T1-w), T2-weighted (T2-w) and fluid-attenuated inversion recovery (FLAIR) MRI voxel intensities. Each MRI study has a manual lesion segmentation that we use to train and validate the supervised classification algorithms. Our main finding is that the differences in predictive performance are due more to differences in the feature vectors, rather than the machine learning or classification algorithms. Features that incorporate information from neighboring voxels in the brain were found to increase performance substantially. For lesion segmentation, we conclude that it is better to use simple, interpretable, and fast algorithms, such as logistic regression, linear discriminant analysis, and quadratic discriminant analysis, and to develop the features to improve performance. PMID:24781953

A comparison of supervised machine learning algorithms and feature vectors for MS lesion segmentation using multimodal structural MRI.

PubMed

Sweeney, Elizabeth M; Vogelstein, Joshua T; Cuzzocreo, Jennifer L; Calabresi, Peter A; Reich, Daniel S; Crainiceanu, Ciprian M; Shinohara, Russell T

2014-01-01

Machine learning is a popular method for mining and analyzing large collections of medical data. We focus on a particular problem from medical research, supervised multiple sclerosis (MS) lesion segmentation in structural magnetic resonance imaging (MRI). We examine the extent to which the choice of machine learning or classification algorithm and feature extraction function impacts the performance of lesion segmentation methods. As quantitative measures derived from structural MRI are important clinical tools for research into the pathophysiology and natural history of MS, the development of automated lesion segmentation methods is an active research field. Yet, little is known about what drives performance of these methods. We evaluate the performance of automated MS lesion segmentation methods, which consist of a supervised classification algorithm composed with a feature extraction function. These feature extraction functions act on the observed T1-weighted (T1-w), T2-weighted (T2-w) and fluid-attenuated inversion recovery (FLAIR) MRI voxel intensities. Each MRI study has a manual lesion segmentation that we use to train and validate the supervised classification algorithms. Our main finding is that the differences in predictive performance are due more to differences in the feature vectors, rather than the machine learning or classification algorithms. Features that incorporate information from neighboring voxels in the brain were found to increase performance substantially. For lesion segmentation, we conclude that it is better to use simple, interpretable, and fast algorithms, such as logistic regression, linear discriminant analysis, and quadratic discriminant analysis, and to develop the features to improve performance.

Structural Characterization of Ginsenosides from Flower Buds of Panax ginseng by RRLC-Q-TOF MS.

PubMed

Wu, Wei; Lu, Ziyan; Teng, Yaran; Guo, Yingying; Liu, Shuying

2016-02-01

Ginseng flower bud as a part of Panax ginseng has received much attention as a valuable functional food with medicinal potential. A few studies focused on systematic and comprehensive studies on its major ingredients. This study aims to rapidly characterize ginsenosides in ginseng flower buds and provide scientific basis for developing functional food, exploiting pharmaceutical effects and making full use of ginseng resources. A rapid resolution liquid chromatography coupled with quadrupole-time-of-flight mass spectrometry (RRLC-Q-TOF-MS) method was developed for rapid qualitative and quantitative analysis of ginsenosides in ginseng flower buds. The compounds were identified by comparing retention time of the reference standards, accurate mass measurement and the fragment ions obtained from RRLC-Q-TOF-MS/MS analyses. A total of 14 kinds of ginsenosides were identified and 5 kinds of malonyl-ginsenosides were first tentatively identified in ginseng flower buds. Ten kinds of main ginsenosides were quantitatively analyzed. The developed RRLC-Q-TOF-MS method was demonstrated as an effective analytical means for rapid characterization of the ginsenosides in flower buds of P. ginseng. The research result is valuable for quality control, assessment of authenticity and stability evaluation of ginseng flower buds. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Switching of the core structures of glycosphingolipids from globo- and lacto- to ganglio-series upon human embryonic stem cell differentiation.

PubMed

Liang, Yuh-Jin; Kuo, Huan-Hsien; Lin, Chi-Hung; Chen, Yen-Ying; Yang, Bei-Chia; Cheng, Yuan-Yuan; Yu, Alice L; Khoo, Kay-Hooi; Yu, John

2010-12-28

A systematic survey of expression profiles of glycosphingolipids (GSLs) in two hESC lines and their differentiated embryoid body (EB) outgrowth with three germ layers was carried out using immunofluorescence, flow cytometry, and MALDI-MS and MS/MS analyses. In addition to the well-known hESC-specific markers stage-specific embryonic antigen 3 (SSEA-3) and SSEA-4, we identified several globosides and lacto-series GSLs, previously unrevealed in hESCs, including Gb(4)Cer, Lc(4)Cer, fucosyl Lc(4)Cer, Globo H, and disialyl Gb(5)Cer. During hESC differentiation into EBs, MS analysis revealed a clear-cut switch in the core structures of GSLs from globo- and lacto- to ganglio-series, which was not as evident by immunostaining with antibodies against SSEA-3 and SSEA-4, owing to their cross-reactivities with various glycosphingolipids. Such a switch was attributable to altered expression of key glycosyltransferases (GTs) in the biosynthetic pathways by the up-regulation of ganglio-series-related GTs with simultaneous down-regulation of globo- and lacto-series-related GTs. Thus, these results provide insights into the unique stage-specific transition and mechanism for alterations of GSL core structures during hESC differentiation. In addition, unique glycan structures uncovered by MS analyses may serve as surface markers for further delineation of hESCs and help identify of their functional roles not only in hESCs but also in cancers.

Top-down approach for the direct characterization of low molecular weight heparins using LC-FT-MS.

PubMed

Li, Lingyun; Zhang, Fuming; Zaia, Joseph; Linhardt, Robert J

2012-10-16

Low molecular heparins (LMWHs) are structurally complex, heterogeneous, polydisperse, and highly negatively charged mixtures of polysaccharides. The direct characterization of LMWH is a major challenge for currently available analytical technologies. Electrospray ionization (ESI) liquid chromatography-mass spectrometry (LC-MS) is a powerful tool for the characterization complex biological samples in the fields of proteomics, metabolomics, and glycomics. LC-MS has been applied to the analysis of heparin oligosaccharides, separated by size exclusion, reversed phase ion-pairing chromatography, and chip-based amide hydrophilic interaction chromatography (HILIC). However, there have been limited applications of ESI-LC-MS for the direct characterization of intact LMWHs (top-down analysis) due to their structural complexity, low ionization efficiency, and sulfate loss. Here we present a simple and reliable HILIC-Fourier transform (FT)-ESI-MS platform to characterize and compare two currently marketed LMWH products using the top-down approach requiring no special sample preparation steps. This HILIC system relies on cross-linked diol rather than amide chemistry, affording highly resolved chromatographic separations using a relatively high percentage of acetonitrile in the mobile phase, resulting in stable and high efficiency ionization. Bioinformatics software (GlycReSoft 1.0) was used to automatically assign structures within 5-ppm mass accuracy.

The Protein Information Management System (PiMS): a generic tool for any structural biology research laboratory

PubMed Central

Morris, Chris; Pajon, Anne; Griffiths, Susanne L.; Daniel, Ed; Savitsky, Marc; Lin, Bill; Diprose, Jonathan M.; Wilter da Silva, Alan; Pilicheva, Katya; Troshin, Peter; van Niekerk, Johannes; Isaacs, Neil; Naismith, James; Nave, Colin; Blake, Richard; Wilson, Keith S.; Stuart, David I.; Henrick, Kim; Esnouf, Robert M.

2011-01-01

The techniques used in protein production and structural biology have been developing rapidly, but techniques for recording the laboratory information produced have not kept pace. One approach is the development of laboratory information-management systems (LIMS), which typically use a relational database schema to model and store results from a laboratory workflow. The underlying philosophy and implementation of the Protein Information Management System (PiMS), a LIMS development specifically targeted at the flexible and unpredictable workflows of protein-production research laboratories of all scales, is described. PiMS is a web-based Java application that uses either Postgres or Oracle as the underlying relational database-management system. PiMS is available under a free licence to all academic laboratories either for local installation or for use as a managed service. PMID:21460443

Online structural elucidation of alkaloids and other constituents in crude extracts and cultured cells of Nandina domestica by combination of LC-MS/MS, LC-NMR, and LC-CD analyses.

PubMed

Iwasa, Kinuko; Takahashi, Teturo; Nishiyama, Yumi; Moriyasu, Masataka; Sugiura, Makiko; Takeuchi, Atsuko; Tode, Chisato; Tokuda, Harukuni; Takeda, Kazuyoshi

2008-08-01

The combination of NMR, MS, and CD data permitted the structural elucidation including the absolute configuration of the known alkaloids and unknown components in the extract matrix solution of Nandina domestica without isolation and sample purification prior to the coupling experiments. Unstable natural stereoisomers were identified by LC-NMR and LC-MS. Five known alkaloids, (S)-isoboldine, (S)-domesticine, (S)-nantenine, sinoacutine, and menispermine, were identified from N. domestica. O-Methylpallidine and (E, E)-, (E, Z)-, and (Z, Z)-terrestribisamide were also characterized for the first time from this plant. Known jatrorrhizine, palmatine, and berberine and unknown (R)-carnegine and (E, E)-, (E, Z)-, and (Z, Z)-terrestribisamide were identified in the callus of N. domestica.

The Protein Information Management System (PiMS): a generic tool for any structural biology research laboratory.

PubMed

Morris, Chris; Pajon, Anne; Griffiths, Susanne L; Daniel, Ed; Savitsky, Marc; Lin, Bill; Diprose, Jonathan M; da Silva, Alan Wilter; Pilicheva, Katya; Troshin, Peter; van Niekerk, Johannes; Isaacs, Neil; Naismith, James; Nave, Colin; Blake, Richard; Wilson, Keith S; Stuart, David I; Henrick, Kim; Esnouf, Robert M

2011-04-01

The techniques used in protein production and structural biology have been developing rapidly, but techniques for recording the laboratory information produced have not kept pace. One approach is the development of laboratory information-management systems (LIMS), which typically use a relational database schema to model and store results from a laboratory workflow. The underlying philosophy and implementation of the Protein Information Management System (PiMS), a LIMS development specifically targeted at the flexible and unpredictable workflows of protein-production research laboratories of all scales, is described. PiMS is a web-based Java application that uses either Postgres or Oracle as the underlying relational database-management system. PiMS is available under a free licence to all academic laboratories either for local installation or for use as a managed service.

Stabilization of Proteins and Noncovalent Protein Complexes during Electrospray Ionization by Amino Acid Additives.

PubMed

Zhang, Hua; Lu, Haiyan; Chingin, Konstantin; Chen, Huanwen

2015-07-21

Ionization of proteins and noncovalent protein complexes with minimal disturbance to their native structure presents a great challenge for biological mass spectrometry (MS). In living organisms, the native structure of intracellular proteins is commonly stabilized by solute amino acids (AAs) accumulated in cells at very high concentrations. Inspired by nature, we hypothesized that AAs could also pose a stabilizing effect on the native structure of proteins and noncovalent protein complexes during ionization. To test this hypothesis, here we explored MS response for various protein complexes upon the addition of free AAs at mM concentrations into the electrospray ionization (ESI) solution. Thermal activation of ESI droplets in the MS inlet capillary was employed as a model destabilizing factor during ionization. Our results indicate that certain AAs, in particular proline (Pro), pose considerable positive effect on the stability of noncovalent protein complexes in ESI-MS without affecting the signal intensity of protein ions and original protein-ligand equilibrium, even when added at the 20 mM concentration. The data suggest that the degree of protein stabilization is primarily determined by the osmolytic and ampholytic characteristics of AA solutes. The highest stability and visibility of noncovalent protein complexes in ESI-MS are achieved using AA additives with neutral isoelectric point, moderate proton affinity, and unfavorable interaction with the native protein state. Overall, our results indicate that the simple addition of free amino acids into the working solution can notably improve the stability and accuracy of protein analysis by native ESI-MS.

A data-independent acquisition workflow for qualitative screening of new psychoactive substances in biological samples.

PubMed

Kinyua, Juliet; Negreira, Noelia; Ibáñez, María; Bijlsma, Lubertus; Hernández, Félix; Covaci, Adrian; van Nuijs, Alexander L N

2015-11-01

Identification of new psychoactive substances (NPS) is challenging. Developing targeted methods for their analysis can be difficult and costly due to their impermanence on the drug scene. Accurate-mass mass spectrometry (AMMS) using a quadrupole time-of-flight (QTOF) analyzer can be useful for wide-scope screening since it provides sensitive, full-spectrum MS data. Our article presents a qualitative screening workflow based on data-independent acquisition mode (all-ions MS/MS) on liquid chromatography (LC) coupled to QTOFMS for the detection and identification of NPS in biological matrices. The workflow combines and structures fundamentals of target and suspect screening data processing techniques in a structured algorithm. This allows the detection and tentative identification of NPS and their metabolites. We have applied the workflow to two actual case studies involving drug intoxications where we detected and confirmed the parent compounds ketamine, 25B-NBOMe, 25C-NBOMe, and several predicted phase I and II metabolites not previously reported in urine and serum samples. The screening workflow demonstrates the added value for the detection and identification of NPS in biological matrices.

Metabolomic Approach for Discrimination of Four- and Six-Year-Old Red Ginseng (Panax ginseng) Using UPLC-QToF-MS.

PubMed

Shin, Jung-Sub; Park, Hee-Won; In, Gyo; Seo, Hyun Kyu; Won, Tae Hyung; Jang, Kyoung Hwa; Cho, Byung-Goo; Han, Chang Kyun; Shin, Jongheon

2016-09-01

Panax ginseng C.A. MEYER is one of the most popular medicinal herbs in Asia and the chemical constituents are changed by processing methods such as steaming or sun drying. Metabolomic analysis was performed to distinguish age discrimination of four- and six-year-old red ginseng using ultra-performance liquid chromatography quadruple time of flight mass spectrometry (UPLC-QToF-MS) with multivariate statistical analysis. Principal component analysis (PCA) showed clear discrimination between extracts of red ginseng of different ages and suggest totally six discrimination markers (two for four-year-old and four for six-year-old red ginseng). Among these, one marker was isolated and the structure determined by NMR spectroscopic analysis was 13-cis-docosenamide (marker 6-1) from six-year-old red ginseng. This is the first report of a metabolomic study regarding the age differentiation of red ginseng using UPLC-QToF-MS and determination of the structure of the marker. These results will contribute to the quality control and standardization as well as provide a scientific basis for pharmacological research on red ginseng.

cAMP-dependent protein kinase (PKA) complexes probed by complementary differential scanning fluorimetry and ion mobility–mass spectrometry

PubMed Central

Byrne, Dominic P.; Vonderach, Matthias; Ferries, Samantha; Brownridge, Philip J.; Eyers, Claire E.; Eyers, Patrick A.

2016-01-01

cAMP-dependent protein kinase (PKA) is an archetypal biological signaling module and a model for understanding the regulation of protein kinases. In the present study, we combine biochemistry with differential scanning fluorimetry (DSF) and ion mobility–mass spectrometry (IM–MS) to evaluate effects of phosphorylation and structure on the ligand binding, dynamics and stability of components of heteromeric PKA protein complexes in vitro. We uncover dynamic, conformationally distinct populations of the PKA catalytic subunit with distinct structural stability and susceptibility to the physiological protein inhibitor PKI. Native MS of reconstituted PKA R2C2 holoenzymes reveals variable subunit stoichiometry and holoenzyme ablation by PKI binding. Finally, we find that although a ‘kinase-dead’ PKA catalytic domain cannot bind to ATP in solution, it interacts with several prominent chemical kinase inhibitors. These data demonstrate the combined power of IM–MS and DSF to probe PKA dynamics and regulation, techniques that can be employed to evaluate other protein-ligand complexes, with broad implications for cellular signaling. PMID:27444646

Mass spectrometry characterization for N-glycosylation of immunoglobulin Y from hen egg yolk.

PubMed

Sheng, Long; He, Zhenjiao; Liu, Yaping; Ma, Meihu; Cai, Zhaoxia

2018-03-01

Immunoglobulin Y (IgY) is a new therapeutic antibody that exists in hen egg yolk. It is a glycoprotein, not much is known about its N-glycan structures, site occupancy and site-specific N-glycosylation. In this study, purified protein from hen egg yolk was identified as IgY based on SDS-PAGE and MALDI-TOF/TOF MS. N-glycan was released from IgY using peptide-N4-(N-acetyl-beta-glucosaminyl) asparagine-amidase treatment, and the molecular weight of IgY was calculated using the difference between the molecular weight of IgY and deglycosylated IgY. Two potential N-Glycosylation sites (ASN 308 and ASN 409 ) were detected on IgY by nanoLC-ESI MS. Sugar chains were separated using normal phase liquid chromatography after fluorescence labeling, and 17 N-glycan structures were confirmed using ESI-MS. The sugar chain pattern contained high-mannose oligosaccharide, hybrid oligosaccharide and complex oligosaccharide. These results could lead to other important information regarding IgY glycosylation. Copyright © 2017 Elsevier B.V. All rights reserved.

Structural Characterization of Monomers and Oligomers of D-Amino Acid-Containing Peptides Using T-Wave Ion Mobility Mass Spectrometry

NASA Astrophysics Data System (ADS)

Pang, Xueqin; Jia, Chenxi; Chen, Zhengwei; Li, Lingjun

2017-01-01

The D-residues are crucial to biological function of D-amino acid containing peptides (DAACPs). Previous ion mobility mass spectrometry (IM-MS) studies revealing oligomerization patterns of amyloid cascade demonstrated conversion from native soluble unstructured assembly to fibril ß-sheet oligomers, which has been implicated in amyloid diseases, such as Alzheimer's disease and type 2 diabetes. Although neuropeptides are typically present at very low concentrations in circulation, their local concentrations could be much higher in large dense core vesicles, forming dimers or oligomers. We studied the oligomerization of protonated and metal-adducted achatin I and dermorphin peptide isomers with IM-MS. Our results suggested that dimerization, oligomerization, and metal adduction augment the structural differences between D/L peptide isomers compared to protonated monomers. Dimers and oligomers enhanced the structural differences between D/L peptide isomers in both aqueous and organic solvent system. Furthermore, some oligomer forms were only observed for either D- or L-isomers, indicating the importance of chiral center in oligomerization process. The oligomerization patterns of D/L isomers appear to be similar. Potassium adducts were detected to enlarge the structural differences between D/L isomers.

Crosslinking Constraints and Computational Models as Complementary Tools in Modeling the Extracellular Domain of the Glycine Receptor

PubMed Central

Liu, Zhenyu; Szarecka, Agnieszka; Yonkunas, Michael; Speranskiy, Kirill; Kurnikova, Maria; Cascio, Michael

2014-01-01

The glycine receptor (GlyR), a member of the pentameric ligand-gated ion channel superfamily, is the major inhibitory neurotransmitter-gated receptor in the spinal cord and brainstem. In these receptors, the extracellular domain binds agonists, antagonists and various other modulatory ligands that act allosterically to modulate receptor function. The structures of homologous receptors and binding proteins provide templates for modeling of the ligand-binding domain of GlyR, but limitations in sequence homology and structure resolution impact on modeling studies. The determination of distance constraints via chemical crosslinking studies coupled with mass spectrometry can provide additional structural information to aid in model refinement, however it is critical to be able to distinguish between intra- and inter-subunit constraints. In this report we model the structure of GlyBP, a structural and functional homolog of the extracellular domain of human homomeric α1 GlyR. We then show that intra- and intersubunit Lys-Lys crosslinks in trypsinized samples of purified monomeric and oligomeric protein bands from SDS-polyacrylamide gels may be identified and differentiated by MALDI-TOF MS studies of limited resolution. Thus, broadly available MS platforms are capable of providing distance constraints that may be utilized in characterizing large complexes that may be less amenable to NMR and crystallographic studies. Systematic studies of state-dependent chemical crosslinking and mass spectrometric identification of crosslinked sites has the potential to complement computational modeling efforts by providing constraints that can validate and refine allosteric models. PMID:25025226

Obseration of flow regime transition in CFB riser using an LDV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yue, Paul C.; Mei, Joseph S.; Shadle, Lawrence J.

2011-01-01

The solids flow in a circulating fluidized bed (CFB) riser is often described to have a core-annular structure. For a given superficial gas velocity, at the initial introduction of solids into a riser a flow structure of dilute upflow regime exists. Continuing to increase the solids flow in the riser transitions the flow structure to the core-annular flow regime. However, with further increase of solids flow a condition is reached, depending on the superficial gas velocity, where all the solids across the riser cross section flow upwards, even those at the wall. When the solids flux, solids fraction and gasmore » velocity are relatively high, such a condition is described as the dense phase suspense upflow (DSU) regime. In this paper we report our observations of these flow regime transitions by using a laser Doppler velocimeter (LDV) to monitor the upward and downward particle flow velocities at and near the riser wall of the National Energy Technology Laboratory’s 30.4 centimeters diameter CFB cold flow model. The particles were high density polyethylene (PPE) spheres with a Sauter mean diameter of 861 micron and a density of 800 kg/m3. Three superficial gas velocities of 6.55 m/s, 10.67 m/s and 13.72 m/s were used in this study. For the case of superficial gas velocity 6.55 m/s, the experimental data show that the transition from dilute upflow to core-annular flow occurred when the solids flux was about 7 kg/m{sup 2}-s and the transition from core-annular flow to dense suspension upflow was about 147 kg/m{sup 2}-s. As the superficial gas velocity was increased to 10.67 m/s the corresponding flow regime transitions were at 34 kg/m{sup 2}-s and 205 kg/m{sup 2}-s, respectively. For the case of superficial gas velocity of 13.72 m/s the data showed no distinct transition of flow regimes. The particles were all upflow for the range of solids fluxes from 10 kg/m{sup 2}-s to 286 kg/m{sup 2}-s.« less

An Interlaboratory Evaluation of Drift Tube Ion Mobility–Mass Spectrometry Collision Cross Section Measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stow, Sarah M.; Causon, Tim J.; Zheng, Xueyun

Collision cross section (CCS) measurements resulting from ion mobility-mass spectrometry (IM-MS) experiments provide a promising orthogonal dimension of structural information in MS-based analytical separations. As with any molecular identifier, interlaboratory standardization must precede broad range integration into analytical workflows. In this study, we present a reference drift tube ion mobility mass spectrometer (DTIM-MS) where improvements on the measurement accuracy of experimental parameters influencing IM separations provide standardized drift tube, nitrogen CCS values (DTCCSN2) for over 120 unique ion species with the lowest measurement uncertainty to date. The reproducibility of these DTCCSN2 values are evaluated across three additional laboratories on amore » commercially available DTIM-MS instrument. The traditional stepped field CCS method performs with a relative standard deviation (RSD) of 0.29% for all ion species across the three additional laboratories. The calibrated single field CCS method, which is compatible with a wide range of chromatographic inlet systems, performs with an average, absolute bias of 0.54% to the standardized stepped field DTCCSN2 values on the reference system. The low RSD and biases observed in this interlaboratory study illustrate the potential of DTIM-MS for providing a molecular identifier for a broad range of discovery based analyses.« less

Analysis of human serum lipoprotein lipid composition using MALDI-TOF mass spectrometry.

PubMed

Hidaka, Hiroya; Hanyu, Noboru; Sugano, Mitsutoshi; Kawasaki, Kenji; Yamauchi, Kazuyoshi; Katsuyama, Tsutomu

2007-01-01

This study used matrix-assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF MS) to identify all lipid classes in human serum lipoproteins. After the major lipoproteins classes were isolated from serum by ultracentrifugation, the lipids were extracted and mixed with 2,5-dihydroxybenzoic acid (2,5-DHB) dissolved in Folch's solution (chloroform/methanol 2:1, v/v). MALDI-TOF MS analysis of the samples identified phospholipids (PLs), lysophospholipids (lysoPLs), sphingolipids (SLs), triglycerides (TGs), cholesteryl esters (CEs), and free cholesterol; it also showed the characteristics of individual fatty acid chains in serum lipids. MALDI-TOF MS allowed analysis of strongly hydrophobic and non-polar molecules such as CEs and TGs as well as hydrophilic molecules such as phospholipids. Direct analysis of fatty acids was not possible. The concentrations of lipids were not consistent with the ion peak intensities, since the extent of polarity affected the ionization characteristics of the molecules. However, lipid molecules with similar molecular structures but various fatty acid chains, such as phosphatidylcholine (PCs), were analyzed quantitatively by MALDI-TOF MS. Quantitative measurement of cholesterol was possible with the use of an internal standard. This study shows that MALDI-TOF MS can be used for direct investigation and quantitative analysis of the phospholipid composition of serum lipoproteins.

Symptom variability, affect and physical activity in ambulatory persons with multiple sclerosis: Understanding patterns and time-bound relationships.

PubMed

Kasser, Susan L; Goldstein, Amanda; Wood, Phillip K; Sibold, Jeremy

2017-04-01

Individuals with multiple sclerosis (MS) experience a clinical course that is highly variable with daily fluctuations in symptoms significantly affecting functional ability and quality of life. Yet, understanding how MS symptoms co-vary and associate with physical and psychological health is unclear. The purpose of the study was to explore variability patterns and time-bound relationships across symptoms, affect, and physical activity in individuals with MS. The study employed a multivariate, replicated, single-subject repeated-measures (MRSRM) design and involved four individuals with MS. Mood, fatigue, pain, balance confidence, and losses of balance were measured daily over 28 days by self-report. Physical activity was also measured daily over this same time period via accelerometry. Dynamic factor analysis (DFA) was used to determine the dimensionality and lagged relationships across the variables. Person-specific models revealed considerable time-dependent co-variation patterns as well as pattern variation across subjects. Results also offered insight into distinct variability structures at varying levels of disability. Modeling person-level variability may be beneficial for addressing the heterogeneity of experiences in individuals with MS and for understanding temporal and dynamic interrelationships among perceived symptoms, affect, and health outcomes in this group. Copyright © 2016 Elsevier Inc. All rights reserved.

Alkaloids Profiling of Fumaria capreolata by Analytical Platforms Based on the Hyphenation of Gas Chromatography and Liquid Chromatography with Quadrupole-Time-of-Flight Mass Spectrometry.

PubMed

Contreras, María Del Mar; Bribi, Noureddine; Gómez-Caravaca, Ana María; Gálvez, Julio; Segura-Carretero, Antonio

2017-01-01

Two analytical platforms, gas chromatography (GC) coupled to quadrupole-time-of-flight (QTOF) mass spectrometry (MS) and reversed-phase ultrahigh performance liquid chromatography (UHPLC) coupled to diode array (DAD) and QTOF detection, were applied in order to study the alkaloid profile of Fumaria capreolata . The use of these mass analyzers enabled tentatively identifying the alkaloids by matching their accurate mass signals and suggested molecular formulae with those previously reported in libraries and databases. Moreover, the proposed structures were corroborated by studying their fragmentation pattern obtained by both platforms. In this way, 8 and 26 isoquinoline alkaloids were characterized using GC-QTOF-MS and RP-UHPLC-DAD-QTOF-MS, respectively, and they belonged to the following subclasses: protoberberine, protopine, aporphine, benzophenanthridine, spirobenzylisoquinoline, morphinandienone, and benzylisoquinoline. Moreover, the latter analytical method was selected to determine at 280 nm the concentration of protopine (9.6 ± 0.7 mg/g), a potential active compound of the extract. In conclusion, although GC-MS has been commonly used for the analysis of this type of phytochemicals, RP-UHPLC-DAD-QTOF-MS provided essential complementary information. This analytical method can be applied for the quality control of phytopharmaceuticals containing Fumaria extracts currently found in the market.

Alkaloids Profiling of Fumaria capreolata by Analytical Platforms Based on the Hyphenation of Gas Chromatography and Liquid Chromatography with Quadrupole-Time-of-Flight Mass Spectrometry

PubMed Central

Bribi, Noureddine; Gómez-Caravaca, Ana María

2017-01-01

Two analytical platforms, gas chromatography (GC) coupled to quadrupole-time-of-flight (QTOF) mass spectrometry (MS) and reversed-phase ultrahigh performance liquid chromatography (UHPLC) coupled to diode array (DAD) and QTOF detection, were applied in order to study the alkaloid profile of Fumaria capreolata. The use of these mass analyzers enabled tentatively identifying the alkaloids by matching their accurate mass signals and suggested molecular formulae with those previously reported in libraries and databases. Moreover, the proposed structures were corroborated by studying their fragmentation pattern obtained by both platforms. In this way, 8 and 26 isoquinoline alkaloids were characterized using GC-QTOF-MS and RP-UHPLC-DAD-QTOF-MS, respectively, and they belonged to the following subclasses: protoberberine, protopine, aporphine, benzophenanthridine, spirobenzylisoquinoline, morphinandienone, and benzylisoquinoline. Moreover, the latter analytical method was selected to determine at 280 nm the concentration of protopine (9.6 ± 0.7 mg/g), a potential active compound of the extract. In conclusion, although GC-MS has been commonly used for the analysis of this type of phytochemicals, RP-UHPLC-DAD-QTOF-MS provided essential complementary information. This analytical method can be applied for the quality control of phytopharmaceuticals containing Fumaria extracts currently found in the market. PMID:29348751

Theonellapeptolide IIIe, a new cyclic peptolide from the New Zealand deep water sponge, Lamellomorpha strongylata.

PubMed

Li, S; Dumdei, E J; Blunt, J W; Munro, M H; Robinson, W T; Pannell, L K

1998-06-26

The structure, stereochemistry, and conformation of theonellapeptolide IIIe (1), a new 36-membered ring cyclic peptolide from the New Zealand deep-water sponge Lamellomorpha strongylata, is described. The sequence of the cytotoxic peptolide was determined through a combination of NMR and MS-MS techniques and confirmed by X-ray crystal structure analysis, which, with chiral HPLC, established the absolute stereochemistry.

High-performance liquid chromatography–tandem mass spectrometry in the identification and determination of phase I and phase II drug metabolites

PubMed Central

Kolářová, L.; Nobilis, M.

2008-01-01

Applications of tandem mass spectrometry (MS/MS) techniques coupled with high-performance liquid chromatography (HPLC) in the identification and determination of phase I and phase II drug metabolites are reviewed with an emphasis on recent papers published predominantly within the last 6 years (2002–2007) reporting the employment of atmospheric pressure ionization techniques as the most promising approach for a sensitive detection, positive identification and quantitation of metabolites in complex biological matrices. This review is devoted to in vitro and in vivo drug biotransformation in humans and animals. The first step preceding an HPLC-MS bioanalysis consists in the choice of suitable sample preparation procedures (biomatrix sampling, homogenization, internal standard addition, deproteination, centrifugation, extraction). The subsequent step is the right optimization of chromatographic conditions providing the required separation selectivity, analysis time and also good compatibility with the MS detection. This is usually not accessible without the employment of the parent drug and synthesized or isolated chemical standards of expected phase I and sometimes also phase II metabolites. The incorporation of additional detectors (photodiode-array UV, fluorescence, polarimetric and others) between the HPLC and MS instruments can result in valuable analytical information supplementing MS results. The relation among the structural changes caused by metabolic reactions and corresponding shifts in the retention behavior in reversed-phase systems is discussed as supporting information for identification of the metabolite. The first and basic step in the interpretation of mass spectra is always the molecular weight (MW) determination based on the presence of protonated molecules [M+H]+ and sometimes adducts with ammonium or alkali-metal ions, observed in the positive-ion full-scan mass spectra. The MW determination can be confirmed by the [M-H]- ion for metabolites providing a signal in negative-ion mass spectra. MS/MS is a worthy tool for further structural characterization because of the occurrence of characteristic fragment ions, either MSn analysis for studying the fragmentation patterns using trap-based analyzers or high mass accuracy measurements for elemental composition determination using time of flight based or Fourier transform mass analyzers. The correlation between typical functional groups found in phase I and phase II drug metabolites and corresponding neutral losses is generalized and illustrated for selected examples. The choice of a suitable ionization technique and polarity mode in relation to the metabolite structure is discussed as well. PMID:18345532

Multiple stage MS in analysis of plasma, serum, urine and in vitro samples relevant to clinical and forensic toxicology.

PubMed

Meyer, Golo M; Maurer, Hans H; Meyer, Markus R

2016-01-01

This paper reviews MS approaches applied to metabolism studies, structure elucidation and qualitative or quantitative screening of drugs (of abuse) and/or their metabolites. Applications in clinical and forensic toxicology were included using blood plasma or serum, urine, in vitro samples, liquids, solids or plant material. Techniques covered are liquid chromatography coupled to low-resolution and high-resolution multiple stage mass analyzers. Only PubMed listed studies published in English between January 2008 and January 2015 were considered. Approaches are discussed focusing on sample preparation and mass spectral settings. Comments on advantages and limitations of these techniques complete the review.

Structure determination of disease associated peak AAA from l-Tryptophan implicated in the eosinophilia-myalgia syndrome.

PubMed

Klarskov, Klaus; Gagnon, Hugo; Boudreault, Pierre-Luc; Normandin, Chad; Plancq, Baptiste; Marsault, Eric; Gleich, Gerald J; Naylor, Stephen

2018-01-05

The eosinophilia-myalgia syndrome (EMS) outbreak of 1989 that occurred in the USA and elsewhere was caused by the ingestion of l-Tryptophan (L-Trp) solely manufactured by the Japanese company Showa Denko K.K. (SD). Six compounds present in the SD L-Trp were reported to be case-associated contaminants. However, "one" of these compounds, Peak AAA has remained structurally uncharacterized, despite the fact that it was described as "the only statistically significant (p=0.0014) contaminant". Here, we employ on-line microcapillary-high performance liquid chromatography-electrospray ionization mass spectrometry (LC-MS), and tandem mass spectrometry (MS/MS) to determine that Peak AAA is in fact two structurally related isomers. Peak AAA 1 and Peak AAA 2 differed in LC retention times, and were determined by accurate mass-LC-MS to both have a protonated molecular ion (MH +) of mass 343.239Da (Da), corresponding to a molecular formula of C 21 H 30 N 2 O 2, and possessing eight degrees of unsaturation (DoU) for the non-protonated molecule. By comparing the LC-MS and LC-MS-MS retention times and spectra with authentic synthetic standards, Peak AAA 1 was identified as the intermolecular condensation product of L-Trp with anteiso 7-methylnonanoic acid, to afford (S)-2-amino-3-(2-((S,E)-7-methylnon-1-en-1-yl)-1H-indol-3-yl)propanoic acid. Peak AAA 2 was determined to be a condensation product of L-Trp with decanoic acid, which produced (S)-2-amino-3-(2-((E)-dec-1-en-1-yl)-1H-indol-3-yl)propanoic acid. Copyright © 2017 Elsevier B.V. All rights reserved.

Structure of indazole N1-oxide derivatives studied by X-ray, theoretical methods, 1H, 13C, 15N NMR and EI/MS

NASA Astrophysics Data System (ADS)

Gerpe, Alejandra; Piro, Oscar E.; Cerecetto, Hugo; González, Mercedes

2007-12-01

A series of indazole N1-oxide derivatives has been spectroscopically studied in solution using 1H, 13C, and 15N NMR based on pulsed field gradient selected PFG 1H sbnd X (X = 13C and 15N) gHMQC and gHMBC experiments. Some indazoles were prepared using a new methodology to compare its spectral and structural data with the indazole N1-oxide parent compounds. The 13C resonances of the indazole N1-oxide carbon 3 and 7a demonstrate the N-oxide push-electron capability. The 15N resonances of the indazole N-oxide, nitrogen 1, are near to 30 ppm more shielded than the corresponding values in the indazole heterocycle (deoxygenated form). Moreover, the structures of one indazole and one indazole N-oxide were unambiguously confirmed by X-ray crystallography. The solid state structures were contrasted with the theoretical ones obtained in vacuo at different calculus level. The aromaticity of the derivatives was studied analyzing the H sbnd H coupling constants of indazole's aromatic hydrogens and measuring C sbnd C distances in the solid state. The fragmentation that takes place in EI/MS was gathered for all the indazole N-oxide derivatives and the general fragmentation pattern analyzed.

Experimental and Theoretical Investigation of Sodiated Multimers of Steroid Epimers with Ion Mobility-Mass Spectrometry

NASA Astrophysics Data System (ADS)

Chouinard, Christopher D.; Cruzeiro, Vinícius Wilian D.; Roitberg, Adrian E.; Yost, Richard A.

2017-02-01

Ion mobility-mass spectrometry (IM-MS) has recently seen increased use in the analysis of small molecules, especially in the field of metabolomics, for increased breadth of information and improved separation of isomers. In this study, steroid epimers androsterone and trans-androsterone were analyzed with IM-MS to investigate differences in their relative mobilities. Although sodiated monomers exhibited very similar collision cross-sections (CCS), baseline separation was observed for the sodiated dimer species (RS = 1.81), with measured CCS of 242.6 and 256.3 Å2, respectively. Theoretical modeling was performed to determine the most energetically stable structures of solution-phase and gas-phase monomer and dimer structures. It was revealed that these epimers differ in their preferred dimer binding mode in solution phase: androsterone adopts a R=O - Na+ - OH—R' configuration, whereas trans-androsterone adopts a R=O - Na+ - O=R' configuration. This difference contributes to a significant structural variation, and subsequent CCS calculations based on these structures relaxed in the gas phase were in agreement with experimentally measured values (ΔCCS 5%). Additionally, these calculations accurately predicted the relative difference in mobility between the epimers. This study illustrates the power of combining experimental and theoretical results to better elucidate gas-phase structures.

Glycoproteomics of cerebrospinal fluid in neurodegenerative disease

NASA Astrophysics Data System (ADS)

Sihlbom, Carina; Davidsson, Pia; Emmett, Mark R.; Marshall, Alan G.; Nilsson, Carol L.

2004-05-01

Cerebrospinal fluid (CSF) from individual patients with Alzheimer's disease (AD) was separated by narrow range two-dimensional (2D) gel electrophoresis and analyzed by electrospray FT-ICR MS in this glycoproteomic study. Because several altered proteins in the comparison between AD patients and healthy controls individuals are isoforms of glycoproteins, it is important to determine if the modifying glycans are also altered. FT-ICR MS and fragmentation of glycopeptides with infrared multiphoton dissociation (IRMPD) offers abundant fragment ions through breakage at the glycosidic linkages with excellent mass accuracy, which facilitates the structural determination of the site-specific N-linked glycosylation. We present results from a structural comparison of proteins from three AD patients and three control individuals of different glycosylated isomers of [alpha]-1-antitrypsin, [beta]-trace and apolipoprotein J.

Low Mass MS/MS Fragments of Protonated Amino Acids Used for Distinction of Their 13C- Isotopomers in Metabolic Studies

NASA Astrophysics Data System (ADS)

Ma, Xin; Dagan, Shai; Somogyi, Árpád; Wysocki, Vicki H.; Scaraffia, Patricia Y.

2013-04-01

Glu, Gln, Pro, and Ala are the main amino acids involved in ammonia detoxification in mosquitoes. In order to develop a tandem mass spectrometry method (MS2) to monitor each carbon of the above isotopically-labeled 13C-amino acids for metabolic studies, the compositions and origins of atoms in fragments of the protonated amino acid should be first elucidated. Thus, various electrospray (ESI)-based MS2 tools were employed to study the fragmentation of these unlabeled and isotopically-labeled amino acids and better understand their dissociation pathways. A broad range of fragments, including previously-undescribed low m/z fragments was revealed. The formulae of the fragments (from m/z 130 down to m/z 27) were confirmed by their accurate masses. The structures and conformations of the larger fragments of Glu were also explored by ion mobility mass spectrometry (IM-MS) and gas-phase hydrogen/deuterium exchange (HDX) experiments. It was found that some low m/z fragments ( m/z 27-30) are common to Glu, Gln, Pro, and Ala. The origins of carbons in these small fragments are discussed and additional collision induced dissociation (CID) MS2 fragmentation pathways are proposed for them. It was also found that small fragments (≤ m/z 84) of protonated, methylated Glu, and methylated Gln are the same as those of the underivatized Glu and Gln. Taken together, the new approach of utilizing low m/z fragments can be applied to distinguish, identify, and quantify 13C-amino acids labeled at various positions, either in the backbone or side chain.

Iron chelation and multiple sclerosis

PubMed Central

Weigel, Kelsey J.; Lynch, Sharon G.; LeVine, Steven M.

2014-01-01

Histochemical and MRI studies have demonstrated that MS (multiple sclerosis) patients have abnormal deposition of iron in both gray and white matter structures. Data is emerging indicating that this iron could partake in pathogenesis by various mechanisms, e.g., promoting the production of reactive oxygen species and enhancing the production of proinflammatory cytokines. Iron chelation therapy could be a viable strategy to block iron-related pathological events or it can confer cellular protection by stabilizing hypoxia inducible factor 1α, a transcription factor that normally responds to hypoxic conditions. Iron chelation has been shown to protect against disease progression and/or limit iron accumulation in some neurological disorders or their experimental models. Data from studies that administered a chelator to animals with experimental autoimmune encephalomyelitis, a model of MS, support the rationale for examining this treatment approach in MS. Preliminary clinical studies have been performed in MS patients using deferoxamine. Although some side effects were observed, the large majority of patients were able to tolerate the arduous administration regimen, i.e., 6–8 h of subcutaneous infusion, and all side effects resolved upon discontinuation of treatment. Importantly, these preliminary studies did not identify a disqualifying event for this experimental approach. More recently developed chelators, deferasirox and deferiprone, are more desirable for possible use in MS given their oral administration, and importantly, deferiprone can cross the blood–brain barrier. However, experiences from other conditions indicate that the potential for adverse events during chelation therapy necessitates close patient monitoring and a carefully considered administration regimen. PMID:24397846

Analysis of Translocation-Competent Secretory Proteins by HDX-MS.

PubMed

Tsirigotaki, A; Papanastasiou, M; Trelle, M B; Jørgensen, T J D; Economou, A

2017-01-01

Protein folding is an intricate and precise process in living cells. Most exported proteins evade cytoplasmic folding, become targeted to the membrane, and then trafficked into/across membranes. Their targeting and translocation-competent states are nonnatively folded. However, once they reach the appropriate cellular compartment, they can fold to their native states. The nonnative states of preproteins remain structurally poorly characterized since increased disorder, protein sizes, aggregation propensity, and the observation timescale are often limiting factors for typical structural approaches such as X-ray crystallography and NMR. Here, we present an alternative approach for the in vitro analysis of nonfolded translocation-competent protein states and their comparison with their native states. We make use of hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS), a method based on differentiated isotope exchange rates in structured vs unstructured protein states/regions, and highly dynamic vs more rigid regions. We present a complete structural characterization pipeline, starting from the preparation of the polypeptides to data analysis and interpretation. Proteolysis and mass spectrometric conditions for the analysis of the labeled proteins are discussed, followed by the analysis and interpretation of HDX-MS data. We highlight the suitability of HDX-MS for identifying short structured regions within otherwise highly flexible protein states, as illustrated by an exported protein example, experimentally tested in our lab. Finally, we discuss statistical analysis in comparative HDX-MS. The protocol is applicable to any protein and protein size, exhibiting slow or fast loss of translocation competence. It could be easily adapted to more complex assemblies, such as the interaction of chaperones with nonnative protein states. © 2017 Elsevier Inc. All rights reserved.

5-Acetyl-6-methyl-4-aryl-3,4-dihydropyrimidin-2(1H)-ones: As potent urease inhibitors; synthesis, in vitro screening, and molecular modeling study.

PubMed

Shamim, Shahbaz; Khan, Khalid Mohammed; Salar, Uzma; Ali, Farman; Lodhi, Muhammad Arif; Taha, Muhammad; Khan, Farman Ali; Ashraf, Sajda; Ul-Haq, Zaheer; Ali, Muhammad; Perveen, Shahnaz

2018-02-01

5-Acetyl-6-methyl-4-aryl-3,4-dihydropyrimidin-2(1H)-ones 1-43 were synthesized in a "one-pot" three component reaction and structurally characterized by various spectroscopic techniques such as 1 H, 13 C NMR, EI-MS, HREI-MS, and IR. All compounds were evaluated for their in vitro urease inhibitory activity. It is worth mentioning that except derivatives 1, 11, 12, and 14, all were found to be more potent than the standard thiourea (IC 50  = 21.25 ± 0.15 µM) and showed their urease inhibitory potential in the range of IC 50  = 3.70 ± 0.5-20.14 ± 0.1 µM. Structure-activity relationship (SAR) was rationalized by looking at the varying structural features of the molecules. However, molecular modeling study was performed to confirm the binding interactions of the molecules (ligand) with the active site of enzyme. Copyright © 2017 Elsevier Inc. All rights reserved.

Magnifying Endoscopy with Narrow Band Imaging of Early Gastric Cancer: Correlation with Histopathology and Mucin Phenotype

PubMed Central

Ok, Kyung-Sun; Kim, Gwang Ha; Park, Do Youn; Lee, Hyun Jeong; Jeon, Hye Kyung; Baek, Dong Hoon; Lee, Bong Eun; Song, Geun Am

2016-01-01

Background/Aims Magnifying endoscopy with narrow band imaging (ME-NBI) is a useful modality for the detailed visualization of microsurface (MS) and microvascular (MV) structures in the gastrointestinal tract. This study aimed to determine whether the MS and MV patterns in ME-NBI differ according to the histologic type, invasion depth, and mucin phenotype of early gastric cancers (EGCs). Methods The MS and MV patterns of 160 lesions in 160 patients with EGC who underwent ME-NBI before endoscopic or surgical resection were prospectively collected and analyzed. EGCs were categorized as either differentiated or undifferentiated and as either mucosal or submucosal, and their mucin phenotypes were determined via immunohistochemistry of the tumor specimens. Results Differentiated tumors mainly displayed an oval and/or tubular MS pattern and a fine network or loop MV pattern, whereas undifferentiated tumors mainly displayed an absent MS pattern and a corkscrew MV pattern. The destructive MS pattern was associated with submucosal invasion, and this association was more prominent in the differentiated tumors than in the undifferentiated tumors. MUC5AC expression was increased in lesions with either a papillary or absent MS pattern and a corkscrew MV pattern, whereas MUC6 expression was increased in lesions with a papillary MS pattern and a loop MV pattern. CD10 expression was more frequent in lesions with a fine network MV pattern. Conclusions ME-NBI can be useful for predicting the histopathology and mucin phenotype of EGCs. PMID:27021504

Mindfulness-based interventions in multiple sclerosis: beneficial effects of Tai Chi on balance, coordination, fatigue and depression

PubMed Central

2014-01-01

Background Patients suffering from Multiple Sclerosis (MS) experience a wide array of symptoms, including balance problems, mobility impairment, fatigue and depression. Physical exercise has recently been acknowledged as a treatment option complementary to medication. However, information regarding putative effects of structured exercise programs on neurological symptoms is sparse. Tai Chi, a Chinese martial art incorporating physical exercise and mindfulness training, has been shown to yield health benefits in various neurological groups. It seems particularly suitable for patients with motoric deficits as it challenges coordination and balance. The purpose of the current study was to explore the therapeutic value of structured Tai Chi training for coordination, balance, fatigue and depression in mildly disabled MS patients. Methods A sample of 32 MS patients (Expanded Disability Status Scale, EDSS < 5) was examined. A structured Tai Chi course was devised and a Tai Chi group participated in two weekly sessions of 90 minutes duration for six months, while a comparison group received treatment as usual (TAU). Both groups were examined prior to and following the six-months interval with regards to balance and coordination performance as well as measures of fatigue, depression and life satisfaction. Results Following the intervention, the Tai Chi group showed significant, consistent improvements in balance, coordination, and depression, relative to the TAU group (range of effect-sizes: partial η2 = 0.16 – 0.20). Additionally, life satisfaction improved (partial η2 = 0.31). Fatigue deteriorated in the comparison group, whereas it remained relatively stable in the Tai Chi group (partial η2 = 0.24). Conclusions The consistent pattern of results confirms that Tai Chi holds therapeutic potential for MS patients. Further research is needed to determine underlying working mechanisms, and to verify the results in a larger sample and different MS subgroups. PMID:25145392

First Identification of 5,11-Dideoxytetrodotoxin in Marine Animals, and Characterization of Major Fragment Ions of Tetrodotoxin and Its Analogs by High Resolution ESI-MS/MS

PubMed Central

Yotsu-Yamashita, Mari; Abe, Yuka; Kudo, Yuta; Ritson-Williams, Raphael; Paul, Valerie J.; Konoki, Keiichi; Cho, Yuko; Adachi, Masaatsu; Imazu, Takuya; Nishikawa, Toshio; Isobe, Minoru

2013-01-01

Even though tetrodotoxin (TTX) is a widespread toxin in marine and terrestrial organisms, very little is known about the biosynthetic pathway used to produce it. By describing chemical structures of natural analogs of TTX, we can start to identify some of the precursors that might be important for TTX biosynthesis. In the present study, an analog of TTX, 5,11-dideoxyTTX, was identified for the first time in natural sources, the ovary of the pufferfish and the pharynx of a flatworm (planocerid sp. 1), by comparison with totally synthesized (−)-5,11-dideoxyTTX, using high resolution ESI-LC-MS. Based on the presence of 5,11-dideoxyTTX together with a series of known deoxy analogs, 5,6,11-trideoxyTTX, 6,11-dideoxyTTX, 11-deoxyTTX, and 5-deoxyTTX, in these animals, we predicted two routes of stepwise oxidation pathways in the late stages of biosynthesis of TTX. Furthermore, high resolution masses of the major fragment ions of TTX, 6,11-dideoxyTTX, and 5,6,11-trideoxyTTX were also measured, and their molecular formulas and structures were predicted to compare them with each other. Although both TTX and 5,6,11-trideoxyTTX give major fragment ions that are very close, m/z 162.0660 and 162.1020, respectively, they are distinguishable and predicted to be different molecular formulas. These data will be useful for identification of TTXs using high resolution LC-MS/MS. PMID:23924959

Characterization of the thermolysis products of Nafion membrane: A potential source of perfluorinated compounds in the environment

NASA Astrophysics Data System (ADS)

Feng, Mingbao; Qu, Ruijuan; Wei, Zhongbo; Wang, Liansheng; Sun, Ping; Wang, Zunyao

2015-05-01

The thermal decomposition of Nafion N117 membrane, a typical perfluorosulfonic acid membrane that is widely used in various chemical technologies, was investigated in this study. Structural identification of thermolysis products in water and methanol was performed using liquid chromatography-electrospray ionization-tandem mass spectrometry (LC/ESI-MS/MS). The fluoride release was studied using an ion-chromatography system, and the membrane thermal stability was characterized by thermogravimetric analysis. Notably, several types of perfluorinated compounds (PFCs) including perfluorocarboxylic acids were detected and identified. Based on these data, a thermolysis mechanism was proposed involving cleavage of both the polymer backbone and its side chains by attack of radical species. This is the first systematic report on the thermolysis products of Nafion by simulating its high-temperature operation and disposal process via incineration. The results of this study indicate that Nafion is a potential environmental source of PFCs, which have attracted growing interest and concern in recent years. Additionally, this study provides an analytical justification of the LC/ESI-MS/MS method for characterizing the degradation products of polymer electrolyte membranes. These identifications can substantially facilitate an understanding of their decomposition mechanisms and offer insight into the proper utilization and effective management on these membranes.

The thalamus and multiple sclerosis

PubMed Central

Minagar, Alireza; Barnett, Michael H.; Benedict, Ralph H.B.; Pelletier, Daniel; Pirko, Istvan; Sahraian, Mohamad Ali; Frohman, Elliott

2013-01-01

The paired thalamic nuclei are gray matter (GM) structures on both sides of the third ventricle that play major roles in cortical activation, relaying sensory information to the higher cortical centers that influence cognition. Multiple sclerosis (MS) is an immune-mediated disease of the human CNS that affects both the white matter (WM) and GM. A number of clinical observations as well as recent neuropathologic and neuroimaging studies have clearly demonstrated extensive involvement of the thalamus, basal ganglia, and neocortex in patients with MS. Modern MRI techniques permit visualization of GM lesions and measurement of atrophy. These contemporary methods have fundamentally altered our understanding of the pathophysiologic nature of MS. Evidence confirms the contention that GM injury can be detected in the earliest phases of MS, and that iron deposition and atrophy of deep gray nuclei are closely related to the magnitude of inflammation. Extensive involvement of GM, and particularly of the thalamus, is associated with a wide range of clinical manifestations including cognitive decline, motor deficits, fatigue, painful syndromes, and ocular motility disturbances in patients with MS. In this review, we characterize the neuropathologic, neuroimaging, and clinical features of thalamic involvement in MS. Further, we underscore the contention that neuropathologic and neuroimaging correlative investigations of thalamic derangements in MS may elucidate not heretofore considered pathobiological underpinnings germane to understanding the ontogeny, magnitude, and progression of the disease process. PMID:23296131

The thalamus and multiple sclerosis: modern views on pathologic, imaging, and clinical aspects.

PubMed

Minagar, Alireza; Barnett, Michael H; Benedict, Ralph H B; Pelletier, Daniel; Pirko, Istvan; Sahraian, Mohamad Ali; Frohman, Elliott; Zivadinov, Robert

2013-01-08

The paired thalamic nuclei are gray matter (GM) structures on both sides of the third ventricle that play major roles in cortical activation, relaying sensory information to the higher cortical centers that influence cognition. Multiple sclerosis (MS) is an immune-mediated disease of the human CNS that affects both the white matter (WM) and GM. A number of clinical observations as well as recent neuropathologic and neuroimaging studies have clearly demonstrated extensive involvement of the thalamus, basal ganglia, and neocortex in patients with MS. Modern MRI techniques permit visualization of GM lesions and measurement of atrophy. These contemporary methods have fundamentally altered our understanding of the pathophysiologic nature of MS. Evidence confirms the contention that GM injury can be detected in the earliest phases of MS, and that iron deposition and atrophy of deep gray nuclei are closely related to the magnitude of inflammation. Extensive involvement of GM, and particularly of the thalamus, is associated with a wide range of clinical manifestations including cognitive decline, motor deficits, fatigue, painful syndromes, and ocular motility disturbances in patients with MS. In this review, we characterize the neuropathologic, neuroimaging, and clinical features of thalamic involvement in MS. Further, we underscore the contention that neuropathologic and neuroimaging correlative investigations of thalamic derangements in MS may elucidate not heretofore considered pathobiological underpinnings germane to understanding the ontogeny, magnitude, and progression of the disease process.

Enhanced separation and analysis procedure reveals production of tri-acylated mannosylerythritol lipids by Pseudozyma aphidis.

PubMed

Goossens, Eliane; Wijnants, Marc; Packet, Dirk; Lemière, Filip

2016-11-01

Mannosylerythritol lipids (MELs) are one of the most promising biosurfactants because of their high fermentation yields (>100 g l -1 ) and during the last two decades they have gained a lot of attention due to their interesting self-assembling properties and biological activities. In this study, MELs were produced by fed-batch bioreactor fermentation of rapeseed oil with Pseudozyma aphidis MUCL 27852. This high-level MEL-producing yeast secretes four conventional MEL structures, -A, -B, -C and -D, which differ in their degree of acetylation. During our research, unknown compounds synthesized by P. aphidis were detected by thin-layer chromatography. The unknown compounds were separated by flash chromatography and identified as tri-acylated MELs by high-performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS). The third fatty acid chain on the tri-acylated MELs was positioned on the primary alcohol of the erythritol moiety and comprised long-chain acids, mainly oleic and linoleic acid, which are not found in conventional di-acylated MELs. Furthermore, the LC-MS analysis time of conventional MELs was reduced to almost one-third by switching from HPLC-MS/MS to ultraperformance liquid chromatography tandem mass spectrometry (UPLC-MS/MS). Provided optimization of the fermentation yield, P. aphidis could be an interesting novel producer of tri-acylated MELs and, thereby expand the supply and applicability of biosurfactants.

HDAC inhibitors, MS-275 and salermide, potentiates the anticancer effect of EF24 in human pancreatic cancer cells.

PubMed

Yar Saglam, Atiye Seda; Yilmaz, Akin; Onen, Hacer Ilke; Alp, Ebru; Kayhan, Handan; Ekmekci, Abdullah

2016-01-01

Histone deacetylases (HDACs) play a major role in the regulation of chromatin structure and gene expression by changing acetylation status of histone and non-histone proteins. MS-275 (entinostat, MS) is a well-known benzamide-based HDACI and Salermide (SAL), a reverse amide compound HDACI, have antiproliferative effects on several human cancer cells. In this study, we aimed to investigate the effects of HDACIs (MS and SAL) alone and/or combined use with EF24 (EF), a novel synthetic curcumin analog, on human pancreatic cancer cell line (BxPC-3). In vitro, BxPC-3 cells were exposed to varying concentrations of MS, SAL with or without EF, and their effects on cell viability, acetylated Histone H3 and H4 levels, cytotoxicity, and cleaved caspase 3 levels, and cell cycle distribution were measured. The viability of BxPC-3 cells decreased significantly after treatment with EF, MS and SAL treatments. MS and SAL treatment increased the acetylation of histone H3 and H4 in a dose dependent manner. MS and SAL alone or combined with EF were increased the number of cells in G1 phase. In addition, treatment with agents significantly decreased the ratio of cell in G2/M phase. There were significant dose-dependent increases at cleaved Caspase 3 levels after MS treatment but not after SAL treatment. Our results showed that HDAC inhibitors (MS and SAL), when combined with EF, may effectively reduce pancreatic cancer cell (BxPC-3) progression and stop the cell cycle at G1 phase. Further molecular analyses are needed to understand the fundamental molecular consequences of HDAC inhibition in pancreas cancer cells.

Multi- and unisensory visual flash illusions.

PubMed

Courtney, Jon R; Motes, Michael A; Hubbard, Timothy L

2007-01-01

The role of stimulus structure in multisensory and unisensory interactions was examined. When a flash (17 ms) was accompanied by multiple tones (each 7 ms, SOA < or =100 ms) multiple flashes were reported, and this effect has been suggested to reflect the role of stimulus continuity in multisensory interactions. In experiments 1 and 2 we examined if stimulus continuity would affect concurrently presented stimuli. When a relatively longer flash (317 ms) was accompanied by multiple tones (each 7 ms), observers reported perceiving multiple flashes. In experiment 3 we tested whether a flash presented near fixation would induce an illusory flash further in the periphery. One flash (17 ms) presented 5 degrees below fixation was reported as multiple flashes if presented with two flashes (each 17 ms, SOA =100 ms) 2 degrees above fixation. The extent to which these data support a phenomenological continuity principle and whether this principle applies to unisensory perception is discussed.

The Differential Interactions of Peroxisome Proliferator-Activated Receptor [gamma] Ligands with Tyr473 Is a Physical Basis for Their Unique Biological Activities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Einstein, Monica; Akiyama, Taro E.; Castriota, Gino A.

2008-08-01

Despite their proven antidiabetic efficacy, widespread use of peroxisome proliferator-activated receptor (PPAR){gamma} agonists has been limited by adverse cardiovascular effects. To overcome this shortcoming, selective PPAR{gamma} modulators (SPPAR{gamma}Ms) have been identified that have antidiabetic efficacy comparable with full agonists with improved tolerability in preclinical species. The results of structural studies support the proposition that SPPAR{gamma}Ms interact with PPAR{gamma} differently from full agonists, thereby providing a physical basis for their novel activities. Herein, we describe a novel PPAR{gamma} ligand, SPPAR{gamma}M2. This compound was a partial agonist in a cell-based transcriptional activity assay, with diminished adipogenic activity and an attenuated gene signaturemore » in cultured human adipocytes. X-ray cocrystallography studies demonstrated that, unlike rosiglitazone, SPPAR{gamma}M2 did not interact with the Tyr473 residue located within helix 12 of the ligand binding domain (LBD). Instead, SPPAR{gamma}M2 was found to bind to and activate human PPAR{gamma} in which the Tyr473 residue had been mutated to alanine (hPPAR{gamma}Y473A), with potencies similar to those observed with the wild-type receptor (hPPAR{gamma}WT). In additional studies, we found that the intrinsic binding and functional potencies of structurally distinct SPPAR{gamma}Ms were not diminished by the Y473A mutation, whereas those of various thiazolidinedione (TZD) and non-TZD PPAR{gamma} full agonists were reduced in a correlative manner. These results directly demonstrate the important role of Tyr473 in mediating the interaction of full agonists but not SPPAR{gamma}Ms with the PPAR{gamma} LBD, thereby providing a precise molecular determinant for their differing pharmacologies.« less

Use of Ambient Ionization High-Resolution Mass Spectrometry for the Kinetic Analysis of Organic Surface Reactions.

PubMed

Sen, Rickdeb; Escorihuela, Jorge; Smulders, Maarten M J; Zuilhof, Han

2016-04-12

In contrast to homogeneous systems, studying the kinetics of organic reactions on solid surfaces remains a difficult task due to the limited availability of appropriate analysis techniques that are general, high-throughput, and capable of offering quantitative, structural surface information. Here, we demonstrate how direct analysis in real time mass spectrometry (DART-MS) complies with above considerations and can be used for determining interfacial kinetic parameters. The presented approach is based on the use of a MS tag that--in principle--allows application to other reactions. To show the potential of DART-MS, we selected the widely applied strain-promoted alkyne-azide cycloaddition (SPAAC) as a model reaction to elucidate the effects of the nanoenvironment on the interfacial reaction rate.

Polymer Analysis by Liquid Chromatography/Electrospray Ionization Time-of-Flight Mass Spectrometry.

PubMed

Nielen, M W; Buijtenhuijs, F A

1999-05-01

Hyphenation of liquid chromatography (LC) techniques with electrospray ionization (ESI) orthogonal acceleration time-of-flight (oa-TOF) mass spectrometry (MS) provides both MS-based structural information and LC-based quantitative data in polymer analysis. In one experimental setup, three different LC modes are interfaced with MS:  size-exclusion chromatography (SEC/MS), gradient polymer elution chromatography (GPEC/MS), and liquid chromatography at the critical point of adsorption (LCCC/MS). In SEC/MS, both absolute mass calibration of the SEC column based on the polymer itself and determination of monomers and end groups from the mass spectra are achieved. GPEC/MS shows detailed chemical heterogeneity of the polymer and the chemical composition distribution within oligomer groups. In LCCC/MS, the retention behavior is primarily governed by chemical heterogeneities, such as different end group functionalities, and quantitative end group calculations can be easily made. The potential of these methods and the benefit of time-of-flight analyzers in polymer analysis are discussed using SEC/MS of a polydisperse poly(methyl methacrylate) sample, GPEC/MS of dipropoxylated bisphenol A/adipic acid polyester resin, LCCC/MS of alkylated poly(ethylene glycol), and LCCC/MS of terephthalic acid/neopentyl glycol polyester resin.