Analysis of Glycoproteins in Human Serum by Means of Glycospecific Magnetic Bead Separation and LC-MALDI-TOF/TOF Analysis with Automated Glycopeptide Detection

PubMed Central

Sparbier, Katrin; Asperger, Arndt; Resemann, Anja; Kessler, Irina; Koch, Sonja; Wenzel, Thomas; Stein, Günter; Vorwerg, Lars; Suckau, Detlev; Kostrzewa, Markus

2007-01-01

Comprehensive proteomic analyses require efficient and selective pre-fractionation to facilitate analysis of post-translationally modified peptides and proteins, and automated analysis workflows enabling the detection, identification, and structural characterization of the corresponding peptide modifications. Human serum contains a high number of glycoproteins, comprising several orders of magnitude in concentration. Thereby, isolation and subsequent identification of low-abundant glycoproteins from serum is a challenging task. selective capturing of glycopeptides and -proteins was attained by means of magnetic particles specifically functionalized with lectins or boronic acids that bind to various structural motifs. Human serum was incubated with differentially functionalized magnetic micro-particles (lectins or boronic acids), and isolated proteins were digested with trypsin. Subsequently, the resulting complex mixture of peptides and glycopeptides was subjected to LC-MALDI analysis and database searching. In parallel, a second magnetic bead capturing was performed on the peptide level to separate and analyze by LC-MALDI intact glycopeptides, both peptide sequence and glycan structure. Detection of glycopeptides was achieved by means of a software algorithm that allows extraction and characterization of potential glycopeptide candidates from large LC-MALDI-MS/MS data sets, based on N-glycopeptide-specific fragmentation patterns and characteristic fragment mass peaks, respectively. By means of fast and simple glycospecific capturing applied in conjunction with extensive LC-MALDI-MS/MS analysis and novel data analysis tools, a high number of low-abundant proteins were identified, comprising known or predicted glycosylation sites. According to the specific binding preferences of the different types of beads, complementary results were obtained from the experiments using either magnetic ConA-, LCA-, WGA-, and boronic acid beads, respectively. PMID:17916798

Multi-elemental analysis of aqueous geochemical samples by quadrupole inductively coupled plasma-mass spectrometry (ICP-MS)

USGS Publications Warehouse

Wolf, Ruth E.; Adams, Monique

2015-01-01

Typically, quadrupole inductively coupled plasma-mass spectrometry (ICP-MS) is used to determine as many as 57 major, minor, and trace elements in aqueous geochemical samples, including natural surface water and groundwater, acid mine drainage water, and extracts or leachates from geological samples. The sample solution is aspirated into the inductively coupled plasma (ICP) which is an electrodeless discharge of ionized argon gas at a temperature of approximately 6,000 degrees Celsius. The elements in the sample solution are subsequently volatilized, atomized, and ionized by the ICP. The ions generated are then focused and introduced into a quadrupole mass filter which only allows one mass to reach the detector at a given moment in time. As the settings of the mass analyzer change, subsequent masses are allowed to impact the detector. Although the typical quadrupole ICP-MS system is a sequential scanning instrument (determining each mass separately), the scan speed of modern instruments is on the order of several thousand masses per second. Consequently, typical total sample analysis times of 2–3 minutes are readily achievable for up to 57 elements.

LC/MS/MS analysis of the endogenous dimethyltryptamine hallucinogens, their precursors, and major metabolites in rat pineal gland microdialysate.

PubMed

Barker, Steven A; Borjigin, Jimo; Lomnicka, Izabela; Strassman, Rick

2013-12-01

We report a qualitative liquid chromatography-tandem mass spectrometry (LC/MS/MS) method for the simultaneous analysis of the three known N,N-dimethyltryptamine endogenous hallucinogens, their precursors and metabolites, as well as melatonin and its metabolic precursors. The method was characterized using artificial cerebrospinal fluid (aCSF) as the matrix and was subsequently applied to the analysis of rat brain pineal gland-aCSF microdialysate. The method describes the simultaneous analysis of 23 chemically diverse compounds plus a deuterated internal standard by direct injection, requiring no dilution or extraction of the samples. The results demonstrate that this is a simple, sensitive, specific and direct approach to the qualitative analysis of these compounds in this matrix. The protocol also employs stringent MS confirmatory criteria for the detection and confirmation of the compounds examined, including exact mass measurements. The excellent limits of detection and broad scope make it a valuable research tool for examining the endogenous hallucinogen pathways in the central nervous system. We report here, for the first time, the presence of N,N-dimethyltryptamine in pineal gland microdialysate obtained from the rat. Copyright © 2013 John Wiley & Sons, Ltd.

5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK--Setting the analysis frame.

PubMed

Stephan, Christian; Hamacher, Michael; Blüggel, Martin; Körting, Gerhard; Chamrad, Daniel; Scheer, Christian; Marcus, Katrin; Reidegeld, Kai A; Lohaus, Christiane; Schäfer, Heike; Martens, Lennart; Jones, Philip; Müller, Michael; Auyeung, Kevin; Taylor, Chris; Binz, Pierre-Alain; Thiele, Herbert; Parkinson, David; Meyer, Helmut E; Apweiler, Rolf

2005-09-01

The Bioinformatics Committee of the HUPO Brain Proteome Project (HUPO BPP) meets regularly to execute the post-lab analyses of the data produced in the HUPO BPP pilot studies. On July 7, 2005 the members came together for the 5th time at the European Bioinformatics Institute (EBI) in Hinxton, UK, hosted by Rolf Apweiler. As a main result, the parameter set of the semi-automated data re-analysis of MS/MS spectra has been elaborated and the subsequent work steps have been defined.

Discovery and Identification of Dimethylsilanediol as a Contaminant in ISS Potable Water

NASA Technical Reports Server (NTRS)

Rutz, Jeffrey A.; Schultz, John R.; Kuo, C. Mike; Cole, Hraold E.; Manuel, Sam; Curtis, Matthew; Jones, Patrick R.; Sparkman, O. David; McCoy, J. Torin

2010-01-01

In September of 2010, analysis of ISS potable water samples was undertaken to determine the contaminant responsible for a rise in total organic carbon (TOC). As analysis of the routine target list of organic compounds did not reveal the contaminant, efforts to look for unknown compounds was initiated, resulting in an unknown peak being discovered in the gas chromatography/mass spectrometry (GC/MS) analysis for glycols. A mass spectrum of the contaminant was then generated by concentrating one of the samples by evaporation and analyzing by GC/MS in full-scan mode. Although a computer match of the compound s identity could not be obtained with the instrument s database, a search with a more up to date mass spectral library yielded a good match with dimethylsilanediol (DMSD). Inductively Coupled Plasma/Mass Spectrometry (ICP/MS) analyses showed abnormally high silicon levels in the samples, confirming that the unknown contained silicon. DMSD was then synthesized to confirm the identification and provide a standard to develop a calibration curve. Further confirmation was provided by external Direct Analysis in Real Time (DART) GC/MS analysis. A preliminary GC/MS method was then developed and archived samples from various locations on ISS were analyzed to determine the extent of the contamination and provide data for troubleshooting. This paper describes these events in more detail as well as problems encountered in routine GC/MS analyses and the subsequent development of high performance liquid chromatography and LC/MS/MS methods for quantitation of DMSD.

Software Analysis of Uncorrelated MS1 Peaks for Discovery of Post-Translational Modifications.

PubMed

Pascal, Bruce D; West, Graham M; Scharager-Tapia, Catherina; Flefil, Ricardo; Moroni, Tina; Martinez-Acedo, Pablo; Griffin, Patrick R; Carvalloza, Anthony C

2015-12-01

The goal in proteomics to identify all peptides in a complex mixture has been largely addressed using various LC MS/MS approaches, such as data dependent acquisition, SRM/MRM, and data independent acquisition instrumentation. Despite these developments, many peptides remain unsequenced, often due to low abundance, poor fragmentation patterns, or data analysis difficulties. Many of the unidentified peptides exhibit strong evidence in high resolution MS(1) data and are frequently post-translationally modified, playing a significant role in biological processes. Proteomics Workbench (PWB) software was developed to automate the detection and visualization of all possible peptides in MS(1) data, reveal candidate peptides not initially identified, and build inclusion lists for subsequent MS(2) analysis to uncover new identifications. We used this software on existing data on the autophagy regulating kinase Ulk1 as a proof of concept for this method, as we had already manually identified a number of phosphorylation sites Dorsey, F. C. et al (J. Proteome. Res. 8(11), 5253-5263 (2009)). PWB found all previously identified sites of phosphorylation. The software has been made freely available at http://www.proteomicsworkbench.com . Graphical Abstract ᅟ.

Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics

PubMed Central

Brusniak, Mi-Youn; Bodenmiller, Bernd; Campbell, David; Cooke, Kelly; Eddes, James; Garbutt, Andrew; Lau, Hollis; Letarte, Simon; Mueller, Lukas N; Sharma, Vagisha; Vitek, Olga; Zhang, Ning; Aebersold, Ruedi; Watts, Julian D

2008-01-01

Background Quantitative proteomics holds great promise for identifying proteins that are differentially abundant between populations representing different physiological or disease states. A range of computational tools is now available for both isotopically labeled and label-free liquid chromatography mass spectrometry (LC-MS) based quantitative proteomics. However, they are generally not comparable to each other in terms of functionality, user interfaces, information input/output, and do not readily facilitate appropriate statistical data analysis. These limitations, along with the array of choices, present a daunting prospect for biologists, and other researchers not trained in bioinformatics, who wish to use LC-MS-based quantitative proteomics. Results We have developed Corra, a computational framework and tools for discovery-based LC-MS proteomics. Corra extends and adapts existing algorithms used for LC-MS-based proteomics, and statistical algorithms, originally developed for microarray data analyses, appropriate for LC-MS data analysis. Corra also adapts software engineering technologies (e.g. Google Web Toolkit, distributed processing) so that computationally intense data processing and statistical analyses can run on a remote server, while the user controls and manages the process from their own computer via a simple web interface. Corra also allows the user to output significantly differentially abundant LC-MS-detected peptide features in a form compatible with subsequent sequence identification via tandem mass spectrometry (MS/MS). We present two case studies to illustrate the application of Corra to commonly performed LC-MS-based biological workflows: a pilot biomarker discovery study of glycoproteins isolated from human plasma samples relevant to type 2 diabetes, and a study in yeast to identify in vivo targets of the protein kinase Ark1 via phosphopeptide profiling. Conclusion The Corra computational framework leverages computational innovation to enable biologists or other researchers to process, analyze and visualize LC-MS data with what would otherwise be a complex and not user-friendly suite of tools. Corra enables appropriate statistical analyses, with controlled false-discovery rates, ultimately to inform subsequent targeted identification of differentially abundant peptides by MS/MS. For the user not trained in bioinformatics, Corra represents a complete, customizable, free and open source computational platform enabling LC-MS-based proteomic workflows, and as such, addresses an unmet need in the LC-MS proteomics field. PMID:19087345

Bayesian Normalization Model for Label-Free Quantitative Analysis by LC-MS

PubMed Central

Nezami Ranjbar, Mohammad R.; Tadesse, Mahlet G.; Wang, Yue; Ressom, Habtom W.

2016-01-01

We introduce a new method for normalization of data acquired by liquid chromatography coupled with mass spectrometry (LC-MS) in label-free differential expression analysis. Normalization of LC-MS data is desired prior to subsequent statistical analysis to adjust variabilities in ion intensities that are not caused by biological differences but experimental bias. There are different sources of bias including variabilities during sample collection and sample storage, poor experimental design, noise, etc. In addition, instrument variability in experiments involving a large number of LC-MS runs leads to a significant drift in intensity measurements. Although various methods have been proposed for normalization of LC-MS data, there is no universally applicable approach. In this paper, we propose a Bayesian normalization model (BNM) that utilizes scan-level information from LC-MS data. Specifically, the proposed method uses peak shapes to model the scan-level data acquired from extracted ion chromatograms (EIC) with parameters considered as a linear mixed effects model. We extended the model into BNM with drift (BNMD) to compensate for the variability in intensity measurements due to long LC-MS runs. We evaluated the performance of our method using synthetic and experimental data. In comparison with several existing methods, the proposed BNM and BNMD yielded significant improvement. PMID:26357332

A novel sampling method for identification of endogenous skin surface compounds by use of DART-MS and MALDI-MS.

PubMed

Mess, Aylin; Enthaler, Bernd; Fischer, Markus; Rapp, Claudius; Pruns, Julia K; Vietzke, Jens-Peter

2013-01-15

Identification of endogenous skin surface compounds is an intriguing challenge in comparative skin investigations. Notably, this short communication is focused on the analysis of small molecules, e.g. natural moisturizing factor (NMF) components and lipids, using a novel sampling method with DIP-it samplers for non-invasive examination of the human skin surface. As a result, extraction of analytes directly from the skin surface by use of various solvents can be replaced with the mentioned procedure. Screening of measureable compounds is achieved by direct analysis in real time mass spectrometry (DART-MS) without further sample preparation. Results are supplemented by dissolving analytes from the DIP-it samplers by use of different solvents, and subsequent matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) measurements. An interesting comparison of the mentioned MS techniques for determination of skin surface compounds in the mass range of 50-1000 Da is presented. Copyright © 2012 Elsevier B.V. All rights reserved.

Nonreductive chemical release of intact N-glycans for subsequent labeling and analysis by mass spectrometry.

PubMed

Yuan, Jiangbei; Wang, Chengjian; Sun, Yujiao; Huang, Linjuan; Wang, Zhongfu

2014-10-01

A novel strategy is proposed, using cost-saving chemical reactions to generate intact free reducing N-glycans and their fluorescent derivatives from glycoproteins for subsequent analysis. N-Glycans without core α-1,3-linked fucose are released in reducing form by selective hydrolysis of the N-type carbohydrate-peptide bond of glycoproteins under a set of optimized mild alkaline conditions and are comparable to those released by commonly used peptide-N-glycosidase (PNGase) F in terms of yield without any detectable side reaction (peeling or deacetylation). The obtained reducing glycans can be routinely derivatized with 2-aminobenzoic acid (2-AA), 1-phenyl-3-methyl-5-pyrazolone (PMP), and potentially some other fluorescent reagents for comprehensive analysis. Alternatively, the core α-1,3-fucosylated N-glycans are released in mild alkaline medium and derivatized with PMP in situ, and their yields are comparable to those obtained using commonly used PNGase A without conspicuous peeling reaction or any detectable deacetylation. Using this new technique, the N-glycans of a series of purified glycoproteins and complex biological samples were successfully released and analyzed by electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry (MS/MS), demonstrating its general applicability to glycomic studies. Copyright © 2014 Elsevier Inc. All rights reserved.

MASS SPECTROMETRY OF FATTY ALDEHYDES

PubMed Central

Berdyshev, Evgeny V.

2011-01-01

Fatty aldehydes are important components of the cellular lipidome. Significant interest has been developed towards the analysis of the short chain α,β-unsaturated and hydroxylated aldehydes formed as a result of oxidation of polyunsaturated fatty acids. Multiple gas chromatography-mass spectrometry (GC/MS) and subsequently liquid chromatography-mass spectrometry (LC/MS) approaches have been developed to identify and quantify short-chain as well as long-chain fatty aldehydes. Due to the ability to non-enzymaticaly form Schiff bases with amino groups of proteins, lipids, and with DNA guanidine, free aldehydes are viewed as a marker or metric of fatty acid oxidation and not the part of intracellular signaling pathways which has significantly limited the overall attention this group of molecules have received. This review provides an overview of current GC/MS and LC/MS approaches of fatty aldehyde analysis as well as discusses technical challenges standing in the way of free fatty aldehyde quantitation. PMID:21930240

Analysis of a G protein-coupled receptor for neurotensin by liquid chromatography-electrospray ionization-mass spectrometry.

PubMed

Ho, Jenny T C; White, Jim F; Grisshammer, Reinhard; Hess, Sonja

2008-05-01

The type 1 neurotensin receptor (NTS1) belongs to the G protein-coupled receptor (GPCR) family. GPCRs are involved in important physiological processes, but for many GPCRs ligand binding sites and other structural features have yet to be elucidated. Comprehensive analyses by mass spectrometry (MS) could address such issues, but they are complicated by the hydrophobic nature of the receptors. Recombinant NTS1 must be purified in the presence of detergents to maintain solubility and functionality of the receptor, to allow testing of ligand, or to allow G protein interaction. However, detergents are detrimental to MS analyses. Hence, steps need to be taken to substitute the detergents with MS-compatible polar/organic solvents. Here we report the characterization of NTS1 by electrospray ionization (ESI)-MS with emphasis on methods to transfer intact NTS1 or its proteolytic peptides into compatible solvents by protein precipitation and liquid chromatography (LC) prior to ESI-MS analyses. Molecular mass measurement of intact recombinant NTS1 was performed using a mixture of chloroform/methanol/aqueous trifluoroacetic acid as the mobile phase for size exclusion chromatography-ESI-MS analysis. In a separate experiment, NTS1 was digested with a combination of cyanogen bromide and trypsin and/or chymotrypsin. Subsequent reversed phase LC-ESI-tandem MS analysis resulted in greater than 80% sequence coverage of the NTS1 protein, including all seven transmembrane domains. This work represents the first comprehensive analysis of recombinant NTS1 using MS.

Automated Liquid Microjunction Surface Sampling-HPLC-MS/MS Analysis of Drugs and Metabolites in Whole-Body Thin Tissue Sections

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

Kertesz, Vilmos; Van Berkel, Gary J

A fully automated liquid extraction-based surface sampling system utilizing a commercially available autosampler coupled to high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) detection is reported. Discrete spots selected for droplet-based sampling and automated sample queue generation for both the autosampler and MS were enabled by using in-house developed software. In addition, co-registration of spatially resolved sampling position and HPLC-MS information to generate heatmaps of compounds monitored for subsequent data analysis was also available in the software. The system was evaluated with whole-body thin tissue sections from propranolol dosed rat. The hands-free operation of the system was demonstrated by creating heatmapsmore » of the parent drug and its hydroxypropranolol glucuronide metabolites with 1 mm resolution in the areas of interest. The sample throughput was approximately 5 min/sample defined by the time needed for chromatographic separation. The spatial distributions of both the drug and its metabolites were consistent with previous studies employing other liquid extraction-based surface sampling methodologies.« less

A molecular beam/quadrupole mass spectrometer system with synchronized beam modulation and digital waveform analysis

NASA Technical Reports Server (NTRS)

Pellett, G. L.; Adams, B. R.

1983-01-01

A performance evaluation is conducted for a molecular beam/mass spectrometer (MB/MS) system, as applied to a 1-30 torr microwave-discharge flow reactor (MWFR) used in the formation of the methylperoxy radical and a study of its subsequent destruction in the presence or absence of NO(x). The modulated MB/MS system is four-staged and differentially pumped. The results obtained by the MWFR study is illustrative of overall system performance, including digital waveform analysis; significant improvements over previous designs are noted in attainable S/N ratio, detection limit, and accuracy.

A novel approach for quantitation of glucosylceramide in human dried blood spot using LC-MS/MS.

PubMed

Ji, Allena Ji; Wang, Haixing; Ziso-Qejvanaj, Enida; Zheng, Kefei; Chung, Lee Lee; Foley, Timothy; Chuang, Wei-Lien; Richards, Susan; Sung, Crystal

2015-01-01

Glucosylceramide, an efficacy biomarker for Gaucher Type 1 disease, exhibits poor solubility in polar solvents and whole blood which makes it difficult to prepare a homogenous blood standard. We developed a novel method using standard addition approach by spiking a small volume of analyte solution on the surface of prespotted dried blood spot. The whole spots were punched out for subsequent extraction and LC-MS/MS analysis. The assay performance met all validation acceptance criteria. Glucosylceramide concentrations in 50 paired plasma and dry blood spot samples obtained from Gaucher Type 1 patients were tested and the results demonstrated the feasibility of using the DBS method for clinical biomarker monitoring. The new approach greatly improves assay precision and accuracy.

Computational mass spectrometry for small molecules

PubMed Central

2013-01-01

The identification of small molecules from mass spectrometry (MS) data remains a major challenge in the interpretation of MS data. This review covers the computational aspects of identifying small molecules, from the identification of a compound searching a reference spectral library, to the structural elucidation of unknowns. In detail, we describe the basic principles and pitfalls of searching mass spectral reference libraries. Determining the molecular formula of the compound can serve as a basis for subsequent structural elucidation; consequently, we cover different methods for molecular formula identification, focussing on isotope pattern analysis. We then discuss automated methods to deal with mass spectra of compounds that are not present in spectral libraries, and provide an insight into de novo analysis of fragmentation spectra using fragmentation trees. In addition, this review shortly covers the reconstruction of metabolic networks using MS data. Finally, we list available software for different steps of the analysis pipeline. PMID:23453222

Analysis of waterborne paints by gas chromatography-mass spectrometry with a temperature-programmable pyrolyzer.

PubMed

Nakamura, S; Takino, M; Daishima, S

2001-04-06

Gas chromatography-mass spectrometry (GC-MS) with a temperature-programmable pyrolyzer was used for the analysis of waterborne paints. Evolved gas analysis (EGA) profiles of the waterborne paints were obtained by this temperature-programmed pyrolysis directly coupled with MS via a deactivated metal capillary tube. The EGA profile suggested the optimal thermal desorption conditions for solvents and additives and the subsequent optimal pyrolysis temperature for the remaining polymeric material. Polymers were identified from pyrograms with the assistance of a new polymer library. The solvents were identified from the electron ionization mass spectra with the corresponding chemical ionization mass spectra. The additive was identified as zinc pyrithione by comparison with authentic standard. Zinc pyrithione cannot be analyzed by GC-MS as it is. However, the thermal decomposition products of zinc pyrithione could be detected. The information on the decomposition temperature and products was useful for the identification of the original compound.

Unravelling Orbital Climatic Cycles from Devonian Magnetic Susceptibility Signal - The Quest for a Better Age Model for the Lochkovian and Pragian Stages (Czech Republic)

NASA Astrophysics Data System (ADS)

da Silva, A. C.; Chadimova, L.; Hladil, J.; Slavik, L.; Hilgen, F. J.; Dekkers, M. J.

2015-12-01

The uncertainties on the Devonian stage boundaries are currently in the order of several millions of years. When shown to reflect a detrital signal, which is influenced by climatic variations, Magnetic Susceptibility (MS) has been proven as a useful tool for identifying climatic cycles; which can subsequently be used to improve the time scale. Here, we focus on two sections from the Prague Synform (Czech Republic) cutting through the Lochkovian, Pragian and the lower part of the Emsian. Sedimentation is rhythmic, dominated by slightly clayey offshore limestones, being mostly calciturbidites and hemipelagites. We provide hysteresis analysis in order to get insight into the nature and the origin of the magnetic minerals driving the variation in the MS signal. The results point to a MS signal mostly carried by clay minerals. Subsequently, to improve estimation of the duration of the stages, we apply different spectral analysis techniques on this MS signal. From the Continuous Wavelet Transform (CWT), Evolutive Harmonic Analysis (EHA) and field observations, we subdivide the section into portions with a steady sedimentation rate (a first estimate of this rate is also delivered by these analyzes). Then, we apply Multitaper Method (MTM) and Multitaper harmonic Analysis (F-test) and extract the frequencies reaching 95% Confidence Level. These frequencies are then implemented into the Average Spectral Misfit procedures (ASM) which enables comparison with orbital targets. By combining these different techniques, 405 kyr cyclicty is identifed, a powerful duration paleochronometer. These new results indicate a duration of 7.7 ± 2 Myr for the Lochkovian stage and of 1.7 Myr ± 1.4 for the Pragian stage (compared to respectively 8.4 ± 6 Myr and 3.2 ± 5.4 Myr in the 2012 Geological Time Scale).

Software Analysis of Uncorrelated MS1 Peaks for Discovery of Post-Translational Modifications

NASA Astrophysics Data System (ADS)

Pascal, Bruce D.; West, Graham M.; Scharager-Tapia, Catherina; Flefil, Ricardo; Moroni, Tina; Martinez-Acedo, Pablo; Griffin, Patrick R.; Carvalloza, Anthony C.

2015-12-01

The goal in proteomics to identify all peptides in a complex mixture has been largely addressed using various LC MS/MS approaches, such as data dependent acquisition, SRM/MRM, and data independent acquisition instrumentation. Despite these developments, many peptides remain unsequenced, often due to low abundance, poor fragmentation patterns, or data analysis difficulties. Many of the unidentified peptides exhibit strong evidence in high resolution MS1 data and are frequently post-translationally modified, playing a significant role in biological processes. Proteomics Workbench (PWB) software was developed to automate the detection and visualization of all possible peptides in MS1 data, reveal candidate peptides not initially identified, and build inclusion lists for subsequent MS2 analysis to uncover new identifications. We used this software on existing data on the autophagy regulating kinase Ulk1 as a proof of concept for this method, as we had already manually identified a number of phosphorylation sites Dorsey, F. C. et al (J. Proteome. Res. 8(11), 5253-5263 (2009)). PWB found all previously identified sites of phosphorylation. The software has been made freely available at http://www.proteomicsworkbench.com .

Dual mechanisms in the perceptual processing of click train temporal regularity.

PubMed

Phillips, Dennis P; Dingle, Rachel N; Hall, Susan E; Jang, Moragh

2012-07-01

Two experiments measured human sensitivity to temporal jitter in 25-click trains with inter-click intervals (ICIs) between 5 and 100 ms. In a naturalistic experiment using wideband clicks, jitter thresholds were a nonmonotonic function of ICI, peaking for ICIs near 40-60 ms. In a subsequent experiment, clicks were high-passed and presented against a low-frequency noise masker. Jitter threshold vs ICI functions lost the positive slope over short ICIs but retained the negative slope at long ICIs. The same behavior was seen in click rate discrimination tasks. Different processes mediate regularity analysis for click trains with ICIs above and below 40-60 ms.

Highly efficient proteome analysis with combination of protein pre-fractionation by preparative microscale solution isoelectric focusing and identification by μRPLC-MS/MS with serially coupled long microcolumn.

PubMed

Tao, Dingyin; Sun, Liangliang; Zhu, Guijie; Liang, Yu; Liang, Zhen; Zhang, Lihua; Zhang, Yukui

2011-01-01

To improve the efficiency of proteome analysis, a strategy with the combination of protein pre-fractionation by preparative microscale solution isoelectric focusing, peptide separation by μRPLC with serially coupled long microcolumn and protein identification by ESI-MS/MS was proposed. By preparative microscale solution isoelectric focusing technique, proteins extracted from whole cell lysates of Escherichia coli were fractionated into five chambers divided by isoelectric membranes, respectively with pH range from 3.0 to 4.6, 4.6 to 5.4, 5.4 to 6.2, 6.2 to 7.0 and 7.0 to 10.0. Compared to the traditional on-gel IFF, the protein recovery could be obviously improved to over 95%. Subsequently, the enriched and fractionated proteins in each chamber were digested, and further separated by a 30-cm long serially coupled RP microcolumn. Through the detection by ESI-MS/MS, about 200 proteins were identified in each fraction, and in total 835 proteins were identified even with one-dimensional μRPLC-MS/MS system. All these results demonstrate that by such a combination strategy, highly efficient proteome analysis could be achieved, not only due to the in-solution protein enrichment and pre-fractionation with improved protein recovery but also owing to the increased separation capacity of serially coupled long μRPLC columns. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Liver plasma membranes: an effective method to analyze membrane proteome.

PubMed

Cao, Rui; Liang, Songping

2012-01-01

Plasma membrane proteins are critical for the maintenance of biological systems and represent important targets for the treatment of disease. The hydrophobicity and low abundance of plasma membrane proteins make them difficult to analyze. The protocols given here are the efficient isolation/digestion procedures for liver plasma membrane proteomic analysis. Both protocol for the isolation of plasma membranes and protocol for the in-gel digestion of gel-embedded plasma membrane proteins are presented. The later method allows the use of a high detergent concentration to achieve efficient solubilization of hydrophobic plasma membrane proteins while avoiding interference with the subsequent LC-MS/MS analysis.

Bone protein extraction without demineralization using principles from hydroxyapatite chromatography.

PubMed

Cleland, Timothy P; Vashishth, Deepak

2015-03-01

Historically, extraction of bone proteins has relied on the use of demineralization to better retrieve proteins from the extracellular matrix; however, demineralization can be a slow process that restricts subsequent analysis of the samples. Here, we developed a novel protein extraction method that does not use demineralization but instead uses a methodology from hydroxyapatite chromatography where high concentrations of ammonium phosphate and ammonium bicarbonate are used to extract bone proteins. We report that this method has a higher yield than those with previously published small-scale extant bone extractions, with and without demineralization. Furthermore, after digestion with trypsin and subsequent high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) analysis, we were able to detect several extracellular matrix and vascular proteins in addition to collagen I and osteocalcin. Our new method has the potential to isolate proteins within a short period (4h) and provide information about bone proteins that may be lost during demineralization or with the use of denaturing agents. Copyright © 2014 Elsevier Inc. All rights reserved.

Study of sample preparation for determination of endocannabinoids and analogous compounds in human serum by LC-MS/MS in MRM mode.

PubMed

Luque-Córdoba, D; Calderón-Santiago, M; Luque de Castro, M D; Priego-Capote, F

2018-08-01

Endocannabinoids are lipids with a key role in physiological processes such as the immune response or the metabolism. This involvement explains their association to pathologies such as cancer, obesity or multiple sclerosis. The determination of endocannabinoids constitutes a challenge for clinical laboratories due to the variety of biological matrices and the wide range of concentrations at which they can be found. This research deals with the comparison of three sample preparation strategies (viz., on-line SPE, off-line SPE for interferents removal, and protein precipitation) for subsequent LC-MS/MS analysis of 14 endocannabinoids and analogous compounds in serum. As a result, the on-line coupling between SPE and LC-MS/MS is proposed as the best approach for this determination. The proposed method allows full automation of the overall process, shortening of the analysis time, and avoidance of errors associated with sample preparation steps. The improvement in sensitivity and selectivity thus achieved allows obtaining quantification limits at the pg mL -1 level, which makes possible the application of the method for clinical studies. Copyright © 2018 Elsevier B.V. All rights reserved.

Maternal Serum and Amniotic Fluid Inhibin A Levels in Women who Subsequently Develop Severe Preeclampsia

PubMed Central

Kim, Shin-Young; Yang, Jae-Hyug; Kim, Moon-Young; Ahn, Hyun-Kyong; Shin, Joong-Sik; Choi, Jun-Seek; Park, So-Yeon; Kim, Jin-Mi; Lee, Bom-Yi; Kim, Do-Jin

2006-01-01

The purpose of this study was to evaluate whether maternal serum (MS) and amniotic fluid (AF) inhibin A levels are elevated in patients who subsequently develop severe preecalmpsia, and to investigate the correlation between MS and AF inhibin A levels in the second trimester. The study included 40 patients who subsequently developed severe preecalmpsia and 80 normal pregnant women. Inhibin A levels in MS and AF were measured with enzyme-linked immunosorbent assay (ELISA). The MS and AF inhibin A levels in patients who developed severe preeclampsia were significantly higher than those in the control group (both for p<0.001). There was a positive correlation between MS and AF inhibin A levels in patients who developed severe preeclampsia (r=0.397, p=0.011), but not in the control group (r=0.185, p=0.126). The best cutoff values of MS and AF inhibin A levels for the prediction of severe preeclampsia were 427 pg/mL and 599 pg/mL, respectively; the estimated ORs that were associated with these cut-off values were 9.95 (95% CI 3.8-25.9, p<0.001) and 6.0 (95% CI 2.3-15.8, p<0.001). An elevated level of inhibin A in MS and AF at the time of second trimester amniocentesis may be a risk factor for the subsequent development of severe preeclampsia. PMID:16778388

Quantitation of intracellular purine intermediates in different Corynebacteria using electrospray LC-MS/MS.

PubMed

Peifer, Susanne; Schneider, Konstantin; Nürenberg, Gudrun; Volmer, Dietrich A; Heinzle, Elmar

2012-11-01

Intermediates of the purine biosynthesis pathway play key roles in cellular metabolism including nucleic acid synthesis and signal mediation. In addition, they are also of major interest to the biotechnological industry as several intermediates either possess flavor-enhancing characteristics or are applied in medical therapy. In this study, we have developed an analytical method for quantitation of 12 intermediates from the purine biosynthesis pathway including important nucleotides and their corresponding nucleosides and nucleobases. The approach comprised a single-step acidic extraction/quenching procedure, followed by quantitative electrospray LC-MS/MS analysis. The assay was validated in terms of accuracy, precision, reproducibility, and applicability for complex biological matrices. The method was subsequently applied for determination of free intracellular pool sizes of purine biosynthetic pathway intermediates in the two Gram-positive bacteria Corynebacterium glutamicum and Corynebacterium ammoniagenes. Importantly, no ion pair reagents were applied in this approach as usually required for liquid chromatography analysis of large classes of diverse metabolites.

The development and validation of an UHPLC–MS/MS method for the rapid quantification of the antiretroviral agent dapivirine in human plasma

PubMed Central

Seserko, Lauren A; Emory, Joshua F; Hendrix, Craig W; Marzinke, Mark A

2014-01-01

Background Dapivirine is a non-nucleoside reverse transcriptase inhibitor designed to prevent HIV-1 viral replication and subsequent propagation. A sensitive method is required to quantify plasma concentrations to assess drug efficacy. Results Dapivirine-spiked plasma was combined with acetonitrile containing deuterated IS and was processed for analysis. The method has an analytical measuring range from 20 to 10,000 pg/ml. For the LLOQ, low, mid and high QCs, intra- and inter-assay precision (%CV) ranged from 5.58 to 13.89% and 5.23 to 13.36%, respectively, and intra- and inter-day accuracy (% deviation) ranged from -5.61 to 0.75% and -4.30 to 6.24%, respectively. Conclusion A robust and sensitive LC–MS/MS assay for the high-throughput quantification of the antiretroviral drug dapivirine in human plasma was developed and validated following bioanalytical validation guidelines. The assay meets criteria for the analysis of samples from large research trials. PMID:24256358

The development and validation of an UHPLC-MS/MS method for the rapid quantification of the antiretroviral agent dapivirine in human plasma.

PubMed

Seserko, Lauren A; Emory, Joshua F; Hendrix, Craig W; Marzinke, Mark A

2013-11-01

Dapivirine is a non-nucleoside reverse transcriptase inhibitor designed to prevent HIV-1 viral replication and subsequent propagation. A sensitive method is required to quantify plasma concentrations to assess drug efficacy. Dapivirine-spiked plasma was combined with acetonitrile containing deuterated IS and was processed for analysis. The method has an analytical measuring range from 20 to 10,000 pg/ml. For the LLOQ, low, mid and high QCs, intra- and inter-assay precision (%CV) ranged from 5.58 to 13.89% and 5.23 to 13.36%, respectively, and intra- and inter-day accuracy (% deviation) ranged from -5.61 to 0.75% and -4.30 to 6.24%, respectively. A robust and sensitive LC-MS/MS assay for the high-throughput quantification of the antiretroviral drug dapivirine in human plasma was developed and validated following bioanalytical validation guidelines. The assay meets criteria for the analysis of samples from large research trials.

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

Quantitative twoplex glycan analysis using 12C6 and 13C6 stable isotope 2-aminobenzoic acid labelling and capillary electrophoresis mass spectrometry.

PubMed

Váradi, Csaba; Mittermayr, Stefan; Millán-Martín, Silvia; Bones, Jonathan

2016-12-01

Capillary electrophoresis (CE) offers excellent efficiency and orthogonality to liquid chromatographic (LC) separations for oligosaccharide structural analysis. Combination of CE with high resolution mass spectrometry (MS) for glycan analysis remains a challenging task due to the MS incompatibility of background electrolyte buffers and additives commonly used in offline CE separations. Here, a novel method is presented for the analysis of 2-aminobenzoic acid (2-AA) labelled glycans by capillary electrophoresis coupled to mass spectrometry (CE-MS). To ensure maximum resolution and excellent precision without the requirement for excessive analysis times, CE separation conditions including the concentration and pH of the background electrolyte, the effect of applied pressure on the capillary inlet and the capillary length were evaluated. Using readily available 12/13 C 6 stable isotopologues of 2-AA, the developed method can be applied for quantitative glycan profiling in a twoplex manner based on the generation of extracted ion electropherograms (EIE) for 12 C 6 'light' and 13 C 6 'heavy' 2-AA labelled glycan isotope clusters. The twoplex quantitative CE-MS glycan analysis platform is ideally suited for comparability assessment of biopharmaceuticals, such as monoclonal antibodies, for differential glycomic analysis of clinical material for potential biomarker discovery or for quantitative microheterogeneity analysis of different glycosylation sites within a glycoprotein. Additionally, due to the low injection volume requirements of CE, subsequent LC-MS analysis of the same sample can be performed facilitating the use of orthogonal separation techniques for structural elucidation or verification of quantitative performance.

Neural processing of recollection, familiarity and priming at encoding: evidence from a forced-choice recognition paradigm.

PubMed

Meng, Yingfang; Ye, Xiaohong; Gonsalves, Brian D

2014-10-17

The distinction between neural mechanisms of explicit and implicit expressions of memory has been well studied at the retrieval stage, but less at encoding. In addition, dissociations obtained in many studies are complicated by methodological difficulties in obtaining process-pure measures of different types of memory. In this experiment, we applied a subsequent memory paradigm and a two-stage forced-choice recognition test to classify study ERP data into four categories: subsequent remembered (later retrieved accompanied by detailed information), subsequent known (later retrieved accompanied by a feeling of familiarity), subsequent primed (later retrieved without conscious awareness) and subsequent forgotten (not retrieved). Differences in subsequent memory effects (DM effects) were measured by comparing ERP waveform associated with later memory based on recollection, familiarity or priming with ERP waveform for later forgotten items. The recollection DM effect involved a robust sustained (onset at 300 ms) prefrontal positive-going DM effect which was right-lateralized, and a later (onset at 800 ms) occipital negative-going DM effect. Familiarity involved an earlier (300-400 ms) prefrontal positive-going DM effect and a later (500-600 ms) parietal positive-going DM effect. Priming involved a negative-going DM effect which onset at 600 ms, mainly distributed over anterior brain sites. These results revealed a sequence of components that represented cognitive processes underlying the encoding of verbal information into episodic memory, and separately supported later remembering, knowing and priming. Copyright © 2014 Elsevier B.V. All rights reserved.

Metabolic Analysis

NASA Astrophysics Data System (ADS)

Tolstikov, Vladimir V.

Analysis of the metabolome with coverage of all of the possibly detectable components in the sample, rather than analysis of each individual metabolite at a given time, can be accomplished by metabolic analysis. Targeted and/or nontargeted approaches are applied as needed for particular experiments. Monitoring hundreds or more metabolites at a given time requires high-throughput and high-end techniques that enable screening for relative changes in, rather than absolute concentrations of, compounds within a wide dynamic range. Most of the analytical techniques useful for these purposes use GC or HPLC/UPLC separation modules coupled to a fast and accurate mass spectrometer. GC separations require chemical modification (derivatization) before analysis, and work efficiently for the small molecules. HPLC separations are better suited for the analysis of labile and nonvolatile polar and nonpolar compounds in their native form. Direct infusion and NMR-based techniques are mostly used for fingerprinting and snap phenotyping, where applicable. Discovery and validation of metabolic biomarkers are exciting and promising opportunities offered by metabolic analysis applied to biological and biomedical experiments. We have demonstrated that GC-TOF-MS, HPLC/UPLC-RP-MS and HILIC-LC-MS techniques used for metabolic analysis offer sufficient metabolome mapping providing researchers with confident data for subsequent multivariate analysis and data mining.

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.

Brain-heart coupling at the P300 latency is linked to anterior cingulate cortex and insula--a cardio-electroencephalographic covariance tracing study.

PubMed

Panitz, Christian; Wacker, Jan; Stemmler, Gerhard; Mueller, Erik M

2013-09-01

Prior work on the coupling of cortical and cardiac responses to feedback demonstrated that feedback-evoked single-trial EEG magnitudes 300 ms post-stimulus predict the degree of subsequent cardiac acceleration. The main goal of the current study was to explore the neural sources of this phenomenon using (a) independent component analysis in conjunction with dipole fitting and (b) low resolution electromagnetic tomography (LORETA) in N=14 participants who performed a gambling task with feedback presented after each trial. It was shown that independent components localized near anterior cingulate cortex produced robust within-subjects correlations with feedback-evoked heart-period, suggesting that anterior cingulate cortex activity 300ms after feedback presentation predicts the strength of subsequent cardiac acceleration. Moreover, interindividual differences in evoked left insular cortex LORETA-estimated activity at around 300ms moderated within-subjects EEG-heart period correlations. These results suggest that key regions of central autonomic control are involved in cortico-cardiac coupling evoked by feedback stimuli. Copyright © 2013 Elsevier B.V. All rights reserved.

Influence of growing conditions on metabolite profile of Ammi visnaga umbels with special reference to bioactive furanochromones and pyranocoumarins.

PubMed

Sellami, Hela Kallel; Napolitano, Assunta; Masullo, Milena; Smiti, Samira; Piacente, Sonia; Pizza, Cosimo

2013-11-01

The medicinal plant Ammi visnaga is a valuable source of furanochromones and pyranocoumarins used as vasodilator agents. Its ability to germinate under unfavourable growth conditions, such as saline soil and hypoxia characterizing clay soils and marshes ecosystems, prompted us to qualitatively characterize secondary metabolites in umbels of A. visnaga plants grown under different conditions (in field, hydroponically controlled, and contrasted by salinity and/or hypoxia) by HPLC-ESI/IT/MS(n) analysis. Subsequently, the quantitative analysis of the bioactive compounds, above all furanochromones and pyranocoumarins, was carried out by HPLC-ESI/QqQ/MS/MS. The results show the influence of growing conditions on the quali-quantitative profile of A. visnaga secondary metabolites and evidence that hydroponic culture leads to increased level of A. visnaga active principles. Furthermore, two furanochromones never reported before were identified and characterized by 1D- and 2D-NMR analysis. Copyright © 2013 Elsevier Ltd. All rights reserved.

Isolation and chemical analysis of nanoparticles from English ivy (Hedera helix L.)

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

Lenaghan, Scott C; Burris, Jason N; Chourey, Karuna

It was discovered that adventitious roots of English ivy secreted a high strength adhesive containing uniform nanoparticles. These nanoparticles were hypothesized to be organic in nature. Subsequent studies have revealed several applications for these nanoparticles, but their chemical composition remained unknown. Here, we describe an isolation procedure to obtain gram quantities of ivy nanoparticles from adventitious roots. In addition, ultraviolet/visible (UV/Vis) spectroscopy, inductively coupled plasma mass spectrometry (ICP-MS), elemental analysis, fourier transform infrared spectroscopy (FTIR), and gel electrophoresis were conducted to identify the chemical nature of the ivy nanoparticles. Based on this comprehensive analysis, we conclude that the ivy nanoparticlesmore » are proteinaceous consisting of 51.77% carbon, 4.72% nitrogen, and 0.32% sulfur, without the presence of metals. Liquid chromatography tandem mass spectrometry (LC-MS/MS) based protein profiling revealed the presence of at least 6 proteins, including heat shock proteins and other large molecular weight proteins. Identification of these protein candidates will facilitate gene discovery and bioproduction of ivy nanoparticles.« less

Assessment of a new method for the analysis of decomposition gases of polymers by a combining thermogravimetric solid-phase extraction and thermal desorption gas chromatography mass spectrometry.

PubMed

Duemichen, E; Braun, U; Senz, R; Fabian, G; Sturm, H

2014-08-08

For analysis of the gaseous thermal decomposition products of polymers, the common techniques are thermogravimetry, combined with Fourier transformed infrared spectroscopy (TGA-FTIR) and mass spectrometry (TGA-MS). These methods offer a simple approach to the decomposition mechanism, especially for small decomposition molecules. Complex spectra of gaseous mixtures are very often hard to identify because of overlapping signals. In this paper a new method is described to adsorb the decomposition products during controlled conditions in TGA on solid-phase extraction (SPE) material: twisters. Subsequently the twisters were analysed with thermal desorption gas chromatography mass spectrometry (TDS-GC-MS), which allows the decomposition products to be separated and identified using an MS library. The thermoplastics polyamide 66 (PA 66) and polybutylene terephthalate (PBT) were used as example polymers. The influence of the sample mass and of the purge gas flow during the decomposition process was investigated in TGA. The advantages and limitations of the method were presented in comparison to the common analysis techniques, TGA-FTIR and TGA-MS. Copyright © 2014 Elsevier B.V. All rights reserved.

Impact of Net Atrioventricular Compliance on Clinical Outcome in Mitral Stenosis

PubMed Central

Nunes, Maria Carmo P.; Hung, Judy; Barbosa, Marcia M.; Esteves, William A.; Carvalho, Vinicius T.; Lodi-Junqueira, Lucas; Fonseca Neto, Cirilo P.; Tan, Timothy C.; Levine, Robert A.

2014-01-01

Background Net atrioventricular compliance (Cn) has been reported to be an important determinant of pulmonary hypertension in mitral stenosis (MS). We hypothesized that, as Cn reflects hemodynamic consequences of MS, it may be useful in assessing prognosis. To date, limited data with an assumed Cn cutoff have indicated the need for larger prospective studies. This prospective study was designed to determine the impact of Cn on clinical outcome and its contribution to pulmonary pressure in MS. In addition, we aimed to identify a cutoff value of Cn for outcome prediction in this setting. Methods and Results A total of 128 patients with rheumatic MS without other significant valve disease were prospectively enrolled. Comprehensive echocardiography was performed and Doppler-derived Cn estimated using a previously validated equation. The endpoint was either mitral valve intervention or death. Cn was an important predictor of pulmonary pressure, regardless of classic measures of MS severity. During a median follow-up of 22 months, the endpoint was reached in 45 patients (35%). Baseline Cn predicted outcome, adding prognostic information beyond that provided by mitral valve area and functional status. Cn ≤ 4 mL/mmHg best predicted unfavorable outcome in derivation and validation sets. A subgroup analysis including only initially asymptomatic patients with moderate to severe MS without initial indication for intervention (40.6 % of total) demonstrated that baseline Cn predicted subsequent adverse outcome even after adjusting for classic measures of hemodynamic MS severity (hazard ratio [HR] 0.33, 95% confidence interval [CI] 0.14–0.79, p = 0.013). Conclusions Cn contributes to pulmonary hypertension beyond of stenosis severity itself. In a wide spectrum of MS severity, Cn is a powerful predictor of adverse outcome, adding prognostic value to clinical data and mitral valve area. Importantly, baseline Cn predicts a progressive course with subsequent need for intervention in initially asymptomatic patients. Cn assessment therefore has potential value for clinical risk stratification and monitoring in MS patients. PMID:24097419

Discovery and Identification of Dimethylsilanediol as a Contaminant in ISS Potable Water

NASA Technical Reports Server (NTRS)

Rutz, Jeffrey A.; Schultz, John R.; Kuo, C. Mike; Curtis, Matthew; Jones, Patrick R.; Sparkman, O. David; McCoy, J. Torin

2011-01-01

In September 2010, analysis of ISS potable water samples was undertaken to determine the contaminant(s) responsible for a rise of total organic carbon (TOC) in the Water Processor Assembly (WPA) product water. As analysis of the routine target list of organic compounds did not reveal the contaminant, efforts to look for unknown compounds were initiated, resulting in discovery of an unknown peak in the gas chromatography/mass spectrometry (GC/MS) analysis for glycols. A mass spectrum of the contaminant was then generated by concentrating one of the samples and analyzing it by GC/MS in full-scan mode. Although a computer match of the compound identity could not be obtained with the instrument database, a search with a more up-to-date mass spectral library yielded a good match with dimethylsilanediol (DMSD). Inductively coupled plasma/mass spectrometry (ICP/MS) analyses showed abnormally high silicon levels in the samples, confirming that the unknown compound(s) contained silicon. DMSD was then synthesized to confirm the identification and provide a standard to develop a calibration curve. Further confirmation was provided by external direct analysis in real time time of flight (DART TOF) mass spectrometry. To routinely test for DMSD in the future, a quantitative method was needed. A preliminary GC/MS method was developed and archived samples from various locations on ISS were analyzed to determine the extent of the contamination and provide data for troubleshooting. This paper describes these events in more detail as well as problems encountered in routine GC/MS analyses and the subsequent development of high performance liquid chromatography and LC/MS/MS methods for measuring DMSD.

Analytical procedure for the determination of very volatile organic compounds (C3-C6) in indoor air.

PubMed

Schieweck, Alexandra; Gunschera, Jan; Varol, Deniz; Salthammer, Tunga

2018-05-01

The substance group of very volatile organic compounds (VVOCs) is moving into the focus of indoor air analysis, facing ongoing regulations at international and European levels targeting on indoor air quality and human health. However, there exists at present no validated analysis for the identification and quantification of VVOCs in indoor air. Therefore, the present study targeted on the development of an analytical method in order to sample the maximum possible quantity of VVOCs in indoor air on solid sorbents with subsequent analysis by thermal desorption and coupled gas chromatography/mass spectrometry (TDS-GC/MS). For this purpose, it was necessary to investigate the performance of available sorbents and to optimize the parameters of GC/MS analysis. Stainless steel tubes filled with Carbograph 5TD were applied successfully for low-volume sampling (2-4 l) with minimal breakthrough (< 1%). With the developed method, VVOCs between C 3 and C 6 of different volatility and polarity  can be detected even in trace quantities with low limits of quantitation (LOQ; 1-3 μg m -3 ). Limitations occur for low molecular weight compounds ≤C 3 , especially for polar substances, such as carboxylic acids and for some aldehydes and alcohols. Consequently, established methods for the quantification of these compounds in indoor air cannot be fully substituted yet. At least three different analytical techniques are needed to cover the large spectrum of relevant VVOCs in indoor air. In addition, unexpected reaction products might occur and need to be taken into account to avoid misinterpretation of chromatographic signals. Graphical abstract Solid sorbent sampling of VVOCs (C 3 -C 6 ) in indoor air with subsequent TDS-GC/MS analysis.

Discrimination of honeys using colorimetric sensor arrays, sensory analysis and gas chromatography techniques.

PubMed

Tahir, Haroon Elrasheid; Xiaobo, Zou; Xiaowei, Huang; Jiyong, Shi; Mariod, Abdalbasit Adam

2016-09-01

Aroma profiles of six honey varieties of different botanical origins were investigated using colorimetric sensor array, gas chromatography-mass spectrometry (GC-MS) and descriptive sensory analysis. Fifty-eight aroma compounds were identified, including 2 norisoprenoids, 5 hydrocarbons, 4 terpenes, 6 phenols, 7 ketones, 9 acids, 12 aldehydes and 13 alcohols. Twenty abundant or active compounds were chosen as key compounds to characterize honey aroma. Discrimination of the honeys was subsequently implemented using multivariate analysis, including hierarchical clustering analysis (HCA) and principal component analysis (PCA). Honeys of the same botanical origin were grouped together in the PCA score plot and HCA dendrogram. SPME-GC/MS and colorimetric sensor array were able to discriminate the honeys effectively with the advantages of being rapid, simple and low-cost. Moreover, partial least squares regression (PLSR) was applied to indicate the relationship between sensory descriptors and aroma compounds. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evaluation of two-dimensional electrophoresis and liquid chromatography – tandem mass spectrometry for tissue-specific protein profiling of laser-microdissected plant samples

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

Schad, Martina; Lipton, Mary S.; Giavalisco, Patrick

2005-07-14

Laser microdissection (LM) allows the collection of homogeneous tissue- and cell specific plant samples. The employment of this technique with subsequent protein analysis has thus far not been reported for plant tissues, probably due to the difficulties associated with defining a reasonable cellular morphology and, in parallel, allowing efficient protein extraction from tissue samples. The relatively large sample amount needed for successful proteome analysis is an additional issue that complicates protein profiling on a tissue- or even cell-specific level. In contrast to transcript profiling that can be performed from very small sample amounts due to efficient amplification strategies, there ismore » as yet no amplification procedure for proteins available. In the current study, we compared different tissue preparation techniques prior to LM/laser pressure catapulting (LMPC) with respect to their suitability for protein retrieval. Cryosectioning was identified as the best compromise between tissue morphology and effective protein extraction. After collection of vascular bundles from Arabidopsis thaliana stem tissue by LMPC, proteins were extracted and subjected to protein analysis, either by classical two-dimensional gel electrophoresis (2-DE), or by high-efficiency liquid chromatography (LC) in conjunction with tandem mass spectrometry (MS/MS). Our results demonstrate that both methods can be used with LMPC collected plant material. But because of the significantly lower sample amount required for LC-MS/MS than for 2-DE, the combination of LMPC and LC-MS/MS has a higher potential to promote comprehensive proteome analysis of specific plant tissues.« less

Evaluation of a multiresidue method for measuring fourteen chemical groups of pesticides in water by use of LC-MS-MS.

PubMed

Carvalho, J J; Jerónimo, P C A; Gonçalves, C; Alpendurada, M F

2008-11-01

European Council Directive 98/83/EC on the quality of water intended for human consumption brought a new challenge for water-quality control routine laboratories, mainly on pesticides analysis. Under the guidelines of ISO/IEC 17025:2005, a multiresidue method was developed, validated, implemented in routine, and studied with real samples during a one-year period. The proposed method enables routine laboratories to handle a large number of samples, since 28 pesticides of 14 different chemical groups can be quantitated in a single procedure. The method comprises a solid-phase extraction step and subsequent analysis by liquid chromatography-mass spectrometry (LC-MS-MS). The accuracy was established on the basis of participation in interlaboratory proficiency tests, with encouraging results (majority |z-score| <2), and the precision was consistently analysed over one year. The limits of quantitation (below 0.050 microg L(-1)) are in agreement with the enforced threshold value for pesticides of 0.10 microg L(-1). Overall method performance is suitable for routine use according to accreditation rules, taking into account the data collected over one year.

New Trends in Pesticide Residue Analysis in Cereals, Nutraceuticals, Baby Foods, and Related Processed Consumer Products.

PubMed

Raina-Fulton, Renata

2015-01-01

Pesticide residue methods have been developed for a wide variety of food products including cereal-based foods, nutraceuticals and related plant products, and baby foods. These cereal, fruit, vegetable, and plant-based products provide the basis for many processed consumer products. For cereal and nutraceuticals, which are dry sample products, a modified QuEChERS (quick, easy, cheap, effective, rugged, and safe) method has been used with additional steps to allow wetting of the dry sample matrix and subsequent cleanup using dispersive or cartridge format SPE to reduce matrix effects. More processed foods may have lower pesticide concentrations but higher co-extracts that can lead to signal suppression or enhancement with MS detection. For complex matrixes, GC/MS/MS or LC/electrospray ionization (positive or negative ion)-MS/MS is more frequently used. The extraction and cleanup methods vary with different sample types particularly for cereal-based products, and these different approaches are discussed in this review. General instrument considerations are also discussed.

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

Tao Xia; Liu Bing; Hou Qian

A new route for the economic and efficient treatment of azo dye pollutants is reported, in which surface-modified organic-inorganic hybrid mesoporous silica (MS) spheres were chosen as microreactors for the accumulation and subsequent photodegradation of pollutants in defined regions. The surface-modified silica materials were prepared by anchoring the polycationic species such as poly(allylamine hydrochloride) on MS spheres via a simple wet impregnation method. The as-synthesized spheres with well-defined porous structures exhibited 15 times of accumulating capacity for orange II and Congo red compared to that of the pure MS spheres. Diffuse reflectance UV-vis spectroscopy and confocal laser scanning microscopy demonstratedmore » that the accumulated orange II and CR in defined MS spheres were rapidly degraded in the presence of Fenton reagent under visible radiation. Kinetics analysis in recycling degradation showed that the as-synthesized materials might be utilized as environment-friendly preconcentrators/microreactors for the remediation of dye wastewater.« less

Detection and quantification of cocaine and benzoylecgonine in meconium using solid phase extraction and UPLC/MS/MS.

PubMed

Gunn, Josh; Kriger, Scott; Terrell, Andrea R

2010-01-01

The simultaneous determination and quantification of cocaine and its major metabolite, benzoylecgonine, in meconium using UPLC-MS/MS is described. Ultra-performance liquid chromatography (UPLC) is an emerging analytical technique which draws upon the principles of chromatography to run separations at higher flow rates for increased speed, while simultaneously achieving superior resolution and sensitivity. Extraction of cocaine and benzoylecgonine from the homogenized meconium matrix was achieved with a preliminary protein precipitation or protein 'crash' employing cold acetonitrile, followed by a mixed mode solid phase extraction (SPE). Following elution from the SPE cartridge, eluents were dried down under nitrogen, reconstituted in 200 microL of DI water:acetonitrile (ACN) (75:25), and injected onto the UPLC/MS/MS for analysis. The increased speed and separation efficiency afforded by UPLC, allowed for the separation and subsequent quantification of both analytes in less than 2 min. Analytes were quantified using multiple reaction monitoring (MRM) and six-point calibration curves constructed in negative blood. Limits of detection for both analytes were 3 ng/g and the lower limit of quantitation (LLOQ) was 30 ng/g.

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.

Mass spectrometric analysis of O-linked oligosaccharides from various recombinant expression systems.

PubMed

Kenny, Diarmuid T; Gaunitz, Stefan; Hayes, Catherine A; Gustafsson, Anki; Sjöblom, Magnus; Holgersson, Jan; Karlsson, Niclas G

2013-01-01

Analysis of O-linked glycosylation is one of the main challenges during structural validation of recombinant glycoproteins. With methods available for N-linked glycosylation in regard to oligosaccharide analysis as well as glycopeptide mapping, there are still challenges for O-linked glycan analysis. Here, we present mass spectrometric methodology for O-linked oligosaccharides released by reductive β-elimination. Using LC-MS and LC-MS(2) with graphitized carbon columns, oligosaccharides are analyzed without derivatization. This approach provides a high-throughput method for screening during clonal selection, as well as product structure verification, without impairing sequencing ability. The protocols are exemplified by analysis of glycoproteins from mammalian cell cultures (CHO cells) as well as insect cells and yeast. The data shows that the method can be successfully applied to both neutral and acidic O-linked oligosaccharides, where sialic acid, hexuronic acid, and sulfate are common substituents. Further characterization of O-glycans can be achieved using permethylation. Permethylation of O-linked oligosaccharides followed by direct infusion into the mass spectrometer provide information about oligosaccharide composition, and subsequent MS (n) experiments can be carried out to elucidate oligosaccharide structure including linkage information and sequence.

Automated protein identification by the combination of MALDI MS and MS/MS spectra from different instruments.

PubMed

Levander, Fredrik; James, Peter

2005-01-01

The identification of proteins separated on two-dimensional gels is most commonly performed by trypsin digestion and subsequent matrix-assisted laser desorption ionization (MALDI) with time-of-flight (TOF). Recently, atmospheric pressure (AP) MALDI coupled to an ion trap (IT) has emerged as a convenient method to obtain tandem mass spectra (MS/MS) from samples on MALDI target plates. In the present work, we investigated the feasibility of using the two methodologies in line as a standard method for protein identification. In this setup, the high mass accuracy MALDI-TOF spectra are used to calibrate the peptide precursor masses in the lower mass accuracy AP-MALDI-IT MS/MS spectra. Several software tools were developed to automate the analysis process. Two sets of MALDI samples, consisting of 142 and 421 gel spots, respectively, were analyzed in a highly automated manner. In the first set, the protein identification rate increased from 61% for MALDI-TOF only to 85% for MALDI-TOF combined with AP-MALDI-IT. In the second data set the increase in protein identification rate was from 44% to 58%. AP-MALDI-IT MS/MS spectra were in general less effective than the MALDI-TOF spectra for protein identification, but the combination of the two methods clearly enhanced the confidence in protein identification.

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

Rodriguez, Mark A.; Coker, Eric Nicholas; Griego, James J. M.

High-temperature X-ray diffraction with concurrent gas chromatography (GC) was used to study cobalt disulfide cathode pellets disassembled from thermal batteries. When CoS 2 cathode materials were analyzed in an air environment, oxidation of the K(Br, Cl) salt phase in the cathode led to the formation of K 2SO 4 that subsequently reacted with the pyrite-type CoS 2 phase leading to cathode decomposition between ~260 and 450 °C. Here, independent thermal analysis experiments, i.e. simultaneous thermogravimetric analysis/differential scanning calorimetry/mass spectrometry (MS), augmented the diffraction results and support the overall picture of CoS 2 decomposition. Both gas analysis measurements (i.e. GC andmore » MS) from the independent experiments confirmed the formation of SO 2 off-gas species during breakdown of the CoS 2. In contrast, characterization of the same cathode material under inert conditions showed the presence of CoS 2 throughout the entire temperature range of analysis.« less

Magnetic particles as powerful purification tool for high sensitive mass spectrometric screening procedures.

PubMed

Peter, Jochen F; Otto, Angela M

2010-02-01

The effective isolation and purification of proteins from biological fluids is the most crucial step for a successful protein analysis when only minute amounts are available. While conventional purification methods such as dialysis, ultrafiltration or protein precipitation often lead to a marked loss of protein, SPE with small-sized particles is a powerful alternative. The implementation of particles with superparamagnetic cores facilitates the handling of those particles and allows the application of particles in the nanometer to low micrometer range. Due to the small diameters, magnetic particles are advantageous for increasing sensitivity when using subsequent MS analysis or gel electrophoresis. In the last years, different types of magnetic particles were developed for specific protein purification purposes followed by analysis or screening procedures using MS or SDS gel electrophoresis. In this review, the use of magnetic particles for different applications, such as, the extraction and analysis of DNA/RNA, peptides and proteins, is described.

Use of phenyl/tetrazolyl-functionalized magnetic microspheres and stable isotope labeled internal standards for significant reduction of matrix effect in determination of nine fluoroquinolones by liquid chromatography-quadrupole linear ion trap mass spectrometry.

PubMed

Xu, Fei; Liu, Feng; Wang, Chaozhan; Wei, Yinmao

2018-02-01

In this study, the strategy of unique adsorbent combined with isotope labeled internal standards was used to significantly reduce the matrix effect for the enrichment and analysis of nine fluoroquinolones in a complex sample by liquid chromatography coupled to quadrupole linear ion trap mass spectrometry (LC-QqQ LIT -MS/MS). The adsorbent was prepared conveniently by functionalizing Fe 3 O 4 @SiO 2 microspheres with phenyl and tetrazolyl groups, which could adsorb fluoroquinolones selectively via hydrophobic, electrostatic, and π-π interactions. The established magnetic solid-phase extraction (MSPE) method as well as using stable isotope labeled internal standards in the next MS/MS detection was able to reduce the matrix effect significantly. In the process of LC-QqQ LIT -MS/MS analysis, the precursor and product ions of the analytes were monitored quantitatively and qualitatively on a QTrap system equipped simultaneously with the multiple reaction monitoring (MRM) and enhanced product ion (EPI) scan. Subsequently, the enrichment method combined with LC-QqQ LIT -MS/MS demonstrated good analytical features in terms of linearity (7.5-100.0 ng mL -1 , r > 0.9960), satisfactory recoveries (88.6%-118.3%) with RSDs < 12.0%, LODs = 0.5 μg kg -1 and LOQs = 1.5 μg kg -1 for all tested analytes. Finally, the developed MSPE-LC-QqQ LIT -MS/MS method had been successfully applied to real pork samples for food-safety risk monitoring in Ningxia Province, China. Graphical abstract Mechanism of reducing matrix effect through the as-prepared adsorbent.

Role of carbon nano-materials in the analysis of biological materials by laser desorption/ionization-mass spectrometry.

PubMed

Najam-ul-Haq, M; Rainer, M; Szabó, Z; Vallant, R; Huck, C W; Bonn, G K

2007-03-10

At present, carbon nano-materials are being utilized in various procedures, especially in laser desorption/ionization-mass spectrometry (LDI-MS) for analyzing a range of analytes, which include peptides, proteins, metabolites, and polymers. Matrix-oriented LDI-MS techniques are very well established, with weak organic acids as energy-absorbing substances. Carbon materials, such as nano-tubes and fullerenes are being successfully applied in the small-mass range, where routine matrices have strong background signals. In addition, the role of carbon nano-materials is very well established in the fractionation and purification fields. Modified diamond powder and surfaces are utilized in binding peptides and proteins from complex biological fluids and analyzed by matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS). Polylysine-coated diamond is used for solid-phase extraction to pre-concentrate DNA oligonucleotides. Graphite is useful for desalting, pre-concentration, and as energy-absorbing material (matrix) in desorption/ionization. Carbon nano-tubes in their different derivatized forms are used as matrix materials for the analysis of a range of analytes, such as carbohydrates, amino acids, peptides, proteins, and some environmental samples by LDI-MS. Fullerenes are modified in different ways to bind serum entities analyzed through MALDI/TOF-MS and are subsequently utilized in their identifications. In addition, the fullerenes are a promising matrix in LDI-MS, but improvements are needed.

Development and validation of LC-MS/MS assay for the simultaneous determination of methotrexate, 6-mercaptopurine and its active metabolite 6-thioguanine in plasma of children with acute lymphoblastic leukemia: Correlation with genetic polymorphism.

PubMed

Al-Ghobashy, Medhat A; Hassan, Said A; Abdelaziz, Doaa H; Elhosseiny, Noha M; Sabry, Nirmeen A; Attia, Ahmed S; El-Sayed, Manal H

2016-12-01

Individualized therapy is a recent approach aiming to specify dosage regimen for each patient according to its genetic state. Cancer chemotherapy requires continuous monitoring of the plasma concentration levels of active forms of cytotoxic drugs and subsequent dose adjustment. In order to attain optimum therapeutic efficacy, correlation to pharmacogenetics data is crucial. In this study, a specific, accurate and sensitive liquid chromatography tandem mass spectrometry (LC-MS/MS) has been developed for determination of methotrexate (MTX), 6-mercaptopurine (MP) and its metabolite 6-thioguanine nucleotide (TG) in human plasma. Based on the basic character of the studied compounds, solid phase extraction using a strong cation exchanger was found the optimum approach to achieve good extraction recovery. Chromatographic separation was carried out using RP-HPLC and isocratic elution by acetonitrile: 0.1% aqueous formic acid (85:15v/v) with a flow rate of 0.8mL/min at 40°C. The detection was performed by tandem mass spectrometry in MRM mode via electrospray ionization source in positive ionization mode. Analysis was carried out within 1.0min over a concentration range of 6.25-200.00ng/mL for the studied analytes. Validation was carried out according to FDA guidelines for bioanalytical method validation and satisfactory results were obtained. The applicability of the assay for the monitoring of the MTX, MP and TG and subsequent application to personalized therapy was demonstrated in a clinical study on children with acute lymphoblastic leukemia (ALL). Results confirmed the need for implementation of reliable analysis tools for therapeutic dose adjustment. Copyright © 2016 Elsevier B.V. All rights reserved.

Clinical guidance of community physiotherapists regarding people with MS: professional development and continuity of care.

PubMed

Normann, Britt; Sørgaard, Knut W; Salvesen, Rolf; Moe, Siri

2014-03-01

Clinical guidance to community physiotherapists (cPTs) is an integral part of physiotherapy service offered in hospital outpatient (OP) clinics for people with multiple sclerosis (PwMS). There is currently a lack of knowledge on the significance of such guidance. The aims of this study were 1) to identify the features that cPTs perceive to be significant in clinical guidance and 2) how this guidance may affect the cPTs' subsequent treatment of PwMS. A phenomenological-hermeneutical framework was selected, and qualitative research interviews were performed and complemented with non-participating observations of a strategic sample of nine cPTs who received clinical guidance for their patients. The interviews were recorded and transcribed, and content analysis was conducted by using systematic text condensation, using theories of practice knowledge as analytic perspectives. The results indicate that cPTs identify participation in authentic movement analysis of a familiar patient as significant for professional development. Vital features are evaluation of the interplay between body parts, exploration of improvement of movement embedded in the OP clinic physiotherapist's explanations, followed by discussion. These elements provide access to dynamic elements in practice knowledge that are available only through first-hand experience and promote clinical reasoning through enhanced reflection during action as well as following action. Such guidance suggests direction for subsequent treatment and may enhance the continuity of care, particularly if the cPTs are experienced. Mutual information flow implementing the cPTs' perspective is requested, as are the use of plain language and supervision of the cPTs handling skills. Professional guidance for cPTs in OP clinics for PwMS should be considered when programmes aiming to develop competency in neurological physiotherapy are designed and when continuity of care for PwMS is discussed. More research regarding potential long-term impact of professional guidance in these clinics is requested. Copyright © 2013 John Wiley & Sons, Ltd.

Simultaneous determination of thirteen different steroid hormones using micro UHPLC-MS/MS with on-line SPE system.

PubMed

Márta, Zoltán; Bobály, Balázs; Fekete, Jenő; Magda, Balázs; Imre, Tímea; Mészáros, Katalin Viola; Bálint, Mária; Szabó, Pál Tamás

2018-02-20

Ultratrace analysis of sample components requires excellent analytical performance in terms of limits of quantitation (LOQ). Micro UHPLC coupled to sensitive tandem mass spectrometry provides state of the art solution for such analytical problems. Using on-line SPE with column switching on a micro UHPLC-MS/MS system allowed to decrease LOQ without any complex sample preparation protocol. The presented method is capable of reaching satisfactory low LOQ values for analysis of thirteen different steroid molecules from human plasma without the most commonly used off-line SPE or compound derivatization. Steroids were determined by using two simple sample preparation methods, based on lower and higher plasma steroid concentrations. In the first method, higher analyte concentrations were directly determined after protein precipitation with methanol. The organic phase obtained from the precipitation was diluted with water and directly injected into the LC-MS system. In the second method, low steroid levels were determined by concentrating the organic phase after steroid extraction. In this case, analytes were extracted with ethyl acetate and reconstituted in 90/10 water/acetonitrile following evaporation to dryness. This step provided much lower LOQs, outperforming previously published values. The method has been validated and subsequently applied to clinical laboratory measurement. Copyright © 2017 Elsevier B.V. All rights reserved.

Improved approach for routine monitoring of 129I activity and 129I/127I atom ratio in environmental samples using TMAH extraction and ICP-MS/MS.

PubMed

Yang, Guosheng; Tazoe, Hirofumi; Yamada, Masatoshi

2018-05-30

To reconstruct 131 I deposition and identify the source of radioiodine due to the Fukushima Daiichi Nuclear Power Plant (FDNPP) accident, 129 I activity and 129 I/ 127 I atom ratio should be obtained by preparing and analyzing large numbers of samples economically. In this study, great efforts were made to realize mild TMAH (tetramethyl ammonium hydroxide) extraction of environmental samples at 90 °C to obtain solutions suitable for the following triple-quadrupole inductively coupled plasma-mass spectrometry (ICP-QQQ) MS/MS mode analysis. After releasing iodine from organic matter in the TMAH extraction solution via K 2 S 2 O 8 oxidation, organic matter was removed effectively by solvent extraction and back-extraction to avoid a serious matrix effect during ICP-QQQ analysis. At the same time, interfering elements, especially, Mo, Cd, and In were also removed effectively, to avoid their undesirable interferences during mass spectrometric analysis. In addition, 0.01% (NH 4 ) 2 SO 3 was selected to introduce I - into ICP-QQQ to ensure there was no memory effect and a stable signal was gotten. Subsequently, ICP-QQQ MS/MS mode was applied to further eliminate polyatomic interferences ( 127 I(H 2 and D) + , 97 MoO 2 + , 113 InO + , and 113 CdO + ) and isobaric interference from 129 Xe + . Finally, the developed method was successfully applied to measure 129 I/ 127 I atom ratios ((2.61-27.0) × 10 -7 ) and 129 I activities (3.51-11.4 mBq kg -1 ) in soil samples. The developed method allows a greater number of ordinary laboratories to participate in the field of radioiodine analysis. Copyright © 2018 Elsevier B.V. All rights reserved.

Simplifying sample pretreatment: application of dried blood spot (DBS) method to blood samples, including postmortem, for UHPLC-MS/MS analysis of drugs of abuse.

PubMed

Odoardi, Sara; Anzillotti, Luca; Strano-Rossi, Sabina

2014-10-01

The complexity of biological matrices, such as blood, requires the development of suitably selective and reliable sample pretreatment procedures prior to their instrumental analysis. A method has been developed for the analysis of drugs of abuse and their metabolites from different chemical classes (opiates, methadone, fentanyl and analogues, cocaine, amphetamines and amphetamine-like substances, ketamine, LSD) in human blood using dried blood spot (DBS) and subsequent UHPLC-MS/MS analysis. DBS extraction required only 100μL of sample, added with the internal standards and then three droplets (30μL each) of this solution were spotted on the card, let dry for 1h, punched and extracted with methanol with 0.1% of formic acid. The supernatant was evaporated and the residue was then reconstituted in 100μL of water with 0.1% of formic acid and injected in the UHPLC-MS/MS system. The method was validated considering the following parameters: LOD and LOQ, linearity, precision, accuracy, matrix effect and dilution integrity. LODs were 0.05-1ng/mL and LOQs were 0.2-2ng/mL. The method showed satisfactory linearity for all substances, with determination coefficients always higher than 0.99. Intra and inter day precision, accuracy, matrix effect and dilution integrity were acceptable for all the studied substances. The addition of internal standards before DBS extraction and the deposition of a fixed volume of blood on the filter cards ensured the accurate quantification of the analytes. The validated method was then applied to authentic postmortem blood samples. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Profiling and Imaging Ion Mobility-Mass Spectrometry Analysis of Cholesterol and 7-Dehydrocholesterol in Cells Via Sputtered Silver MALDI

PubMed Central

Xu, Libin; Kliman, Michal; Forsythe, Jay G.; Korade, Zeljka; Hmelo, Anthony B.; Porter, Ned A.; McLean, John A.

2015-01-01

Profiling and imaging of cholesterol and its precursors by mass spectrometry (MS) are important in a number of cholesterol biosynthesis disorders, such as in Smith-Lemli-Opitz syndrome (SLOS), where 7-dehydrocholesterol (7-DHC) is accumulated in affected individuals. SLOS is caused by defects in the enzyme that reduces 7-DHC to cholesterol. However, analysis of sterols is challenging because these hydrophobic olefins are difficult to ionize for MS detection. We report here sputtered silver matrix-assisted laser desorption/ionization (MALDI)-ion mobility-MS (IM-MS) analysis of cholesterol and 7-DHC. In comparison with liquid-based AgNO3 and colloidal Ag nanoparticle (AgNP), sputtered silver NP (10–25 nm) provided the lowest limits-of-detection based on the silver coordinated [cholesterol+Ag]+ and [7-DHC+Ag]+ signals while minimizing dehydrogenation products ([M+Ag-2H]+). When analyzing human fibroblasts that were directly grown on poly-L-lysine-coated ITO glass plates with this technique, in situ, the 7-DHC/cholesterol ratios for both control and SLOS human fibroblasts are readily obtained. The m/z of 491 (specific for [7-DHC+107Ag]+) and 495 (specific for [cholesterol+109Ag]+) were subsequently imaged using MALDI-IM-MS. MS images were co-registered with optical images of the cells for metabolic ratio determination. From these comparisons, ratios of 7-DHC/cholesterol for SLOS human fibroblasts are distinctly higher than in control human fibroblasts. Thus, this strategy demonstrates the utility for diagnosing/assaying the severity of cholesterol biosynthesis disorders in vitro. PMID:25822928

Profiling and Imaging Ion Mobility-Mass Spectrometry Analysis of Cholesterol and 7-Dehydrocholesterol in Cells Via Sputtered Silver MALDI

NASA Astrophysics Data System (ADS)

Xu, Libin; Kliman, Michal; Forsythe, Jay G.; Korade, Zeljka; Hmelo, Anthony B.; Porter, Ned A.; McLean, John A.

2015-06-01

Profiling and imaging of cholesterol and its precursors by mass spectrometry (MS) are important in a number of cholesterol biosynthesis disorders, such as in Smith-Lemli-Opitz syndrome (SLOS), where 7-dehydrocholesterol (7-DHC) is accumulated in affected individuals. SLOS is caused by defects in the enzyme that reduces 7-DHC to cholesterol. However, analysis of sterols is challenging because these hydrophobic olefins are difficult to ionize for MS detection. We report here sputtered silver matrix-assisted laser desorption/ionization (MALDI)-ion mobility-MS (IM-MS) analysis of cholesterol and 7-DHC. In comparison with liquid-based AgNO3 and colloidal Ag nanoparticle (AgNP), sputtered silver NP (10-25 nm) provided the lowest limits-of-detection based on the silver coordinated [cholesterol + Ag]+ and [7-DHC + Ag]+ signals while minimizing dehydrogenation products ([M + Ag-2H]+). When analyzing human fibroblasts that were directly grown on poly-L-lysine-coated ITO glass plates with this technique, in situ, the 7-DHC/cholesterol ratios for both control and SLOS human fibroblasts are readily obtained. The m/z of 491 (specific for [7-DHC + 107Ag]+) and 495 (specific for [cholesterol + 109Ag]+) were subsequently imaged using MALDI-IM-MS. MS images were co-registered with optical images of the cells for metabolic ratio determination. From these comparisons, ratios of 7-DHC/cholesterol for SLOS human fibroblasts are distinctly higher than in control human fibroblasts. Thus, this strategy demonstrates the utility for diagnosing/assaying the severity of cholesterol biosynthesis disorders in vitro.

Smoking and multiple sclerosis: A systematic review and meta-analysis using the Bradford Hill criteria for causation.

PubMed

Degelman, Michelle L; Herman, Katya M

2017-10-01

Despite being one of the most common neurological disorders globally, the cause(s) of multiple sclerosis (MS) remain unknown. Cigarette smoking has been studied with regards to both the development and progression of MS. The Bradford Hill criteria for causation can contribute to a more comprehensive evaluation of a potentially causal risk factor-disease outcome relationship. The objective of this systematic review and meta-analysis was to assess the relationship between smoking and both MS risk and MS progression, subsequently applying Hill's criteria to further evaluate the likelihood of causal associations. The Medline, EMBASE, CINAHL, PsycInfo, and Cochrane Library databases were searched for relevant studies up until July 28, 2015. A random-effects meta-analysis was conducted for three outcomes: MS risk, conversion from clinically isolated syndrome (CIS) to clinically definite multiple sclerosis (CDMS), and progression from relapsing-remitting multiple sclerosis (RRMS) to secondary-progressive multiple sclerosis (SPMS). Dose-response relationships and risk factor interactions, and discussions of mechanisms and analogous associations were noted. Hill's criteria were applied to assess causality of the relationships between smoking and each outcome. The effect of second-hand smoke exposure was also briefly reviewed. Smoking had a statistically significant association with both MS risk (conservative: OR/RR 1.54, 95% CI [1.46-1.63]) and SPMS risk (HR 1.80, 95% CI [1.04-3.10]), but the association with progression from CIS to CDMS was non-significant (HR 1.13, 95% CI [0.73-1.76]). Using Hill's criteria, there was strong evidence of a causal role of smoking in MS risk, but only moderate evidence of a causal association between smoking and MS progression. Heterogeneity in study designs and target populations, inconsistent results, and an overall scarcity of studies point to the need for more research on second-hand smoke exposure in relation to MS prior to conducting a detailed meta-analysis. This first review to supplement systematic review and meta-analytic methods with Hill's criteria to analyze the smoking-MS association provides evidence supporting the causal involvement of smoking in the development and progression of MS. Smoking prevention and cessation programs and policies should consider MS as an additional health risk when aiming to reduce smoking prevalence in the population. Copyright © 2017 Elsevier B.V. All rights reserved.

Application of the MIDAS approach for analysis of lysine acetylation sites.

PubMed

Evans, Caroline A; Griffiths, John R; Unwin, Richard D; Whetton, Anthony D; Corfe, Bernard M

2013-01-01

Multiple Reaction Monitoring Initiated Detection and Sequencing (MIDAS™) is a mass spectrometry-based technique for the detection and characterization of specific post-translational modifications (Unwin et al. 4:1134-1144, 2005), for example acetylated lysine residues (Griffiths et al. 18:1423-1428, 2007). The MIDAS™ technique has application for discovery and analysis of acetylation sites. It is a hypothesis-driven approach that requires a priori knowledge of the primary sequence of the target protein and a proteolytic digest of this protein. MIDAS essentially performs a targeted search for the presence of modified, for example acetylated, peptides. The detection is based on the combination of the predicted molecular weight (measured as mass-charge ratio) of the acetylated proteolytic peptide and a diagnostic fragment (product ion of m/z 126.1), which is generated by specific fragmentation of acetylated peptides during collision induced dissociation performed in tandem mass spectrometry (MS) analysis. Sequence information is subsequently obtained which enables acetylation site assignment. The technique of MIDAS was later trademarked by ABSciex for targeted protein analysis where an MRM scan is combined with full MS/MS product ion scan to enable sequence confirmation.

Analytical Methodologies for Detection of Gamma-Valerolactone, Delta-Valerolactone, Acephate and Azinphos Methyl and Their Associated Metabolites in Complex Biological Matrices

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

Zink, E.; Clark, R.; Grant, K.

2005-01-01

Non-invasive biomonitoring for chemicals of interest in law enforcement and similar monitoring of pesticides, together with their metabolites, can not only save money but can lead to faster medical attention for individuals exposed to these chemicals. This study describes methods developed for the analysis of gamma-valerolactone (GVL), delta-valerolactone (DVL), acephate, and azinphos methyl in saliva and serum. Liquid chromatography/mass spectrometry (LC/MS) operated in the negative and positive ion mode and gas chromatography/mass spectrometry (GC/MS) were used to analyze GVL and DVL. Although both analytical techniques worked well, lower detection limits were obtained with GC/MS. The lactones and their corresponding sodiummore » salts were spiked into both saliva and serum. The lactones were isolated from saliva or serum using newly developed extraction techniques and then subsequently analyzed using GC/MS. The sodium salts of the lactones are nonvolatile and require derivatization prior to analysis by this method. N-methyl-N-(t-butyldimethylsilyl)-trifluoroacetamide (MTBSTFA) was ultimately selected as the reagent for derivatization because the acidic conditions required for reactions with diazomethane caused the salts to undergo intramolecular cyclization to the corresponding lactones. In vitro studies were conducted using rat liver microsomes to determine other metabolites associated with these compounds. Azinphos methyl and acephate are classified as organophosphate pesticides, and are known to be cholinesterase inhibitors in humans and insects, causing neurotoxicity. For this reason they have both exposure and environmental impact implications. These compounds were spiked into serum and saliva and prepared for analysis by GC/MS. Continuation of this research would include analysis by GC/MS under positive ion mode to determine the parent ions of the unknown metabolites. Further research is planned through an in vivo analysis of the lactones and pesticides. These methodologies could be extended for further analysis of other similar compounds.« less

Analytical Methodologies for Detection of Gamma-valerolactone, Delta-valerolactone, Acephate, and Azinphos Methyl and their Associated Metabolites in Complex Biological Matrices

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

Zink, Erika M.; Clark, Ryan J.; Grant, Karen E.

2005-01-01

Non-invasive biomonitoring for chemicals of interest in law enforcement and similar monitoring of pesticides together with their metabolites can not only save money but can lead to faster medical attention for individuals exposed to these chemicals. This study describes methods developed for the analysis of gamma-valerolactone (GVL), delta-valerolactone (DVL), acephate, and azinphos methyl in saliva and serum. Liquid chromatography/mass spectrometry (LC/MS) operated in the negative ion mode and in the positive ion mode and gas chromatography/mass spectrometry (GC/MS) were used to analyze GVL and DVL. Although both analytical techniques worked well, lower detection limits were obtained with GC/MS. The lactonesmore » and their corresponding sodium salts were spiked into both saliva and serum. The lactones were isolated from saliva or serum using newly developed extraction techniques and then subsequently analyzed using GC/MS. The sodium salts of the lactones are nonvolatile and require derivatization prior to analysis by this method. N-methyl-N-(t-butyldimethylsilyl)-trifluoroacetamide (MTBSTFA) was ultimately selected as the reagent for derivatization because the acidic conditions required for reactions with diazomethane caused the salts to undergo intramolecular cyclization to the corresponding lactones. In vitro studies were conducted using rat liver microsomes to determine other metabolites associated with these compounds. Azinphos methyl and acephate are classified as organophosphate pesticides, and are known to be cholinesterase inhibitors in humans and insects, causing neurotoxicity. For this reason they have both exposure and environmental impact implications. These compounds were spiked into serum and saliva and prepared for analysis by GC/MS. Continuation of this research would include analysis by GC/MS under positive ion mode to determine the parent ions of the unknown metabolites. Further research is planned through an in vivo analysis of the lactones and pesticides. These methodologies could be extended for further analysis of other similar compounds as well as chemical and biological warfare agents.« less

Liquid microjunction surface sampling coupled with high-pressure liquid chromatography-electrospray ionization-mass spectrometry for analysis of drugs and metabolites in whole-body thin tissue sections.

PubMed

Kertesz, Vilmos; Van Berkel, Gary J

2010-07-15

In this work, a commercially available autosampler was adapted to perform direct liquid microjunction (LMJ) surface sampling followed by a high-pressure liquid chromatography (HPLC) separation of the extract components and detection with electrospray ionization mass spectrometry (ESI-MS). To illustrate the utility of coupling a separation with this direct liquid extraction based surface sampling approach, four different organs (brain, lung, kidney, and liver) from whole-body thin tissue sections of propranolol dosed and control mice were examined. The parent drug was observed in the chromatograms of the surface sampling extracts from all the organs of the dosed mouse examined. In addition, two isomeric phase II metabolites of propranolol (an aliphatic and an aromatic hydroxypropranolol glucuronide) were observed in the chromatograms of the extracts from lung, kidney, and liver. Confirming the presence of one or the other or both of these glucuronides in the extract from the various organs was not possible without the separation. These drug and metabolite data obtained using the LMJ surface sampling/HPLC-MS method and the results achieved by analyzing similar samples by conventional extraction of the tissues and subsequent HPLC-MS analysis were consistent. The ability to directly and efficiently sample from thin tissue sections via a liquid extraction and then perform a subsequent liquid phase separation increases the utility of this liquid extraction surface sampling approach.

Teaching Experimental Design Using a GC MS Analysis of Cocaine on Money: A Cross-Disciplinary Laboratory 1254 Christopher A. Heimbuck and Nathan W. Bower Quantitative Determination of Nicotine and Cotinine in Urine and Sputum Using a Combined SPME-GC/MS Method

NASA Astrophysics Data System (ADS)

Witter, A. E.; Klinger, D. M.; Fan, X.; Lam, M.; Mathers, D. T.; Mabury, S. A.

2002-10-01

The forensic analysis of cocaine on currencies was optimized using a fractional, two-level experimental design that compared methanol and HCl extraction, SPE versus heptane pre-concentration, and extracted versus total ion chromatography. Subsequent student-initiated questions about levels of cocaine on U.S. and world currencies helped make connections to societal issues while teaching method optimization and chromatography. A significant correlation was found between the levels of cocaine and the age of the bills. Levels of cocaine on various world currencies followed expected drug-trafficking patterns with the highest levels found in the most developed countries.

Rapid Analysis of the Size Distribution of Metal-Containing Aerosol

PubMed Central

Park, Jae Hong; Mudunkotuwa, Imali A.; Crawford, Kathryn J.; Anthony, T. Renée; Grassian, Vicki H.; Peters, Thomas M.

2017-01-01

Conventional methods to measure the metallic content of particles by size are time consuming and expensive, requiring collection of particles with a cascade impactor and subsequent metals analysis by inductively coupled plasma mass spectrometry (ICP-MS). In this work, we describe a rapid way to measure the size distribution of metal-containing particles from 10 nm to 20 μm, using a nano micro-orifice uniform-deposit impactor (nano-MOUDI) to size-selective and collect particles that are then analyzed with a field portable X-ray fluorescence (FP-XRF) to determine metal composition and concentration. The nano-MOUDI was used to sample a stainless-steel aerosol produced by a spark discharge system. The particle-laden substrates were then analyzed directly with FP-XRF and then with ICP-MS. Results from FP-XRF were linearly correlated with results from ICP-MS (R2 = 0.91 for Fe and R2 = 0.84 for Cr). Although the FP-XRF was unable to detect Fe particles at mass per substrate loadings less than 2.5 μg effectively, it produced results similar to those using the ICP-MS at a mass per substrate loading greater than 2.5 μg. PMID:28871214

Petroleomic Analysis of Bio- Oils from the Fast Pyrolysis or Biomass: Laser Desorption Ionization-Linear Ion Trap-Orbitrap mass Spectrometry Approach

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

Smith, Erica A.; Lee, Young Jin

2010-08-23

Fast pyrolysis of biomass produces bio-oils that can be upgraded into biofuels. Despite similar physical properties to petroleum, the chemical properties of bio-oils are quite different and their chemical compositions, particularly those of non-volatile compounds, are not well-known. Here, we report the first time attempt at analyzing bio-oils using high-resolution mass spectrometry (MS), which employed laser desorption ionization-linear ion trap-Orbitrap MS. Besides a few limitations, we could determine chemical compositions for over 100 molecular compounds in a bio-oil sample produced from the pyrolysis of a loblolly pine tree. These compounds consist of 3-6 oxygens and 9-17 double-bond equivalents (DBEs). Amongmore » those, O{sub 4} compounds with a DBE of 9-13 were most abundant. Unlike petroleum oils, the lack of nearby molecules within a {+-}2 Da mass window for major components enabled clear isolation of precursor ions for subsequent MS/MS structural investigations. Petroleomic analysis and a comparison to low-mass components in hydrolytic lignin suggest that they are dimers and trimers of depolymerized lignin.« less

Regio- and stereospecific analysis of glycerolipids.

PubMed

Kuksis, Arnis; Itabashi, Yutaka

2005-06-01

In recent years researchers have recognized the potential value of comprehensive lipid profiling (lipidomics), which was invented and promoted by lipidologists who recognized the many valuable applications that grew out of the fields of DNA profiling (genomics) and protein profiling (proteonomics). Through lipid class-selective intrasource ionization and subsequent analysis of two-dimensional cross-peak intensities, the chemical identity and mass composition of individual molecular species of most lipid classes can now be determined in a chloroform extract. There remains, however, the necessity to distinguish the enantiomers and isobaric regioisomers resulting from enzymatic and chemical reactions, which conventional high performance liquid chromatography/mass spectrometry (HPLC/MS) has been slow to accommodate, and tandem MS unable to provide. While reversed-phase HPLC can separate regioisomers, normal-phase HPLC can resolve diastereomers, and chiral-phase HPLC can effect dramatic resolution of enantiomers, the full potential of the combined systems has seldom been exploited. The present chapter calls attention to both recent and earlier combinations of these methodologies with mass spectrometry, which allows the HPLC/ESI (electrospray ionization)-MS/MS separation and identification of enantiomeric diacylglycerols, triacylglycerols, and glycerophospholipids as well as their isobaric regioisomers. These developments permit further expansion of lipid profiling (lipidomics) and better understanding of lipid metabolism.

Twoplex 12/13 C6 aniline stable isotope and linkage-specific sialic acid labeling 2D-LC-MS workflow for quantitative N-glycomics.

PubMed

Albrecht, Simone; Mittermayr, Stefan; Smith, Josh; Martín, Silvia Millán; Doherty, Margaret; Bones, Jonathan

2017-01-01

Quantitative glycomics represents an actively expanding research field ranging from the discovery of disease-associated glycan alterations to the quantitative characterization of N-glycans on therapeutic proteins. Commonly used analytical platforms for comparative relative quantitation of complex glycan samples include MALDI-TOF-MS or chromatographic glycan profiling with subsequent data alignment and statistical evaluation. Limitations of such approaches include run-to-run technical variation and the potential introduction of subjectivity during data processing. Here, we introduce an offline 2D LC-MS E workflow for the fractionation and relative quantitation of twoplex isotopically labeled N-linked oligosaccharides using neutral 12 C 6 and 13 C 6 aniline (Δmass = 6 Da). Additional linkage-specific derivatization of sialic acids using 4-(4,6-dimethoxy-1,3,5-trizain-2-yl)-4-methylmorpholinium chloride offered simultaneous and advanced in-depth structural characterization. The potential of the method was demonstrated for the differential analysis of structurally defined N-glycans released from serum proteins of patients diagnosed with various stages of colorectal cancer. The described twoplex 12 C 6 / 13 C 6 aniline 2D LC-MS platform is ideally suited for differential glycomic analysis of structurally complex N-glycan pools due to combination and analysis of samples in a single LC-MS injection and the associated minimization in technical variation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Small-scale enzymatic digestion of glycoproteins and proteoglycans for analysis of oligosaccharides by LC-MS and FACE gel electrophoresis.

PubMed

Estrella, Ruby P; Whitelock, John M; Roubin, Rebecca H; Packer, Nicolle H; Karlsson, Niclas G

2009-01-01

Structural characterization of oligosaccharides from proteoglycans and other glycoproteins is greatly enhanced through the use of mass spectrometry and gel electrophoresis. Sample preparation for these sensitive techniques often requires enzymatic treatments to produce oligosaccharide sequences for subsequent analysis. This chapter describes several small-scale methods for in-gel, on-blot, and in-solution enzymatic digestions in preparation for graphitized carbon liquid chromatography-mass spectrometry (LC-MS) analysis, with specific applications indicated for glycosaminoglycans (GAGs) and N-linked oligosaccharides. In addition, accompanying procedures for oligosaccharide reduction by sodium borohydride, sample desalting via carbon microcolumn, desialylation by sialidase enzyme treatment, and small-scale oligosaccharide species fractionation are included. Fluorophore-assisted carbohydrate electrophoresis (FACE) is another useful method to isolate derivatized oligosaccharides. Overall, the modularity of these techniques provides ease and flexibility for use in conjunction with mass spectrometric and electrophoretic tools for glycomic research studies.

Unstable simple volatiles and gas chromatography-tandem mass spectrometry analysis of essential oil from the roots bark of Oplopanax horridus extracted by supercritical fluid extraction.

PubMed

Shao, Li; Bao, Mei-Hua; Ouyang, Dong-Sheng; Wang, Chong-Zhi; Yuan, Chun-Su; Zhou, Hong-Hao; Huang, Wei-Hua

2014-11-27

Volatile oil from the root bark of Oplopanax horridus is regarded to be responsible for the clinical uses of the title plant as a respiratory stimulant and expectorant. Therefore, a supercritical fluid extraction method was first employed to extract the volatile oil from the roots bark of O. horridus, which was subsequently analyzed by GC/MS. Forty-eight volatile compounds were identified by GC/MS analysis, including (S,E)-nerolidol (52.5%), τ-cadinol (21.6%) and S-falcarinol (3.6%). Accordingly, the volatile oil (100 g) was subjected to chromatographic separation and purification. As a result, the three compounds, (E)-nerolidol (2 g), τ-cadinol (62 mg) and S-falcarinol (21 mg), were isolated and purified from the volatile oil, the structures of which were unambiguously elucidated by detailed spectroscopic analysis including 1D- and 2D-NMR techniques.

Analysis of yellow "fat" deposits on Inuit boots.

PubMed

Edwards, Howell G M; Stern, Ben; Burgio, Lucia; Kite, Marion

2009-08-01

Irregular residues of a yellow deposit that was assumed to be seal fat used for waterproofing were observed in the creases of the outer surface of a pair of Inuit boots from Arctic Canada. A sample of this deposit detached from one of these areas on these boots was examined initially by FT-Raman microscopy, from which interesting and rather surprising results demanded further analysis using FT-IR and GC-MS. The non-destructive Raman spectroscopic analysis yielded spectra which indicated the presence of a tree resin from the Pinaceae sp. The Raman spectra were also characteristic of a well-preserved keratotic protein and indicative of adherent skin. Subsequent FT-IR spectroscopic analysis supported the attribution of a Pinaceae resin to the yellow deposit. GC-MS analysis of the same deposits identified the presence of pimaric, sandaracopimaric, dehydroabietic and abietic acids, all indicative of an aged Pinaceae resin. These results confirmed that the Inuit people had access to tree resins which they probably used as a waterproofing agent.

Rapid analysis of the skin irritant p-phenylenediamine (PPD) in henna products using atmospheric solids analysis probe mass spectrometry.

PubMed

Chen, Weiyang; Nkosi, Thobile A N; Combrinck, Sandra; Viljoen, Alvaro M; Cartwright-Jones, Catherine

2016-09-05

Henna (Lawsonia inermis) is applied to stain keratin, present in hair, skin and fingernails, a red-orange or rust colour. Producers of temporary tattoos mix the aromatic amine compound, para-phenylenediamine (PPD) into natural henna to create 'black henna' that rapidly stains the skin black. However, PPD may cause severe delayed hypersensitivity reactions following skin contact. This study proposes a rapid direct-analysis method to detect and identify PPD using an atmospheric solids analysis probe (ASAP) coupled to a Q-ToF mass spectrometer (MS). Since laborious, multistep methods of analysis to determine PPD are undesirable, due to the instability of the compound in solution, a screening method involving no sample preparation steps was developed. Experiments were carried out to optimise the corona current, sample cone voltage, source temperature, and desolvation gas temperature to determine ideal ASAP-Q-ToF-MS analysing conditions. Eleven of the 109 henna samples, originating from various countries, tested positive for PPD when henna products were screened using ASAP-MS, without any form of sample preparation other than grinding. Ultra-performance liquid chromatography electrospray ionisation-mass spectrometry (UPLC-Q-ToF-MS) was subsequently used to confirm the results from ASAP and to determine the concentrations of PPD in henna products. The allergen was detected in the same eleven samples, with concentrations ranging from 0.05-4.21% (w/w). It can be concluded that the sensitivity of the ASAP-MS technique is sufficient (limit of detection=0.025% w/w) to allow screening of henna samples for the presence of PPD. This relatively new technique can be applied to commercial products without extraction, sample treatment or chromatographic separation. Copyright © 2016 Elsevier B.V. All rights reserved.

Synthesis and analytical follow-up of the mineralization of a new fluorosurfactant prototype.

PubMed

Peschka, M; Fichtner, N; Hierse, W; Kirsch, P; Montenegro, E; Seidel, M; Wilken, R D; Knepper, T P

2008-08-01

Fluorinated surfactants have become essential in numerous technical applications due to their unparalleled effectiveness and efficiency. The environmental persistence of the non-biodegradable perfluorinated alkyl moiety has become a matter of concern. Therefore, it was searched for new molecules with chemically stable fluorinated end groups which can be microbially transformed into labile fluorinated substances. One prototype substance, 10-(trifluoromethoxy)decane-1-sulfonate, has shown biomineralization. Monitoring the formation of metabolites over time elucidated the mechanism of biotransformation. Analysis was performed utilizing liquid chromatography-single quadrupole mass spectrometry (LC-MS) and quadrupole-time of flight tandem mass spectrometry (QqTOF-MS). It was possible to distinguish between two major degradation pathways of the fluorinated alkylsulfonate derivative: (i) a desulfonation and subsequent oxidation and degradation of the alkyl chain being predominant and (ii) an insertion of oxygen with a subsequent cleavage and degradation of the molecule. The utilized trifluoromethoxy-endgroup resulted in instable trifluoromethanol after degradation of the alkyl chain, which led to a high degree of mineralization of the molecule.

Optimization of Sample Preparation and Instrumental Parameters for the Rapid Analysis of Drugs of Abuse in Hair samples by MALDI-MS/MS Imaging

NASA Astrophysics Data System (ADS)

Flinders, Bryn; Beasley, Emma; Verlaan, Ricky M.; Cuypers, Eva; Francese, Simona; Bassindale, Tom; Clench, Malcolm R.; Heeren, Ron M. A.

2017-08-01

Matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) has been employed to rapidly screen longitudinally sectioned drug user hair samples for cocaine and its metabolites using continuous raster imaging. Optimization of the spatial resolution and raster speed were performed on intact cocaine contaminated hair samples. The optimized settings (100 × 150 μm at 0.24 mm/s) were subsequently used to examine longitudinally sectioned drug user hair samples. The MALDI-MS/MS images showed the distribution of the most abundant cocaine product ion at m/z 182. Using the optimized settings, multiple hair samples obtained from two users were analyzed in approximately 3 h: six times faster than the standard spot-to-spot acquisition method. Quantitation was achieved using longitudinally sectioned control hair samples sprayed with a cocaine dilution series. A multiple reaction monitoring (MRM) experiment was also performed using the `dynamic pixel' imaging method to screen for cocaine and a range of its metabolites, in order to differentiate between contaminated hairs and drug users. Cocaine, benzoylecgonine, and cocaethylene were detectable, in agreement with analyses carried out using the standard LC-MS/MS method. [Figure not available: see fulltext.

Infectious mononucleosis and multiple sclerosis - Updated review on associated risk.

PubMed

Sheik-Ali, Sharaf

2017-05-01

There has been substantial evidence accumulating on the role of infectious mononucleosis (IM) and the subsequent risk of obtaining Multiple Sclerosis (MS). Up to date studies not previously explored were reviewed by the author to further clarify the association. Medline and Web of Science were searched with no time constraints for articles exploring an association between Multiple Sclerosis and Infectious Mononucleosis. 24 articles were found, totalling 1063 cases and 13,227 cohort/controls. 23/24 (96%) articles reported a significant association of Infectious Mononucleosis on the risk of subsequent multiple sclerosis. Overall, new literature on IM and risk of MS categorically supports the association. Future work should focus on other risk factors such as age and gender on IM and subsequent risk of MS. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

A novel mice model of metabolic syndrome: the high-fat-high-fructose diet-fed ICR mice.

PubMed

Zhuhua, Zhang; Zhiquan, Wang; Zhen, Yang; Yixin, Niu; Weiwei, Zhang; Xiaoyong, Li; Yueming, Liu; Hongmei, Zhang; Li, Qin; Qing, Su

2015-01-01

Currently, the metabolic syndrome (MS) is occurring at growing rates worldwide, raising extensive concerns on the mechanisms and therapeutic interventions for this disorder. Herein, we described a novel method of establishing MS model in rodents. Male Institute of Cancer Research (ICR) mice were fed with high-fat-high-fructose (HFHF) diet or normal chow (NC) respectively for 12 weeks. Metabolic phenotypes were assessed by glucose tolerance test, insulin tolerance test and hyperinsulinemic-euglycemic clamp. Blood pressure was measured by a tail-cuff system. At the end of the experiment, mice were sacrificed, and blood and tissues were harvested for subsequent analysis. Serum insulin levels were measured by ELISA, and lipid profiles were determined biochemically. The HFHF diet-fed ICR mice exhibited obvious characteristics of the components of MS, including obvious obesity, severe insulin resistance, hyperinsulinemia, dislipidemia, significant hypertension and hyperuricemia. Our data suggest that HFHF diet-fed ICR mice may be a robust and efficient animal model that could well mimic the basic pathogenesis of human MS.

Visualization procedures for proteins and peptides on flat-bed monoliths and their effects on matrix-assisted laser-desorption/ionization time-of-flight mass spectrometric detection.

PubMed

Wouters, Bert; Vanhoutte, Dominique J D; Aarnoutse, Petra; Visser, Adriaan; Stassen, Catherine; Devreese, Bart; Kok, Wim Th; Schoenmakers, Peter J; Eeltink, Sebastiaan

2013-04-19

The present study concerns the application of visualization methods, i.e. coomassie-brilliant-blue-R staining (CBB-R), silver-nitrate staining, and fluorescamine labeling, and subsequent MALDI-MS analysis of intact proteins and peptides on the surface of flat-bed monoliths, intended for spatial two-dimensional chromatographic separations. The use of 100-μm thick macroporous poly(butyl methacrylate-co-ethylene dimethacrylate) flat-bed monoliths renders a fixation step obsolete, so that CBB-R and silver-nitrate staining and destaining could be achieved in 10-15 min as opposed to up to 24h, as is typical on 2D-PAGE gels. The detection limits remained comparable. The compatibility of the monolithic layer with subsequent MALDI-MS analysis of individual proteins and peptide spots was investigated with regards to mass accuracy, mass precision, resolution, and signal intensity. When comparing results from MALDI-MS analysis of proteins and peptides on a flat-bed monolith to results obtained directly on stainless-steel target plates, significant losses in mass precision, signal intensity, and an increased variation in resolution were observed. In addition, a loss in signal intensity up to two orders of magnitude was observed when using monolithic layers. After CCB-R and silver-nitrate staining and destaining to disrupt the protein-dye complexes no MALDI spectra with significant S/N ratios could be achieved. After fluorescamine labeling heterogeneous signals were observed, which resulted from a distribution in the number of fluorescence-labeled lysine groups and from the presence of labeled derivatives that had undergone condensation reactions. Copyright © 2013 Elsevier B.V. All rights reserved.

Analysis of formononetin from black cohosh (Actaea racemosa).

PubMed

Jiang, B; Kronenberg, F; Balick, M J; Kennelly, E J

2006-07-01

Black cohosh has been widely used as an herbal medicine for the treatment of symptoms related to menopause in America and Europe during the past several decades, but the bioactive constituents are still unknown. Formononetin is an isoflavone with known estrogen-like activity. This compound was first reported to be isolated from black cohosh in 1985, but subsequent research in 2002 using HPLC-PDA and LC-MS revealed no evidence to show the presence of formononetin in 13 populations of American black cohosh. A more recent report published in 2004 claimed to detect formononetin in an extract of black cohosh rhizomes using a TLC-fluorescent densitometry method. To further resolve these conflicting reports, we analyzed black cohosh roots and rhizomes for the presence of formononetin, using a combined TLC, HPLC-PDA and LC-MS method. We examined both methanolic and aqueous methanolic black cohosh extracts by HPLC-PDA and LC-MS methods, and did not detect formononetin in any extracts. We further determined the limits of detection of formononetin by HPLC-PDA and LC-MS. Our experimental results indicated that the sensitivity and accuracy of the HPLC-PDA and LC-MS methods for the analysis of formononetin were slightly higher than those of the reported fluorescent method, suggesting that the HPLC-PDA and LC-MS methods were reliable for the analysis of formononetin from black cohosh. We also repeated the reported TLC method to concentrate two fractions from a modern black cohosh sample and an 86-year-old black cohosh sample, respectively, and then analyzed these two fractions for formononetin using the HPLC-PDA and LC-MS method instead of the fluorescent method. Formononetin was not detected by HPLC-PDA or LC-MS. From the results of the present study it is not reasonable to attribute the estrogen-like activity of black cohosh extracts to formononetin.

Evidence of gushing induction by Penicillium oxalicum proteins.

PubMed

Vogt, E I; Kupfer, V M; Vogel, R F; Niessen, L

2017-03-01

The aim of this study was to elucidate whether grape-associated fungi exert an influence on gushing by their production of surface-active compounds. In preliminary experiments, 58 grape-associated isolates of species within Penicillium and Aspergillus genera were tested for their ability to modify the surface activity of culture supernatants. As the genus Penicillium had a higher potential to change surface activity, further research focused on that genus. Subsequently, supernatants of 36 Penicillium isolates were assessed for their potential to induce gushing in a model system. Isolates of Penicillium oxalicum had the highest potential. Different external factors were investigated for their influence on the intensity of gushing. By using reversed-phase high performance liquid chromatography and subsequent MALDI-TOF MS, SDS-PAGE and nano-ESI-LC-MS/MS analysis, two proteins in the exoproteome of P. oxalicum were identified, which could be linked to the induction of gushing. Our results suggest that infection of grapes by P. oxalicum may contribute to gushing in sparkling wine. In contrast to gushing of beer, the reason for its development in sparkling wine is widely unexplored. Nonetheless, sparkling wine producers have also been affected by this economically damaging phenomenon. This study has first suggested about the occurrence of primary gushing in sparkling wine. © 2016 The Society for Applied Microbiology.

Differentiation of perceptual and semantic subsequent memory effects using an orthographic paradigm.

PubMed

Kuo, Michael C C; Liu, Karen P Y; Ting, Kin Hung; Chan, Chetwyn C H

2012-11-27

This study aimed to differentiate perceptual and semantic encoding processes using subsequent memory effects (SMEs) elicited by the recognition of orthographs of single Chinese characters. Participants studied a series of Chinese characters perceptually (by inspecting orthographic components) or semantically (by determining the object making sounds), and then made studied or unstudied judgments during the recognition phase. Recognition performance in terms of d-prime measure in the semantic condition was higher, though not significant, than that of the perceptual condition. The between perceptual-semantic condition differences in SMEs at P550 and late positive component latencies (700-1000ms) were not significant in the frontal area. An additional analysis identified larger SME in the semantic condition during 600-1000ms in the frontal pole regions. These results indicate that coordination and incorporation of orthographic information into mental representation is essential to both task conditions. The differentiation was also revealed in earlier SMEs (perceptual>semantic) at N3 (240-360ms) latency, which is a novel finding. The left-distributed N3 was interpreted as more efficient processing of meaning with semantically learned characters. Frontal pole SMEs indicated strategic processing by executive functions, which would further enhance memory. Copyright © 2012 Elsevier B.V. All rights reserved.

Role of biofilm roughness and hydrodynamic conditions in Legionella pneumophila adhesion to and detachment from simulated drinking water biofilms.

PubMed

Shen, Yun; Monroy, Guillermo L; Derlon, Nicolas; Janjaroen, Dao; Huang, Conghui; Morgenroth, Eberhard; Boppart, Stephen A; Ashbolt, Nicholas J; Liu, Wen-Tso; Nguyen, Thanh H

2015-04-07

Biofilms in drinking water distribution systems (DWDS) could exacerbate the persistence and associated risks of pathogenic Legionella pneumophila (L. pneumophila), thus raising human health concerns. However, mechanisms controlling adhesion and subsequent detachment of L. pneumophila associated with biofilms remain unclear. We determined the connection between L. pneumophila adhesion and subsequent detachment with biofilm physical structure characterization using optical coherence tomography (OCT) imaging technique. Analysis of the OCT images of multispecies biofilms grown under low nutrient condition up to 34 weeks revealed the lack of biofilm deformation even when these biofilms were exposed to flow velocity of 0.7 m/s, typical flow for DWDS. L. pneumophila adhesion on these biofilm under low flow velocity (0.007 m/s) positively correlated with biofilm roughness due to enlarged biofilm surface area and local flow conditions created by roughness asperities. The preadhered L. pneumophila on selected rough and smooth biofilms were found to detach when these biofilms were subjected to higher flow velocity. At the flow velocity of 0.1 and 0.3 m/s, the ratio of detached cell from the smooth biofilm surface was from 1.3 to 1.4 times higher than that from the rough biofilm surface, presumably because of the low shear stress zones near roughness asperities. This study determined that physical structure and local hydrodynamics control L. pneumophila adhesion to and detachment from simulated drinking water biofilm, thus it is the first step toward reducing the risk of L. pneumophila exposure and subsequent infections.

Quantification of dimethylsulfoniopropionate (DMSP) in Acropora spp. of reef-building coral using mass spectrometry with deuterated internal standard.

PubMed

Swan, Hilton B; Deschaseaux, Elisabeth S M; Jones, Graham B; Eyre, Bradley D

2017-03-01

Dimethylsulfoniopropionate (DMSP) in scleractinian coral is usually analysed indirectly as dimethylsulfide (DMS) using gas chromatography (GC) with a sulfur-specific detector. We developed a headspace GC method for mass spectral analysis of DMSP in branching coral where hexa-deuterated DMSP (d 6 -DMSP) was added to samples and standards to optimise the analytical precision and quantitative accuracy. Using this indirect HS-GC-MS method, we show that common coral sample handling techniques did not alter DMSP concentrations in Acropora aspera and that endogenous DMS was insignificant compared to the store of DMSP in A. aspera. Field application of the indirect HS-GC-MS method in all seasons over a 5-year period at Heron Island in the southern Great Barrier Reef indicated that healthy colonies of A. aspera ordinarily seasonally conserve their branch tip store of DMSP; however, this store increased to a higher concentration under extended thermal stress conditions driven by a strong El Niño Southern Oscillation event. A liquid chromatography mass spectral method (LC-MS) was subsequently developed for direct analysis of DMSP in branching coral, also utilising the d 6 -DMSP internal standard. The quantitative comparison of DMSP in four species of Acropora coral by indirect HS-GC-MS and direct LC-MS analyses gave equivalent concentrations in A. aspera only; in the other three species, HS-GC-MS gave consistently higher concentrations, indicating that indirect analysis of DMSP may lead to artificially high values for some coral species. Graphical Abstract Dimethylsulfoniopropionate (DMSP) was quantified in Acropora spp. of branching coral using deuterated stable isotope dilution mass spectrometry.

Wipe selection for the analysis of surface materials containing chemical warfare agent nitrogen mustard degradation products by ultra-high pressure liquid chromatography-tandem mass spectrometry.

PubMed

Willison, Stuart A

2012-12-28

Degradation products arising from nitrogen mustard chemical warfare agent were deposited on common urban surfaces and determined via surface wiping, wipe extraction, and liquid chromatography–tandem mass spectrometry detection. Wipes investigated included cotton gauze, glass fiber filter, non-woven polyester fiber and filter paper, and surfaces included several porous (vinyl tile, painted drywall, wood) and mostly non-porous (laminate, galvanized steel, glass) surfaces. Wipe extracts were analyzed by ultra-high pressure liquid chromatography–tandem mass spectrometry (UPLC–MS/MS) and compared with high performance liquid chromatography–tandem mass spectrometry (HPLC–MS/MS) results. An evaluation of both techniques suggests UPLC–MS/MS provides a quick and sensitive analysis of targeted degradation products in addition to being nearly four times faster than a single HPLC run, allowing for greater throughput during a wide-spread release concerning large-scale contamination and subsequent remediation events. Based on the overall performance of all tested wipes, filter paper wipes were selected over other wipes because they did not contain interferences or native species (TEA and DEA) associated with the target analytes, resulting in high percent recoveries and low background levels during sample analysis. Other wipes, including cotton gauze, would require a pre-cleaning step due to the presence of large quantities of native species or interferences of the targeted analytes. Percent recoveries obtained from a laminate surface were 47–99% for all nitrogen mustard degradation products. The resulting detection limits achieved from wipes were 0.2 ng/cm(2) for triethanolamine (TEA), 0.03 ng/cm(2) for N-ethyldiethanolamine (EDEA), 0.1 ng/cm(2) for N-methyldiethanolamine (MDEA), and 0.1 ng/cm(2) for diethanolamine (DEA).

Risk Factors for Failure of Male Slings and Artificial Urinary Sphincters: Results from a Large Middle European Cohort Study.

PubMed

Hüsch, Tanja; Kretschmer, Alexander; Thomsen, Frauke; Kronlachner, Dominik; Kurosch, Martin; Obaje, Alice; Anding, Ralf; Pottek, Tobias; Rose, Achim; Olianas, Roberto; Friedl, Alexander; Hübner, Wilhelm; Homberg, Roland; Pfitzenmaier, Jesco; Grein, Ulrich; Queissert, Fabian; Naumann, Carsten Maik; Schweiger, Josef; Wotzka, Carola; Nyarangi-Dix, Joanne; Hofmann, Torben; Ulm, Kurt; Bauer, Ricarda M; Haferkamp, Axel

2017-01-01

We analysed the impact of predefined risk factors: age, diabetes, history of pelvic irradiation, prior surgery for stress urinary incontinence (SUI), prior urethral stricture, additional procedure during SUI surgery, duration of incontinence, ASA-classification and cause for incontinence on failure and complications in male SUI surgery. We retrospectively identified 506 patients with an artificial urinary sphincter (AUS) and 513 patients with a male sling (MS) in a multicenter cohort study. Complication rates were correlated to the risk factors in univariate analysis. Subsequently, a multivariate logistic regression adjusted to the risk factors was performed. A p value <0.05 was considered statistically significant. A history of pelvic irradiation was an independent risk factor for explantation in AUS (p < 0.001) and MS (p = 0.018). Moreover, prior urethral stricture (p = 0.036) and higher ASA-classification (p = 0.039) were positively correlated with explantation in univariate analysis for AUS. Urethral erosion was correlated with prior urethral stricture (p < 0.001) and a history of pelvic irradiation (p < 0.001) in AUS. Furthermore, infection was correlated with additional procedures during SUI surgery in univariate analysis (p = 0.037) in MS. We first identified the correlation of higher ASA-classification and explantation in AUS. Nevertheless, only a few novel risk factors had a significant influence on the failure of MS or AUS. © 2016 S. Karger AG, Basel.

Rapid LC-MS/MS quantification of the major benzodiazepines and their metabolites on dried blood spots using a simple and cost-effective sample pretreatment.

PubMed

Déglon, Julien; Versace, François; Lauer, Estelle; Widmer, Christèle; Mangin, Patrice; Thomas, Aurélien; Staub, Christian

2012-06-01

Dried blood spots (DBS) sampling has gained popularity in the bioanalytical community as an alternative to conventional plasma sampling, as it provides numerous benefits in terms of sample collection and logistics. The aim of this work was to show that these advantages can be coupled with a simple and cost-effective sample pretreatment, with subsequent rapid LC-MS/MS analysis for quantitation of 15 benzodiazepines, six metabolites and three Z-drugs. For this purpose, a simplified offline procedure was developed that consisted of letting a 5-µl DBS infuse directly into 100 µl of MeOH, in a conventional LC vial. The parameters related to the DBS pretreatment, such as extraction time or internal standard addition, were investigated and optimized, demonstrating that passive infusion in a regular LC vial was sufficient to quantitatively extract the analytes of interest. The method was validated according to international criteria in the therapeutic concentration ranges of the selected compounds. The presented strategy proved to be efficient for the rapid analysis of the selected drugs. Indeed, the offline sample preparation was reduced to a minimum, using a small amount of organic solvent and consumables, without affecting the accuracy of the method. Thus, this approach enables simple and rapid DBS analysis, even when using a non-DBS-dedicated autosampler, while lowering the costs and environmental impact.

Metabolic profiling of body fluids and multivariate data analysis.

PubMed

Trezzi, Jean-Pierre; Jäger, Christian; Galozzi, Sara; Barkovits, Katalin; Marcus, Katrin; Mollenhauer, Brit; Hiller, Karsten

2017-01-01

Metabolome analyses of body fluids are challenging due pre-analytical variations, such as pre-processing delay and temperature, and constant dynamical changes of biochemical processes within the samples. Therefore, proper sample handling starting from the time of collection up to the analysis is crucial to obtain high quality samples and reproducible results. A metabolomics analysis is divided into 4 main steps: 1) Sample collection, 2) Metabolite extraction, 3) Data acquisition and 4) Data analysis. Here, we describe a protocol for gas chromatography coupled to mass spectrometry (GC-MS) based metabolic analysis for biological matrices, especially body fluids. This protocol can be applied on blood serum/plasma, saliva and cerebrospinal fluid (CSF) samples of humans and other vertebrates. It covers sample collection, sample pre-processing, metabolite extraction, GC-MS measurement and guidelines for the subsequent data analysis. Advantages of this protocol include: •Robust and reproducible metabolomics results, taking into account pre-analytical variations that may occur during the sampling process•Small sample volume required•Rapid and cost-effective processing of biological samples•Logistic regression based determination of biomarker signatures for in-depth data analysis.

Monitoring of CoS 2 reactions using high-temperature XRD coupled with gas chromatography (GC)

DOE PAGES

Rodriguez, Mark A.; Coker, Eric Nicholas; Griego, James J. M.; ...

2016-04-18

High-temperature X-ray diffraction with concurrent gas chromatography (GC) was used to study cobalt disulfide cathode pellets disassembled from thermal batteries. When CoS 2 cathode materials were analyzed in an air environment, oxidation of the K(Br, Cl) salt phase in the cathode led to the formation of K 2SO 4 that subsequently reacted with the pyrite-type CoS 2 phase leading to cathode decomposition between ~260 and 450 °C. Here, independent thermal analysis experiments, i.e. simultaneous thermogravimetric analysis/differential scanning calorimetry/mass spectrometry (MS), augmented the diffraction results and support the overall picture of CoS 2 decomposition. Both gas analysis measurements (i.e. GC andmore » MS) from the independent experiments confirmed the formation of SO 2 off-gas species during breakdown of the CoS 2. In contrast, characterization of the same cathode material under inert conditions showed the presence of CoS 2 throughout the entire temperature range of analysis.« less

Application of mass spectrometry based electronic nose and chemometrics for fingerprinting radiation treatment

NASA Astrophysics Data System (ADS)

Gupta, Sumit; Variyar, Prasad S.; Sharma, Arun

2015-01-01

Volatile compounds were isolated from apples and grapes employing solid phase micro extraction (SPME) and subsequently analyzed by GC/MS equipped with a transfer line without stationary phase. Single peak obtained was integrated to obtain total mass spectrum of the volatile fraction of samples. A data matrix having relative abundance of all mass-to-charge ratios was subjected to principal component analysis (PCA) and linear discriminant analysis (LDA) to identify radiation treatment. PCA results suggested that there is sufficient variability between control and irradiated samples to build classification models based on supervised techniques. LDA successfully aided in segregating control from irradiated samples at all doses (0.1, 0.25, 0.5, 1.0, 1.5, 2.0 kGy). SPME-MS with chemometrics was successfully demonstrated as simple screening method for radiation treatment.

MALDI-TOF Mass Spectrometry Enables a Comprehensive and Fast Analysis of Dynamics and Qualities of Stress Responses of Lactobacillus paracasei subsp. paracasei F19

PubMed Central

Schott, Ann-Sophie; Behr, Jürgen; Quinn, Jennifer; Vogel, Rudi F.

2016-01-01

Lactic acid bacteria (LAB) are widely used as starter cultures in the manufacture of foods. Upon preparation, these cultures undergo various stresses resulting in losses of survival and fitness. In order to find conditions for the subsequent identification of proteomic biomarkers and their exploitation for preconditioning of strains, we subjected Lactobacillus (Lb.) paracasei subsp. paracasei TMW 1.1434 (F19) to different stress qualities (osmotic stress, oxidative stress, temperature stress, pH stress and starvation stress). We analysed the dynamics of its stress responses based on the expression of stress proteins using MALDI-TOF mass spectrometry (MS), which has so far been used for species identification. Exploiting the methodology of accumulating protein expression profiles by MALDI-TOF MS followed by the statistical evaluation with cluster analysis and discriminant analysis of principle components (DAPC), it was possible to monitor the expression of low molecular weight stress proteins, identify a specific time point when the expression of stress proteins reached its maximum, and statistically differentiate types of adaptive responses into groups. Above the specific result for F19 and its stress response, these results demonstrate the discriminatory power of MALDI-TOF MS to characterize even dynamics of stress responses of bacteria and enable a knowledge-based focus on the laborious identification of biomarkers and stress proteins. To our knowledge, the implementation of MALDI-TOF MS protein profiling for the fast and comprehensive analysis of various stress responses is new to the field of bacterial stress responses. Consequently, we generally propose MALDI-TOF MS as an easy and quick method to characterize responses of microbes to different environmental conditions, to focus efforts of more elaborate approaches on time points and dynamics of stress responses. PMID:27783652

Comprehensive Analysis of Protein Modifications by Top-down Mass Spectrometry

PubMed Central

Zhang, Han; Ge, Ying

2012-01-01

Mass spectrometry (MS)-based proteomics is playing an increasingly important role in cardiovascular research. Proteomics includes not only identification and quantification of proteins, but also the characterization of protein modifications such as post-translational modifications and sequence variants. The conventional bottom-up approach, involving proteolytic digestion of proteins into small peptides prior to MS analysis, is routinely used for protein identification and quantification with high throughput and automation. Nevertheless, it has limitations in the analysis of protein modifications mainly due to the partial sequence coverage and loss of connections among modifications on disparate portions of a protein. An alternative approach, top-down MS, has emerged as a powerful tool for the analysis of protein modifications. The top-down approach analyzes whole proteins directly, providing a “bird’s eye” view of all existing modifications. Subsequently, each modified protein form can be isolated and fragmented in the mass spectrometer to locate the modification site. The incorporation of the non-ergodic dissociation methods such as electron capture dissociation (ECD) greatly enhances the top-down capabilities. ECD is especially useful for mapping labile post-translational modifications which are well-preserved during the ECD fragmentation process. Top-down MS with ECD has been successfully applied to cardiovascular research with the unique advantages in unraveling the molecular complexity, quantifying modified protein forms, complete mapping of modifications with full sequence coverage, discovering unexpected modifications, and identifying and quantifying positional isomers and determining the order of multiple modifications. Nevertheless, top-down MS still needs to overcome some technical challenges to realize its full potential. Herein, we reviewed the advantages and challenges of top-down methodology with a focus on its application in cardiovascular research. PMID:22187450

Technical basis for the reduction of the maximum temperature TGA-MS analysis of oxide samples from the 3013 destructive examination program

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

Scogin, J. H.

2016-03-24

Thermogravimetric analysis with mass spectroscopy of the evolved gas (TGA-MS) is used to quantify the moisture content of materials in the 3013 destructive examination (3013 DE) surveillance program. Salts frequently present in the 3013 DE materials volatilize in the TGA and condense in the gas lines just outside the TGA furnace. The buildup of condensate can restrict the flow of purge gas and affect both the TGA operations and the mass spectrometer calibration. Removal of the condensed salts requires frequent maintenance and subsequent calibration runs to keep the moisture measurements by mass spectroscopy within acceptable limits, creating delays in processingmore » samples. In this report, the feasibility of determining the total moisture from TGA-MS measurements at a lower temperature is investigated. A temperature of the TGA-MS analysis which reduces the complications caused by the condensation of volatile materials is determined. Analysis shows that an excellent prediction of the presently measured total moisture value can be made using only the data generated up to 700 °C and there is a sound physical basis for this estimate. It is recommended that the maximum temperature of the TGA-MS determination of total moisture for the 3013 DE program be reduced from 1000 °C to 700 °C. It is also suggested that cumulative moisture measurements at 550 °C and 700°C be substituted for the measured value of total moisture in the 3013 DE database. Using these raw values, any of predictions of the total moisture discussed in this report can be made.« less

Neural correlates of encoding processes predicting subsequent cued recall and source memory.

PubMed

Angel, Lucie; Isingrini, Michel; Bouazzaoui, Badiâa; Fay, Séverine

2013-03-06

In this experiment, event-related potentials were used to examine whether the neural correlates of encoding processes predicting subsequent successful recall differed from those predicting successful source memory retrieval. During encoding, participants studied lists of words and were instructed to memorize each word and the list in which it occurred. At test, they had to complete stems (the first four letters) with a studied word and then make a judgment of the initial temporal context (i.e. list). Event-related potentials recorded during encoding were segregated according to subsequent memory performance to examine subsequent memory effects (SMEs) reflecting successful cued recall (cued recall SME) and successful source retrieval (source memory SME). Data showed a cued recall SME on parietal electrode sites from 400 to 1200 ms and a late inversed cued recall SME on frontal sites in the 1200-1400 ms period. Moreover, a source memory SME was reported from 400 to 1400 ms on frontal areas. These findings indicate that patterns of encoding-related activity predicting successful recall and source memory are clearly dissociated.

Comparison of three officinal species of Callicarpa based on a biochemome profiling strategy with UHPLC-IT-MS and chemometrics analysis.

PubMed

Chen, Meng-Lu; Chang, Wen-Qi; Zhou, Jian-Liang; Yin, Ying-Hao; Xia, Wen-Rui; Liu, Jian-Qun; Liu, Li-Fang; Xin, Gui-Zhong

2017-10-25

Traditional Chinese medicine (TCM) materials with closely related species are frequently fungible in clinical use. Therefore, holistic comparison of the composition in bioactive compounds is essential to evaluate whether they are equivalent in efficacy. Taking three officinal species of Callicarpa as a case, we proposed and validated a standardized strategy for the discrimination of closely related TCM materials, which focused on the extraction, profiling and multivariate statistical analysis of their biochemome. Firstly, serial liquid-liquid extractions were utilized to prepare different batches of Callicarpa biochemome, and the preparation yields were utilized for the normalization of sampling quantity prior to UHPLC-IT-MS analysis. Secondly, 34 compounds, including 19 phenylethanoid glycosides, 10 flavonoids and 5 terpenoids, were identified based on an untargeted UHPLC-IT-MS method. Thirdly, method validation of linearity, precision and stability showed that the UHPLC-IT-MS system was qualified (R 2 >0.995, RSD<15%) for subsequent biochemome profiling. After PCA and PLS-DA analysis, 30 marker compounds were screened and demonstrated to be of good predictability using genetic algorithm optimized support vector machines. Finally, a heatmap visualization was employed for clarifying the distribution of marker compounds, which could be helpful to determine whether the three Callicarpa species are, in fact, equivalent substitutes. This study provides a standardized biochemome profiling strategy for systemic comparison analysis of closely related TCM materials, which shows promising perspectives in tracking the supply chain of pharmaceutical suppliers. Copyright © 2017 Elsevier B.V. All rights reserved.

Uterine disease and its effect on subsequent reproductive performance of dairy cattle: a comparison of two cow-side diagnostic methods.

PubMed

Šavc, Miha; Duane, Mary; O'Grady, Luke E; Somers, Joris R; Beltman, Marijke E

2016-11-01

The aim of this study was to compare vaginal mucus scoring and ultrasonographic assessment of uterine content as predictors of future reproductive performance of dairy cows. Holstein-Friesian cows (n = 493) from seven commercial dairy farms were enrolled in this study. All cows received one prebreeding examination (PBE) between 21 and 38 days after parturition. During the PBE, vaginal mucus was scored (MS) and the transrectal ultrasonographic examination of the uterus to assess content (UTS) took place. The MS was scored on a scale of 0 to 3 using a Metricheck device and appearance of the uterus on transrectal ultrasound was scored on a scale of 0 to 4 based on the presence and consistency of intraluminal fluid. Other data collected from each cow included the farm ID (F_ID), conception rate to first service, length of breeding window, lactation number, calving month, body condition score (BCS) at calving, BCS loss after calving, BCS at PBE, days in milk at PBE, 305 day milk yield, economic breeding index (EBI), EBI fertility subindex and EBI health subindex. For each cow these parameters were analyzed using univariate Cox proportional hazard model to evaluate the effect of variables on the reproductive performance, measured as positive pregnancy status (PS) at the end of the breeding season. Receiver-operating characteristic analysis of the diagnostic tests compared with each other took place as well. Cows with positive UTS were 7.75 times more likely to have a positive MS as well (P < 0.01). The PS hazard ratios for cows with UTS0, 1, 2, 3, and 4 were 1; 0.84; 0.53; 0.78; 0.28, respectively (P < 0.001). For the cows with MS0, 1, 2, and 3, the PR hazard ratios were 1; 1.02; 0.51; 0.75; respectively (P = 0.01). Conception rate to first service, breeding window, and PS were significantly better for the cows with UTS0, 1 and 2 compared with the cows with UTS3-4 and MS2+3 (68%; 18%, [P = 0.020]; 29; 75 days, [P = 0.001]; 95%; 55%; [P = 0.010], respectively). There was a significant effect of days in milk at PBE in relation to the subsequent PS (P = 0.04). Cows in lactation number 5 or more were less likely (r = 0.69) to get in calf before the end of the breeding season than cows in their first lactation. Cows that calved later in the season were less likely to become pregnant before the end of the breeding season (P < 0.03). Younger cows (lactation <5) and cows with MS and UTS scores of 0 and -1 had significantly better reproductive performance (P < 0.04). Receiver-operating characteristic analysis showed that MS did not always reflect UTS, but cows with positive UTS were 7.75 times more likely to have a positive MS (P < 0.01) and a high UTS had a larger negative effect on time to PS than a high MS (P < 0.05). In conclusion, both prebreeding vaginal mucus evaluation with the Metricheck device and an ultrasound scan of the uterus serve as a good predictor of the subsequent PS. There is overlap between the two systems, but the best predictor for future reproductive outcome of the cow is a combination of both. Copyright © 2016 Elsevier Inc. All rights reserved.

Direct Detection of Biotinylated Proteins by Mass Spectrometry

PubMed Central

2015-01-01

Mass spectrometric strategies to identify protein subpopulations involved in specific biological functions rely on covalently tagging biotin to proteins using various chemical modification methods. The biotin tag is primarily used for enrichment of the targeted subpopulation for subsequent mass spectrometry (MS) analysis. A limitation of these strategies is that MS analysis does not easily discriminate unlabeled contaminants from the labeled protein subpopulation under study. To solve this problem, we developed a flexible method that only relies on direct MS detection of biotin-tagged proteins called “Direct Detection of Biotin-containing Tags” (DiDBiT). Compared with conventional targeted proteomic strategies, DiDBiT improves direct detection of biotinylated proteins ∼200 fold. We show that DiDBiT is applicable to several protein labeling protocols in cell culture and in vivo using cell permeable NHS-biotin and incorporation of the noncanonical amino acid, azidohomoalanine (AHA), into newly synthesized proteins, followed by click chemistry tagging with biotin. We demonstrate that DiDBiT improves the direct detection of biotin-tagged newly synthesized peptides more than 20-fold compared to conventional methods. With the increased sensitivity afforded by DiDBiT, we demonstrate the MS detection of newly synthesized proteins labeled in vivo in the rodent nervous system with unprecedented temporal resolution as short as 3 h. PMID:25117199

Identification and in vitro cytotoxicity of ochratoxin A degradation products formed during coffee roasting.

PubMed

Cramer, Benedikt; Königs, Maika; Humpf, Hans-Ulrich

2008-07-23

The mycotoxin ochratoxin A is degraded by up to 90% during coffee roasting. In order to investigate this degradation, model heating experiments with ochratoxin A were carried out, and the reaction products were analyzed by HPLC-DAD and HPLC-MS/MS. Two ochratoxin A degradation products were identified, and their structure and absolute configuration were determined. As degradation reactions, the isomerization to 14-(R)-ochratoxin A and the decarboxylation to 14-decarboxy-ochratoxin A were identified. Subsequently, an analytical method for the determination of these compounds in roasted coffee was developed. Quantification was carried out by HPLC-MS/MS and the use of stable isotope dilution analysis. By using this method for the analysis of 15 coffee samples from the German market, it could be shown that, during coffee roasting, the ochratoxin A diastereomer 14-(R)-ochratoxin A was formed in amounts of up to 25.6% relative to ochratoxin A. The decarboxylation product was formed only in traces. For toxicity evaluations, first preliminary cell culture assays were performed with the two new substances. Both degradation products exhibited higher IC50 values and caused apoptotic effects with higher concentrations than ochratoxin A in cultured human kidney epithelial cells. Thus, these cell culture data suggest that the degradation products are less cytotoxic than ochratoxin A.

iPhos: a toolkit to streamline the alkaline phosphatase-assisted comprehensive LC-MS phosphoproteome investigation

PubMed Central

2014-01-01

Background Comprehensive characterization of the phosphoproteome in living cells is critical in signal transduction research. But the low abundance of phosphopeptides among the total proteome in cells remains an obstacle in mass spectrometry-based proteomic analysis. To provide a solution, an alternative analytic strategy to confidently identify phosphorylated peptides by using the alkaline phosphatase (AP) treatment combined with high-resolution mass spectrometry was provided. While the process is applicable, the key integration along the pipeline was mostly done by tedious manual work. Results We developed a software toolkit, iPhos, to facilitate and streamline the work-flow of AP-assisted phosphoproteome characterization. The iPhos tookit includes one assister and three modules. The iPhos Peak Extraction Assister automates the batch mode peak extraction for multiple liquid chromatography mass spectrometry (LC-MS) runs. iPhos Module-1 can process the peak lists extracted from the LC-MS analyses derived from the original and dephosphorylated samples to mine out potential phosphorylated peptide signals based on mass shift caused by the loss of some multiples of phosphate groups. And iPhos Module-2 provides customized inclusion lists with peak retention time windows for subsequent targeted LC-MS/MS experiments. Finally, iPhos Module-3 facilitates to link the peptide identifications from protein search engines to the quantification results from pattern-based label-free quantification tools. We further demonstrated the utility of the iPhos toolkit on the data of human metastatic lung cancer cells (CL1-5). Conclusions In the comparison study of the control group of CL1-5 cell lysates and the treatment group of dasatinib-treated CL1-5 cell lysates, we demonstrated the applicability of the iPhos toolkit and reported the experimental results based on the iPhos-facilitated phosphoproteome investigation. And further, we also compared the strategy with pure DDA-based LC-MS/MS phosphoproteome investigation. The results of iPhos-facilitated targeted LC-MS/MS analysis convey more thorough and confident phosphopeptide identification than the results of pure DDA-based analysis. PMID:25521246

Fast time-resolved aerosol collector: proof of concept

NASA Astrophysics Data System (ADS)

Yu, X.-Y.; Cowin, J. P.; Iedema, M. J.; Ali, H.

2010-10-01

Atmospheric particles can be collected in the field on substrates for subsequent laboratory analysis via chemically sensitive single particle methods such as scanning electron microscopy with energy dispersive x-ray analysis. With moving substrates time resolution of seconds to minutes can be achieved. In this paper, we demonstrate how to increase the time resolution when collecting particles on a substrate to a few milliseconds to provide real-time information. Our fast time-resolved aerosol collector ("Fast-TRAC") microscopically observes the particle collection on a substrate and records an on-line video. Particle arrivals are resolved to within a single frame (4-17 ms in this setup), and the spatial locations are matched to the subsequent single particle analysis. This approach also provides in-situ information on particle size and number concentration. Applications are expected in airborne studies of cloud microstructure, pollution plumes, and surface long-term monitoring.

Fast time-resolved aerosol collector: proof of concept

NASA Astrophysics Data System (ADS)

Yu, X.-Y.; Cowin, J. P.; Iedema, M. J.; Ali, H.

2010-06-01

Atmospheric particles can be collected in the field on substrates for subsequent laboratory analysis via chemically sensitive single particle methods such as scanning electron microscopy with energy dispersive x-ray analysis. With moving substrates time resolution of seconds to minutes can be achieved. In this paper, we demonstrate how to increase the time resolution when collecting particles on a substrate to a few milliseconds to provide real-time information. Our fast time-resolved aerosol collector ("Fast-TRAC") microscopically observes the particle collection on a substrate and records an on-line video. Particle arrivals are resolved to within a single frame (4-17 ms in this setup), and the spatial locations are matched to the subsequent single particle analysis. This approach also provides in-situ information on particle size and number concentration. Applications are expected in airborne studies of cloud microstructure, pollution plumes, and surface long-term monitoring.

Hooked differential mobility spectrometry apparatus and method therefore

DOEpatents

Shvartsburg, Alexandre A [Richland, WA; Tang, Keqi [Richland, WA; Ibrahim, Yehia M [Richland, WA; Smith, Richard D [Richland, WA

2009-02-17

Disclosed are a device and method for improved interfacing of differential mobility spectrometry (DMS) or field asymmetric waveform ion mobility spectrometry (FAIMS) analyzers of substantially planar geometry to subsequent or preceding instrument stages. Interfacing is achieved using curved DMS elements, where a thick ion beam emitted by planar DMS analyzers or injected into them for ion filtering is compressed to the gap median by DMS ion focusing effect in a spatially inhomogeneous electric field. Resulting thinner beams are more effectively transmitted through necessarily constrained conductance limit apertures to subsequent instrument stages operated at a pressure lower than DMS, and/or more effectively injected into planar DMS analyzers. The technology is synergetic with slit apertures, slit aperture/ion funnels, and high-pressure ion funnel interfaces known in the art which allow for increasing cross-sectional area of MS inlets. The invention may be used in integrated analytical platforms, including, e.g., DMS/MS, LC/DMS/MS, and DMS/IMS/MS that could replace and/or enhance current LC/MS methods, e.g., for proteomics research.

Mechanisms contributing to the thermal analysis of waste incineration bottom ash and quantification of different carbon species.

PubMed

Rocca, Stefania; van Zomeren, André; Costa, Giulia; Dijkstra, Joris J; Comans, Rob N J; Lombardi, Francesco

2013-02-01

The focus of this study was to identify the main compounds affecting the weight changes of bottom ash (BA) in conventional loss on ignition (LOI) tests and to obtain a better understanding of the individual processes in heterogeneous (waste) materials such as BA. Evaluations were performed on BA samples from a refuse derived fuel incineration (RDF-I) plant and a hospital waste incineration (HW-I) plant using thermogravimetric analysis and subsequent mass spectrometry (TG-MS) analysis of the gaseous thermal decomposition products. Results of TG-MS analysis on RDF-I BA indicated that the LOI measured at 550°C was due to moisture evaporation and dehydration of Ca(OH)(2) and hydrocalumite. Results for the HW-I BA showed that LOI at 550°C was predominantly related to the elemental carbon (EC) content of the sample. Decomposition of CaCO(3) around 700°C was identified in both materials. In addition, we have identified reaction mechanisms that underestimate the EC and overestimate the CaCO(3) contents of the HW-I BA during TG-MS analyses. These types of artefacts are expected to occur also when conventional LOI methods are adopted, in particular for materials that contain CaO/Ca(OH)(2) in combination with EC and/or organic carbon, such as e.g. municipal solid waste incineration (MSWI) bottom and fly ashes. We suggest that the same mechanisms that we have found (i.e. in situ carbonation) can also occur during combustion of the waste in the incinerator (between 450 and 650°C) demonstrating that the presence of carbonate in bottom ash is not necessarily indicative for weathering. These results may also give direction to further optimization of waste incineration technologies with regard to stimulating in situ carbonation during incineration and subsequent potential improvement of the leaching behavior of bottom ash. Copyright © 2012 Elsevier Ltd. All rights reserved.

MALDI-TOF MS typing of a nosocomial methicillin-resistant Staphylococcus aureus outbreak in a neonatal intensive care unit.

PubMed

Steensels, Deborah; Deplano, Ariane; Denis, Olivier; Simon, Anne; Verroken, Alexia

2017-08-01

The early detection of a methicillin-resistant Staphylococcus aureus (MRSA) outbreak is decisive to control its spread and rapidly initiate adequate infection control measures. Therefore, prompt determination of epidemiologic relatedness of clinical MRSA isolates is essential. Genetic typing methods have a high discriminatory power but their availability remains restricted. In this study, we aimed to challenge matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) as a typing tool of a nosocomial MRSA outbreak in a neonatal intensive care unit. Over a 2-year period, 15 MRSA isolates were recovered from patients (n = 14) and health care workers (n = 1) at the neonatal intensive care unit. Five reference strains were included for comparison. Identification was performed by MALDI-TOF MS and susceptibility profiles determined by automated broth microdilution. Typing analysis by MALDI-TOF MS included mean spectrum profiles and subsequent dendrogram creation using BioNumerics software. Results were compared with spa typing and pulsed-field gel electrophoresis (PFGE). Our study showed good concordance (93%) between PFGE, spa typing, and MALDI-TOF MS for the outbreak-related MRSA strains. MALDI-TOF MS typing showed excellent typeability and discriminatory power but showed poor reproducibility. This study is one of the first to document the potential usefulness of MALDI-TOF MS with standardized data analysis as a typing tool for investigating a nosocomial MRSA outbreak. A concordance of 93% compared to reference typing techniques was observed. However, because of poor reproducibility, long-term follow-up of prospective isolated strains is not practical for routine use. Further studies are needed to confirm our observations.

CIG-P: Circular Interaction Graph for Proteomics.

PubMed

Hobbs, Christopher K; Leung, Michelle; Tsang, Herbert H; Ebhardt, H Alexander

2014-10-31

A typical affinity purification coupled to mass spectrometry (AP-MS) experiment includes the purification of a target protein (bait) using an antibody and subsequent mass spectrometry analysis of all proteins co-purifying with the bait (aka prey proteins). Like any other systems biology approach, AP-MS experiments generate a lot of data and visualization has been challenging, especially when integrating AP-MS experiments with orthogonal datasets. We present Circular Interaction Graph for Proteomics (CIG-P), which generates circular diagrams for visually appealing final representation of AP-MS data. Through a Java based GUI, the user inputs experimental and reference data as file in csv format. The resulting circular representation can be manipulated live within the GUI before exporting the diagram as vector graphic in pdf format. The strength of CIG-P is the ability to integrate orthogonal datasets with each other, e.g. affinity purification data of kinase PRPF4B in relation to the functional components of the spliceosome. Further, various AP-MS experiments can be compared to each other. CIG-P aids to present AP-MS data to a wider audience and we envision that the tool finds other applications too, e.g. kinase - substrate relationships as a function of perturbation. CIG-P is available under: http://sourceforge.net/projects/cig-p/

Online immunocapture ICP-MS for the determination of the metalloprotein ceruloplasmin in human serum.

PubMed

Bernevic, Bogdan; El-Khatib, Ahmed H; Jakubowski, Norbert; Weller, Michael G

2018-04-02

The human copper-protein ceruloplasmin (Cp) is the major copper-containing protein in the human body. The accurate determination of Cp is mandatory for the reliable diagnosis of several diseases. However, the analysis of Cp has proven to be difficult. The aim of our work was a proof of concept for the determination of a metalloprotein-based on online immunocapture ICP-MS. The immuno-affinity step is responsible for the enrichment and isolation of the analyte from serum, whereas the compound-independent quantitation with ICP-MS delivers the sensitivity, precision, and large dynamic range. Off-line ELISA (enzyme-linked immunosorbent assay) was used in parallel to confirm the elution profile of the analyte with a structure-selective method. The total protein elution was observed with the 32 S mass trace. The ICP-MS signals were normalized on a 59 Co signal. The human copper-protein Cp could be selectively determined. This was shown with pure Cp and with a sample of human serum. The good correlation with off-line ELISA shows that Cp could be captured and eluted selectively from the anti-Cp affinity column and subsequently determined by the copper signal of ICP-MS.

Proteomics-Based Analysis of Protein Complexes in Pluripotent Stem Cells and Cancer Biology.

PubMed

Sudhir, Putty-Reddy; Chen, Chung-Hsuan

2016-03-22

A protein complex consists of two or more proteins that are linked together through protein-protein interactions. The proteins show stable/transient and direct/indirect interactions within the protein complex or between the protein complexes. Protein complexes are involved in regulation of most of the cellular processes and molecular functions. The delineation of protein complexes is important to expand our knowledge on proteins functional roles in physiological and pathological conditions. The genetic yeast-2-hybrid method has been extensively used to characterize protein-protein interactions. Alternatively, a biochemical-based affinity purification coupled with mass spectrometry (AP-MS) approach has been widely used to characterize the protein complexes. In the AP-MS method, a protein complex of a target protein of interest is purified using a specific antibody or an affinity tag (e.g., DYKDDDDK peptide (FLAG) and polyhistidine (His)) and is subsequently analyzed by means of MS. Tandem affinity purification, a two-step purification system, coupled with MS has been widely used mainly to reduce the contaminants. We review here a general principle for AP-MS-based characterization of protein complexes and we explore several protein complexes identified in pluripotent stem cell biology and cancer biology as examples.

Proteomics-Based Analysis of Protein Complexes in Pluripotent Stem Cells and Cancer Biology

PubMed Central

Sudhir, Putty-Reddy; Chen, Chung-Hsuan

2016-01-01

A protein complex consists of two or more proteins that are linked together through protein–protein interactions. The proteins show stable/transient and direct/indirect interactions within the protein complex or between the protein complexes. Protein complexes are involved in regulation of most of the cellular processes and molecular functions. The delineation of protein complexes is important to expand our knowledge on proteins functional roles in physiological and pathological conditions. The genetic yeast-2-hybrid method has been extensively used to characterize protein-protein interactions. Alternatively, a biochemical-based affinity purification coupled with mass spectrometry (AP-MS) approach has been widely used to characterize the protein complexes. In the AP-MS method, a protein complex of a target protein of interest is purified using a specific antibody or an affinity tag (e.g., DYKDDDDK peptide (FLAG) and polyhistidine (His)) and is subsequently analyzed by means of MS. Tandem affinity purification, a two-step purification system, coupled with MS has been widely used mainly to reduce the contaminants. We review here a general principle for AP-MS-based characterization of protein complexes and we explore several protein complexes identified in pluripotent stem cell biology and cancer biology as examples. PMID:27011181

Acute myeloid leukaemia diagnosed by intra-oral myeloid sarcoma. A case report.

PubMed

Papamanthos, Mattheos K; Kolokotronis, Alexandros E; Skulakis, Haralampos E; Fericean, Angela-Monika A; Zorba, Matina T; Matiakis, Apostolos T

2010-06-01

Myeloid sarcoma (MS) is a rare extramedullary malignant tumor composed of immature myeloid cells. It is strongly associated with a well known or covert acute myeloid leukaemia, chronic myeloproliferative diseases or myelodysplastic syndromes. Intraoral MS scarcely occurs. An unusual case of acute myeloid leukaemia, which was diagnosed by mandibular MS that was developed in the alveolar socket after a dental extraction, is reported. The histological examination (including immunohistochemical analysis) of a subsequent biopsy showed infiltration of the oral mucosa by neoplastic cells. This lesion was therefore classified as acute myeloid leukaemia. The patient was referred to oncologists that confirmed the initial diagnosis. The patient underwent chemotherapy and the mandibular tumor disappeared. Forty days later, a relapse of the disease, which appeared as a great-ulcerated lesion, was developed in the hard palate. Thirty days after the second chemotherapy had finished, a new intraoral tumor was developed in the vestibular maxillary gingiva. Review of the literature shows no report of intraoral relapse and particularly multiple relapse of a MS that involves the oral cavity. Even though MS is encountered infrequently in the oral cavity, it should be considered in the differential diagnosis of conditions (especially tumors) with a similar clinical appearance.

Acute Myeloid Leukaemia Diagnosed by Intra-Oral Myeloid Sarcoma. A Case Report

PubMed Central

Papamanthos, Mattheos K.; Skulakis, Haralampos E.; Fericean, Angela-Monika A.; Zorba, Matina T.; Matiakis, Apostolos T.

2010-01-01

Myeloid sarcoma (MS) is a rare extramedullary malignant tumor composed of immature myeloid cells. It is strongly associated with a well known or covert acute myeloid leukaemia, chronic myeloproliferative diseases or myelodysplastic syndromes. Intraoral MS scarcely occurs. An unusual case of acute myeloid leukaemia, which was diagnosed by mandibular MS that was developed in the alveolar socket after a dental extraction, is reported. The histological examination (including immunohistochemical analysis) of a subsequent biopsy showed infiltration of the oral mucosa by neoplastic cells. This lesion was therefore classified as acute myeloid leukaemia. The patient was referred to oncologists that confirmed the initial diagnosis. The patient underwent chemotherapy and the mandibular tumor disappeared. Forty days later, a relapse of the disease, which appeared as a great-ulcerated lesion, was developed in the hard palate. Thirty days after the second chemotherapy had finished, a new intraoral tumor was developed in the vestibular maxillary gingiva. Review of the literature shows no report of intraoral relapse and particularly multiple relapse of a MS that involves the oral cavity. Even though MS is encountered infrequently in the oral cavity, it should be considered in the differential diagnosis of conditions (especially tumors) with a similar clinical appearance. PMID:20512638

High-sensitivity analysis of naturally occurring sugar chains, using a novel fluorescent linker molecule.

PubMed

Sato, Masaki; Ito, Yuji; Arima, Naomichi; Baba, Masanori; Sobel, Michael; Wakao, Masahiro; Suda, Yasuo

2009-07-01

To analyse the binding of sugar chains to proteins, viruses and cells, the surface plasmon resonance (SPR) technique is very convenient and effective because it is a real-time, non-destructive detection system. Key to this method is linker compounds for immobilization of the sugar chains to the gold-coated chip for SPR. Also, well-designed fluorescent labelling reagents are essential when analysing the structure of trace amounts of sugar chains derived from natural sources, such as glycoproteins on the surface of specific cells. In this report, we developed a novel linker molecule, named 'f-mono', which has both of these properties: simple immobilization chemistry and a fluorescent label. Since the molecule contains a 2,5-diaminopyridyl group and a thioctic acid group, conjugation with sugar chains can be achieved using the well-established reductive amination reaction. This conjugate of sugar chain and fluorescent linker (fluorescent ligand-conjugate, FLC) has fluorescent properties (ex. 335 nm, em. 380 nm), and as little as 1 microg of FLC can be easily purified using HPLC with a fluorescent detector. MS and MS/MS analysis of the FLC is also possible. As a +2 Da larger MS peak ([M + H + 2](+) ion) was always associated with the theoretical MS peak ([M + H](+)) (due to the reduction of the thioctic acid moiety), the MS peaks of the FLC were easily found, even using unfractionated crude samples. Immobilization of the FLC onto gold-coated chips, and their subsequent SPR analyses were successively accomplished, as had been performed previously using non-fluorescent ligand conjugates.

An improved pseudotargeted metabolomics approach using multiple ion monitoring with time-staggered ion lists based on ultra-high performance liquid chromatography/quadrupole time-of-flight mass spectrometry.

PubMed

Wang, Yang; Liu, Fang; Li, Peng; He, Chengwei; Wang, Ruibing; Su, Huanxing; Wan, Jian-Bo

2016-07-13

Pseudotargeted metabolomics is a novel strategy integrating the advantages of both untargeted and targeted methods. The conventional pseudotargeted metabolomics required two MS instruments, i.e., ultra-high performance liquid chromatography/quadrupole-time- of-flight mass spectrometry (UHPLC/Q-TOF MS) and UHPLC/triple quadrupole mass spectrometry (UHPLC/QQQ-MS), which makes method transformation inevitable. Furthermore, the picking of ion pairs from thousands of candidates and the swapping of the data between two instruments are the most labor-intensive steps, which greatly limit its application in metabolomic analysis. In the present study, we proposed an improved pseudotargeted metabolomics method that could be achieved on an UHPLC/Q-TOF/MS instrument operated in the multiple ion monitoring (MIM) mode with time-staggered ion lists (tsMIM). Full scan-based untargeted analysis was applied to extract the target ions. After peak alignment and ion fusion, a stepwise ion picking procedure was used to generate the ion lists for subsequent single MIM and tsMIM. The UHPLC/Q-TOF tsMIM MS-based pseudotargeted approach exhibited better repeatability and a wider linear range than the UHPLC/Q-TOF MS-based untargeted metabolomics method. Compared to the single MIM mode, the tsMIM significantly increased the coverage of the metabolites detected. The newly developed method was successfully applied to discover plasma biomarkers for alcohol-induced liver injury in mice, which indicated its practicability and great potential in future metabolomics studies. Copyright © 2016 Elsevier B.V. All rights reserved.

UPLC-MS/MS analysis for antioxidant components of Lycii Fructus based on spectrum-effect relationship.

PubMed

Zhang, Xian-Fei; Chen, Juan; Yang, Jun-Li; Shi, Yan-Ping

2018-04-01

Lycii Fructus is widely cultivated in the Northwest China. It is well-known for its antiaging effect in traditional Chinese medicines (TCMs), but the effective components are not clear. In this work, the ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) was used to study the antioxidant components of Lycii Fructus through analyzing the spectrum-effect relationship, and the positive correlation components with antioxidant activity were partially identified. The extractums of Lycii Fructus were adsorbed with macroporous resin, and then eluted with water and 30%, 60%, 90% ethanol in turn. The extract fraction eluted with 60% ethanol was determined as the best, and was taken for subsequent experiments. With the above separation method, UPLC fingerprints of thirty batches of Lycii Fructus (from different areas) were obtained, and thirty common peaks were selected through similarity analysis (SA). Combined with the data of the 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS) assays, the spectrum-effect relationship was studied. The results showed that the main peaks with antioxidant activity were P14, P26, P8, and P21 for DPPH, and P26, P14, P21, and P19 for ABTS. Using the UPLC-MS/MS data, peaks P14, P19, P21, and P30 were respectively identified as chlorogenic acid, quercetin, kaempferol, and isorhamnetin, and then the results were confirmed through comparison with the standards and other references. Finally, their strong antioxidant activities were validated experimentally. Copyright © 2017 Elsevier B.V. All rights reserved.

An Integrated Strategy to Qualitatively Differentiate Components of Raw and Processed Viticis Fructus Based on NIR, HPLC and UPLC-MS Analysis.

PubMed

Diao, Jiayin; Xu, Can; Zheng, Huiting; He, Siyi; Wang, Shumei

2018-06-21

Viticis Fructus is a traditional Chinese herbal drug processed by various methods to achieve different clinical purposes. Thermal treatment potentially alters chemical composition, which may impact on effectiveness and toxicity. In order to interpret the constituent discrepancies of raw versus processed (stir-fried) Viticis Fructus, a multivariate detection method (NIR, HPLC, and UPLC-MS) based on metabonomics and chemometrics was developed. Firstly, synergy interval partial least squares and partial least squares-discriminant analysis were employed to screen the distinctive wavebands (4319 - 5459 cm -1 ) based on preprocessed near-infrared spectra. Then, HPLC with principal component analysis was performed to characterize the distinction. Subsequently, a total of 49 compounds were identified by UPLC-MS, among which 42 compounds were eventually characterized as having a significant change during processing via the semiquantitative volcano plot analysis. Moreover, based on the partial least squares-discriminant analysis, 16 compounds were chosen as characteristic markers that could be in close correlation with the discriminatory near-infrared wavebands. Together, all of these characterization techniques effectively discriminated raw and processed products of Viticis Fructus. In general, our work provides an integrated way of classifying Viticis Fructus, and a strategy to explore discriminatory chemical markers for other traditional Chinese herbs, thus ensuring safety and efficacy for consumers. Georg Thieme Verlag KG Stuttgart · New York.

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.

Peptide Array X-Linking (PAX): A New Peptide-Protein Identification Approach

PubMed Central

Okada, Hirokazu; Uezu, Akiyoshi; Soderblom, Erik J.; Moseley, M. Arthur; Gertler, Frank B.; Soderling, Scott H.

2012-01-01

Many protein interaction domains bind short peptides based on canonical sequence consensus motifs. Here we report the development of a peptide array-based proteomics tool to identify proteins directly interacting with ligand peptides from cell lysates. Array-formatted bait peptides containing an amino acid-derived cross-linker are photo-induced to crosslink with interacting proteins from lysates of interest. Indirect associations are removed by high stringency washes under denaturing conditions. Covalently trapped proteins are subsequently identified by LC-MS/MS and screened by cluster analysis and domain scanning. We apply this methodology to peptides with different proline-containing consensus sequences and show successful identifications from brain lysates of known and novel proteins containing polyproline motif-binding domains such as EH, EVH1, SH3, WW domains. These results suggest the capacity of arrayed peptide ligands to capture and subsequently identify proteins by mass spectrometry is relatively broad and robust. Additionally, the approach is rapid and applicable to cell or tissue fractions from any source, making the approach a flexible tool for initial protein-protein interaction discovery. PMID:22606326

Diagnosis by Volatile Organic Compounds in Exhaled Breath from Lung Cancer Patients Using Support Vector Machine Algorithm

PubMed Central

Sakumura, Yuichi; Koyama, Yutaro; Tokutake, Hiroaki; Hida, Toyoaki; Sato, Kazuo; Itoh, Toshio; Akamatsu, Takafumi; Shin, Woosuck

2017-01-01

Monitoring exhaled breath is a very attractive, noninvasive screening technique for early diagnosis of diseases, especially lung cancer. However, the technique provides insufficient accuracy because the exhaled air has many crucial volatile organic compounds (VOCs) at very low concentrations (ppb level). We analyzed the breath exhaled by lung cancer patients and healthy subjects (controls) using gas chromatography/mass spectrometry (GC/MS), and performed a subsequent statistical analysis to diagnose lung cancer based on the combination of multiple lung cancer-related VOCs. We detected 68 VOCs as marker species using GC/MS analysis. We reduced the number of VOCs and used support vector machine (SVM) algorithm to classify the samples. We observed that a combination of five VOCs (CHN, methanol, CH3CN, isoprene, 1-propanol) is sufficient for 89.0% screening accuracy, and hence, it can be used for the design and development of a desktop GC-sensor analysis system for lung cancer. PMID:28165388

Bioprospecting Chemical Diversity and Bioactivity in a Marine Derived Aspergillus terreus.

PubMed

Adpressa, Donovon A; Loesgen, Sandra

2016-02-01

A comparative metabolomic study of a marine derived fungus (Aspergillus terreus) grown under various culture conditions is presented. The fungus was grown in eleven different culture conditions using solid agar, broth cultures, or grain based media (OSMAC). Multivariate analysis of LC/MS data from the organic extracts revealed drastic differences in the metabolic profiles and guided our subsequent isolation efforts. The compound 7-desmethylcitreoviridin was isolated and identified, and is fully described for the first time. In addition, 16 known fungal metabolites were also isolated and identified. All compounds were elucidated by detailed spectroscopic analysis and tested for antibacterial activities against five human pathogens and tested for cytotoxicity. This study demonstrates that LC/MS based multivariate analysis provides a simple yet powerful tool to analyze the metabolome of a single fungal strain grown under various conditions. This approach allows environmentally-induced changes in metabolite expression to be rapidly visualized, and uses these differences to guide the discovery of new bioactive molecules. Copyright © 2016 Verlag Helvetica Chimica Acta AG, Zürich.

Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis.

PubMed

Yang, Chao; He, Zengyou; Yu, Weichuan

2009-01-06

In mass spectrometry (MS) based proteomic data analysis, peak detection is an essential step for subsequent analysis. Recently, there has been significant progress in the development of various peak detection algorithms. However, neither a comprehensive survey nor an experimental comparison of these algorithms is yet available. The main objective of this paper is to provide such a survey and to compare the performance of single spectrum based peak detection methods. In general, we can decompose a peak detection procedure into three consequent parts: smoothing, baseline correction and peak finding. We first categorize existing peak detection algorithms according to the techniques used in different phases. Such a categorization reveals the differences and similarities among existing peak detection algorithms. Then, we choose five typical peak detection algorithms to conduct a comprehensive experimental study using both simulation data and real MALDI MS data. The results of comparison show that the continuous wavelet-based algorithm provides the best average performance.

Diagnosis by Volatile Organic Compounds in Exhaled Breath from Lung Cancer Patients Using Support Vector Machine Algorithm.

PubMed

Sakumura, Yuichi; Koyama, Yutaro; Tokutake, Hiroaki; Hida, Toyoaki; Sato, Kazuo; Itoh, Toshio; Akamatsu, Takafumi; Shin, Woosuck

2017-02-04

Monitoring exhaled breath is a very attractive, noninvasive screening technique for early diagnosis of diseases, especially lung cancer. However, the technique provides insufficient accuracy because the exhaled air has many crucial volatile organic compounds (VOCs) at very low concentrations (ppb level). We analyzed the breath exhaled by lung cancer patients and healthy subjects (controls) using gas chromatography/mass spectrometry (GC/MS), and performed a subsequent statistical analysis to diagnose lung cancer based on the combination of multiple lung cancer-related VOCs. We detected 68 VOCs as marker species using GC/MS analysis. We reduced the number of VOCs and used support vector machine (SVM) algorithm to classify the samples. We observed that a combination of five VOCs (CHN, methanol, CH₃CN, isoprene, 1-propanol) is sufficient for 89.0% screening accuracy, and hence, it can be used for the design and development of a desktop GC-sensor analysis system for lung cancer.

A novel mice model of metabolic syndrome: the high-fat-high-fructose diet-fed ICR mice

PubMed Central

Zhuhua, Zhang; Zhiquan, Wang; Zhen, Yang; Yixin, Niu; Weiwei, Zhang; Xiaoyong, Li; Yueming, Liu; Hongmei, Zhang; Li, Qin; Qing, Su

2015-01-01

Currently, the metabolic syndrome (MS) is occurring at growing rates worldwide, raising extensive concerns on the mechanisms and therapeutic interventions for this disorder. Herein, we described a novel method of establishing MS model in rodents. Male Institute of Cancer Research (ICR) mice were fed with high-fat-high-fructose (HFHF) diet or normal chow (NC) respectively for 12 weeks. Metabolic phenotypes were assessed by glucose tolerance test, insulin tolerance test and hyperinsulinemic-euglycemic clamp. Blood pressure was measured by a tail-cuff system. At the end of the experiment, mice were sacrificed, and blood and tissues were harvested for subsequent analysis. Serum insulin levels were measured by ELISA, and lipid profiles were determined biochemically. The HFHF diet-fed ICR mice exhibited obvious characteristics of the components of MS, including obvious obesity, severe insulin resistance, hyperinsulinemia, dislipidemia, significant hypertension and hyperuricemia. Our data suggest that HFHF diet-fed ICR mice may be a robust and efficient animal model that could well mimic the basic pathogenesis of human MS. PMID:26134356

Mass spectrometric imaging of red fluorescent protein in breast tumor xenografts.

PubMed

Chughtai, Kamila; Jiang, Lu; Post, Harm; Winnard, Paul T; Greenwood, Tiffany R; Raman, Venu; Bhujwalla, Zaver M; Heeren, Ron M A; Glunde, Kristine

2013-05-01

Mass spectrometric imaging (MSI) in combination with electrospray mass spectrometry (ESI-MS) is a powerful technique for visualization and identification of a variety of different biomolecules directly from thin tissue sections. As commonly used tools for molecular reporting, fluorescent proteins are molecular reporter tools that have enabled the elucidation of a multitude of biological pathways and processes. To combine these two approaches, we have performed targeted MS analysis and MALDI-MSI visualization of a tandem dimer (td)Tomato red fluorescent protein, which was expressed exclusively in the hypoxic regions of a breast tumor xenograft model. For the first time, a fluorescent protein has been visualized by both optical microscopy and MALDI-MSI. Visualization of tdTomato by MALDI-MSI directly from breast tumor tissue sections will allow us to simultaneously detect and subsequently identify novel molecules present in hypoxic regions of the tumor. MS and MALDI-MSI of fluorescent proteins, as exemplified in our study, is useful for studies in which the advantages of MS and MSI will benefit from the combination with molecular approaches that use fluorescent proteins as reporters.

A Comparative Analysis of Computational Approaches to Relative Protein Quantification Using Peptide Peak Intensities in Label-free LC-MS Proteomics Experiments

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

Matzke, Melissa M.; Brown, Joseph N.; Gritsenko, Marina A.

2013-02-01

Liquid chromatography coupled with mass spectrometry (LC-MS) is widely used to identify and quantify peptides in complex biological samples. In particular, label-free shotgun proteomics is highly effective for the identification of peptides and subsequently obtaining a global protein profile of a sample. As a result, this approach is widely used for discovery studies. Typically, the objective of these discovery studies is to identify proteins that are affected by some condition of interest (e.g. disease, exposure). However, for complex biological samples, label-free LC-MS proteomics experiments measure peptides and do not directly yield protein quantities. Thus, protein quantification must be inferred frommore » one or more measured peptides. In recent years, many computational approaches to relative protein quantification of label-free LC-MS data have been published. In this review, we examine the most commonly employed quantification approaches to relative protein abundance from peak intensity values, evaluate their individual merits, and discuss challenges in the use of the various computational approaches.« less

Chemical profiling and quantitation of bioactive compounds in Platycladi Cacumen by UPLC-Q-TOF-MS/MS and UPLC-DAD.

PubMed

Zhuang, Bo; Bi, Zhi-Ming; Wang, Zi-Yuan; Duan, Li; Lai, Chang-Jiang-Sheng; Liu, E-Hu

2018-05-30

Platycladi Cacumen (PC) is a traditional Chinese medicine used for the treatment of hemorrhages, cough, asthma and hair loss. To get a better understanding of the chemical constituents in PC, ultra-high performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry (UPLC-Q-TOF-MS/MS) and diagnostic ion filtering strategy were firstly employed for chemical profiling of PC. A total of 43 compounds including organic acids and derivatives, flavonoids as well as phenylpropanolds were unambiguously or reasonably identified. Coumarin and lignan were reported for the first time in PC. Chemical variation of 39 batches of PC from different geographical origins and 10 batches of processed product of PC was subsequently investigated by quantitation of nine major flavonoids. The results determined by UPLC coupled with diode array detection (UPLC-DAD) and hierarchical cluster analysis (HCA) indicated that the contents of flavonoids in PC samples differ greatly. This work provides an efficient approach to comprehensively evaluate the quality of PC. Copyright © 2018 Elsevier B.V. All rights reserved.

Quantitation of repaglinide and metabolites in mouse whole-body thin tissue sections using droplet-based liquid microjunction surface sampling-high-performance liquid chromatography-electrospray ionization tandem mass spectrometry.

PubMed

Chen, Weiqi; Wang, Lifei; Van Berkel, Gary J; Kertesz, Vilmos; Gan, Jinping

2016-03-25

Herein, quantitation aspects of a fully automated autosampler/HPLC-MS/MS system applied for unattended droplet-based surface sampling of repaglinide dosed thin tissue sections with subsequent HPLC separation and mass spectrometric analysis of parent drug and various drug metabolites were studied. Major organs (brain, lung, liver, kidney and muscle) from whole-body thin tissue sections and corresponding organ homogenates prepared from repaglinide dosed mice were sampled by surface sampling and by bulk extraction, respectively, and analyzed by HPLC-MS/MS. A semi-quantitative agreement between data obtained by surface sampling and that by employing organ homogenate extraction was observed. Drug concentrations obtained by the two methods followed the same patterns for post-dose time points (0.25, 0.5, 1 and 2 h). Drug amounts determined in the specific tissues was typically higher when analyzing extracts from the organ homogenates. In addition, relative comparison of the levels of individual metabolites between the two analytical methods also revealed good semi-quantitative agreement. Copyright © 2015 Elsevier B.V. All rights reserved.

Determination of abamectin, doramectin, emamectin, eprinomectin, ivermectin, and moxidectin in milk by liquid chromatography electrospray tandem mass specrometry.

PubMed

Sheridan, Robert; Desjardins, Lucille

2006-01-01

The avermectin and milbemycin families of compounds are derived from naturally occurring yeasts. They have proven to be potent preventatives against a variety of pests such as insects and parasites. Only eprinomectin and moxidectin are currently approved for use on lactating cattle with tolerances in milk of 12 microg/kg for eprinomectin and 40 microg/kg for moxidectin. Detection of misuse or inadvertent contamination in milk requires a sensitive and definitive analytical method. A method has been developed for the determination of 5 avermectins and 1 milbemycin in milk using a simple liquid-liquid extraction and liquid chromatography/tandem mass spectrometry (LC/MS/MS) analysis. Ivermectin (IVR), doramectin (DOR), abamectin (ABA), eprinomectin (EPR), emamectin (EMA), and moxidectin (MOX) were extracted from whole milk by partitioning into acetonitrile with a subsequent solvent exchange into methanol-water. Simultaneous confirmation and quantification were achieved with LC separation, positive electrospray ionization (ESI+), and MS/MS. The limits of detection ranged from 16 pg/g (ppt) for EMA to 1.7 microg/g (ppb) for MOX.

Quantitation of repaglinide and metabolites in mouse whole-body thin tissue sections using droplet-based liquid microjunction surface sampling-high-performance liquid chromatography-electrospray ionization tandem mass spectrometry

DOE PAGES

Chen, Weiqi; Wang, Lifei; Van Berkel, Gary J.; ...

2015-11-03

Herein, quantitation aspects of a fully automated autosampler/HPLC-MS/MS system applied for unattended droplet-based surface sampling of repaglinide dosed thin tissue sections with subsequent HPLC separation and mass spectrometric analysis of parent drug and various drug metabolites was studied. Major organs (brain, lung, liver, kidney, muscle) from whole-body thin tissue sections and corresponding organ homogenates prepared from repaglinide dosed mice were sampled by surface sampling and by bulk extraction, respectively, and analyzed by HPLC-MS/MS. A semi-quantitative agreement between data obtained by surface sampling and that by employing organ homogenate extraction was observed. Drug concentrations obtained by the two methods followed themore » same patterns for post-dose time points (0.25, 0.5, 1 and 2 h). Drug amounts determined in the specific tissues was typically higher when analyzing extracts from the organ homogenates. Furthermore, relative comparison of the levels of individual metabolites between the two analytical methods also revealed good semi-quantitative agreement.« less

Quantitation of repaglinide and metabolites in mouse whole-body thin tissue sections using droplet-based liquid microjunction surface sampling-high-performance liquid chromatography-electrospray ionization tandem mass spectrometry

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

Chen, Weiqi; Wang, Lifei; Van Berkel, Gary J.

Herein, quantitation aspects of a fully automated autosampler/HPLC-MS/MS system applied for unattended droplet-based surface sampling of repaglinide dosed thin tissue sections with subsequent HPLC separation and mass spectrometric analysis of parent drug and various drug metabolites was studied. Major organs (brain, lung, liver, kidney, muscle) from whole-body thin tissue sections and corresponding organ homogenates prepared from repaglinide dosed mice were sampled by surface sampling and by bulk extraction, respectively, and analyzed by HPLC-MS/MS. A semi-quantitative agreement between data obtained by surface sampling and that by employing organ homogenate extraction was observed. Drug concentrations obtained by the two methods followed themore » same patterns for post-dose time points (0.25, 0.5, 1 and 2 h). Drug amounts determined in the specific tissues was typically higher when analyzing extracts from the organ homogenates. Furthermore, relative comparison of the levels of individual metabolites between the two analytical methods also revealed good semi-quantitative agreement.« less

Isolation and structure elucidation of the nucleoside antibiotic strepturidin from Streptomyces albus DSM 40763.

PubMed

Pesic, Alexander; Steinhaus, Britta; Kemper, Sebastian; Nachtigall, Jonny; Kutzner, Hans Jürgen; Höfle, Gerhard; Süssmuth, Roderich D

2014-06-01

The antibiotic strepturidin (1) was isolated from the microorganism Streptomyces albus DSM 40763, and its structure elucidated by spectroscopic methods and chemical degradation studies. The determination of the relative and absolute stereocenters was partially achieved using chiral GC/EI-MS analysis and microderivatization by acetal ring formation and subsequent 2D-NMR analysis of key (1)H,(1)H-NOESY NMR correlations and extraction of (1)H,(13)C coupling constants from (1)H,(13)C-HMBC NMR spectra. Based on these results, a biosynthesis model was proposed.

Multivariate analysis of progressive thermal desorption coupled gas chromatography-mass spectrometry.

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

Van Benthem, Mark Hilary; Mowry, Curtis Dale; Kotula, Paul Gabriel

Thermal decomposition of poly dimethyl siloxane compounds, Sylgard{reg_sign} 184 and 186, were examined using thermal desorption coupled gas chromatography-mass spectrometry (TD/GC-MS) and multivariate analysis. This work describes a method of producing multiway data using a stepped thermal desorption. The technique involves sequentially heating a sample of the material of interest with subsequent analysis in a commercial GC/MS system. The decomposition chromatograms were analyzed using multivariate analysis tools including principal component analysis (PCA), factor rotation employing the varimax criterion, and multivariate curve resolution. The results of the analysis show seven components related to offgassing of various fractions of siloxanes that varymore » as a function of temperature. Thermal desorption coupled with gas chromatography-mass spectrometry (TD/GC-MS) is a powerful analytical technique for analyzing chemical mixtures. It has great potential in numerous analytic areas including materials analysis, sports medicine, in the detection of designer drugs; and biological research for metabolomics. Data analysis is complicated, far from automated and can result in high false positive or false negative rates. We have demonstrated a step-wise TD/GC-MS technique that removes more volatile compounds from a sample before extracting the less volatile compounds. This creates an additional dimension of separation before the GC column, while simultaneously generating three-way data. Sandia's proven multivariate analysis methods, when applied to these data, have several advantages over current commercial options. It also has demonstrated potential for success in finding and enabling identification of trace compounds. Several challenges remain, however, including understanding the sources of noise in the data, outlier detection, improving the data pretreatment and analysis methods, developing a software tool for ease of use by the chemist, and demonstrating our belief that this multivariate analysis will enable superior differentiation capabilities. In addition, noise and system artifacts challenge the analysis of GC-MS data collected on lower cost equipment, ubiquitous in commercial laboratories. This research has the potential to affect many areas of analytical chemistry including materials analysis, medical testing, and environmental surveillance. It could also provide a method to measure adsorption parameters for chemical interactions on various surfaces by measuring desorption as a function of temperature for mixtures. We have presented results of a novel method for examining offgas products of a common PDMS material. Our method involves utilizing a stepped TD/GC-MS data acquisition scheme that may be almost totally automated, coupled with multivariate analysis schemes. This method of data generation and analysis can be applied to a number of materials aging and thermal degradation studies.« less

Selective Extraction and Purification of Azaspiracids from Blue Mussels ( Mytilus edulis) Using Boric Acid Gel.

PubMed

Miles, Christopher O; Kilcoyne, Jane; McCarron, Pearse; Giddings, Sabrina D; Waaler, Thor; Rundberget, Thomas; Samdal, Ingunn A; Løvberg, Kjersti E

2018-03-21

Azaspiracids belong to a family of more than 50 polyether toxins originating from marine dinoflagellates such as Azadinium spinosum. All of the azaspiracids reported thus far contain a 21,22-dihydroxy group. Boric acid gel can bind selectively to compounds containing vic-diols or α-hydroxycarboxylic acids via formation of reversible boronate complexes. Here we report use of the gel to selectively capture and release azaspiracids from extracts of blue mussels. Analysis of the extracts and fractions by liquid chromatography-tandem mass spectrometry (LC-MS) showed that this procedure resulted in an excellent cleanup of the azaspiracids in the extract. Analysis by enzyme-linked immunoasorbent assay (ELISA) and LC-MS indicated that most azaspiracid analogues were recovered in good yield by this procedure. The capacity of boric acid gel for azaspiracids was at least 50 μg/g, making this procedure suitable for use in the early stages of preparative purification of azaspiracids. In addition to its potential for concentration of dilute samples, the extensive cleanup provided by boric acid gel fractionation of azaspiracids in mussel samples almost eliminated matrix effects during subsequent LC-MS and could be expected to reduce matrix effects during ELISA analysis. The method may therefore prove useful for quantitative analysis of azaspiracids as part of monitoring programs. Although LC-MS data showed that okadaic acid analogues also bound to the gel, this was much less efficient than for azaspiracids under the conditions used. The boric acid gel methodology is potentially applicable to other important groups of natural toxins containing diols including ciguatoxins, palytoxins, pectenotoxins, tetrodotoxin, trichothecenes, and toxin glycosides.

Carbonyl group containing products from nopinone oxidation

NASA Astrophysics Data System (ADS)

Kahnt, A.; Iinuma, Y.; Heinold, A.; Böge, O.; Herrmann, H.

2010-12-01

Biogenic volatile organic compounds (BVOC) such as isoprene, monoterpenes and sesquiterpenes account for a large fraction of the fluxes of atmospheric non-methane hydrocarbons. Their atmospheric degradation leads to multifunctional oxidation products that can contribute to aerosol growth. In particular, semi-volatile carbonyl compounds that are formed during the early stage of the BVOC oxidation play an important role in the formation of subsequent secondary organic aerosol (SOA) compounds. In this study, a series of aerosol chamber experiments were performed to better understand the OH initiated oxidation of nopinone and subsequent oxidation products in both the gas- and particle-phase. Nopinone is a first generation oxidation product of β-pinene and has been rarely studied for its oxidation products (Calogirou et al., 1999). The gas- and particle-phase products were sampled using a denuder/filter setup. The combination of XAD-4 and 2,4-dinitrophenylhydrazine was applied on the denuder surface to enable in-situ derivatisation of carbonyl compounds. After extraction and sample purification, the derivatised carbonyl compounds were analysed with HPLC/(-)ESI-TOFMS. The data obtained from the denuder sample analysis were compared to the data obtained from the concurrent PTR-MS measurement. The PTR-MS was used in the scan mode during the OH reactions to detect unknown gaseous oxidation products. The selected ion mode was used for some of the experiments to determine the time evolution of certain compounds. The off-line denuder sample analysis enabled us to elucidate the structures of unknown compounds whereas the PTR-MS delivers the time series of oxidation products . The influences of NOx and seed particle acidity on gas- and particle-phase product distributions will be presented. References: A. Calogirou, N.R. Jensen, C.J. Nielsen, D. Kotzias, J. Hjorth, Environmental Science & Technology 33 (1999) 453.

Real-time breath analysis with active capillary plasma ionization-ambient mass spectrometry.

PubMed

Bregy, Lukas; Sinues, Pablo Martinez-Lozano; Nudnova, Maryia M; Zenobi, Renato

2014-06-01

On-line analysis of exhaled human breath is a growing area in analytical science, for applications such as fast and non-invasive medical diagnosis and monitoring. In this work, we present a novel approach based on ambient ionization of compounds in breath and subsequent real-time mass spectrometric analysis. We introduce a plasma ionization source for this purpose, which has no need for additional gases, is very small, and is easily interfaced with virtually any commercial atmospheric pressure ionization mass spectrometer (API-MS) without major modifications. If an API-MS instrument exists in a laboratory, the cost to implement this technology is only around [Formula: see text]500, far less than the investment for a specialized mass spectrometric system designed for volatile organic compounds (VOCs) analysis. In this proof-of-principle study we were able to measure mass spectra of exhaled human breath and found these to be comparable to spectra obtained with other electrospray-based methods. We detected over 100 VOCs, including relevant metabolites like fatty acids, with molecular weights extending up to 340 Da. In addition, we were able to monitor the time-dependent evolution of the peaks and show the enhancement of the metabolism after a meal. We conclude that this approach may complement current methods to analyze breath or other types of vapors, offering an affordable option to upgrade any pre-existing API-MS to a real-time breath analyzer.

Analysis of polyethylene microplastics in environmental samples, using a thermal decomposition method.

PubMed

Dümichen, Erik; Barthel, Anne-Kathrin; Braun, Ulrike; Bannick, Claus G; Brand, Kathrin; Jekel, Martin; Senz, Rainer

2015-11-15

Small polymer particles with a diameter of less than 5 mm called microplastics find their way into the environment from polymer debris and industrial production. Therefore a method is needed to identify and quantify microplastics in various environmental samples to generate reliable concentration values. Such concentration values, i.e. quantitative results, are necessary for an assessment of microplastic in environmental media. This was achieved by thermal extraction in thermogravimetric analysis (TGA), connected to a solid-phase adsorber. These adsorbers were subsequently analysed by thermal desorption gas chromatography mass spectrometry (TDS-GC-MS). In comparison to other chromatographic methods, like pyrolyse gas chromatography mass spectrometry (Py-GC-MS), the relatively high sample masses in TGA (about 200 times higher than used in Py-GC-MS) analysed here enable the measurement of complex matrices that are not homogenous on a small scale. Through the characteristic decomposition products known for every kind of polymer it is possible to identify and even to quantify polymer particles in various matrices. Polyethylene (PE), one of the most important representatives for microplastics, was chosen as an example for identification and quantification. Copyright © 2015 Elsevier Ltd. All rights reserved.

Fast filtration sampling protocol for mammalian suspension cells tailored for phosphometabolome profiling by capillary ion chromatography - tandem mass spectrometry.

PubMed

Kvitvang, Hans F N; Bruheim, Per

2015-08-15

Capillary ion chromatography (capIC) is the premium separation technology for low molecular phosphometabolites and nucleotides in biological extracts. Removal of excessive amounts of salt during sample preparation stages is a prerequisite to enable high quality capIC separation in combination with reproducible and sensitive MS detection. Existing sampling protocols for mammalian cells used for GC-MS and LC-MS metabolic profiling can therefore not be directly applied to capIC separations. Here, the development of a fast filtration sampling protocol for mammalian suspension cells tailored for quantitative profiling of the phosphometabolome on capIC-MS/MS is presented. The whole procedure from sampling the culture to transfer of filter to quenching and extraction solution takes less than 10s. To prevent leakage it is critical that a low vacuum pressure is applied, and satisfactorily reproducibility was only obtained by usage of a vacuum pressure controlling device. A vacuum of 60mbar was optimal for filtration of multiple myeloma Jjn-3 cell cultures through 5μm polyvinylidene (PVDF) filters. A quick deionized water (DI-water) rinse step prior to extraction was tested, and significantly higher metabolite yields were obtained during capIC-MS/MS analyses in this extract compared to extracts prepared by saline and reduced saline (25%) washing steps only. In addition, chromatographic performance was dramatically improved. Thus, it was verified that a quick DI-water rinse is tolerated by the cells and can be included as the final stage during filtration. Over 30 metabolites were quantitated in JJN-3 cell extracts by using the optimized sampling protocol with subsequent capIC-MS/MS analysis, and up to 2 million cells can be used in a single filtration step for the chosen filter and vacuum pressure. The technical set-up is also highly advantageous for microbial metabolome filtration protocols after optimization of vacuum pressure and washing solutions, and the reduced salt content of the extract will also improve the quality of LC-MS analysis due to lower salt adduct ion formation. Copyright © 2015 Elsevier B.V. All rights reserved.

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.

Chemometric Data Analysis for Deconvolution of Overlapped Ion Mobility Profiles

NASA Astrophysics Data System (ADS)

Zekavat, Behrooz; Solouki, Touradj

2012-11-01

We present the details of a data analysis approach for deconvolution of the ion mobility (IM) overlapped or unresolved species. This approach takes advantage of the ion fragmentation variations as a function of the IM arrival time. The data analysis involves the use of an in-house developed data preprocessing platform for the conversion of the original post-IM/collision-induced dissociation mass spectrometry (post-IM/CID MS) data to a Matlab compatible format for chemometric analysis. We show that principle component analysis (PCA) can be used to examine the post-IM/CID MS profiles for the presence of mobility-overlapped species. Subsequently, using an interactive self-modeling mixture analysis technique, we show how to calculate the total IM spectrum (TIMS) and CID mass spectrum for each component of the IM overlapped mixtures. Moreover, we show that PCA and IM deconvolution techniques provide complementary results to evaluate the validity of the calculated TIMS profiles. We use two binary mixtures with overlapping IM profiles, including (1) a mixture of two non-isobaric peptides (neurotensin (RRPYIL) and a hexapeptide (WHWLQL)), and (2) an isobaric sugar isomer mixture of raffinose and maltotriose, to demonstrate the applicability of the IM deconvolution.

A simple method to identify ether lipids in spermatozoa samples by MALDI-TOF mass spectrometry.

PubMed

Nimptsch, Ariane; Fuchs, Beate; Süß, Rosmarie; Zschörnig, Kristin; Jakop, Ulrike; Göritz, Frank; Schiller, Jürgen; Müller, Karin

2013-08-01

Plasmalogens (alkenylacyl glycerophospholipids) are important lipid constituents of many tissues and cells (e.g., selected spermatozoa). Since the molecular weights of plasmalogens overlap with that of diacyl- or alkyl acyl lipids, sophisticated mass spectrometry (MS; including MS/MS) analysis is normally used for the unequivocal identification of plasmalogens. We will show here that a simple matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (without MS/MS capability) in combination with acidic hydrolysis and subsequent derivatization with 2,4-dinitrophenylhydrazine (DNPH) and/or digestion with phospholipase A2 (PLA2) is sufficient to determine the contributions of ether lipids in spermatozoa extracts. As neither diacyl nor alkylacyl lipids are sensitive to acids and do not react with DNPH, the comparison of the mass spectra before and after treatment with acids and/or DNPH addition readily provides unequivocal information about the plasmalogen content. Additionally, the released aldehydes are readily converted into the 2,4-dinitrophenylhydrazones and can be easily identified in the corresponding negative ion mass spectra. Finally, PLA2 digestion is very useful in confirming the presence of plasmalogens. The suggested method was validated by analyzing roe deer, bovine, boar, and domestic cat spermatozoa extracts and comparing the results with isolated phospholipids.

Secondary Organic Aerosol Formation from Glyoxal: photochemical versus dark uptake and reversible versus irreversible SOA formation

NASA Astrophysics Data System (ADS)

Waxman, E.; Slowik, J. G.; Kampf, C. J.; Timkovsky, J.; Noziere, B.; Praplan, A. P.; Pfaffenberger, L.; Holzinger, R.; Hoffmann, T.; Dommen, J.; Prevot, A. S.; Baltensperger, U.; Volkamer, R.

2011-12-01

Glyoxal forms secondary organic aerosol (SOA) by partitioning to the aerosol aqueous phase according to Henry's law. The subsequent processing by heterogeneous and multiphase reactions shifts the partitioning towards aerosols. Currently it is not well understood whether these reactions result in reversible or irreversible SOA formation, and what parameters influence the rate limiting step of multiphase processing. We conducted a series of simulation chamber experiments at PSI in April and May 2011 to investigate processing under dark conditions, UV and/or visible light irradiated conditions, and in the presence and absence of OH radicals. Experiments used ammonium sulfate or ammonium sulfate/fulvic acid mixtures as seed aerosols, and were conducted between 50% and 85% relative humidity at approximately constant RH over the course of any given experiment. Glyoxal was produced photochemically from acetylene, using HONO photolysis as the OH radical source. Gas-phase glyoxal was measured by the CU LED-Cavity Enhanced-DOAS. The Thermal-Desorption Proton-Transfer-Reaction Mass Spectrometer (TD-PTR-MS) and Ion Chromatography Mass Spectrometer (IC-MS) monitored both gas and aerosol-phase organic reaction products. Particle composition was monitored by High-Resolution Time-of-Flight Aerosol Mass Spectrometry (HR-ToF-AMS), and HPLC-ESI MS/MS and LC-MS analysis of filter samples.

Secondary Organic Aerosol Formation from Glyoxal: photochemical versus dark uptake and reversible versus irreversible SOA formation

NASA Astrophysics Data System (ADS)

Waxman, E.; Slowik, J.; Kampf, C.; Timkovsky, J.; Noziere, B.; Praplan, A.; Pffafenberger, L.; Holzinger, R.; Hoffmann, T.; Dommen, J.; Prevot, A.; Baltensperger, U.; Volkamer, R.

2012-04-01

Glyoxal forms secondary organic aerosol (SOA) by partitioning to the aerosol aqueous phase according to Henry's law. The subsequent processing by heterogeneous and multiphase reactions shifts the partitioning towards aerosols. Currently it is not well understood whether these reactions result in reversible or irreversible SOA formation, and what parameters influence the rate limiting step of multiphase processing. We conducted a series of simulation chamber experiments at PSI in April and May 2011 to investigate processing under dark conditions, UV and/or visible light irradiated conditions, and in the presence and absence of OH radicals. Experiments used ammonium sulfate or ammonium sulfate/fulvic acid mixtures as seed aerosols, and were conducted between 50% and 85% relative humidity at approximately constant RH over the course of any given experiment. Glyoxal was produced photochemically from acetylene, using HONO photolysis as the OH radical source. Gas-phase glyoxal was measured by the CU LED-Cavity Enhanced-DOAS. The Thermal-Desorption Proton-Transfer-Reaction Mass Spectrometer (TD-PTR-MS) and Ion Chromatography Mass Spectrometer (IC-MS) monitored both gas and aerosol-phase organic reaction products. Particle composition was monitored by High-Resolution Time-of-Flight Aerosol Mass Spectrometry (HR-ToF-AMS), and HPLC-ESI MS/MS and LC-MS analysis of filter samples.

MS4a4B, a CD20 homologue in T cells, inhibits T cell propagation by modulation of cell cycle.

PubMed

Xu, Hui; Yan, Yaping; Williams, Mark S; Carey, Gregory B; Yang, Jingxian; Li, Hongmei; Zhang, Guang-Xian; Rostami, Abdolmohamad

2010-11-01

MS4a4B, a CD20 homologue in T cells, is a novel member of the MS4A gene family in mice. The MS4A family includes CD20, FcεRIβ, HTm4 and at least 26 novel members that are characterized by their structural features: with four membrane-spanning domains, two extracellular domains and two cytoplasmic regions. CD20, FcεRIβ and HTm4 have been found to function in B cells, mast cells and hematopoietic cells respectively. However, little is known about the function of MS4a4B in T cell regulation. We demonstrate here that MS4a4B negatively regulates mouse T cell proliferation. MS4a4B is highly expressed in primary T cells, natural killer cells (NK) and some T cell lines. But its expression in all malignant T cells, including thymoma and T hybridoma tested, was silenced. Interestingly, its expression was regulated during T cell activation. Viral vector-driven overexpression of MS4a4B in primary T cells and EL4 thymoma cells reduced cell proliferation. In contrast, knockdown of MS4a4B accelerated T cell proliferation. Cell cycle analysis showed that MS4a4B regulated T cell proliferation by inhibiting entry of the cells into S-G2/M phase. MS4a4B-mediated inhibition of cell cycle was correlated with upregulation of Cdk inhibitory proteins and decreased levels of Cdk2 activity, subsequently leading to inhibition of cell cycle progression. Our data indicate that MS4a4B negatively regulates T cell proliferation. MS4a4B, therefore, may serve as a modulator in the negative-feedback regulatory loop of activated T cells.

Evidence for electron-based ion generation in radio-frequency ionization.

PubMed

Olaitan, Abayomi D; Zekavat, Behrooz; Solouki, Touradj

2016-01-01

Radio-frequency ionization (RFI) is a novel ionization method coupled to mass spectrometry (MS) for analysis of semi-volatile and volatile organic compounds (VOCs). Despite the demonstrated capabilities of RFI MS for VOC analysis in both positive- and negative-ion modes, mechanism of RFI is not completely understood. Improved understanding of the ion generation process in RFI should expand its utility in MS. Here, we studied the possibility of electron emission in RFI using both direct charged particle current measurements and indirect electron detection in a 9.4-T Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometer. We show that RF-generated electrons can be trapped in the ICR cell and, subsequently, reacted with neutral hexafluorobenzene (C6 F6 ) molecules to generate C6 F6 (●-) . Intensity of observed C6 F6 (●-) species correlated with the number of trapped electrons and decreased as a function of electron quenching period. We also measured the electron attachment rate constant of hexafluorobenzene using a post-RF electron trapping experiment. Measured electron attachment rate constant of hexafluorobenzene (1.19 (±0.53) × 10(-9)  cm(3)  molecule(-1)  s(-1) ) for post-RF FT-ICR MS agreed with the previously reported value (1.60 (±0.30) × 10(-9)  cm(3)  molecule(-1)  s(-1) ) from low-pressure ICR MS measurements. Experimental results from direct and indirect electron measurements suggest that RFI process involves RF-generated electrons under ultrahigh vacuum conditions. Copyright © 2015 John Wiley & Sons, Ltd.

Proteomic analysis of Pinus radiata needles: 2-DE map and protein identification by LC/MS/MS and substitution-tolerant database searching.

PubMed

Valledor, Luis; Castillejo, Maria A; Lenz, Christof; Rodríguez, Roberto; Cañal, Maria J; Jorrín, Jesús

2008-07-01

Pinus radiata is one of the most economically important forest tree species, with a worldwide production of around 370 million m (3) of wood per year. Current selection of elite trees to be used in conservation and breeding programes requires the physiological and molecular characterization of available populations. To identify key proteins related to tree growth, productivity and responses to environmental factors, a proteomic approach is being utilized. In this paper, we present the first report of the 2-DE protein reference map of physiologically mature P. radiata needles, as a basis for subsequent differential expression proteomic studies related to growth, development, biomass production and responses to stresses. After TCA/acetone protein extraction of needle tissue, 549 +/- 21 well-resolved spots were detected in Coommassie-stained gels within the 5-8 pH and 10-100 kDa M(r) ranges. The analytical and biological variance determined for 450 spots were of 31 and 42%, respectively. After LC/MS/MS analysis of in-gel tryptic digested spots, proteins were identified by using the novel Paragon algorithm that tolerates amino acid substitution in the first-pass search. It allowed the confident identification of 115 out of the 150 protein spots subjected to MS, quite unusual high percentage for a poor sequence database, as is the case of P. radiata. Proteins were classified into 12 or 18 groups based on their corresponding cell component or biological process/pathway categories, respectively. Carbohydrate metabolism and photosynthetic enzymes predominate in the 2-DE protein profile of P. radiata needles.

Determination of doping peptides via solid-phase microelution and accurate-mass quadrupole time-of-flight LC-MS.

PubMed

Cuervo, Darío; Loli, Cynthia; Fernández-Álvarez, María; Muñoz, Gloria; Carreras, Daniel

2017-10-15

A complete analytical protocol for the determination of 25 doping-related peptidic drugs and 3 metabolites in urine was developed by means of accurate-mass quadrupole time-of-flight (Q-TOF) LC-MS analysis following solid-phase extraction (SPE) on microplates and conventional SPE pre-treatment for initial testing and confirmation, respectively. These substances included growth hormone releasing factors, gonadotropin releasing factors and anti-diuretic hormones, with molecular weights ranging from 540 to 1320Da. Optimal experimental conditions were stablished after investigation of different parameters concerning sample preparation and instrumental analysis. Weak cation exchange SPE followed by C18 HPLC chromatography and accurate mass detection provided the required sensitivity and selectivity for all the target peptides under study. 2mg SPE on 96-well microplates can be used in combination with full scan MS detection for the initial testing, thus providing a fast, cost-effective and high-throughput protocol for the processing of a large batch of samples simultaneously. On the other hand, extraction on 30mg SPE cartridges and subsequent target MS/MS determination was the protocol of choice for confirmatory purposes. The methodology was validated in terms of selectivity, recovery, matrix effect, precision, sensitivity (limit of detection, LOD), cross contamination, carryover, robustness and stability. Recoveries ranged from 6 to 70% (microplates) and 17-95% (cartridges), with LODs from 0.1 to 1ng/mL. The suitability of the method was assessed by analyzing different spiked or excreted urines containing some of the target substances. Copyright © 2017 Elsevier B.V. All rights reserved.

EFFECTS OF ANESTHESIA (MS222) ON LIVER BIOTRANSFORMATION IN RAINBOW TROUT (ONCORHYNCHUS MYKISS)

EPA Science Inventory

Tricaine methanesulfonate (3-aminobenzoic acid ethyl ester methanesulfonate; MS222) is a widely used fish anaesthetic. While there have been several studies addressing the impact of its use on subsequently measured biotransformation rates, the measured influence on normal functio...

Principal component analysis of normalized full spectrum mass spectrometry data in multiMS-toolbox: An effective tool to identify important factors for classification of different metabolic patterns and bacterial strains.

PubMed

Cejnar, Pavel; Kuckova, Stepanka; Prochazka, Ales; Karamonova, Ludmila; Svobodova, Barbora

2018-06-15

Explorative statistical analysis of mass spectrometry data is still a time-consuming step. We analyzed critical factors for application of principal component analysis (PCA) in mass spectrometry and focused on two whole spectrum based normalization techniques and their application in the analysis of registered peak data and, in comparison, in full spectrum data analysis. We used this technique to identify different metabolic patterns in the bacterial culture of Cronobacter sakazakii, an important foodborne pathogen. Two software utilities, the ms-alone, a python-based utility for mass spectrometry data preprocessing and peak extraction, and the multiMS-toolbox, an R software tool for advanced peak registration and detailed explorative statistical analysis, were implemented. The bacterial culture of Cronobacter sakazakii was cultivated on Enterobacter sakazakii Isolation Agar, Blood Agar Base and Tryptone Soya Agar for 24 h and 48 h and applied by the smear method on an Autoflex speed MALDI-TOF mass spectrometer. For three tested cultivation media only two different metabolic patterns of Cronobacter sakazakii were identified using PCA applied on data normalized by two different normalization techniques. Results from matched peak data and subsequent detailed full spectrum analysis identified only two different metabolic patterns - a cultivation on Enterobacter sakazakii Isolation Agar showed significant differences to the cultivation on the other two tested media. The metabolic patterns for all tested cultivation media also proved the dependence on cultivation time. Both whole spectrum based normalization techniques together with the full spectrum PCA allow identification of important discriminative factors in experiments with several variable condition factors avoiding any problems with improper identification of peaks or emphasis on bellow threshold peak data. The amounts of processed data remain still manageable. Both implemented software utilities are available free of charge from http://uprt.vscht.cz/ms. Copyright © 2018 John Wiley & Sons, Ltd.

Relationship between gait initiation and disability in individuals affected by multiple sclerosis.

PubMed

Galli, Manuela; Coghe, Giancarlo; Sanna, Paola; Cocco, Eleonora; Marrosu, Maria Giovanna; Pau, Massimiliano

2015-11-01

This study analyzes how multiple sclerosis (MS) does affect one of the most common voluntary activities in life: the gait initiation (GI). The main aim of the work is to characterize the execution of this task by measuring and comparing relevant parameters based on center of pressure (COP) patterns and to study the relationship between these and the level of expanded disability status scale (EDSS). To this aim, 95 MS subjects with an average EDSS score of 2.4 and 35 healthy subjects were tested using a force platform during the transition from standing posture to gait. COP time-series were acquired and processed to extract a number of parameters related to the trajectory followed by the COP. The statistical analysis revealed that only a few measurements were statistically different between the two groups and only these were subsequently correlated with EDSS score. The correlation analysis underlined that a progressive alteration of the task execution can be directly related with the increase of EDSS score. These finding suggest that most of the impairment found in people with MS comes from the first part of the COP pattern, the anticipatory postural adjustments (APAs). The central nervous system performs APAs before every voluntary movement to minimize balance perturbation due to the movement itself. Gait Initiation's APAs consist in some ankle muscles contractions that induce a backward COP shift to the swing limb. The analysis here performed highlighted that MS affected patients have a reduced posterior COP shift that reveals that the anticipatory mechanism is impaired. Copyright © 2015 Elsevier B.V. All rights reserved.

Development of a sensitive and selective liquid chromatography-mass spectrometry method for high throughput analysis of paralytic shellfish toxins using graphitised carbon solid phase extraction.

PubMed

Boundy, Michael J; Selwood, Andrew I; Harwood, D Tim; McNabb, Paul S; Turner, Andrew D

2015-03-27

Routine regulatory monitoring of paralytic shellfish toxins (PST) commonly employs oxidative derivitisation and complex liquid chromatography fluorescence detection methods (LC-FL). The pre-column oxidation LC-FL method is currently implemented in New Zealand and the United Kingdom. When using this method positive samples are fractionated and two different oxidations are required to confirm the identity and quantity of each PST analogue present. There is a need for alternative methods that are simpler, provide faster turnaround times and have improved detection limits. Hydrophilic interaction liquid chromatography (HILIC) HPLC-MS/MS analysis of PST has been used for research purposes, but high detection limits and substantial sample matrix issues have prevented it from becoming a viable alternative for routine monitoring purposes. We have developed a HILIC UPLC-MS/MS method for paralytic shellfish toxins with an optimised desalting clean-up procedure on inexpensive carbon solid phase extraction cartridges for reduction of matrix interferences. This represents a major technical breakthrough and allows sensitive, selective and rapid analysis of paralytic shellfish toxins from a variety of sample types, including many commercially produced bivalve molluscan shellfish species. Additionally, this analytical approach avoids the need for complex calculations to determine sample toxicity, as unlike other methods each PST analogue is able to be quantified as a single resolved peak. This article presents the method development and optimisation information. A thorough single laboratory validation study has subsequently been performed and this data will be presented elsewhere. Copyright © 2015 Elsevier B.V. All rights reserved.

Characteristics of downward leaders in a cloud-to-ground lightning strike on a lightning rod

NASA Astrophysics Data System (ADS)

Wang, Caixia; Sun, Zhuling; Jiang, Rubin; Tian, Yangmeng; Qie, Xiushu

2018-05-01

A natural downward negative cloud-to-ground (CG) lightning was observed at a close distance of 370 m by using electric field change measurements and a high-speed camera at 5400 frames per second (fps). Two subsequent leader-return strokes of the lightning hit a lightning rod installed on the top of a seven-story building in Beijing city, while the grounding point for the stepped leader-first return stroke was 12 m away, on the roof of the building. The 2-D average speed of the downward stepped leader (L1) before the first return stroke (R1) was approximately 5.1 × 104 m/s during its propagation over the 306 m above the building, and those before the subsequent strokes (R2 and R3) ranged from 1.1 × 106 m/s to 2.2 × 106 m/s. An attempted leader (AL) occurred 201 ms after R1 and 10 ms before R2 reached approximately 99 m above the roof and failed to connect to the ground. The 2-D average speed of the AL was approximately 7.4 × 104 m/s. The luminosity at tip of the leader was brighter than the channel behind it. The leader inducing the R2 with an alteration of terminating point was a dart-stepped leader (DSL), which propagated through the channel of AL and continued to develop downward with new branches at about 17 m above the roof. The 2-D speed of the DSL at the bottom 99 m was 6.6 × 105 m/s. The average time interval between the stepped pulses of the DSL was approximately 10 μs, smaller than that of L1 with value of about 17 μs. The average step lengths of the DSL were approximately 6.6 m. The study shows that the stepped leader-first return stroke of lightning will not always hit the tip of a tall metal rod due to the significant branching property of the leader. However, under certain conditions, the subsequent return strokes may alter the grounding point to the tip of a tall metal rod. For the lightning rod, the protection against subsequent return strokes may be better than that against the first return stroke.

High-resolution droplet-based fractionation of nano-LC separations onto microarrays for MALDI-MS analysis.

PubMed

Küster, Simon K; Pabst, Martin; Jefimovs, Konstantins; Zenobi, Renato; Dittrich, Petra S

2014-05-20

We present a robust droplet-based device, which enables the fractionation of ultralow flow rate nanoflow liquid chromatography (nano-LC) eluate streams at high frequencies and high peak resolution. This is achieved by directly interfacing the separation column to a micro T-junction, where the eluate stream is compartmentalized into picoliter droplets. This immediate compartmentalization prevents peak dispersion during eluate transport and conserves the chromatographic performance. Subsequently, nanoliter eluate fractions are collected at a rate of one fraction per second on a high-density microarray to retain the separation with high temporal resolution. Chromatographic separations of up to 45 min runtime can thus be archived on a single microarray possessing 2700 sample spots. The performance of this device is demonstrated by fractionating the separation of a tryptic digest of a known protein mixture onto the microarray chip and subsequently analyzing the sample archive using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Resulting peak widths are found to be significantly reduced compared to standard continuous flow spotting technologies as well as in comparison to a conventional nano-LC-electrospray ionization-mass spectrometry interface. Moreover, we demonstrate the advantage of our high-definition nanofractionation device by applying two different MALDI matrices to all collected fractions in an alternating fashion. Since the information that is obtained from a MALDI-MS measurement depends on the choice of MALDI matrix, we can extract complementary information from neighboring spots containing almost identical composition but different matrices.

[Qualitative analysis of bis-(3'-5')-cyclic dimeric adenosine monophosphate of Porphyromonas gingivalis by high performance liquid chromatography coupled with mass spectrometry].

PubMed

Yongmei, Tan; Xiaojun, Yang; Juan, Du; Wanghong, Zhao; Xiaodan, Chen; Jin, Hou

2016-06-01

To test whether Porphyromonas gingivalis (P. gingivalis) could produce bacterial signal molecule, bis-(3'-5')-cyclic dimeric adenosine monophosphate (c-di-AMP) and lay the foundation for explorations of its roles in life metabolism and periodontitis immunity of P. gingivalis. P. gingivalis standard strain ATCC33277 was used as the experimental strain to extract nucleic acids from the bacteria. Then, c-di-AMP was detected using high performance liquid chromatography coupled with mass spectrometry (HPLC-MS/MS). Subsequently, HPLC was used to validate the sample further. Based on the signal/noise (S/N) for 3 : 1, the limit of determination of HPLC-MS/MS for peak time of c-di-AMP standard substances was 7.49 min and nucleic acid extractions from P. gingivalis was 8.82 min (S/N > 3). Further confirmation of HPLC showed that nucleic acid extractions from both P. gingivalis and c-di-AMP standard substances pre- sented goal absorbent peaks at 15.7 min, with the same ultraviolet absorbent spectrum. The nucleic acid extrac- tions from P. gingivalis contained c-di-AMP, which shows that P. gingivalis could produce c-di-AMP.

Two-dimensional proteome reference maps for the soybean cyst nematode Heterodera glycines

USDA-ARS?s Scientific Manuscript database

Two-dimensional electrophoresis (2-DE) reference maps of Heterodera glycines were constructed. After in-gel digestion with trypsin, 803 spots representing 426 proteins were subsequently identified by LC-MS/MS. Proteins with annotated function were further categorized by Gene Ontology. Results showed...

Diagnosis of glutaric aciduria type 1 by measuring 3-hydroxyglutaric acid in dried urine spots by liquid chromatography tandem mass spectrometry.

PubMed

Al-Dirbashi, Osama Y; Kölker, Stefan; Ng, Dione; Fisher, Lawrence; Rupar, Tony; Lepage, Nathalie; Rashed, Mohamed S; Santa, Tomofumi; Goodman, Stephen I; Geraghty, Michael T; Zschocke, Johannes; Christensen, Ernst; Hoffmann, Georg F; Chakraborty, Pranesh

2011-02-01

Accumulation of glutaric acid (GA) and 3-hydroxyglutaric acid (3HGA) in body fluids is the biochemical hallmark of type 1 glutaric aciduria (GA1), a disorder characterized by acute striatal degeneration and a subsequent dystonia. To date, methods for quantification of 3HGA are mainly based on stable isotope dilution gas chromatography mass spectrometry (GC-MS) and require extensive sample preparation. Here we describe a simple liquid chromatography tandem MS (LC-MS/MS) method to quantify this important metabolite in dried urine spots (DUS). This method is based on derivatization with 4-[2-(N,N-dimethylamino)ethylaminosulfonyl]-7-(2-aminoethylamino)-2,1,3-benzoxadiazole (DAABD-AE). Derivatization was adopted to improve the chromatographic and mass spectrometric properties of the studied analytes. Derivatization was performed directly on a 3.2-mm disc of DUS as a sample without extraction. Sample mixture was heated at 60°C for 45 min, and 5 μl of the reaction solution was analyzed by LC-MS/MS. Reference ranges obtained were in excellent agreement with the literature. The method was applied retrospectively for the analysis of DUS samples from established low- and high-excreter GA1 patients as well as controls (n = 100). Comparison of results obtained versus those obtained by GC-MS was satisfactory (n = 14). In populations with a high risk of GA1, this approach will be useful as a primary screening method for high- or low-excreter variants. In these populations, however, DUS analysis should not be implemented before completing a parallel comparative study with the standard screening method (i.e., molecular testing). In addition, follow-up DUS GA and 3HGA testing of babies with elevated dried blood spot C5DC acylcarnitines will be useful as a first-tier diagnostic test, thus reducing the number of cases requiring enzymatic and molecular analyses to establish or refute the diagnosis of GA1.

Emotionally negative pictures increase attention to a subsequent auditory stimulus.

PubMed

Tartar, Jaime L; de Almeida, Kristen; McIntosh, Roger C; Rosselli, Monica; Nash, Allan J

2012-01-01

Emotionally negative stimuli serve as a mechanism of biological preparedness to enhance attention. We hypothesized that emotionally negative stimuli would also serve as motivational priming to increase attention resources for subsequent stimuli. To that end, we tested 11 participants in a dual sensory modality task, wherein emotionally negative pictures were contrasted with emotionally neutral pictures and each picture was followed 600 ms later by a tone in an auditory oddball paradigm. Each trial began with a picture displayed for 200 ms; half of the trials began with an emotionally negative picture and half of the trials began with an emotionally neutral picture; 600 ms following picture presentation, the participants heard either an oddball tone or a standard tone. At the end of each trial (picture followed by tone), the participants categorized, with a button press, the picture and tone combination. As expected, and consistent with previous studies, we found an enhanced visual late positive potential (latency range=300-700 ms) to the negative picture stimuli. We further found that compared to neutral pictures, negative pictures resulted in early attention and orienting effects to subsequent tones (measured through an enhanced N1 and N2) and sustained attention effects only to the subsequent oddball tones (measured through late processing negativity, latency range=400-700 ms). Number pad responses to both the picture and tone category showed the shortest response latencies and greatest percentage of correct picture-tone categorization on the negative picture followed by oddball tone trials. Consistent with previous work on natural selective attention, our results support the idea that emotional stimuli can alter attention resource allocation. This finding has broad implications for human attention and performance as it specifically shows the conditions in which an emotionally negative stimulus can result in extended stimulus evaluation. Copyright © 2011 Elsevier B.V. All rights reserved.

Global analysis of glycoproteins identifies markers of endotoxin tolerant monocytes and GPR84 as a modulator of TNFα expression.

PubMed

Müller, Mario M; Lehmann, Roland; Klassert, Tilman E; Reifenstein, Stella; Conrad, Theresia; Moore, Christoph; Kuhn, Anna; Behnert, Andrea; Guthke, Reinhard; Driesch, Dominik; Slevogt, Hortense

2017-04-12

Exposure of human monocytes to lipopolysaccharide (LPS) induces a temporary insensitivity to subsequent LPS challenges, a cellular state called endotoxin tolerance. In this study, we investigated the LPS-induced global glycoprotein expression changes of tolerant human monocytes and THP-1 cells to identify markers and glycoprotein targets capable to modulate the immunosuppressive state. Using hydrazide chemistry and LC-MS/MS analysis, we analyzed glycoprotein expression changes during a 48 h LPS time course. The cellular snapshots at different time points identified 1491 glycoproteins expressed by monocytes and THP-1 cells. Label-free quantitative analysis revealed transient or long-lasting LPS-induced expression changes of secreted or membrane-anchored glycoproteins derived from intracellular membrane coated organelles or from the plasma membrane. Monocytes and THP-1 cells demonstrated marked differences in glycoproteins differentially expressed in the tolerant state. Among the shared differentially expressed glycoproteins G protein-coupled receptor 84 (GPR84) was identified as being capable of modulating pro-inflammatory TNFα mRNA expression in the tolerant cell state when activated with its ligand Decanoic acid.

Quantitative proteomic analysis reveals proteins involved in the neurotoxicity of marine medaka Oryzias melastigma chronically exposed to inorganic mercury.

PubMed

Wang, Yuyu; Wang, Dazhi; Lin, Lin; Wang, Minghua

2015-01-01

Mercury is a ubiquitous environmental contaminant which exerts neurotoxicity upon animals. Nevertheless, the molecular mechanisms involved in inorganic mercury neurotoxicity are unknown. We investigated protein profiles of marine medaka, chronically exposed to mercuric chloride using two-dimensional difference gel electrophoresis (2D-DIGE) and matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-TOF-TOF MS) analysis. The mercury accumulation and ultrastructure were also examined in the brain. The results showed that mercury was significantly accumulated in the treated brain, and subsequently caused a noticeable damage. The comparison of 2D-DIGE protein profiles between the control and treatment revealed that 16 protein spots were remarkably altered in abundance, which were further submitted for MALDI-TOF-TOF MS analysis. The identified proteins indicated that inorganic mercury may cause neurotoxicity through the induction of oxidative stress, cytoskeletal assembly dysfunction and metabolic disorders. Thus, this study provided a basis for a better understanding of the molecular mechanisms involved in mercury neurotoxicity. Copyright © 2014 Elsevier Ltd. All rights reserved.

Relapse May Serve as a Mediator Variable in Longitudinal Outcomes in Multiple Sclerosis.

PubMed

Stone, Lael Anne; Cutter, Gary Raymond; Fisher, Elizabeth; Richert, Nancy; McCartin, Jennifer; Ohayon, Joan; Bash, Craig; McFarland, Henry

2016-05-01

Contrast-enhancing lesions (CEL) on magnetic resonance imaging (MRI) are believed to represent inflammatory disease activity in multiple sclerosis (MS), but their relationship to subsequent long-term disability and progression is unclear, particularly at longer time periods such as 8-10 years. Between 1989 and 1994, 111 MS patients were seen at the National Institutes of Health for clinical evaluations and 3 monthly contrast-enhanced MRI scans. Of these, 94 patients were re-evaluated a mean of 8 years later (range 6.1-10.5 years) with a single MRI scan and clinical evaluation. CEL number and volume were determined at baseline and follow-up. The number of relapses was ascertained over the follow-up period and annualized relapse rates were calculated. Other MRI parameters, such as T2 hyperintensity volume, T1 volume, and brain parenchymal fraction, were also calculated. While there was no direct correlation between CEL number or volume at baseline and disability status at follow-up, CEL measures at baseline did correlate with number of relapses observed in the subsequent years, and the number of relapses in turn correlated with subsequent disability as well as transition to progressive MS. While number and volume of CEL at baseline do not directly correlate with disability in the longer term in MS, our data suggest that 1 route to disability involves relapses as a mediator variable in the causal sequence of MS progression from CEL to disability. Further studies using relapse as a mediator variable in a larger data set may be warranted. Copyright © 2015 by the American Society of Neuroimaging.

MALDI Orbitrap Mass Spectrometry Profiling of Dysregulated Sulfoglycosphingolipids in Renal Cell Carcinoma Tissues

NASA Astrophysics Data System (ADS)

Jirásko, Robert; Holčapek, Michal; Khalikova, Maria; Vrána, David; Študent, Vladimír; Prouzová, Zuzana; Melichar, Bohuslav

2017-08-01

Matrix-assisted laser desorption/ionization coupled with Orbitrap mass spectrometry (MALDI-Orbitrap-MS) is used for the clinical study of patients with renal cell carcinoma (RCC), as the most common type of kidney cancer. Significant changes in sulfoglycosphingolipid abundances between tumor and autologous normal kidney tissues are observed. First, sulfoglycosphingolipid species in studied RCC samples are identified using high mass accuracy full scan and tandem mass spectra. Subsequently, optimization, method validation, and statistical evaluation of MALDI-MS data for 158 tissues of 80 patients are discussed. More than 120 sulfoglycosphingolipids containing one to five hexosyl units are identified in human RCC samples based on the systematic study of their fragmentation behavior. Many of them are recorded here for the first time. Multivariate data analysis (MDA) methods, i.e., unsupervised principal component analysis (PCA) and supervised orthogonal partial least square discriminant analysis (OPLS-DA), are used for the visualization of differences between normal and tumor samples to reveal the most up- and downregulated lipids in tumor tissues. Obtained results are closely correlated with MALDI mass spectrometry imaging (MSI) and histologic staining. Important steps of the present MALDI-Orbitrap-MS approach are also discussed, such as the selection of best matrix, correct normalization, validation for semiquantitative study, and problems with possible isobaric interferences on closed masses in full scan mass spectra.

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.

Reproducible Tissue Homogenization and Protein Extraction for Quantitative Proteomics Using MicroPestle-Assisted Pressure-Cycling Technology.

PubMed

Shao, Shiying; Guo, Tiannan; Gross, Vera; Lazarev, Alexander; Koh, Ching Chiek; Gillessen, Silke; Joerger, Markus; Jochum, Wolfram; Aebersold, Ruedi

2016-06-03

The reproducible and efficient extraction of proteins from biopsy samples for quantitative analysis is a critical step in biomarker and translational research. Recently, we described a method consisting of pressure-cycling technology (PCT) and sequential windowed acquisition of all theoretical fragment ions-mass spectrometry (SWATH-MS) for the rapid quantification of thousands of proteins from biopsy-size tissue samples. As an improvement of the method, we have incorporated the PCT-MicroPestle into the PCT-SWATH workflow. The PCT-MicroPestle is a novel, miniaturized, disposable mechanical tissue homogenizer that fits directly into the microTube sample container. We optimized the pressure-cycling conditions for tissue lysis with the PCT-MicroPestle and benchmarked the performance of the system against the conventional PCT-MicroCap method using mouse liver, heart, brain, and human kidney tissues as test samples. The data indicate that the digestion of the PCT-MicroPestle-extracted proteins yielded 20-40% more MS-ready peptide mass from all tissues tested with a comparable reproducibility when compared to the conventional PCT method. Subsequent SWATH-MS analysis identified a higher number of biologically informative proteins from a given sample. In conclusion, we have developed a new device that can be seamlessly integrated into the PCT-SWATH workflow, leading to increased sample throughput and improved reproducibility at both the protein extraction and proteomic analysis levels when applied to the quantitative proteomic analysis of biopsy-level samples.

Long-Term Data Reveal Rate and Risk Factors for Subsequent Surgeries Following Initial ACL Reconstruction

MedlinePlus

... and Risk Factors for Subsequent Surgeries Following Initial ACL Reconstruction By Colleen Labbe, M.S. | December 1, 2013 ... surgery to reconstruct a torn anterior cruciate ligament (ACL) eventually need to have additional surgery on the ...

Phosphorylation of αB-crystallin supports reactive astrogliosis in demyelination

PubMed Central

Yoon, Jane; van Horssen, Jack; Han, May H.; Bollyky, Paul L.; Palmer, Theo D.; Steinman, Lawrence

2017-01-01

The small heat shock protein αB-crystallin (CRYAB) has been implicated in multiple sclerosis (MS) pathogenesis. Earlier studies have indicated that CRYAB inhibits inflammation and attenuates clinical disease when administered in the experimental autoimmune encephalomyelitis model of MS. In this study, we evaluated the role of CRYAB in primary demyelinating events. Using the cuprizone model of demyelination, a noninflammatory model that allows the analysis of glial responses in MS, we show that endogenous CRYAB expression is associated with increased severity of demyelination. Moreover, we demonstrate a strong correlation between the expression of CRYAB and the extent of reactive astrogliosis in demyelinating areas and in in vitro assays. In addition, we reveal that CRYAB is differentially phosphorylated in astrocytes in active demyelinating MS lesions, as well as in cuprizone-induced lesions, and that this phosphorylation is required for the reactive astrocyte response associated with demyelination. Furthermore, taking a proteomics approach to identify proteins that are bound by the phosphorylated forms of CRYAB in primary cultured astrocytes, we show that there is clear differential binding of protein targets due to the specific phosphorylation of CRYAB. Subsequent Ingenuity Pathway Analysis of these targets reveals implications for intracellular pathways and biological processes that could be affected by these modifications. Together, these findings demonstrate that astrocytes play a pivotal role in demyelination, making them a potential target for therapeutic intervention, and that phosphorylation of CRYAB is a key factor supporting the pathogenic response of astrocytes to oligodendrocyte injury. PMID:28196893

On-line solid phase extraction using the Prospekt-2 coupled with a liquid chromatography/tandem mass spectrometer for the determination of dextromethorphan, dextrorphan and guaifenesin in human plasma.

PubMed

Kuhlenbeck, Debbie L; Eichold, Thomas H; Hoke, Steven H; Baker, Timothy R; Mensen, Robert; Wehmeyer, Kenneth R

2005-01-01

An on-line liquid chromatography/tandem mass spectrometry (LC-MS/MS) procedure, using the Prospekt- 2 system, was developed and used for the determination of the levels of the active ingredients of cough/cold medications in human plasma matrix. The experimental configuration allows direct plasma injection by performing on- line solid phase extraction (SPE) on small cartridge columns prior to elution of the analyte(s) onto the analytical column and subsequent MS/MS detection. The quantitative analysis of three analytes with differing polarities, dextromethorphan (DEX), dextrorphan (DET) and guaifenesin (GG) in human plasma presented a significant challenge. Using stable-isotope-labeled internal standards for each analyte, the Prospekt-2 on-line methodology was evaluated for sensitivity, suppression, accuracy, precision, linearity, analyst time, analysis time, cost, carryover and ease of use. The lower limit of quantitation for the on-line SPE procedure for DEX, DET and GG was 0.05, 0.05 and 5.0 ng mL(-1), respectively, using a 0.1 mL sample volume. The linear range for DEX and DET was 0.05-50 ng mL(-1) and was 5-5,000 ng mL(-1) for GG. Accuracy and precision data for five different levels of QC samples were collected over three separate days. Accuracy ranged from 90% to 112% for all three analytes, while the precision, as measured by the %RSD, ranged from 1.5% to 16.0%

A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments.

PubMed

Moulder, Robert; Filén, Jan-Jonas; Salmi, Jussi; Katajamaa, Mikko; Nevalainen, Olli S; Oresic, Matej; Aittokallio, Tero; Lahesmaa, Riitta; Nyman, Tuula A

2005-07-01

The options available for processing quantitative data from isotope coded affinity tag (ICAT) experiments have mostly been confined to software specific to the instrument of acquisition. However, recent developments with data format conversion have subsequently increased such processing opportunities. In the present study, data sets from ICAT experiments, analysed with liquid chromatography/tandem mass spectrometry (MS/MS), using an Applied Biosystems QSTAR Pulsar quadrupole-TOF mass spectrometer, were processed in triplicate using separate mass spectrometry software packages. The programs Pro ICAT, Spectrum Mill and SEQUEST with XPRESS were employed. Attention was paid towards the extent of common identification and agreement of quantitative results, with additional interest in the flexibility and productivity of these programs. The comparisons were made with data from the analysis of a specifically prepared test mixture, nine proteins at a range of relative concentration ratios from 0.1 to 10 (light to heavy labelled forms), as a known control, and data selected from an ICAT study involving the measurement of cytokine induced protein expression in human lymphoblasts, as an applied example. Dissimilarities were detected in peptide identification that reflected how the associated scoring parameters favoured information from the MS/MS data sets. Accordingly, there were differences in the numbers of peptides and protein identifications, although from these it was apparent that both confirmatory and complementary information was present. In the quantitative results from the three programs, no statistically significant differences were observed.

Analysis of oversulfation in biglycan chondroitin/dermatan sulfate oligosaccharides by chip-based nanoelectrospray ionization multistage mass spectrometry.

PubMed

Flangea, Corina; Sisu, Eugen; Seidler, Daniela G; Zamfir, Alina D

2012-01-15

Biglycan (BGN) is a small proteoglycan that consists of a protein core containing leucine-rich repeat regions and two glycosaminoglycan (GAG) chains of either chondroitin sulfate (CS) or dermatan sulfate (DS) type. The development of novel, highly efficient analytical methods for structural identification of BGN-derived CS/DS motifs, possibly implicated in biological events, is currently the focus of research. In this work, an improved analytical method based on fully automated chip-nanoelectrospray ionization (nanoESI) in conjunction with high-capacity ion trap (HCT) multistage mass spectrometry (MS) by collision-induced dissociation (CID) was for the first time applied to BGN CS/DS oligosaccharide analysis. The CS/DS chains were released from transfected 293 BGN by β-elimination. The chain was digested with AC I lyase, and the resulting mixture was purified and subsequently separated by size exclusion chromatography (SEC). Di- and tetrasaccharide fractions were pooled and characterized in detail using the developed chip-nanoESI protocol. The chip-nanoESI MS profile in the negative ion mode revealed the presence of under-, regularly, and oversulfated species in both di- and tetrasaccharide fractions. CID MS(2)-MS(3) yielded sequence patterns consistent with unusual oversulfated 4,5-Δ-GlcA(2S)-GalNAc(4S) and 4,5-Δ-GlcA(2S)-GalNAc(6S)-IdoA(2S)-GalNAc(6S) motifs. Copyright © 2011 Elsevier Inc. All rights reserved.

First LC/MS determination of cyanazine amide, cyanazine acid, and cyanazine in groundwater samples

USGS Publications Warehouse

Ferrer, Imma; Thurman, E.M.; Barceló, Damià

2000-01-01

Cyanazine and two of its major metabolites, cyanazine amide and cyanazine acid, were measured at trace levels in groundwater using liquid chromatography/atmospheric pressure chemical ionization/mass spectrometry (LC/APCI/MS). Solid-phase extraction was carried out by passing 20 mL of groundwater sample through a cartridge containing a polymeric phase (PLRP-s), with recoveries ranging from 99 to 108% (n = 5). Using LC/MS detection in positive ion mode, useful structural information was obtained by increasing the fragmentor voltage, thus permitting the unequivocal identification of these compounds in groundwater samples with low sample volumes. The fragmentation of the amide, carboxylic acid, and cyano group was observed for both metabolites and cyanazine, respectively, leading to a diagnostic ion at m/z 214. Method detection limits were in the range of 0.002−0.005 μg/L for the three compounds. Finally, the newly developed method was evaluated for the analysis of groundwater samples from New York containing the compounds under study and presents evidence that the metabolites, cyanazine acid, and cyanazine amide may leach to groundwater and serve as sources for deisopropylatrazine. The combination of on-line SPE and LC/APCI/MS represents an important advance in environmental analysis of herbicide metabolites in groundwater since it demonstrates that trace amounts of polar metabolites may be determined rapidly. Furthermore, the presence of both cyanazine amide and cyanazine acid indicate that another degradation product, deisopropylatrazine, may be occurring at depth because of the subsequent degradation of cyanazine.

Simultaneous extraction of propofol and propofol glucuronide from hair followed by validated LC-MS/MS analyses.

PubMed

Maas, Alexandra; Maier, Christoph; Iwersen-Bergmann, Stefanie; Madea, Burkhard; Hess, Cornelius

2017-11-30

Besides its clinical application, the anaesthetic agent propofol is being increasingly misused, mostly by healthcare professionals, and its abuse potential gained worldwide attention after the tragic death of Michael Jackson in 2009. Due to the short duration of its narcotic effects, propofol abuse is especially easy to hide compared with the use of other recreational drugs. However, propofol possesses a very narrow therapeutic window between the desired effect and potentially fatal toxicity, making abuse of the drug extremely dangerous even in experienced physicians. Consequently, it is important that forensic laboratories possess a sensitive and specific method for the detection of chronic propofol abuse. We present a simple, fast and reliable method to simultaneously extract propofol and its main metabolite propofol glucuronide from hair, followed by sensitive LC-MS/MS analyses, allowing to determine a chronic propofol abuse. Difficulties regarding the detection of propofol using LC-MS/MS were solved by using a derivatization reaction with 2-fluoro-1-methylpyridinium-p-toluene-sulfonate and triethylamine. Reliability of extraction method and subsequent LC-MS/MS analyses was confirmed under consideration of the validation parameters selectivity, linearity, accuracy and precision, analytical limits, processed sample stability, matrix effects and recovery. Appropriate quantification (LLOQ=10pg/mg hair) and detection limits (3.6pg/mg hair for propofol and 7.8 pg/mg hair for propofol glucuronide) could be achieved, enabling to detect even small amounts of both analytes. Applicability of the method was confirmed by analysis of three human hair samples from deceased with suspicion of chronic propofol abuse. Copyright © 2017 Elsevier B.V. All rights reserved.

Analysis of the differentially expressed low molecular weight peptides in human serum via an N-terminal isotope labeling technique combining nano-liquid chromatography/matrix-assisted laser desorption/ionization mass spectrometry.

PubMed

Leng, Jiapeng; Zhu, Dong; Wu, Duojiao; Zhu, Tongyu; Zhao, Ningwei; Guo, Yinlong

2012-11-15

Peptidomics analysis of human serum is challenging due to the low abundance of serum peptides and interference from the complex matrix. This study analyzed the differentially expressed (DE) low molecular weight peptides in human serum integrating a DMPITC-based N-terminal isotope labeling technique with nano-liquid chromatography and matrix-assisted laser desorption/ionization mass spectrometry (nano-LC/MALDI-MS). The workflow introduced a [d(6)]-4,6-dimethoxypyrimidine-2-isothiocyanate (DMPITC)-labeled mixture of aliquots from test samples as the internal standard. The spiked [d(0)]-DMPITC-labeled samples were separated by nano-LC then spotted on the MALDI target. Both quantitative and qualitative studies for serum peptides were achieved based on the isotope-labeled peaks. The DMPITC labeling technique combined with nano-LC/MALDI-MS not only minimized the errors in peptide quantitation, but also allowed convenient recognition of the labeled peptides due to the 6 Da mass difference. The data showed that the entire research procedure as well as the subsequent data analysis method were effective, reproducible, and sensitive for the analysis of DE serum peptides. This study successfully established a research model for DE serum peptides using DMPITC-based N-terminal isotope labeling and nano-LC/MALDI-MS. Application of the DMPITC-based N-terminal labeling technique is expected to provide a promising tool for the investigation of peptides in vivo, especially for the analysis of DE peptides under different biological conditions. Copyright © 2012 John Wiley & Sons, Ltd.

Liquid Microjunction Surface Sampling Coupled with High-Pressure Liquid Chromatography-Electrospray Ionization-Mass Spectrometry for Analysis of Drugs and Metabolites in Whole-Body Thin Tissue Sections

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

Kertesz, Vilmos; Van Berkel, Gary J

2010-01-01

In this work, a commercially available autosampler was adapted to perform direct liquid microjunction (LMJ) surface sampling followed by a high-pressure liquid chromatography (HPLC) separation of the extract components and detection with electrospray ionization mass spectrometry (ESI-MS). To illustrate the utility of coupling a separation with this direct liquid extraction based surface sampling approach, four different organs (brain, lung, kidney, and liver) from whole-body thin tissue sections of propranolol dosed and control mice were examined. The parent drug was observed in the chromatograms of the surface sampling extracts from all the organs of the dosed mouse examined. In addition, twomore » isomeric phase II metabolites of propranolol (an aliphatic and an aromatic hydroxypropranolol glucuronide) were observed in the chromatograms of the extracts from lung, kidney, and liver. Confirming the presence of one or the other or both of these glucuronides in the extract from the various organs was not possible without the separation. These drug and metabolite data obtained using the LMJ surface sampling/HPLC-MS method and the results achieved by analyzing similar samples by conventional extraction of the tissues and subsequent HPLC-MS analysis were consistent.« less

Bio-oil Analysis Using Negative Electrospray Ionization: Comparative Study of High-Resolution Mass Spectrometers and Phenolic versus Sugaric Components

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

Smith, Erica A.; Park, Soojin; Klein, Adam T.

2012-05-16

We have previously demonstrated that a petroleomic analysis could be performed for bio-oils and revealed the complex nature of bio-oils for the nonvolatile phenolic compounds (Smith, E.; Lee, Y. J. Energy Fuels 2010, 24, 5190−5198). As a subsequent study, we have adapted electrospray ionization in negative-ion mode to characterize a wide variety of bio-oil compounds. A comparative study of three common high-resolution mass spectrometers was performed to validate the methodology and to investigate the differences in mass discrimination and resolution. The mass spectrum is dominated by low mass compounds with m/z of 100–250, with some compounds being analyzable by gasmore » chromatography–mass spectrometry (GC–MS). We could characterize over 800 chemical compositions, with only about 40 of them being previously known in GC–MS. This unveiled a much more complex nature of bio-oils than typically shown by GC–MS. The pyrolysis products of cellulose and hemicellulose, particularly polyhydroxy cyclic hydrocarbons (or what we call “sugaric” compounds), such as levoglucosan, could be effectively characterized with this approach. Phenolic compounds from lignin pyrolysis could be clearly distinguished in a contour map of double bond equivalent (DBE) versus the number of carbons from these sugaric compounds.« less

Proteomic profiling of an undefined microbial consortium cultured in fermented dairy manure: Methods development.

PubMed

Hanson, Andrea J; Paszczynski, Andrzej J; Coats, Erik R

2016-03-01

The production of polyhydroxyalkanoates (PHA; bioplastics) from waste or surplus feedstocks using mixed microbial consortia (MMC) and aerobic dynamic feeding (ADF) is a growing field within mixed culture biotechnology. This study aimed to optimize a 2DE workflow to investigate the proteome dynamics of an MMC synthesizing PHA from fermented dairy manure. To mitigate the challenges posed to effective 2DE by this complex sample matrix, the bacterial biomass was purified using Accudenz gradient centrifugation (AGC) before protein extraction. The optimized 2DE method yielded high-quality gels suitable for quantitative comparative analysis and subsequent protein identification by LC-MS/MS. The optimized 2DE method could be adapted to other proteomic investigations involving MMC in complex organic or environmental matrices. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Optical progression characteristics of an interesting natural downward bipolar lightning flash

NASA Astrophysics Data System (ADS)

Chen, Luwen; Lu, Weitao; Zhang, Yijun; Wang, Daohong

2015-01-01

high-speed cameras, Lightning Attachment Process Observation Systems, and fast and slow electrical antennas, we documented a downward bipolar lightning flash that contained one first positive stroke with a peak current of 142 kA and five subsequent negative strokes hitting on a 90 m tall structure on 29 July 2010 in Guangzhou City, China. All the six strokes propagated along the same viewed channel established by the first positive return stroke. The leader which preceded the positive return stroke propagated downward without any branches at a two-dimensional (2-D) speed of 2.5 × 106 m/s. An upward connecting leader with a length of about 80 m was observed in response to the downward positive leader. The 10-90% risetimes of the return strokes' optical pulses ranged from 2.2 µs to 3.2 µs, while the widths from the 10% wavefront to the 50% wave tail ranged from 56.5 µs to 83.1 µs, and the half peak widths ranged from 53.4 µs to 81.6 µs. All the return strokes exhibited similar speeds, ranging from 1.0 × 108 m/s to 1.3 × 108 m/s. Each of the return strokes was followed by a continuing current stage (CC). The first positive stroke CC lasted more than 150 ms, much larger than all the subsequent negative stroke CC, ranging from 13 ms to 70 ms.

Advanced functional materials in solid phase extraction for ICP-MS determination of trace elements and their species - A review.

PubMed

He, Man; Huang, Lijin; Zhao, Bingshan; Chen, Beibei; Hu, Bin

2017-06-22

For the determination of trace elements and their species in various real samples by inductively coupled plasma mass spectrometry (ICP-MS), solid phase extraction (SPE) is a commonly used sample pretreatment technique to remove complex matrix, pre-concentrate target analytes and make the samples suitable for subsequent sample introduction and measurements. The sensitivity, selectivity/anti-interference ability, sample throughput and application potential of the methodology of SPE-ICP-MS are greatly dependent on SPE adsorbents. This article presents a general overview of the use of advanced functional materials (AFMs) in SPE for ICP-MS determination of trace elements and their species in the past decade. Herein the AFMs refer to the materials featuring with high adsorption capacity, good selectivity, fast adsorption/desorption dynamics and satisfying special requirements in real sample analysis, including nanometer-sized materials, porous materials, ion imprinting polymers, restricted access materials and magnetic materials. Carbon/silica/metal/metal oxide nanometer-sized adsorbents with high surface area and plenty of adsorption sites exhibit high adsorption capacity, and porous adsorbents would provide more adsorption sites and faster adsorption dynamics. The selectivity of the materials for target elements/species can be improved by using physical/chemical modification, ion imprinting and restricted accessed technique. Magnetic adsorbents in conventional batch operation offer unique magnetic response and high surface area-volume ratio which provide a very easy phase separation, greater extraction capacity and efficiency over conventional adsorbents, and chip-based magnetic SPE provides a versatile platform for special requirement (e.g. cell analysis). The performance of these adsorbents for the determination of trace elements and their species in different matrices by ICP-MS is discussed in detail, along with perspectives and possible challenges in the future development. Copyright © 2017 Elsevier B.V. All rights reserved.

Safety and Effectiveness of Natalizumab: First Report of Interim Results of Post-Marketing Surveillance in Japan.

PubMed

Saida, Takahiko; Yokoyama, Kazumasa; Sato, Ryusuke; Makioka, Haruki; Iizuka, Yukihiko; Hase, Masakazu; Ling, Yan; Torii, Shinichi

2017-12-01

Natalizumab, a humanized anti-α4 integrin monoclonal antibody, received marketing approval in Japan in 2014 for the treatment of multiple sclerosis (MS). Because the previous large-scale clinical trials of natalizumab were mainly conducted in Europe and North American countries, and data in patients with MS from Japan were limited, we conducted an all-case post-marketing surveillance of natalizumab-treated MS patients from Japan to investigate the safety and effectiveness of natalizumab in a real-world clinical setting in Japan. Here, we report the results of an interim analysis. During the observation period of 2 years, all patients who were treated with natalizumab subsequent to its approval in Japan were followed. The effectiveness of natalizumab was assessed by examining the changes in expanded disability status scale (EDSS) score and annualized relapse rate (ARR) from baseline. Safety was assessed by analyzing the incidence of adverse drug reactions (ADRs). The safety analysis included 106 patients (mean age 39.3 years; women 62.3%) whose data were collected until the data lock point (February 7, 2016). The effectiveness analysis included 75 patients. The majority of patients had relapsing-remitting MS (93/106 patients; 87.7%). The mean length of treatment exposure in the present study was 6.6 months. During the 2-year observation period, no significant change in the EDSS was observed, while the ARR decreased significantly from baseline (72.9% reduction, p = 0.001). ADRs and serious ADRs were observed in 11.3% and 3.8% of patients, respectively; however, no new safety concerns were detected. No patient had progressive multifocal leukoencephalopathy (PML) during the present study period. The safety and effectiveness of natalizumab were confirmed in Japanese patients with MS in clinical practice. Nevertheless, potential risks including PML require continuous, careful observation. Biogen Japan Ltd (Tokyo, Japan).

An integrated strategy using UPLC-QTOF-MSE and UPLC-QTOF-MRM (enhanced target) for pharmacokinetics study of wine processed Schisandra Chinensis fructus in rats.

PubMed

Liu, Kuangyi; Song, Yonggui; Liu, Yali; Peng, Mi; Li, Hanyun; Li, Xueliang; Feng, Bingwei; Xu, Pengfei; Su, Dan

2017-05-30

Currently the pharmacokinetic (PK) research of herbal medicines is still limited and facing critical technical challenges on quantitative analysis of multi-components from biological matrices which often accompanied by lacking of authentic standards and low concentration. This present work contributes to the development of an integrated strategy for extensive pharmacokinetics assessments, and a selective and sensitive method independent of authentic standards for multi-components analysis based on the use of ultra-performance liquid chromatography/quadrupole-time-of-flight/MS E (UPLC-TOF-MS E ) and UPLC-TOF-MRM (rnhanced target). Initially, phytochemicals were identified by UPLC-TOF-MS E analysis, subsequently the identified components were matched with authentic standards and pre-classified, and UPLC-QTOF-MRM method optimized and developed. To guarantee reliable results, three rules are necessary: (1) detection with a mass error of less than 5ppm; (2) same class chemical compositions with structural high similarity between analytes with and without authentic reference substance; (3) a matching retention time between TOF-MRM mode and TOF-MS E within 0.2min. The developed and validated method was applied for the simultaneous determination of 12 lignans in rat plasma after administered with wine processed Schisandra Chinensis fructus (WPSCF) extract. Such an approach was found capable of providing extensive pharmacokinetic profiles of multi-components absorbed into blood after oral administrated with WPSCF extract. The results also indicated that significant difference in pharmacokinetics parameters of dibenzocyclooctadiene lignans was observed between schizandrin and gomisin compounds. For lignans, the absorption via gastrointestinal tract were all rapid and maintained relatively long retention time, especially for schisantherin A and schisantherin B with higher plasma exposure. Copyright © 2017 Elsevier B.V. All rights reserved.

Molecular modeling and cytotoxicity of diffractaic acid: HP-β-CD inclusion complex encapsulated in microspheres.

PubMed

Silva, Camilla V N S; Barbosa, Jéssica A P; Ferraz, Milena S; Silva, Nicácio H; Honda, Neli K; Rabello, Marcelo M; Hernandes, Marcelo Z; Bezerra, Beatriz P; Cavalcanti, Isabella M F; Ayala, Alejandro P; Santos, Noemia P S; Santos-Magalhães, Nereide S

2016-11-01

In this pioneer study, 2-hydroxypropyl-β-cyclodextrin (HP-β-CD) was used to improve the solubility of the diffractaic acid (DA) via inclusion complex (DA:HP-β-CD). Subsequently, DA:HP-β-CD was incorporated into poly-ε-caprolactone (PCL) microspheres (DA:HP-β-CD-MS). Microspheres containing DA (DA-MS) or DA:HP-β-CD (DA:HP-β-CD-MS) were prepared using the multiple W/O/W emulsion-solvent evaporation technique. The phase-solubility diagram of DA in HP-β-CD (10-50mM) showed an A L type curve with a stability constant K 1:1 =821M -1 . 1 H NMR, FTIR, X-ray diffraction and thermal analysis showed changes in the molecular environment of DA in DA:HP-β-CD. The molecular modeling approach suggests a guest-host complex formation between the carboxylic moiety of both DA and the host (HP-β-CD). The mean particle size of the microspheres were ∅ DA-MS =5.23±1.65μm and ∅ DA:HP-β-CD-MS =4.11±1.39μm, respectively. The zeta potential values of the microspheres were ζ DA-MS =-7.85±0.32mV and ζ DA:HP-β-CD-MS =-6.93±0.46mV. Moreover, the encapsulation of DA:HP-β-CD into microspheres resulted in a more slower release (k 2 =0.042±0.001; r 2 =0.996) when compared with DA-MS (k 2 =0.183±0.005; r 2 =0.996). The encapsulation of DA or DA:HP-β-CD into microspheres reduced the cytotoxicity of DA (IC 50 =43.29μM) against Vero cells (IC 50 of DA-MS=108.48μM and IC 50 of DA:HP-β-CD-MS=142.63μM). Copyright © 2016 Elsevier B.V. All rights reserved.

Viral exposures and MS outcome in a prospective cohort of children with acquired demyelination.

PubMed

Makhani, Naila; Banwell, Brenda; Tellier, Raymond; Yea, Carmen; McGovern, Suzanne; O'Mahony, Julia; Ahorro, Jean M; Arnold, Douglas; Sadovnick, A Dessa; Marrie, Ruth A; Bar-Or, Amit

2016-03-01

Epstein-Barr virus (EBV) infection is associated with increased multiple sclerosis (MS) risk. Recently, cytomegalovirus (CMV) infection has been proposed as a protective factor against MS development. We determined EBV, herpes simplex virus, varicella-zoster virus and CMV seroprevalence in 247 prospectively followed children with acquired demyelinating syndromes (ADS). Remote EBV infection was more common in children with MS than those with monophasic ADS while CMV infection was more common in children with monophasic ADS. Children displaying evidence of remote EBV without CMV infection were at highest risk of subsequent MS diagnosis. Viral infection repertoire detected at ADS provides important prognostic information. © The Author(s), 2015.

On the Reproducibility of Label-Free Quantitative Cross-Linking/Mass Spectrometry

NASA Astrophysics Data System (ADS)

Müller, Fränze; Fischer, Lutz; Chen, Zhuo Angel; Auchynnikava, Tania; Rappsilber, Juri

2018-02-01

Quantitative cross-linking/mass spectrometry (QCLMS) is an emerging approach to study conformational changes of proteins and multi-subunit complexes. Distinguishing protein conformations requires reproducibly identifying and quantifying cross-linked peptides. Here we analyzed the variation between multiple cross-linking reactions using bis[sulfosuccinimidyl] suberate (BS3)-cross-linked human serum albumin (HSA) and evaluated how reproducible cross-linked peptides can be identified and quantified by LC-MS analysis. To make QCLMS accessible to a broader research community, we developed a workflow that integrates the established software tools MaxQuant for spectra preprocessing, Xi for cross-linked peptide identification, and finally Skyline for quantification (MS1 filtering). Out of the 221 unique residue pairs identified in our sample, 124 were subsequently quantified across 10 analyses with coefficient of variation (CV) values of 14% (injection replica) and 32% (reaction replica). Thus our results demonstrate that the reproducibility of QCLMS is in line with the reproducibility of general quantitative proteomics and we establish a robust workflow for MS1-based quantitation of cross-linked peptides.

The lager yeast Saccharomyces pastorianus removes and transforms Fusarium trichothecene mycotoxins during fermentation of brewer's wort.

PubMed

Nathanail, Alexis V; Gibson, Brian; Han, Li; Peltonen, Kimmo; Ollilainen, Velimatti; Jestoi, Marika; Laitila, Arja

2016-07-15

An investigation was conducted to determine the fate of deoxynivalenol, deoxynivalenol-3-glucoside, HT-2 toxin and T-2 toxin, during a four-day fermentation with the lager yeast Saccharomyces pastorianus. The influence of excessive mycotoxin concentrations on yeast growth, productivity and viability were also assessed. Mycotoxins were dosed at varying concentrations to 11.5° Plato wort. Analysis of yeast revealed that presence of the toxins even at concentrations up to 10,000 μg/L had little or no effect on sugar utilisation, alcohol production, pH, yeast growth or cell viability. Of the dosed toxin amounts 9-34% were removed by the end of fermentation, due to physical binding and/or biotransformation by yeast. Deoxynivalenol-3-glucoside was not reverted to its toxic precursor during fermentation. Processing of full-scan liquid chromatography-quadrupole time-of-flight-mass spectrometry (LC-QTOF-MS) data with MetaboLynx and subsequent LC-QTOF-MS/MS measurements resulted in annotation of several putative metabolites. De(acetylation), glucosylation and sulfonation were the main metabolic pathways activated. Copyright © 2016 Elsevier Ltd. All rights reserved.

Establishing Long-Term Efficacy in Chronic Disease: Use of Recursive Partitioning and Propensity Score Adjustment to Estimate Outcome in MS

PubMed Central

Goodin, Douglas S.; Jones, Jason; Li, David; Traboulsee, Anthony; Reder, Anthony T.; Beckmann, Karola; Konieczny, Andreas; Knappertz, Volker

2011-01-01

Context Establishing the long-term benefit of therapy in chronic diseases has been challenging. Long-term studies require non-randomized designs and, thus, are often confounded by biases. For example, although disease-modifying therapy in MS has a convincing benefit on several short-term outcome-measures in randomized trials, its impact on long-term function remains uncertain. Objective Data from the 16-year Long-Term Follow-up study of interferon-beta-1b is used to assess the relationship between drug-exposure and long-term disability in MS patients. Design/Setting To mitigate the bias of outcome-dependent exposure variation in non-randomized long-term studies, drug-exposure was measured as the medication-possession-ratio, adjusted up or down according to multiple different weighting-schemes based on MS severity and MS duration at treatment initiation. A recursive-partitioning algorithm assessed whether exposure (using any weighing scheme) affected long-term outcome. The optimal cut-point that was used to define “high” or “low” exposure-groups was chosen by the algorithm. Subsequent to verification of an exposure-impact that included all predictor variables, the two groups were compared using a weighted propensity-stratified analysis in order to mitigate any treatment-selection bias that may have been present. Finally, multiple sensitivity-analyses were undertaken using different definitions of long-term outcome and different assumptions about the data. Main Outcome Measure Long-Term Disability. Results In these analyses, the same weighting-scheme was consistently selected by the recursive-partitioning algorithm. This scheme reduced (down-weighted) the effectiveness of drug exposure as either disease duration or disability at treatment-onset increased. Applying this scheme and using propensity-stratification to further mitigate bias, high-exposure had a consistently better clinical outcome compared to low-exposure (Cox proportional hazard ratio = 0.30–0.42; p<0.0001). Conclusions Early initiation and sustained use of interferon-beta-1b has a beneficial impact on long-term outcome in MS. Our analysis strategy provides a methodological framework for bias-mitigation in the analysis of non-randomized clinical data. Trial Registration Clinicaltrials.gov NCT00206635 PMID:22140424

Compatibility studies of acyclovir and lactose in physical mixtures and commercial tablets.

PubMed

Monajjemzadeh, Farnaz; Hassanzadeh, Davoud; Valizadeh, Hadi; Siahi-Shadbad, Mohammad R; Mojarrad, Javid Shahbazi; Robertson, Thomas A; Roberts, Michael S

2009-11-01

This study documents drug-excipient incompatibility studies of acyclovir in physical mixtures with lactose and in different tablet brands. Differential scanning calorimetry (DSC) was initially used to assess compatibility of mixtures. The Fourier-transform infrared (FTIR) spectrum was also compared with the spectra of pure drug and excipient. Although DSC results indicated incompatibility with lactose, FTIR spectra were mostly unmodified due to overlapping peaks. Samples of isothermally stressed physical mixture were stored at 95 degrees C for 24 h. The residual drug was monitored using a validated high-performance liquid chromatography (HPLC) assay and data fitting to solid-state kinetic models was performed. The drug loss kinetics followed a diffusion model. The aqueous mixture of drug and excipient was heated in order to prepare an adduct mixture. HPLC analysis revealed one extra peak that was fractionated and subsequently injected into the liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) system. The MRM (Multiple Reaction Monitoring) chromatograms characterized the peak with molecular mass corresponding to an acyclovir-lactose Maillard reaction product. The presence of lactose in commercial tablets was checked using a new TLC method. Overall, the incompatibility of acyclovir with lactose was successfully evaluated using a combination of thermal methods and LC-MS/MS.

Facilitating high resolution mass spectrometry data processing for screening of environmental water samples: An evaluation of two deconvolution tools.

PubMed

Bade, Richard; Causanilles, Ana; Emke, Erik; Bijlsma, Lubertus; Sancho, Juan V; Hernandez, Felix; de Voogt, Pim

2016-11-01

A screening approach was applied to influent and effluent wastewater samples. After injection in a LC-LTQ-Orbitrap, data analysis was performed using two deconvolution tools, MsXelerator (modules MPeaks and MS Compare) and Sieve 2.1. The outputs were searched incorporating an in-house database of >200 pharmaceuticals and illicit drugs or ChemSpider. This hidden target screening approach led to the detection of numerous compounds including the illicit drug cocaine and its metabolite benzoylecgonine and the pharmaceuticals carbamazepine, gemfibrozil and losartan. The compounds found using both approaches were combined, and isotopic pattern and retention time prediction were used to filter out false positives. The remaining potential positives were reanalysed in MS/MS mode and their product ions were compared with literature and/or mass spectral libraries. The inclusion of the chemical database ChemSpider led to the tentative identification of several metabolites, including paraxanthine, theobromine, theophylline and carboxylosartan, as well as the pharmaceutical phenazone. The first three of these compounds are isomers and they were subsequently distinguished based on their product ions and predicted retention times. This work has shown that the use deconvolution tools facilitates non-target screening and enables the identification of a higher number of compounds. Copyright © 2016 Elsevier B.V. All rights reserved.

Development and validation of a quantitative UHPLC-MS/MS method for selected brominated flame retardants in food.

PubMed

Malysheva, Svetlana V; Goscinny, Séverine; Malarvannan, Govindan; Poma, Giulia; Andjelkovic, Mirjana; Voorspoels, Stefan; Covaci, Adrian; Van Loco, Joris

2018-02-01

An ultra-high performance liquid chromatography - tandem mass spectrometry (UHPLC-MS/MS) method was developed and validated (in-house) for the quantification of selected brominated flame retardants (BFRs), including tetrabromobisphenol A (TBBPA), hexabromocyclododecanes (HBCDs), tetrabromobisphenol S (TBBPS) and bromophenols (BPs), in various food matrices. The sample preparation consisted of extraction of TBBPS with acidified acetonitrile followed by a fast dispersive solid-phase extraction (dSPE) clean-up and extraction of the other BFRs with a mixture of hexane and dichloromethane (1:1, v/v) with subsequent clean-up using acidified silica (44%, w/w). The limits of quantification of the method varied widely for the types of food matrices and the different classes of BFRs from 4 pg g -1 wet weight (ww) to 8 ng g -1 ww. For most of the analytes the apparent recovery was in the range 70-120%, and the method precision (under repeatability conditions) was below 20%. The method was successfully applied in proficiency testing exercises as well as for analysis of various food items. Only 25% of the collected food samples contained BFRs, with 4-bromophenol and α-HBCD as the only detected compounds. The contaminated foodstuffs were fish and eggs with concentrations in the range from 48 to 305 pg g -1 ww.

Application of metabonomic strategy to discover an unreported active ingredient in LiuWeiDiHuang pills suppressing beta-glucuronidase.

PubMed

Xie, Baogang; Zhang, Zhirong; Gong, Tao; Zhang, Ningning; Wang, Huiyun; Zou, Huiqing

2015-01-01

Identification of the bioactive ingredient from traditional Chinese medicine (TCM) remains a challenging task by traditional approach that focuses on chemical isolation coupled with biological activity screening. Here, we present a metabonomics-based approach for bioactive ingredient discovery in LiuWeiDiHuang pills (LWPs). First, a non-targeted high-performance liquid chromatography ultraviolet (HPLC-UV) profiling of rat urine was used to discriminate urinary profiling intervened by LWPs. Orthogonal partial least-squares discriminant analysis (OPLS-DA) revealed that eight chromatographic peaks made a significant contribution to the classification of the LWPs group and the control group. Five of these chromatographic peaks were successfully isolated and identified as hippurate, genistein (GT), daidzein (DZ), and glucuronide conjugate of GT and that of DZ by mass spectroscopy (MS). Subsequently, we found that LWPs significantly decreased the activity of intestinal β-glucuronidase by 18 % and exerted a dose-dependent inhibitory effect on rat liver lysosomal fraction, suggesting that LWPs were a β-glucuronidase inhibitor. In the end, by inhibiting β-glucuronidase-guided isolation, D-glucaro-1,4-lactone, a previously unreported ingredient of LWPs, was identified by MS, MS/MS, and nuclear magnetic resonance spectroscopy. Our findings indicated that metabonomics might increase research productivity toward the drug targets and/or bioactive compounds from TCM.

Determination of six polyether antibiotic residues in foods of animal origin by solid phase extraction combined with liquid chromatography-tandem mass spectrometry.

PubMed

Ha, Jing; Song, Ge; Ai, Lian-Feng; Li, Jian-Chen

2016-04-01

A new method using solid phase extraction (SPE) combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS) has been developed for the determination of six polyether antibiotics, including lasalocid, salinomycin, monensin, narasin, madubamycin and nigericin residues, in foods of animal origin. The samples were extracted with acetonitrile and purified by ENVI-Carb SPE columns after comparing the impurity effect and maneuverability of several SPE cartridges. Subsequently, the analytes were separated on a Hypersil Gold column (2.1×150mm, 5μm) and analyzed by MS/MS detection. The limit of quantization (LOQ) for milk and chicken was 0.4μg/kg, and for chicken livers and eggs, it was 1μg/kg. The linearity was satisfactory with a correlation coefficient of >0.9995 at concentrations ranging from 2 to 100μg/L. The average recoveries of the analytes fortified at three levels ranged from 68.2 to 114.3%, and the relative standard deviations ranged from 4.5 to 12.1%. The method was suitable for quantitative analysis and confirmation of polyether antibiotic residues in foods of animal origin. Copyright © 2016 Elsevier B.V. All rights reserved.

Simultaneous LC/MS/MS determination of thiols and disulfides in urine samples based on differential labeling with ferrocene-based maleimides.

PubMed

Seiwert, Bettina; Karst, Uwe

2007-09-15

A method for the simultaneous determination of a series of thiols and disulfides in urine samples has been developed based on the sequential labeling of free and bound thiol functionalities with two ferrocene-based maleimide reagents. The sample is first exposed to N-(2-ferroceneethyl)maleimide, thus leading to the derivatization of free thiol groups in the sample. After quantitative reaction and subsequent reduction of the disulfide-bound thiols by tris(2-carboxyethyl)phosphine, the newly formed thiol functionalities are reacted with ferrocenecarboxylic acid-(2-maleimidoyl)ethylamide. The reaction products are determined by LC/MS/MS in the multiple reaction mode, and precursor ion scan as well as neutral loss scan is applied to detect unknown further thiols. The method was successfully applied to the analysis of free and disulfide-bound thiols in urine samples. Limits of detection are 30 to 110 nM, and the linear range comprises two decades of concentration, thus covering the relevant concentration range of thiols in urine samples. The thiol and disulfide concentrations were referred to the creatinine content to compensate for different sample volumes. As some calibration standards for the disulfides are not commercially available, they were synthesized in an electrochemical flow-through cell. This allowed the synthesis of hetero- and homodimeric disulfides.

Interlaboratory Validation of a Stable Isotope Dilution and Liquid Chromatography Tandem Mass Spectrometry Method for the Determination of Aflatoxins in Milk, Milk-Based Infant Formula, and Feed.

PubMed

Zhang, Kai; Liao, Chia-Ding; Prakash, Shristi; Conway, Michael; Cheng, Hwei-Fang

2018-05-01

An interlaboratory study was conducted to evaluate stable isotope dilution and LC tandem MS (MS/MS) for the determination of aflatoxins B1, B2, G1, G2, and M1 (AFB1, AFB2, AFG1, AFG2, and AFM1) in milk, milk-based infant formula (formula), and feed. Samples were first fortified with five 13C uniformly labeled aflatoxins {[13C]-internal standard (IS)} corresponding to the five native aflatoxins, which were subsequently extracted with acetonitrile-water (50 + 50, v/v), followed by centrifugation, filtration, and LC-MS/MS analysis. In addition to certified milk powder and animal feed, the three participating laboratories also analyzed milk, formula, and feed fortified with the five aflatoxins at concentrations ranging from 0.5 to 50 ng/g. The majority of recoveries ranged from 80 to 120%, with RSDs < 20%. Method LOQs were determined by the three laboratories using the three sample matrixes in replicates (n = 8), and the determined LOQs of AFB1, AFB2, AFG1, AFG2, and AFM1 ranged from 0.1 to 0.91, 0.24 to 0.64, 0.28 to 1.52, 0.19 to 3.80, and 0.12 to 0.45 ng/g, respectively. For detected aflatoxins in the certified materials, all measured concentrations were within ±25% of the certified values. Using [13C]-IS eliminated the need for matrix-matched calibration standards for quantitation, simplified sample preparation, and achieved simultaneous identification and quantitation of the aflatoxins in a simple LC-MS/MS procedure.

Managing Neuropsychological Impairment in Multiple Sclerosis

PubMed Central

Lau, Stephanie; Penner, Iris; Heesen, Christoph; Moritz, Steffen

2015-01-01

Background: Multiple sclerosis (MS) is an inflammatory and neurodegenerative disease of the central nervous system of potential autoimmune origin that is frequently associated with psychological disorders and cognitive deficits, as well as with fatigue, stress, and psychosocial burden. These factors often cause decreased quality of life, social withdrawal, and unemployment. We describe the development of a cognitive-behavioral group intervention based on the concept of metacognition and evaluation of the feasibility and acceptance of the program as a rehabilitation tool. Methods: Metacognitive Training in MS (MaTiMS) consists of six modules, each 90 minutes in duration. We tested acceptance and design of the program in six focus groups (entire sample, n = 27). Framework analysis of transcripts was used to identify key topics and categories. Program modules were revised in accordance with appropriate recommendations of focus group members. We subsequently evaluated MaTiMS in two groups (n = 5, n = 6) in a rehabilitation center. Neuropsychological functioning as well as coping self-efficacy, depression, stress, perceived cognitive deficit, fatigue, and quality of life were assessed. Acceptance of MaTiMS from the patient perspective was also studied. Results: The modules were highly accepted by patients. Pre-post assessments showed significant improvements in the Coping Self Efficacy Scale (P = .007), the Würzburger Fatigue Inventory for MS Score (P = .028), and the Hamburg Quality of Life Questionnaire in Multiple Sclerosis Mood subscale (P = .046). Conclusions: These preliminary results suggest that MaTiMS represents a feasible psychological group training program that may foster improvements in self-efficacy, fatigue, and mood. The next step will be an evaluation of the program in a randomized controlled trial. PMID:26052258

Identification of mycotoxins by UHPLC-QTOF MS in airborne fungi and fungi isolated from industrial paper and antique documents from the Archive of Bogotá.

PubMed

Castillo, Nancy I; Ibáñez, María; Beltrán, Eduardo; Rivera-Monroy, Jhon; Ochoa, Juan Camilo; Páez-Castillo, Mónica; Posada-Buitrago, Martha L; Sulyok, Michael; Hernández, Félix

2016-01-01

Mold deterioration of historical documents in archives and libraries is a frequent and complex phenomenon that may have important economic and cultural consequences. In addition, exposure to toxic fungal metabolites might produce health problems. In this work, samples of broths of fungal species isolated from the documentary material and from indoor environmental samples of the Archive of Bogotá have been analyzed to investigate the presence of mycotoxins. High resolution mass spectrometry made possible to search for a large number of mycotoxins, even without reference standards available at the laboratory. For this purpose, a screening strategy based on ultra-high pressure liquid chromatography coupled to quadrupole-time of flight mass spectrometry (UHPLC-QTOF MS) under MS(E) mode was applied. A customized home-made database containing elemental composition for around 600 mycotoxins was compiled. The presence of the (de)protonated molecule measured at its accurate mass was evaluated in the samples. When a peak was detected, collision induced dissociation fragments and characteristic isotopic ions were also evaluated and used for tentative identification, based on structure compatibility and comparison with literature data (if existing). Up to 44 mycotoxins were tentatively identified by UHPLC-QTOF MS. 34 of these tentative compounds were confirmed by subsequent analysis using a targeted LC-MS/MS method, supporting the strong potential of QTOF MS for identification/elucidation purposes. The presence of mycotoxins in these samples might help to reinforce safety measures for researchers and staff who work on reception, restoration and conservation of archival material, not only at the Archive of Bogotá but worldwide. Copyright © 2015 Elsevier Inc. All rights reserved.

In Situ Analysis of Organics with a Portable Mass Spectrometer

NASA Technical Reports Server (NTRS)

Soparawalla, Santosh

2011-01-01

The search for extra-terrestrial life starts at home. In order to find life on other planets, we start by examining life processes we understand on the earth. Though it may not be possible to see the life in the form of macroscopic organisms, telltale signs of life can exist in the form of small organic molecules such as peptides and amino acids. Our overall goal is to test a portable mass spectrometer (MS) system, the Mini 10.5, for astrobiological applications including in situ hydrocarbon analysis and sediments analysis using an additional automated sample processing system (ASPS). The collaborative research focuses on two current projects in the field of astrobiology. Both projects are geared towards examining organics distributed in extreme environments. One portion of study attempts to qualitatively analyze the effect of volatile organic compounds (VOC) produced by diesel exhaust on lichens growing in the desert. This requires measurements to be taken by bringing the instrument to the Mojave Desert and monitoring atmospheric composition of VOCs in situ. The second project is to evaluate the miniature MS system as a detector for the ASPS extraction system. A major obstacle of any chemometric in situ analysis is the suppression of analyte signal by concomitant signal from the surrounding environment. The ASPS extraction device has been developed at JPL to extract amino acids from sediment samples and elute them in solution. The solution is eluted at a high pH and needs to be conditioned to a more neutral pH so that dissolved amino acids can be readily protonated and subsequently analyzed by electrospray MS.

On-line LC-MS approach combining collision-induced dissociation (CID), electron-transfer dissociation (ETD), and CID of an isolated charge-reduced species for the trace-level characterization of proteins with post-translational modifications.

PubMed

Wu, Shiaw-Lin; Hühmer, Andreas F R; Hao, Zhiqi; Karger, Barry L

2007-11-01

We have expanded our recent on-line LC-MS platform for large peptide analysis to combine collision-induced dissociation (CID), electron-transfer dissociation (ETD), and CID of an isolated charge-reduced (CRCID) species derived from ETD to determine sites of phosphorylation and glycosylation modifications, as well as the sequence of large peptide fragments (i.e., 2000-10,000 Da) from complex proteins, such as beta-casein, epidermal growth factor receptor (EGFR), and tissue plasminogen activator (t-PA) at the low femtomol level. The incorporation of an additional CID activation step for a charge-reduced species, isolated from ETD fragment ions, improved ETD fragmentation when precursor ions with high m/z (approximately >1000) were automatically selected for fragmentation. Specifically, the identification of the exact phosphorylation sites was strengthened by the extensive coverage of the peptide sequence with a near-continuous product ion series. The identification of N-linked glycosylation sites in EGFR and an O-linked glycosylation site in t-PA were also improved through the enhanced identification of the peptide backbone sequence of the glycosylated precursors. The new strategy is a good starting survey scan to characterize enzymatic peptide mixtures over a broad range of masses using LC-MS with data-dependent acquisition, as the three activation steps can provide complementary information to each other. In general, large peptides can be extensively characterized by the ETD and CRCID steps, including sites of modification from the generated, near-continuous product ion series, supplemented by the CID-MS2 step. At the same time, small peptides (e.g.,

Sensitivity of GC-EI/MS, GC-EI/MS/MS, LC-ESI/MS/MS, LC-Ag(+) CIS/MS/MS, and GC-ESI/MS/MS for analysis of anabolic steroids in doping control.

PubMed

Cha, Eunju; Kim, Sohee; Kim, Ho Jun; Lee, Kang Mi; Kim, Ki Hun; Kwon, Oh-Seung; Lee, Jaeick

2015-01-01

This study compared the sensitivity of various separation and ionization methods, including gas chromatography with an electron ionization source (GC-EI), liquid chromatography with an electrospray ionization source (LC-ESI), and liquid chromatography with a silver ion coordination ion spray source (LC-Ag(+) CIS), coupled to a mass spectrometer (MS) for steroid analysis. Chromatographic conditions, mass spectrometric transitions, and ion source parameters were optimized. The majority of steroids in GC-EI/MS/MS and LC-Ag(+) CIS/MS/MS analysis showed higher sensitivities than those obtained with other analytical methods. The limits of detection (LODs) of 65 steroids by GC-EI/MS/MS, 68 steroids by LC-Ag(+) CIS/MS/MS, 56 steroids by GC-EI/MS, 54 steroids by LC-ESI/MS/MS, and 27 steroids by GC-ESI/MS/MS were below cut-off value of 2.0 ng/mL. LODs of steroids that formed protonated ions in LC-ESI/MS/MS analysis were all lower than the cut-off value. Several steroids such as unconjugated C3-hydroxyl with C17-hydroxyl structure showed higher sensitivities in GC-EI/MS/MS analysis relative to those obtained using the LC-based methods. The steroids containing 4, 9, 11-triene structures showed relatively poor sensitivities in GC-EI/MS and GC-ESI/MS/MS analysis. The results of this study provide information that may be useful for selecting suitable analytical methods for confirmatory analysis of steroids. Copyright © 2015 John Wiley & Sons, Ltd.

Structural characterization and identification of iridoid glycosides, saponins, phenolic acids and flavonoids in Flos Lonicerae Japonicae by a fast liquid chromatography method with diode-array detection and time-of-flight mass spectrometry.

PubMed

Qi, Lian-Wen; Chen, Chun-Yun; Li, Ping

2009-10-01

A fast liquid chromatography method with diode-array detection (DAD) and time-of-flight mass spectrometry (TOF-MS) has been developed for analysis of constituents in Flos Lonicerae Japonicae (FLJ), a traditional Chinese medicine derived from the flower bud of Lonicera japonica. The chromatographic analytical time decreased to 25 min without sacrificing resolution using a column packed with 1.8-microm porous particles (4.6 x 50 mm), three times faster than the performance of conventional 5.0-microm columns (4.6 x 150 mm). Four major groups of compounds previously isolated from FLJ were structurally characterized by DAD-TOF-MS: iridoid glycosides showed maximum UV absorption at 240 nm; phenolic acids at 217, 242, and 326 nm; flavonoids at 255 and 355 nm; while saponins had no absorption. In electrospray ionization (ESI)-TOF-MS experiments, elimination of a glucose unit (162 Da), and successive losses of H(2)O, CH(3)OH and CO, were generally observed in iridoid glycosides; saponins were characterized by a series of identical aglycone ions; phenolic acids typically generated a base peak at [M-H-caffeoyl](-) by loss of a caffeic acid unit (162 Da) and several marked quinic acid moiety ions; cleavage of the glycosidic bond (loss of 162 or 308 Da), subsequent losses of H(2)O, CO, RDA and C-ring fragmentation were the most possible fragmentation pathways for flavonoids. By accurate mass measurements within 4 ppm error for each molecular ion and subsequent fragment ions, as well as the 'full mass spectral' information of TOF-MS, a total of 41 compounds including 13 iridoid glycosides, 11 phenolic acids, 7 saponins, and 10 flavonoids were identified in a methanolic extract of FLJ. Copyright (c) 2009 John Wiley & Sons, Ltd.

Validation of a LC-MS/MS Method for Quantifying Urinary Nicotine, Six Nicotine Metabolites and the Minor Tobacco Alkaloids—Anatabine and Anabasine—in Smokers' Urine

PubMed Central

McGuffey, James E.; Wei, Binnian; Bernert, John T.; Morrow, John C.; Xia, Baoyun; Wang, Lanqing; Blount, Benjamin C.

2014-01-01

Tobacco use is a major contributor to premature morbidity and mortality. The measurement of nicotine and its metabolites in urine is a valuable tool for evaluating nicotine exposure and for nicotine metabolic profiling—i.e., metabolite ratios. In addition, the minor tobacco alkaloids—anabasine and anatabine—can be useful for monitoring compliance in smoking cessation programs that use nicotine replacement therapy. Because of an increasing demand for the measurement of urinary nicotine metabolites, we developed a rapid, low-cost method that uses isotope dilution liquid chromatography-tandem mass spectrometry (LC-MS/MS) for simultaneously quantifying nicotine, six nicotine metabolites, and two minor tobacco alkaloids in smokers' urine. This method enzymatically hydrolyzes conjugated nicotine (primarily glucuronides) and its metabolites. We then use acetone pretreatment to precipitate matrix components (endogenous proteins, salts, phospholipids, and exogenous enzyme) that may interfere with LC-MS/MS analysis. Subsequently, analytes (nicotine, cotinine, hydroxycotinine, norcotinine, nornicotine, cotinine N-oxide, nicotine 1′-N-oxide, anatabine, and anabasine) are chromatographically resolved within a cycle time of 13.5 minutes. The optimized assay produces linear responses across the analyte concentrations typically found in urine collected from daily smokers. Because matrix ion suppression may influence accuracy, we include a discussion of conventions employed in this procedure to minimize matrix interferences. Simplicity, low cost, low maintenance combined with high mean metabolite recovery (76–99%), specificity, accuracy (0–10% bias) and reproducibility (2–9% C.V.) make this method ideal for large high through-put studies. PMID:25013964

Identification, Synthesis, and Biological Evaluation of the Major Human Metabolite of NLRP3 Inflammasome Inhibitor MCC950

PubMed Central

2016-01-01

MCC950 is an orally bioavailable small molecule inhibitor of the NOD-like receptor pyrin domain-containing protein 3 (NLRP3) inflammasome that exhibits remarkable activity in multiple models of inflammatory disease. Incubation of MCC950 with human liver microsomes, and subsequent analysis by HPLC–MS/MS, revealed a major metabolite, where hydroxylation of MCC950 had occurred on the 1,2,3,5,6,7-hexahydro-s-indacene moiety. Three possible regioisomers were synthesized, and coelution using HPLC–MS/MS confirmed the structure of the metabolite. Further synthesis of individual enantiomers and coelution studies using a chiral column in HPLC–MS/MS showed the metabolite was R-(+)- N-((1-hydroxy-1,2,3,5,6,7-hexahydro-s-indacen-4-yl)carbamoyl)-4-(2-hydroxypropan-2-yl)furan-2-sulfonamide (2a). Incubation of MCC950 with a panel of cytochrome P450 enzymes showed P450s 2A6, 2C9, 2C18, 2C19, 2J2, and 3A4 catalyze the formation of the major metabolite 2a, with a lower level of activity shown by P450s 1A2 and 2B6. All of the synthesized compounds were tested for inhibition of NLRP3-induced production of the pro-inflammatory cytokine IL-1β from human monocyte derived macrophages. The identified metabolite 2a was 170-fold less potent than MCC950, while one regioisomer had nanomolar inhibitory activity. These findings also give first insight into the SAR of the hexahydroindacene moiety. PMID:27994733

Identification, Synthesis, and Biological Evaluation of the Major Human Metabolite of NLRP3 Inflammasome Inhibitor MCC950.

PubMed

Salla, Manohar; Butler, Mark S; Pelingon, Ruby; Kaeslin, Geraldine; Croker, Daniel E; Reid, Janet C; Baek, Jong Min; Bernhardt, Paul V; Gillam, Elizabeth M J; Cooper, Matthew A; Robertson, Avril A B

2016-12-08

MCC950 is an orally bioavailable small molecule inhibitor of the NOD-like receptor pyrin domain-containing protein 3 (NLRP3) inflammasome that exhibits remarkable activity in multiple models of inflammatory disease. Incubation of MCC950 with human liver microsomes, and subsequent analysis by HPLC-MS/MS, revealed a major metabolite, where hydroxylation of MCC950 had occurred on the 1,2,3,5,6,7-hexahydro- s -indacene moiety. Three possible regioisomers were synthesized, and coelution using HPLC-MS/MS confirmed the structure of the metabolite. Further synthesis of individual enantiomers and coelution studies using a chiral column in HPLC-MS/MS showed the metabolite was R -(+)- N -((1-hydroxy-1,2,3,5,6,7-hexahydro- s -indacen-4-yl)carbamoyl)-4-(2-hydroxypropan-2-yl)furan-2-sulfonamide ( 2a ). Incubation of MCC950 with a panel of cytochrome P450 enzymes showed P450s 2A6, 2C9, 2C18, 2C19, 2J2, and 3A4 catalyze the formation of the major metabolite 2a , with a lower level of activity shown by P450s 1A2 and 2B6. All of the synthesized compounds were tested for inhibition of NLRP3-induced production of the pro-inflammatory cytokine IL-1β from human monocyte derived macrophages. The identified metabolite 2a was 170-fold less potent than MCC950, while one regioisomer had nanomolar inhibitory activity. These findings also give first insight into the SAR of the hexahydroindacene moiety.

Clinical and MRI characterization of MS patients with a pure and severe cognitive onset.

PubMed

Assouad, Rana; Louapre, Celine; Tourbah, Ayman; Papeix, Caroline; Galanaud, Damien; Lubetzki, Catherine; Stankoff, Bruno

2014-11-01

Cognitive and behavioural symptoms are common in multiple sclerosis (MS), but they are rarely the inaugural and predominant manifestation of the disease. Our objective is to characterize the clinical and radiological features of cognitive-multiple sclerosis (cog-MS), defined as MS subjects who entered into the disease with cognitive symptoms, which subsequently remain the predominant manifestation. We describe the disease course, and clinical and radiological features of 18 subjects with a cognitive form of MS. Memory loss and behavioural changes were the primary symptoms at disease onset. They remained prominent and led to severe cognitive impairment during disease course. The main associated manifestations were depression, pathological laughing and/or crying, urinary incontinence and gait disturbance suggestive of high-level gait disorder. Motor, sensory or cerebellar abnormalities were uncommon. During disease course, superimposed neurological relapses occurred in 61% of cases. Brain MRI revealed multiple periventricular lesions that were extensive and confluent in half of cases, and a severe atrophy measured as an increase in the third ventricular width compared to age-matched healthy controls. Gadolinium-enhancing lesions were common (72%). The mean diagnosis delay from disease onset was 2 years. A principal component analysis on the neuropsychological results revealed that verbal memory assessment is complementary to global cognitive functioning evaluation in these patients with severe cognitive deficit. Verbal memory deficit was associated with high EDSS. cog-MS patients might represent a challenging diagnosis, which needs to be individualized for an early management. Copyright © 2014 Elsevier B.V. All rights reserved.

Quantitative determination of dopamine in human plasma by a highly sensitive LC-MS/MS assay: Application in preterm neonates.

PubMed

Zhang, Daping; Wu, Lei; Chow, Diana S-L; Tam, Vincent H; Rios, Danielle R

2016-01-05

The determination of dopamine facilitates better understanding of the complex brain disorders in the central nervous system and the regulation of endocrine system, cardiovascular functions and renal functions in the periphery. The purpose of this study was to develop a highly sensitive and reliable assay for the quantification of dopamine in human neonate plasma. Dopamine was extracted from human plasma by strong cation exchange (SCX) solid phase extraction (SPE), and subsequently derivatized with propionic anhydride. The derivatized analyte was separated by a Waters Acquity UPLC BEH C18 column using gradient elution at 0.4 ml/min with mobile phases A (0.2% formic acid in water [v/v]) and B (MeOH-ACN [v/v, 30:70]). Analysis was performed under positive electrospray ionization tandem mass spectrometer (ESI-MS/MS) in the multiple reaction monitoring (MRM) mode. The stable and relatively non-polar nature of the derivatized analyte enables reliable quantification of dopamine in the range of 10-1000 pg/ml using 200 μl of plasma sample. The method was validated with intra-day and inter-day precision less than 7%, and the intra-day and inter-day accuracy of 91.9-101.9% and 92.3-102.6%, respectively. The validated assay was applied to quantify dopamine levels in two preterm neonate plasma samples. In conclusion, a sensitive and selective LC-MS/MS method has been developed and validated, and successfully used for the determination of plasma dopamine levels in preterm neonates. Copyright © 2015 Elsevier B.V. All rights reserved.

Rapid screening and identification of ACE inhibitors in snake venoms using at-line nanofractionation LC-MS.

PubMed

Mladic, Marija; de Waal, Tessa; Burggraaff, Lindsey; Slagboom, Julien; Somsen, Govert W; Niessen, Wilfried M A; Manjunatha Kini, R; Kool, Jeroen

2017-10-01

This study presents an analytical method for the screening of snake venoms for inhibitors of the angiotensin-converting enzyme (ACE) and a strategy for their rapid identification. The method is based on an at-line nanofractionation approach, which combines liquid chromatography (LC), mass spectrometry (MS), and pharmacology in one platform. After initial LC separation of a crude venom, a post-column flow split is introduced enabling parallel MS identification and high-resolution fractionation onto 384-well plates. The plates are subsequently freeze-dried and used in a fluorescence-based ACE activity assay to determine the ability of the nanofractions to inhibit ACE activity. Once the bioactive wells are identified, the parallel MS data reveals the masses corresponding to the activities found. Narrowing down of possible bioactive candidates is provided by comparison of bioactivity profiles after reversed-phase liquid chromatography (RPLC) and after hydrophilic interaction chromatography (HILIC) of a crude venom. Additional nanoLC-MS/MS analysis is performed on the content of the bioactive nanofractions to determine peptide sequences. The method described was optimized, evaluated, and successfully applied for screening of 30 snake venoms for the presence of ACE inhibitors. As a result, two new bioactive peptides were identified: pELWPRPHVPP in Crotalus viridis viridis venom with IC 50  = 1.1 μM and pEWPPWPPRPPIPP in Cerastes cerastes cerastes venom with IC 50  = 3.5 μM. The identified peptides possess a high sequence similarity to other bradykinin-potentiating peptides (BPPs), which are known ACE inhibitors found in snake venoms.

Characterization of Human Skin Emanations by Solid Phase Microextraction (SPME) Extraction of Volatiles and Subsequent Analysis by Gas Chromatography-Mass Spectrometry (GC-MS)

DTIC Science & Technology

2005-05-06

Figure 12: Overlaid TICs of Multiple Extractions for Donor 18 Figure 13: Two Sets of Twins on Same Day Figure 14: Sectioning of Socks for Sock Odors ...considerations they provoked, i.e. sock odors , induced perspiration, Twister® extraction, and glass beads rubbed on hands (which was ultimately...Substances 2.1.2.1 Socks Worn on Feet for Three to Four Hours To test the viability of collecting odors from fragments of clothing, an experiment was

Urine metabolic fingerprinting using LC-MS and GC-MS reveals metabolite changes in prostate cancer: A pilot study.

PubMed

Struck-Lewicka, Wiktoria; Kordalewska, Marta; Bujak, Renata; Yumba Mpanga, Arlette; Markuszewski, Marcin; Jacyna, Julia; Matuszewski, Marcin; Kaliszan, Roman; Markuszewski, Michał J

2015-01-01

Prostate cancer (CaP) is a leading cause of cancer deaths in men worldwide. The alarming statistics, the currently applied biomarkers are still not enough specific and selective. In addition, pathogenesis of CaP development is not totally understood. Therefore, in the present work, metabolomics study related to urinary metabolic fingerprinting analyses has been performed in order to scrutinize potential biomarkers that could help in explaining the pathomechanism of the disease and be potentially useful in its diagnosis and prognosis. Urine samples from CaP patients and healthy volunteers were analyzed with the use of high performance liquid chromatography coupled with time of flight mass spectrometry detection (HPLC-TOF/MS) in positive and negative polarity as well as gas chromatography hyphenated with triple quadruple mass spectrometry detection (GC-QqQ/MS) in a scan mode. The obtained data sets were statistically analyzed using univariate and multivariate statistical analyses. The Principal Component Analysis (PCA) was used to check systems' stability and possible outliers, whereas Partial Least Squares Discriminant Analysis (PLS-DA) was performed for evaluation of quality of the model as well as its predictive ability using statistically significant metabolites. The subsequent identification of selected metabolites using NIST library and commonly available databases allows for creation of a list of putative biomarkers and related biochemical pathways they are involved in. The selected pathways, like urea and tricarboxylic acid cycle, amino acid and purine metabolism, can play crucial role in pathogenesis of prostate cancer disease. Copyright © 2014 Elsevier B.V. All rights reserved.

Interaction of bacteria and ion-exchange particles and its potential in separation for matrix-assisted laser desorption/ionization mass spectrometric identification of bacteria in water.

PubMed

Guo, Zhongxian; Liu, Ying; Li, Shuping; Yang, Zhaoguang

2009-12-01

Identification of microbial contaminants in drinking water is a challenge to matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) due to low levels of microorganisms in fresh water. To avoid the time-consuming culture step of obtaining enough microbial cells for subsequent MALDI-MS analysis, a combination of membrane filtration and nanoparticles- or microparticles-based magnetic separation is a fast and efficient approach. In this work, the interaction of bacteria and fluidMAG-PAA, a cation-exchange superparamagnetic nanomaterial, was investigated by MALDI-MS analysis and transmission electron microscopy. FluidMAG-PAA selectively captured cells of Salmonella, Bacillus, Enterococcus and Staphylococcus aureus. This capture was attributed to the aggregation of negatively charged nanoparticles on bacterial cell regional surfaces that bear positive charges. Three types of non-porous silica-encapsulated anion-exchange magnetic microparticles (SiMAG-Q, SiMAG-PEI, SiMAG-DEAE) were capable of concentrating a variety of bacteria, and were compared with silica-free, smaller fluidMAG particles. Salmonella, Escherichia coli, Enterococcus and other bacteria spiked in aqueous solutions, tap water and reservoir water were separated and concentrated by membrane filtration and magnetic separation based on these ion-exchange magnetic materials, and then characterized by whole cell MALDI-MS. By comparing with the mass spectra of the isolates and pure cells, bacteria in fresh water can be rapidly detected at 1 x 10(3) colony-forming units (cfu)/mL. Copyright 2009 John Wiley & Sons, Ltd.

Control of corrosive bacterial community by bronopol in industrial water system.

PubMed

Narenkumar, Jayaraman; Ramesh, Nachimuthu; Rajasekar, Aruliah

2018-01-01

Ten aerobic corrosive bacterial strains were isolated from a cooling tower water system (CWS) which were identified based on the biochemical characterization and 16S rRNA gene sequencing. Out of them, dominant corrosion-causing bacteria, namely, Bacillus thuringiensis EN2, Terribacillus aidingensis EN3, and Bacillus oleronius EN9, were selected for biocorrosion studies on mild steel 1010 (MS) in a CWS. The biocorrosion behaviour of EN2, EN3, and EN9 strains was studied using immersion test (weight loss method), electrochemical analysis, and surface analysis. To address the corrosion problems, an anti-corrosive study using a biocide, bronopol was also demonstrated. Scanning electron microscopy and Fourier-transform infrared spectroscopy analyses of the MS coupons with biofilm developed after exposure to CWS confirmed the accumulation of extracellular polymeric substances and revealed that biofilms was formed as microcolonies, which subsequently cause pitting corrosion. In contrast, the biocide system, no pitting type of corrosion, was observed and weight loss was reduced about 32 ± 2 mg over biotic system (286 ± 2 mg). FTIR results confirmed the adsorption of bronopol on the MS metal surface as protective layer (co-ordination of NH 2 -Fe 3+ ) to prevent the biofilm formation and inhibit the corrosive chemical compounds and thus led to reduction of corrosion rate (10 ± 1 mm/year). Overall, the results from WL, EIS, SEM, XRD, and FTIR concluded that bronopol was identified as effective biocide and corrosion inhibitor which controls the both chemical and biocorrosion of MS in CWS.

MALDI-MS/MS with Traveling Wave Ion Mobility for the Structural Analysis of N-Linked Glycans

NASA Astrophysics Data System (ADS)

Harvey, David J.; Scarff, Charlotte A.; Crispin, Max; Scanlan, Christopher N.; Bonomelli, Camille; Scrivens, James H.

2012-11-01

The preference for singly charged ion formation by MALDI makes it a better choice than electrospray ionization for profiling mixtures of N-glycans. For structural analysis, fragmentation of negative ions often yields more informative spectra than fragmentation of positive ones but such ions are more difficult to produce from neutral glycans under MALDI conditions. This work investigates conditions for the formation of both positive and negative ions by MALDI from N-linked glycans released from glycoproteins and their subsequent MS/MS and ion mobility behaviour. 2,4,6-Trihydroxyacetophenone (THAP) doped with ammonium nitrate was found to give optimal ion yields in negative ion mode. Ammonium chloride or phosphate also yielded prominent adducts but anionic carbohydrates such as sulfated N-glycans tended to ionize preferentially. Carbohydrates adducted with all three adducts (phosphate, chloride, and nitrate) produced good negative ion CID spectra but those adducted with iodide and sulfate did not yield fragment ions although they gave stronger signals. Fragmentation paralleled that seen following electrospray ionization providing superior spectra than could be obtained by PSD on MALDI-TOF instruments or with ion traps. In addition, ion mobility drift times of the adducted glycans and the ability of this technique to separate isomers also mirrored those obtained following ESI sample introduction. Ion mobility also allowed profiles to be obtained from samples whose MALDI spectra showed no evidence of such ions allowing the technique to be used in conditions where sample amounts were limiting. The method was applied to N-glycans released from the recombinant human immunodeficiency virus glycoprotein, gp120.

Quantitative determination of tilmicosin in canine serum by high performance liquid chromatography-tandem mass spectrometry.

PubMed

Herrera, Michael; Ding, Haiqing; McClanahan, Robert; Owens, Jane G; Hunter, Robert P

2007-09-15

A highly sensitive and quantitative LC/MS/MS assay for the determination of tilmicosin in serum has been developed and validated. For sample preparation, 0.2 mL of canine serum was extracted with 3 mL of methyl tert-butyl ether. The organic layer was transferred to a new vessel and dried under nitrogen. The sample was then reconstituted for analysis by high performance liquid chromatography-tandem mass spectrometry. A Phenomenex Luna C8(2) analytical column was used for the chromatographic separation. The eluent was subsequently introduced to the mass spectrometer by electrospray ionization. A single range was validated for 50-5000 ng/mL for support of toxicokinetic studies. The inter-day relative error (inaccuracy) for the LLOQ samples ranged from -5.5% to 0.3%. The inter-day relative standard deviations (imprecision) at the respective LLOQ levels were < or =10.1%.

Separation and analysis of trace degradants in a pharmaceutical formulation using on-line capillary isotachophoresis-NMR.

PubMed

Eldridge, Stacie L; Almeida, Valentino K; Korir, Albert K; Larive, Cynthia K

2007-11-15

NMR spectroscopy is widely used in the pharmaceutical industry for the structure elucidation of pharmaceutical impurities, especially when coupled to a separation method, such as HPLC. However, NMR has relatively poor sensitivity compared with other techniques such as mass spectrometry, limiting its applicability in impurity analyses. This limitation is addressed here through the on-line coupling of microcoil NMR with capillary isotachophoresis (cITP), a separation method that can concentrate dilute components by 2-3 orders of magnitude. With this approach, 1H NMR spectra can be acquired for microgram (nanomole) quantities of trace impurities in a complex sample matrix. cITP-NMR was used in this work to isolate and detect 4-aminophenol (PAP) in an acetaminophen sample spiked at the 0.1% level, with no interference from the parent compound. Analysis of an acetaminophen thermal degradation sample revealed resonances of several degradation products in addition to PAP, confirming the effectiveness of on-line cITP-NMR for trace analyses of pharmaceutical formulations. Subsequent LC-MS/MS analysis provided complementary information for the structure elucidation of the unknown degradation products, which were dimers formed during the degradation process.

Proteomic analysis of ligamentum flavum from patients with lumbar spinal stenosis.

PubMed

Kamita, Masahiro; Mori, Taiki; Sakai, Yoshihito; Ito, Sadayuki; Gomi, Masahiro; Miyamoto, Yuko; Harada, Atsushi; Niida, Shumpei; Yamada, Tesshi; Watanabe, Ken; Ono, Masaya

2015-05-01

Lumbar spinal stenosis (LSS) is a syndromic degenerative spinal disease and is characterized by spinal canal narrowing with subsequent neural compression causing gait disturbances. Although LSS is a major age-related musculoskeletal disease that causes large decreases in the daily living activities of the elderly, its molecular pathology has not been investigated using proteomics. Thus, we used several proteomic technologies to analyze the ligamentum flavum (LF) of individuals with LSS. Using comprehensive proteomics with strong cation exchange fractionation, we detected 1288 proteins in these LF samples. A GO analysis of the comprehensive proteome revealed that more than 30% of the identified proteins were extracellular. Next, we used 2D image converted analysis of LC/MS to compare LF obtained from individuals with LSS to that obtained from individuals with disc herniation (nondegenerative control). We detected 64 781 MS peaks and identified 1675 differentially expressed peptides derived from 286 proteins. We verified four differentially expressed proteins (fibronectin, serine protease HTRA1, tenascin, and asporin) by quantitative proteomics using SRM/MRM. The present proteomic study is the first to identify proteins from degenerated and hypertrophied LF in LSS, which will help in studying LSS. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Solid matrix transformation and tracer addition using molten ammonium bifluoride salt as a sample preparation method for laser ablation inductively coupled plasma mass spectrometry.

PubMed

Grate, Jay W; Gonzalez, Jhanis J; O'Hara, Matthew J; Kellogg, Cynthia M; Morrison, Samuel S; Koppenaal, David W; Chan, George C-Y; Mao, Xianglei; Zorba, Vassilia; Russo, Richard E

2017-09-08

Solid sampling and analysis methods, such as laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), are challenged by matrix effects and calibration difficulties. Matrix-matched standards for external calibration are seldom available and it is difficult to distribute spikes evenly into a solid matrix as internal standards. While isotopic ratios of the same element can be measured to high precision, matrix-dependent effects in the sampling and analysis process frustrate accurate quantification and elemental ratio determinations. Here we introduce a potentially general solid matrix transformation approach entailing chemical reactions in molten ammonium bifluoride (ABF) salt that enables the introduction of spikes as tracers or internal standards. Proof of principle experiments show that the decomposition of uranium ore in sealed PFA fluoropolymer vials at 230 °C yields, after cooling, new solids suitable for direct solid sampling by LA. When spikes are included in the molten salt reaction, subsequent LA-ICP-MS sampling at several spots indicate that the spikes are evenly distributed, and that U-235 tracer dramatically improves reproducibility in U-238 analysis. Precisions improved from 17% relative standard deviation for U-238 signals to 0.1% for the ratio of sample U-238 to spiked U-235, a factor of over two orders of magnitude. These results introduce the concept of solid matrix transformation (SMT) using ABF, and provide proof of principle for a new method of incorporating internal standards into a solid for LA-ICP-MS. This new approach, SMT-LA-ICP-MS, provides opportunities to improve calibration and quantification in solids based analysis. Looking forward, tracer addition to transformed solids opens up LA-based methods to analytical methodologies such as standard addition, isotope dilution, preparation of matrix-matched solid standards, external calibration, and monitoring instrument drift against external calibration standards.

Bifunctional activity of deoxyhypusine synthase/hydroxylase from Trichomonas vaginalis.

PubMed

Quintas-Granados, Laura Itzel; Carvajal Gamez, Bertha Isabel; Villalpando, Jose Luis; Ortega-Lopez, Jaime; Arroyo, Rossana; Azuara-Liceaga, Elisa; Álvarez-Sánchez, María Elizbeth

2016-04-01

The Trichomonas vaginalis genome analysis suggested the presence of a putative deoxyhypusine synthase (TvDHS) that catalyzes the posttranslational modification of eIF-5A. Herein, we expressed and purified the recombinant TvDHS (rTvDHS) protein (43 kDa) and the recombinant TveIF-5A (rTveIF-5A) precursor protein (46 kDa). A 41 kDa band of the native TvDHS was recognized by western blot analysis in T. vaginalis total protein extract by a mouse polyclonal anti-rTvDHS antibody. The enzymatic activity of rTvDHS was determined by in vitro rTveIF-5A precursor modification. The modification reaction was performed by using ((3)H)-spermidine, and the biochemical analysis showed that rTvDHS exhibited Km value of 0.6 μM. The rTvDHS activity was inhibited by the spermidine analog, N″-guanyl-1,7-diamino-heptane (GC7). Native gel electrophoresis analysis showed two bands corresponding to an rTvDHS-rTveIF-5A complex and an intermediate form of rTveIF-5A. The two forms were subsequently separated by ion exchange chromatography to identify the hypusine residue by MS/MS analysis. Moreover, mutations in TvDHS showed that the putative HE motif present in this enzyme is involved in the hydroxylation of TveIF-5A. We observed that only hypusine-containing TveIF-5A was bound to an RNA hairpin ERE structure from the cox-2 gene, which contains the AAAUGUCACAC consensus sequence. Interestingly, 2DE-WB assays, using parasites that were grown in DAB-culture conditions and transferred to exogenous putrescine, showed the new isoform of TveIF-5A. In summary, our results indicate that T. vaginalis contains an active TvDHS capable of modifying the precursor TveIF-5A protein, which subsequently exhibits RNA binding activity. Copyright © 2015. Published by Elsevier B.V.

Highly efficient peptide separations in proteomics Part 1. Unidimensional high performance liquid chromatography.

PubMed

Sandra, Koen; Moshir, Mahan; D'hondt, Filip; Verleysen, Katleen; Kas, Koen; Sandra, Pat

2008-04-15

Sample complexity and dynamic range constitute enormous challenges in proteome analysis. The back-end technology in typical proteomics platforms, namely mass spectrometry (MS), can only tolerate a certain complexity, has a limited dynamic range per spectrum and is very sensitive towards ion suppression. Therefore, component overlap has to be minimized for successful mass spectrometric analysis and subsequent protein identification and quantification. The present review describes the advances that have been made in liquid-based separation techniques with focus on the recent developments to boost the resolving power. The review is divided in two parts; the first part deals with unidimensional liquid chromatography and the second part with bi- and multidimensional liquid-based separation techniques. Part 1 mainly focuses on reversed-phase HPLC due to the fact that it is and will, in the near future, remain the technique of choice to be hyphenated with MS. The impact of increasing the column length, decreasing the particle diameter, replacing the traditional packed beds by monolithics, amongst others, is described. The review is complemented with data obtained in the laboratories of the authors.

Hair testing for cocaine and metabolites by GC/MS: criteria to quantitatively assess cocaine use.

PubMed

López-Guarnido, O; Álvarez, I; Gil, F; Rodrigo, L; Cataño, H C; Bermejo, A M; Tabernero, M J; Pla, A; Hernández, A F

2013-08-01

A simple, rapid and sensitive method has been developed and validated for the determination of cocaine and its main metabolites (benzoylecgonine and cocaethylene) in human hair. The method involved solid-phase extraction with an Oasis HLB extraction cartridge and subsequent analysis by GC/MS. The limit of detection was 0.01 ng mg(-1) for cocaine, 0.04 for benzoylecgonine and 0.03 for cocaethylene. The method validation included linearity (with a correlation coefficient >0.99 over the range 0.2-50 ng mg(-1) ), intra- and inter-day precision (always lower than 12%) and accuracy (mean relative error always below 17%) to meet the bioanalytical acceptance criteria. The procedure was further applied to 40 hair samples from self-reported cocaine users arrested by the police who provided a positive urine-analysis for cocaine, and was demonstrated to be suitable for its application in forensic toxicology. New approaches were raised to detect false-negative results that allow a better interpretation of hair testing results. Copyright © 2012 John Wiley & Sons, Ltd.

Graphene oxide-based dispersive solid-phase extraction combined with in situ derivatization and gas chromatography-mass spectrometry for the determination of acidic pharmaceuticals in water.

PubMed

Naing, Nyi Nyi; Li, Sam Fong Yau; Lee, Hian Kee

2015-12-24

A fast and low-cost sample preparation method of graphene based dispersive solid-phase extraction combined with gas chromatography-mass spectrometric (GC-MS) analysis, was developed. The procedure involves an initial extraction with water-immiscible organic solvent, followed by a rapid clean-up using amine functionalized reduced graphene oxide as sorbent. Simple and fast one-step in situ derivatization using trimethylphenylammonium hydroxide was subsequently applied on acidic pharmaceuticals serving as model analytes, ibuprofen, gemfibrozil, naproxen, ketoprofen and diclofenac, before GC-MS analysis. Extraction parameters affecting the derivatization and extraction efficiency such as volume of derivatization agent, effect of desorption solvent, effect of pH and effect of ionic strength were investigated. Under the optimum conditions, the method demonstrated good limits of detection ranging from 1 to 16ngL(-1), linearity (from 0.01 to 50 and 0.05 to 50μgL(-1), depending on the analytes) and satisfactory repeatability of extractions (relative standard deviations, below 13%, n=3). Copyright © 2015 Elsevier B.V. All rights reserved.

Enrichment and Analysis of Non-enzymatically Glycated Peptides: Boronate Affinity Chromatography Coupled with Electron Transfer Dissociation Mass Spectrometry

PubMed Central

Zhang, Qibin; Tang, Ning; Brock, Jonathan W. C.; Mottaz, Heather M.; Ames, Jennifer M.; Baynes, John W.; Smith, Richard D.; Metz, Thomas O.

2008-01-01

Non-enzymatic glycation of peptides and proteins by D-glucose has important implications in the pathogenesis of diabetes mellitus, particularly in the development of diabetic complications. However, no effective high-throughput methods exist for identifying proteins containing this low abundance post-translational modification in bottom-up proteomic studies. In this report, phenylboronate affinity chromatography was used in a two-step enrichment scheme to selectively isolate first glycated proteins and then glycated, tryptic peptides from human serum glycated in vitro. Enriched peptides were subsequently analyzed by alternating electron transfer dissociation (ETD) and collision induced dissociation (CID) tandem mass spectrometry. ETD fragmentation mode permitted identification of a significantly higher number of glycated peptides (87.6% of all identified peptides) versus CID mode (17.0% of all identified peptides), when utilizing enrichment on first the protein and then the peptide level. This study illustrates that phenylboronate affinity chromatography coupled with LC-MS/MS and using ETD as the fragmentation mode is an efficient approach for analysis of glycated proteins and may have broad application in studies of diabetes mellitus. PMID:17488106

An integrated approach utilising chemometrics and GC/MS for classification of chamomile flowers, essential oils and commercial products.

PubMed

Wang, Mei; Avula, Bharathi; Wang, Yan-Hong; Zhao, Jianping; Avonto, Cristina; Parcher, Jon F; Raman, Vijayasankar; Zweigenbaum, Jerry A; Wylie, Philip L; Khan, Ikhlas A

2014-01-01

As part of an ongoing research program on authentication, safety and biological evaluation of phytochemicals and dietary supplements, an in-depth chemical investigation of different types of chamomile was performed. A collection of chamomile samples including authenticated plants, commercial products and essential oils was analysed by GC/MS. Twenty-seven authenticated plant samples representing three types of chamomile, viz. German chamomile, Roman chamomile and Juhua were analysed. This set of data was employed to construct a sample class prediction (SCP) model based on stepwise reduction of data dimensionality followed by principle component analysis (PCA) and partial least squares discriminant analysis (PLS-DA). The model was cross-validated with samples including authenticated plants and commercial products. The model demonstrated 100.0% accuracy for both recognition and prediction abilities. In addition, 35 commercial products and 11 essential oils purported to contain chamomile were subsequently predicted by the validated PLS-DA model. Furthermore, tentative identification of the marker compounds correlated with different types of chamomile was explored. Copyright © 2013 Elsevier Ltd. All rights reserved.

Simultaneous separation and identification of oligomeric procyanidins and anthocyanin-derived pigments in raw red wine by HPLC-UV-ESI-MSn.

PubMed

Pati, S; Losito, I; Gambacorta, G; La Notte, E; Palmisano, F; Zambonin, P G

2006-07-01

Samples of raw red wine (Primitivo di Manduria, Apulia, Southern Italy) were analysed without any pre-treatment (except 1:2 dilution with water) using HPLC with detection based on UV absorbance and Electrospray Ionisation Sequential Mass Spectrometry (ESI-MSn, with n = 1-3) in a series configuration. In particular, absorbance at 520 nm was monitored for UV detection in order to identify pigments responsible for wine colour. On the other hand, two subsequent stages of MS detection based on positive ions were adopted. The first consisted of an explorative MS acquisition, aimed at the individuation of the m/z ratios for positively charged compounds; the second was based on fragmentation of the detected ions within an ion trap analyser, followed by MS/MS and, if required, MS3 acquisitions. The synergy between UV detection and MSn analysis led to the identification of 41 pigments, which can be classified into five groups: grape anthocyanins, pyranoanthocyanins, vinyl-linked anthocyanin-flavanol pigments, ethyl-bridged anthocyanin-flavanol pigments and flavanol-anthocyanin compounds. Many isomeric and oligomeric structures were found within each group. A further class of compounds, not absorbing in the visible spectrum, could be also characterised by ESI-MSn and corresponded to B-type procyanidins, i.e. proanthocyanidins arising from C4-->C8/C4-->C6 couplings between catechin or epicatechin units. In particular, oligomeric structures (from dimers to pentamers), often present with several isomers, were identified and their fragmentation patterns clarified.

Parallel microscope-based fluorescence, absorbance and time-of-flight mass spectrometry detection for high performance liquid chromatography and determination of glucosamine in urine.

PubMed

Xiong, Bo; Wang, Ling-Ling; Li, Qiong; Nie, Yu-Ting; Cheng, Shuang-Shuang; Zhang, Hui; Sun, Ren-Qiang; Wang, Yu-Jiao; Zhou, Hong-Bin

2015-11-01

A parallel microscope-based laser-induced fluorescence (LIF), ultraviolet-visible absorbance (UV) and time-of-flight mass spectrometry (TOF-MS) detection for high performance liquid chromatography (HPLC) was achieved and used to determine glucosamine in urines. First, a reliable and convenient LIF detection was developed based on an inverted microscope and corresponding modulations. Parallel HPLC-LIF/UV/TOF-MS detection was developed by the combination of preceding Microscope-based LIF detection and HPLC coupled with UV and TOF-MS. The proposed setup, due to its parallel scheme, was free of the influence from photo bleaching in LIF detection. Rhodamine B, glutamic acid and glucosamine have been determined to evaluate its performance. Moreover, the proposed strategy was used to determine the glucosamine in urines, and subsequent results suggested that glucosamine, which was widely used in the prevention of the bone arthritis, was metabolized to urines within 4h. Furthermore, its concentration in urines decreased to 5.4mM at 12h. Efficient glucosamine detection was achieved based on a sensitive quantification (LIF), a universal detection (UV) and structural characterizations (TOF-MS). This application indicated that the proposed strategy was sensitive, universal and versatile, and it was capable of improved analysis, especially for analytes with low concentrations in complex samples, compared with conventional HPLC-UV/TOF-MS. Copyright © 2015 Elsevier B.V. All rights reserved.

Methylation-sensitive enrichment of minor DNA alleles using a double-strand DNA-specific nuclease.

PubMed

Liu, Yibin; Song, Chen; Ladas, Ioannis; Fitarelli-Kiehl, Mariana; Makrigiorgos, G Mike

2017-04-07

Aberrant methylation changes, often present in a minor allelic fraction in clinical samples such as plasma-circulating DNA (cfDNA), are potentially powerful prognostic and predictive biomarkers in human disease including cancer. We report on a novel, highly-multiplexed approach to facilitate analysis of clinically useful methylation changes in minor DNA populations. Methylation Specific Nuclease-assisted Minor-allele Enrichment (MS-NaME) employs a double-strand-specific DNA nuclease (DSN) to remove excess DNA with normal methylation patterns. The technique utilizes oligonucleotide-probes that direct DSN activity to multiple targets in bisulfite-treated DNA, simultaneously. Oligonucleotide probes targeting unmethylated sequences generate local double stranded regions resulting to digestion of unmethylated targets, and leaving methylated targets intact; and vice versa. Subsequent amplification of the targeted regions results in enrichment of the targeted methylated or unmethylated minority-epigenetic-alleles. We validate MS-NaME by demonstrating enrichment of RARb2, ATM, MGMT and GSTP1 promoters in multiplexed MS-NaME reactions (177-plex) using dilutions of methylated/unmethylated DNA and in DNA from clinical lung cancer samples and matched normal tissue. MS-NaME is a highly scalable single-step approach performed at the genomic DNA level in solution that combines with most downstream detection technologies including Sanger sequencing, methylation-sensitive-high-resolution melting (MS-HRM) and methylation-specific-Taqman-based-digital-PCR (digital Methylight) to boost detection of low-level aberrant methylation-changes. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Identification of mycotoxins by UHPLC–QTOF MS in airborne fungi and fungi isolated from industrial paper and antique documents from the Archive of Bogotá

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

Castillo, Nancy I.; Ibáñez, María; Beltrán, Eduardo

Mold deterioration of historical documents in archives and libraries is a frequent and complex phenomenon that may have important economic and cultural consequences. In addition, exposure to toxic fungal metabolites might produce health problems. In this work, samples of broths of fungal species isolated from the documentary material and from indoor environmental samples of the Archive of Bogotá have been analyzed to investigate the presence of mycotoxins. High resolution mass spectrometry made possible to search for a large number of mycotoxins, even without reference standards available at the laboratory. For this purpose, a screening strategy based on ultra-high pressure liquidmore » chromatography coupled to quadrupole-time of flight mass spectrometry (UHPLC–QTOF MS) under MS{sup E} mode was applied. A customized home-made database containing elemental composition for around 600 mycotoxins was compiled. The presence of the (de)protonated molecule measured at its accurate mass was evaluated in the samples. When a peak was detected, collision induced dissociation fragments and characteristic isotopic ions were also evaluated and used for tentative identification, based on structure compatibility and comparison with literature data (if existing). Up to 44 mycotoxins were tentatively identified by UHPLC–QTOF MS. 34 of these tentative compounds were confirmed by subsequent analysis using a targeted LC–MS/MS method, supporting the strong potential of QTOF MS for identification/elucidation purposes. The presence of mycotoxins in these samples might help to reinforce safety measures for researchers and staff who work on reception, restoration and conservation of archival material, not only at the Archive of Bogotá but worldwide. - Highlights: • Mold deterioration of historical documents is a frequent and complex phenomenon. • Samples of broths of fungal species isolated from Archive of Bogotá analyzed. • UHPLC–QTOF MS (MS{sup E}) applied for mycotoxins screening, without reference standards. • Customized home-made database for around 600 mycotoxins compiled. • 44 mycotoxins tentatively identified, 34 of which confirmed by LC–MS/MS.« less

Development and optimization of an analytical system for volatile organic compound analysis coming from the heating of interstellar/cometary ice analogues.

PubMed

Abou Mrad, Ninette; Duvernay, Fabrice; Theulé, Patrice; Chiavassa, Thierry; Danger, Grégoire

2014-08-19

This contribution presents an original analytical system for studying volatile organic compounds (VOC) coming from the heating and/or irradiation of interstellar/cometary ice analogues (VAHIIA system) through laboratory experiments. The VAHIIA system brings solutions to three analytical constraints regarding chromatography analysis: the low desorption kinetics of VOC (many hours) in the vacuum chamber during laboratory experiments, the low pressure under which they sublime (10(-9) mbar), and the presence of water in ice analogues. The VAHIIA system which we developed, calibrated, and optimized is composed of two units. The first is a preconcentration unit providing the VOC recovery. This unit is based on a cryogenic trapping which allows VOC preconcentration and provides an adequate pressure allowing their subsequent transfer to an injection unit. The latter is a gaseous injection unit allowing the direct injection into the GC-MS of the VOC previously transferred from the preconcentration unit. The feasibility of the online transfer through this interface is demonstrated. Nanomoles of VOC can be detected with the VAHIIA system, and the variability in replicate measurements is lower than 13%. The advantages of the GC-MS in comparison to infrared spectroscopy are pointed out, the GC-MS allowing an unambiguous identification of compounds coming from complex mixtures. Beyond the application to astrophysical subjects, these analytical developments can be used for all systems requiring vacuum/cryogenic environments.

UV Lamp as a Facile Ozone Source for Structural Analysis of Unsaturated Lipids Via Electrospray Ionization-Mass Spectrometry

NASA Astrophysics Data System (ADS)

Stinson, Craig A.; Zhang, Wenpeng; Xia, Yu

2017-12-01

Ozonolysis of alkene functional groups is a type of highly specific and effective chemical reaction, which has found increasing applications in structural analysis of unsaturated lipids via coupling with mass spectrometry (MS). In this work, we utilized a low-pressure mercury lamp (6 W) to initiate ozonolysis inside electrospray ionization (ESI) sources. By placing the lamp near a nanoESI emitter that partially transmits 185 nm ultraviolet (UV) emission from the lamp, dissolved dioxygen in the spray solution was converted into ozone, which subsequently cleaved the double bonds within fatty acyls of lipids. Solvent conditions, such as presence of water and acid solution pH, were found to be critical in optimizing ozonolysis yields. Fast (on seconds time scale) and efficient (50%-100% yield) ozonolysis was achieved for model unsaturated phospholipids and fatty acids with UV lamp-induced ozonolysis incorporated on a static and an infusion nanoESI source. The method was able to differentiate double bond location isomers and identify the geometry of the double bond based on yield. The analytical utility of UV lamp-induced ozonolysis was further demonstrated by implementation on a liquid chromatography (LC)-MS platform. Ozonolysis was effected in a flow microreactor that was made from ozone permeable tubing, so that ambient ozone produced by the lamp irradiation could diffuse into the reactor and induce online ozonolysis post-LC separation and before ESI-MS.

Surface modified capillary electrophoresis combined with in solution isoelectric focusing and MALDI-TOF/TOF MS: a gel-free multidimensional electrophoresis approach for proteomic profiling--exemplified on human follicular fluid.

PubMed

Hanrieder, Jörg; Zuberovic, Aida; Bergquist, Jonas

2009-04-24

Development of miniaturized analytical tools continues to be of great interest to face the challenges in proteomic analysis of complex biological samples such as human body fluids. In the light of these challenges, special emphasis is put on the speed and simplicity of newly designed technological approaches as well as the need for cost efficiency and low sample consumption. In this study, we present an alternative multidimensional bottom-up approach for proteomic profiling for fast, efficient and sensitive protein analysis in complex biological matrices. The presented setup was based on sample pre-fractionation using microscale in solution isoelectric focusing (IEF) followed by tryptic digestion and subsequent capillary electrophoresis (CE) coupled off-line to matrix assisted laser desorption/ionization time of flight tandem mass spectrometry (MALDI TOF MS/MS). For high performance CE-separation, PolyE-323 modified capillaries were applied to minimize analyte-wall interactions. The potential of the analytical setup was demonstrated on human follicular fluid (hFF) representing a typical complex human body fluid with clinical implication. The obtained results show significant identification of 73 unique proteins (identified at 95% significance level), including mostly acute phase proteins but also protein identities that are well known to be extensively involved in follicular development.

Effective Identification of Akt Interacting Proteins by Two-Step Chemical Crosslinking, Co-Immunoprecipitation and Mass Spectrometry

PubMed Central

Huang, Bill X.; Kim, Hee-Yong

2013-01-01

Akt is a critical protein for cell survival and known to interact with various proteins. However, Akt binding partners that modulate or regulate Akt activation have not been fully elucidated. Identification of Akt-interacting proteins has been customarily achieved by co-immunoprecipitation combined with western blot and/or MS analysis. An intrinsic problem of the method is loss of interacting proteins during procedures to remove non-specific proteins. Moreover, antibody contamination often interferes with the detection of less abundant proteins. Here, we developed a novel two-step chemical crosslinking strategy to overcome these problems which resulted in a dramatic improvement in identifying Akt interacting partners. Akt antibody was first immobilized on protein A/G beads using disuccinimidyl suberate and allowed to bind to cellular Akt along with its interacting proteins. Subsequently, dithiobis[succinimidylpropionate], a cleavable crosslinker, was introduced to produce stable complexes between Akt and binding partners prior to the SDS-PAGE and nanoLC-MS/MS analysis. This approach enabled identification of ten Akt partners from cell lysates containing as low as 1.5 mg proteins, including two new potential Akt interacting partners. None of these but one protein was detectable without crosslinking procedures. The present method provides a sensitive and effective tool to probe Akt-interacting proteins. This strategy should also prove useful for other protein interactions, particularly those involving less abundant or weakly associating partners. PMID:23613850

Software LS-MIDA for efficient mass isotopomer distribution analysis in metabolic modelling.

PubMed

Ahmed, Zeeshan; Zeeshan, Saman; Huber, Claudia; Hensel, Michael; Schomburg, Dietmar; Münch, Richard; Eisenreich, Wolfgang; Dandekar, Thomas

2013-07-09

The knowledge of metabolic pathways and fluxes is important to understand the adaptation of organisms to their biotic and abiotic environment. The specific distribution of stable isotope labelled precursors into metabolic products can be taken as fingerprints of the metabolic events and dynamics through the metabolic networks. An open-source software is required that easily and rapidly calculates from mass spectra of labelled metabolites, derivatives and their fragments global isotope excess and isotopomer distribution. The open-source software "Least Square Mass Isotopomer Analyzer" (LS-MIDA) is presented that processes experimental mass spectrometry (MS) data on the basis of metabolite information such as the number of atoms in the compound, mass to charge ratio (m/e or m/z) values of the compounds and fragments under study, and the experimental relative MS intensities reflecting the enrichments of isotopomers in 13C- or 15 N-labelled compounds, in comparison to the natural abundances in the unlabelled molecules. The software uses Brauman's least square method of linear regression. As a result, global isotope enrichments of the metabolite or fragment under study and the molar abundances of each isotopomer are obtained and displayed. The new software provides an open-source platform that easily and rapidly converts experimental MS patterns of labelled metabolites into isotopomer enrichments that are the basis for subsequent observation-driven analysis of pathways and fluxes, as well as for model-driven metabolic flux calculations.

A matched cohort comparison of clinical outcomes following microsurgical resection or stereotactic radiosurgery for patients with small- and medium-sized vestibular schwannomas.

PubMed

Golfinos, John G; Hill, Travis C; Rokosh, Rae; Choudhry, Osamah; Shinseki, Matthew; Mansouri, Alireza; Friedmann, David R; Thomas Roland, J; Kondziolka, Douglas

2016-12-01

OBJECTIVE A randomized trial that compares clinical outcomes following microsurgery (MS) or stereotactic radiosurgery (SRS) for patients with small- and medium-sized vestibular schwannomas (VSs) is impractical, but would have important implications for clinical decision making. A matched cohort analysis was conducted to evaluate clinical outcomes in patients treated with MS or SRS. METHODS The records of 399 VS patients who were cared for by 2 neurosurgeons and 1 neurotologist between 2001 and 2014 were evaluated. From this data set, 3 retrospective matched cohorts were created to compare hearing preservation (21 matched pairs), facial nerve preservation (83 matched pairs), intervention-free survival, and complication rates (85 matched pairs) between cases managed with SRS and patients managed with MS. Cases were matched for age at surgery (± 10 years) and lesion size (± 0.1 cm). To compare hearing outcomes, cases were additionally matched for preoperative Class A hearing according to the American Academy of Otolaryngology-Head and Neck Surgery guidelines. To compare facial nerve (i.e., cranial nerve [CN] VII) outcomes, cases were additionally matched for preoperative House-Brackmann (HB) score. Investigators who were not involved with patient care reviewed the clinical and imaging records. The reported outcomes were as assessed at the time of the last follow-up, unless otherwise stated. RESULTS The preservation of preoperative Class A hearing status was achieved in 14.3% of MS cases compared with 42.9% of SRS cases (OR 4.5; p < 0.05) after an average follow-up interval of 43.7 months and 30.3 months, respectively. Serviceable hearing was preserved in 42.8% of MS cases compared with 85.7% of SRS cases (OR 8.0; p < 0.01). The rates of postoperative CN VII dysfunction were low for both groups, although significantly higher in the MS group (HB III-IV 11% vs 0% for SRS; OR 21.3; p < 0.01) at a median follow-up interval of 35.7 and 19.0 months for MS and SRS, respectively. There was no difference in the need for subsequent intervention (2 MS patients and 2 SRS patients). CONCLUSIONS At this high-volume center, VS resection or radiosurgery for tumors ≤ 2.8 cm in diameter was associated with low overall morbidity. The need for subsequent intervention was the same in both groups. SRS was associated with improved hearing and facial preservation rates and reduced morbidity, but with a shorter average follow-up period. Facial function was excellent in both groups. Since patients were not randomly selected for surgery, different clinical outcomes may be of different value to individual patients. Both anticipated medical outcomes and patient goals remain the drivers of treatment decisions.

Nontargeted diagnostic ion network analysis (NINA): A software to streamline the analytical workflow for untargeted characterization of natural medicines.

PubMed

Ye, Hui; Zhu, Lin; Sun, Di; Luo, Xiaozhuo; Lu, Gaoyuan; Wang, Hong; Wang, Jing; Cao, Guoxiu; Xiao, Wei; Wang, Zhenzhong; Wang, Guangji; Hao, Haiping

2016-11-30

The characterization of herbal prescriptions serves as a foundation for quality control and regulation of herbal medicines. Previously, the characterization of herbal chemicals from natural medicines often relied on the analysis of signature fragment ions from the acquired tandem mass spectrometry (MS/MS) spectra with prior knowledge of the herbal species present in the herbal prescriptions of interest. Nevertheless, such an approach is often limited to target components, and it risks missing the critical components that we have no prior knowledge of. We previously reported a "diagnostic ion-guided network bridging" strategy. It is a generally applicable and robust approach to analyze unknown substances from complex mixtures in an untargeted manner. In this study, we have developed a standalone software named "Nontargeted Diagnostic Ion Network Analysis (NINA)" with a graphical user interface based on a strategy for post-acquisition data analysis. NINA allows one to rapidly determine the nontargeted diagnostic ions (NIs) by summarizing all of the fragment ions shared by the precursors from the acquired MS/MS spectra. A NI-guided network using bridging components that possess two or more NIs can then be established via NINA. With such a network, we could sequentially identify the structures of all the NIs once a single compound has been identified de novo. The structures of NIs can then be used as "priori" knowledge to narrow the candidates containing the sub-structure of the corresponding NI from the database hits. Subsequently, we applied the NINA software to the characterization of a model herbal prescription, Re-Du-Ning injection, and rapidly identified 56 herbal chemicals from the prescription using an ultra-performance liquid chromatography quadrupole time-of-flight system in the negative mode with no knowledge of the herbal species or herbal chemicals in the mixture. Therefore, we believe the applications of NINA will greatly facilitate the characterization of complex mixtures, such as natural medicines, especially when no advance information is available. In addition to herbal medicines, the NINA-based workflow will also benefit many other fields, such as environmental analysis, nutritional science, and forensic analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

Visual-gustatory interaction: orbitofrontal and insular cortices mediate the effect of high-calorie visual food cues on taste pleasantness.

PubMed

Ohla, Kathrin; Toepel, Ulrike; le Coutre, Johannes; Hudry, Julie

2012-01-01

Vision provides a primary sensory input for food perception. It raises expectations on taste and nutritional value and drives acceptance or rejection. So far, the impact of visual food cues varying in energy content on subsequent taste integration remains unexplored. Using electrical neuroimaging, we assessed whether high- and low-calorie food cues differentially influence the brain processing and perception of a subsequent neutral electric taste. When viewing high-calorie food images, participants reported the subsequent taste to be more pleasant than when low-calorie food images preceded the identical taste. Moreover, the taste-evoked neural activity was stronger in the bilateral insula and the adjacent frontal operculum (FOP) within 100 ms after taste onset when preceded by high- versus low-calorie cues. A similar pattern evolved in the anterior cingulate (ACC) and medial orbitofrontal cortex (OFC) around 180 ms, as well as, in the right insula, around 360 ms. The activation differences in the OFC correlated positively with changes in taste pleasantness, a finding that is an accord with the role of the OFC in the hedonic evaluation of taste. Later activation differences in the right insula likely indicate revaluation of interoceptive taste awareness. Our findings reveal previously unknown mechanisms of cross-modal, visual-gustatory, sensory interactions underlying food evaluation.

Visual-Gustatory Interaction: Orbitofrontal and Insular Cortices Mediate the Effect of High-Calorie Visual Food Cues on Taste Pleasantness

PubMed Central

Ohla, Kathrin; Toepel, Ulrike; le Coutre, Johannes; Hudry, Julie

2012-01-01

Vision provides a primary sensory input for food perception. It raises expectations on taste and nutritional value and drives acceptance or rejection. So far, the impact of visual food cues varying in energy content on subsequent taste integration remains unexplored. Using electrical neuroimaging, we assessed whether high- and low-calorie food cues differentially influence the brain processing and perception of a subsequent neutral electric taste. When viewing high-calorie food images, participants reported the subsequent taste to be more pleasant than when low-calorie food images preceded the identical taste. Moreover, the taste-evoked neural activity was stronger in the bilateral insula and the adjacent frontal operculum (FOP) within 100 ms after taste onset when preceded by high- versus low-calorie cues. A similar pattern evolved in the anterior cingulate (ACC) and medial orbitofrontal cortex (OFC) around 180 ms, as well as, in the right insula, around 360 ms. The activation differences in the OFC correlated positively with changes in taste pleasantness, a finding that is an accord with the role of the OFC in the hedonic evaluation of taste. Later activation differences in the right insula likely indicate revaluation of interoceptive taste awareness. Our findings reveal previously unknown mechanisms of cross-modal, visual-gustatory, sensory interactions underlying food evaluation. PMID:22431974

Purification and high-resolution top-down mass spectrometric characterization of human salivary α-amylase.

PubMed

Peng, Ying; Chen, Xin; Sato, Takuya; Rankin, Scott A; Tsuji, Ryohei F; Ge, Ying

2012-04-03

Human salivary α-amylase (HSAMY) is a major component of salivary secretions, possessing multiple important biological functions. Here we have established three methods to purify HSAMY in human saliva for comprehensive characterization of HSAMY by high-resolution top-down mass spectrometry (MS). Among the three purification methods, the affinity method based on the enzyme-substrate specific interaction between amylase and glycogen is preferred, providing the highest purity HSAMY with high reproducibility. Subsequently, we employed Fourier transform ion cyclotron resonance MS to analyze the purified HSAMY. The predominant form of α-amylase purified from saliva of various races and genders is nonglycosylated with the same molecular weight of 55,881.2, which is 1885.8 lower than the calculated value based on the DNA-predicted sequence. High-resolution MS revealed the truncation of the first 15 N-terminal amino acids (-1858.96) and the subsequent formation of pyroglutamic acid at the new N-terminus Gln (-17.03). More importantly, five disulfide bonds in HSAMY were identified (-10.08) and effectively localized by tandem MS in conjunction with complete and partial reduction by tris (2-carboxyethyl) phosphine. Overall, this study demonstrates that top-down MS combined with affinity purification and partial reduction is a powerful method for rapid purification and complete characterization of large proteins with complex and overlapping disulfide bond patterns.

UVnovo: A De Novo Sequencing Algorithm Using Single Series of Fragment Ions via Chromophore Tagging and 351 nm Ultraviolet Photodissociation Mass Spectrometry

PubMed Central

Robotham, Scott A.; Horton, Andrew P.; Cannon, Joe R.; Cotham, Victoria C.; Marcotte, Edward M.; Brodbelt, Jennifer S.

2016-01-01

De novo peptide sequencing by mass spectrometry represents an important strategy for characterizing novel peptides and proteins, in which a peptide’s amino acid sequence is inferred directly from the precursor peptide mass and tandem mass spectrum (MS/MS or MS3) fragment ions, without comparison to a reference proteome. This method is ideal for organisms or samples lacking a complete or well-annotated reference sequence set. One of the major barriers to de novo spectral interpretation arises from confusion of N- and C-terminal ion series due to the symmetry between b and y ion pairs created by collisional activation methods (or c, z ions for electron-based activation methods). This is known as the ‘antisymmetric path problem’ and leads to inverted amino acid subsequences within a de novo reconstruction. Here, we combine several key strategies for de novo peptide sequencing into a single high-throughput pipeline: high efficiency carbamylation blocks lysine side chains, and subsequent tryptic digestion and N-terminal peptide derivatization with the ultraviolet chromophore AMCA yields peptides susceptible to 351 nm ultraviolet photodissociation (UVPD). UVPD-MS/MS of the AMCA-modified peptides then predominantly produces y ions in the MS/MS spectra, specifically addressing the antisymmetric path problem. Finally, the program UVnovo applies a random forest algorithm to automatically learn from and then interpret UVPD mass spectra, passing results to a hidden Markov model for de novo sequence prediction and scoring. We show this combined strategy provides high performance de novo peptide sequencing, enabling the de novo sequencing of thousands of peptides from an E. coli lysate at high confidence. PMID:26938041

Rationale and design of a randomized controlled, clinical trial investigating a comprehensive exercise stimulus for improving mobility disability outcomes in persons with multiple sclerosis.

PubMed

Motl, Robert W; Pilutti, Lara A; Sandroff, Brian M; Klaren, Rachel; Balantrapu, Swathi; McAuley, Edward; Sosnoff, Jacob J; Fernhall, Bo

2013-05-01

This randomized controlled trial (RCT) examines the effect of a comprehensive exercise training stimulus on physiological function and mobility disability (i.e., problems walking) in individuals with multiple sclerosis (MS) who have walking impairment. This trial will recruit 30 persons with MS across central Illinois who have an Expanded Disability Status Scale score between 4.0 and 6.0, and those persons will be randomized into either the intervention or control arm of the study; the participants will not be blinded regarding group assignment. The intervention will incorporate equal amounts of aerobic, resistance, and balance modes of training delivered 3 times/week with a gradual progression of duration and intensity across a 6-month period. The control will involve stretching along with minimal muscle strengthening stimuli and will be delivered on the same frequency and duration. The primary outcomes will be clinical, kinematic, patient-rated, and physiological measures of mobility disability. The secondary outcomes will be measures of physiological function including aerobic capacity, muscle strength, and balance. This study will lay the foundation for the design of a subsequent Phase II or Phase III RCT by (a) providing effect sizes that can be included in a power analysis for sample size estimation and (b) investigating whether aerobic capacity, muscle strength, and balance are possible factors associated with the beneficial effect of exercise training on walking outcomes. Taken as a whole, the proposed study and our subsequent research agenda has the potential for advancing the management of mobility disability using exercise training in the 2nd stage of MS. Copyright © 2013 Elsevier Inc. All rights reserved.

Development and application of LC–APCI–MS method for biomonitoring of animal and human exposure to imidacloprid.

PubMed

Kavvalakis, Matthaios P; Tzatzarakis, Manolis N; Theodoropoulou, Eleftheria P; Barbounis, Emmanouil G; Tsakalof, Andreas K; Tsatsakis, Aristidis M

2013-11-01

Imidacloprid (IMI) is a relatively new neuro-active neonicotinoid insecticide and nowadays one of the largest selling insecticides worldwide. In the present study a LC–APCI–MS based method was developed and validated for the quantification of imidacloprid and its main metabolite 6-chloronicotinic acid (6- CINA) in urine and hair specimens. The method was tested in biomonitoring of intentionally exposed animals and subsequently applied for biomonitoring of Cretan urban and rural population. The developed analytical method comprises two main steps of analytes isolation from specimen (solid– liquid extraction with methanol for hair, liquid–liquid extraction with methanol for urine) and subsequent instrumental analysis by LC–APCI–MS. The developed method was applied for the monitoring of IMI and 6-ClNA in hair and urine of laboratory animals (rabbits) intentionally fed with insecticide at low or high doses (40 and 80 mg kg(-1) weight d(-1) respectively) for 24 weeks. The analytes were detected in the regularly acquired hair and urine specimens and their found levels were proportional to the feeding dose and time of exposure with the exception of slight decline of IMI levels in high dose fed rabbits after 24 weeks of feeding. This decline can be explained by the induction of IMI metabolizing enzymes by the substrate. After testing on animal models the method was applied for pilot biomonitoring of Crete urban (n = 26) and rural (n = 32) population. Rural but not urban population is exposed to IMI with 21 positive samples (65.6%) and found median concentration 0.03 ng mg(-1). Maximum concentration detected was 27 ng mg(-1)

LC-MS-MS aboard ship: tandem mass spectrometry in the search for phycotoxins and novel toxigenic plankton from the North Sea.

PubMed

Krock, Bernd; Tillmann, Urban; John, Uwe; Cembella, Allan

2008-11-01

Phycotoxins produced by various species of toxigenic microalgae occurring in the plankton are a global threat to the security of seafood resources and the health of humans and coastal marine ecosystems. This has necessitated the development and application of advanced methods in liquid chromatography coupled to mass spectrometry (LC-MS) for monitoring of these compounds, particularly in plankton and shellfish. Most such chemical analyses are conducted in land-based laboratories on stored samples, and thus much information on the near real-time biogeographical distribution and dynamics of phycotoxins in the plankton is unavailable. To resolve this problem, we conducted ship-board analysis of a broad spectrum of phycotoxins collected directly from the water column on an oceanographic cruise along the North Sea coast of Scotland, Norway, and Denmark. We equipped the ship with a triple-quadrupole linear ion-trap hybrid LC-MS-MS system for detection and quantitative analysis of toxins, such as domoic acid, gymnodimine, spirolides, dinophysistoxins, okadaic acid, pectenotoxins, yessotoxins, and azaspiracids (AZAs). We focused particular attention on the detection of AZAs, a group of potent nitrogenous polyether toxins, because the culprit species associated with the occurrence of these toxins in shellfish has been controversial. Marine toxins were analyzed directly from size-fractionated plankton net tows (20 microm mesh size) and Niskin bottle samples from discrete depths, after rapid methanolic extraction but without any further clean-up. Almost all expected phycotoxins were detected in North Sea plankton samples, with domoic acid and 20-methylspirolide G being most abundant. Although AZA was the least abundant of these toxins, the high sensitivity of the LC-MS-MS enabled detailed quantification, indicating that the highest amounts of AZA-1 were present in the southern Skagerrak in the 3-20 microm size-fraction. The direct on-board toxin measurements enabled isolation of plankton from stations with high AZA-1 levels and from the most suspicious size-fraction, i.e. most likely to contain the AZA-producer. A large number (>100) of crude cultures were established by serial dilution and later screened for the presence of AZAs after several weeks growth. From one crude culture containing AZA, a small dinoflagellate was subsequently isolated and brought into pure culture. We have thus proved that even sophisticated mass spectrometers can be operated in ship laboratories without any limitation caused by vibrations of the ship's engine or by wave movement during heavy seas at wind forces up to nine Beaufort. On-board LC-MS-MS is a valuable method for near real-time analysis of phycotoxins in plankton for studies on bloom dynamics and the fate of toxins in the food web, and for characterization and isolation of putatively toxigenic organisms.

Higher rates of metabolic syndrome among women taking zidovudine as compared to tenofovir in rural Africa: preliminary data from the CART-1 study.

PubMed

Labhardt, Niklaus Daniel; Cheleboi, Molisana; Faturyiele, Olatunbosun; Motlatsi, Mokete M; Pfeiffer, Karolin; Lejone, Thabo Ismael; Cerutti, Bernard; Muser, Jürgen; Gupta, Ravi Shankar; Lynen, Lutgarde; Hatz, Christoph

2014-01-01

Due to its side effects stavudine (D4T) has been replaced by zidovudine (AZT) and tenofovir (TDF) in most low- and middle-income countries (LMICs). In 2014 about 38% of adult first-line regimens contain AZT and 62% TDF [1]. Whereas the unfavourable metabolic outcomes of D4T in comparison to TDF have been described extensively, studies from LMICs comparing metabolic profiles between patients on AZT and TDF are scarce. Given the high number of patients in LMICs still taking AZT, data on their metabolic profile are needed. We present rates of metabolic syndrome (MS) in adult patients taking either AZT- or TDF-containing first-line, non-nucleoside reverse transcriptase (NNRTI)-based regimens. Data derived from a cross-sectional multi-disease screening conducted in ten facilities in two rural districts of Lesotho, Southern Africa [2]. Patients were eligible if aged ≥25 years and on NNRTI-containing first-line ART ≥6 months. The MS definition for Africa of the International Diabetes Federation was applied [3]. Assessed potential predictors for MS were age, time on ART, virologic suppression, body-mass index (BMI), alcohol consumption, wealth quintile, NNRTI (nevirapine (NVP) or Efavirenz (EFV)), history of previous D4T exposure and ART-backbone (AZT or TDF). Statistical analyses - stratified for sex - comprised univariate logistic regression for each predictor variable with subsequent construction of a multivariate model including all predictors with an association to MS at a significance level<0.1 in univariate analysis. Out of 1026 patients, 660 (64.3%) were female. MS prevalence was 9.8% (95% CI 6.9-13.4) in men and 22.9% (19.7-26.3) in women. In women, aged ≥35 years, AZT-backbone, NVP-base, BMI ≥25kg/m2 and taking ART for ≥4.5 years were associated with MS in univariate analysis. In the multivariate model only AZT (adjusted odds-ratio: 2.2, 95% CI 1.4-3.6; p=0.001) and BMI ≥25kg/m2 (9.8; 2.8-34.1, p<0.001) were associated with MS. For men, age, higher wealth quintile, history of D4T exposure and BMI were associated with MS in univariate analysis. In the multivariate model only a BMI ≥25kg/m2 was associated with MS (8.9; 3.8-20.9, p<0.001). In rural Lesotho, Southern Africa, the use of AZT instead of TDF among women who are on ART for ≥6 months predisposes to the development of metabolic syndrome. Given that, still 38% of first-line regimens in LMIC contain AZT, this finding needs to be verified in other settings in Sub-Saharan Africa.

MALDI-TOF mass spectrometry following short incubation on a solid medium is a valuable tool for rapid pathogen identification from positive blood cultures.

PubMed

Kohlmann, Rebekka; Hoffmann, Alexander; Geis, Gabriele; Gatermann, Sören

2015-01-01

Rapid identification of the causative microorganism is a key element in appropriate antimicrobial therapy of bloodstream infections. Whereas traditional analysis of positive blood cultures requires subculture over at least 16-24h prior to pathogen identification by, e.g. matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), sample preparation procedures enabling direct MALDI-TOF MS, i.e. without preceding subculture, are associated with additional effort and costs. Hence, we integrated an alternative MALDI-TOF MS approach in diagnostic routine using a short incubation on a solid medium. Positive blood cultures were routinely plated on chocolate agar plates and incubated for 4h (37 °C, 5% CO2). Subsequently, MALDI-TOF MS using a Microflex LT instrument (Bruker Daltonics) and direct smear method was performed once per sample. For successful identification of bacteria at species level, score cut-off values were used as proposed by the manufacturer (≥ 2.0) and in a modified form (≥ 1.5 for MALDI-TOF MS results referring to Gram-positive cocci and ≥ 1.7 for MALDI-TOF MS results referring to bacteria other than Gram-positive cocci). Further data analysis also included an assessment of the clinical impact of the MALDI-TOF MS result. Applying the modified score cut-off values, our approach led to an overall correct species identification in 69.5% with misidentification in 3.4% (original cut-offs: 49.2% and 1.8%, respectively); for Gram-positive cocci, correct identification in 68.4% (100% for Staphylococcus aureus and enterococci, 80% for beta-hemolytic streptococci), for Gram-negative bacteria, correct identification in 97.6%. In polymicrobial blood cultures, in 72.7% one of the pathogens was correctly identified. Results were not reliable for Gram-positive rods and yeasts. The approach was easy to implement in diagnostic routine. In cases with available clinical data and successful pathogen identification, in 51.1% our approach allowed an optimized treatment recommendation. MALDI-TOF MS following 4h pre-culture is a valuable tool for rapid pathogen identification from positive blood cultures, allowing easy integration in diagnostic routine and the opportunity of considerably earlier treatment adaptation. Copyright © 2015 Elsevier GmbH. All rights reserved.

The Human Urine Metabolome

PubMed Central

Bouatra, Souhaila; Aziat, Farid; Mandal, Rupasri; Guo, An Chi; Wilson, Michael R.; Knox, Craig; Bjorndahl, Trent C.; Krishnamurthy, Ramanarayan; Saleem, Fozia; Liu, Philip; Dame, Zerihun T.; Poelzer, Jenna; Huynh, Jessica; Yallou, Faizath S.; Psychogios, Nick; Dong, Edison; Bogumil, Ralf; Roehring, Cornelia; Wishart, David S.

2013-01-01

Urine has long been a “favored” biofluid among metabolomics researchers. It is sterile, easy-to-obtain in large volumes, largely free from interfering proteins or lipids and chemically complex. However, this chemical complexity has also made urine a particularly difficult substrate to fully understand. As a biological waste material, urine typically contains metabolic breakdown products from a wide range of foods, drinks, drugs, environmental contaminants, endogenous waste metabolites and bacterial by-products. Many of these compounds are poorly characterized and poorly understood. In an effort to improve our understanding of this biofluid we have undertaken a comprehensive, quantitative, metabolome-wide characterization of human urine. This involved both computer-aided literature mining and comprehensive, quantitative experimental assessment/validation. The experimental portion employed NMR spectroscopy, gas chromatography mass spectrometry (GC-MS), direct flow injection mass spectrometry (DFI/LC-MS/MS), inductively coupled plasma mass spectrometry (ICP-MS) and high performance liquid chromatography (HPLC) experiments performed on multiple human urine samples. This multi-platform metabolomic analysis allowed us to identify 445 and quantify 378 unique urine metabolites or metabolite species. The different analytical platforms were able to identify (quantify) a total of: 209 (209) by NMR, 179 (85) by GC-MS, 127 (127) by DFI/LC-MS/MS, 40 (40) by ICP-MS and 10 (10) by HPLC. Our use of multiple metabolomics platforms and technologies allowed us to identify several previously unknown urine metabolites and to substantially enhance the level of metabolome coverage. It also allowed us to critically assess the relative strengths and weaknesses of different platforms or technologies. The literature review led to the identification and annotation of another 2206 urinary compounds and was used to help guide the subsequent experimental studies. An online database containing the complete set of 2651 confirmed human urine metabolite species, their structures (3079 in total), concentrations, related literature references and links to their known disease associations are freely available at http://www.urinemetabolome.ca. PMID:24023812

PGCA: An algorithm to link protein groups created from MS/MS data

PubMed Central

Sasaki, Mayu; Hollander, Zsuzsanna; Smith, Derek; McManus, Bruce; McMaster, W. Robert; Ng, Raymond T.; Cohen Freue, Gabriela V.

2017-01-01

The quantitation of proteins using shotgun proteomics has gained popularity in the last decades, simplifying sample handling procedures, removing extensive protein separation steps and achieving a relatively high throughput readout. The process starts with the digestion of the protein mixture into peptides, which are then separated by liquid chromatography and sequenced by tandem mass spectrometry (MS/MS). At the end of the workflow, recovering the identity of the proteins originally present in the sample is often a difficult and ambiguous process, because more than one protein identifier may match a set of peptides identified from the MS/MS spectra. To address this identification problem, many MS/MS data processing software tools combine all plausible protein identifiers matching a common set of peptides into a protein group. However, this solution introduces new challenges in studies with multiple experimental runs, which can be characterized by three main factors: i) protein groups’ identifiers are local, i.e., they vary run to run, ii) the composition of each group may change across runs, and iii) the supporting evidence of proteins within each group may also change across runs. Since in general there is no conclusive evidence about the absence of proteins in the groups, protein groups need to be linked across different runs in subsequent statistical analyses. We propose an algorithm, called Protein Group Code Algorithm (PGCA), to link groups from multiple experimental runs by forming global protein groups from connected local groups. The algorithm is computationally inexpensive and enables the connection and analysis of lists of protein groups across runs needed in biomarkers studies. We illustrate the identification problem and the stability of the PGCA mapping using 65 iTRAQ experimental runs. Further, we use two biomarker studies to show how PGCA enables the discovery of relevant candidate protein group markers with similar but non-identical compositions in different runs. PMID:28562641

An electrophysiological index of changes in risk decision-making strategies.

PubMed

Zhang, Dandan; Gu, Ruolei; Wu, Tingting; Broster, Lucas S; Luo, Yi; Jiang, Yang; Luo, Yue-jia

2013-07-01

Human decision-making is significantly modulated by previously experienced outcomes. Using event-related potentials (ERPs), we examined whether ERP components evoked by outcome feedbacks could serve as biomarkers to signal the influence of current outcome evaluation on subsequent decision-making. In this study, 18 adult volunteers participated in a simple monetary gambling task, in which they were asked to choose between two options that differed in risk. Their decisions were immediately followed by outcome presentation. Temporospatial principle component analysis (PCA) was applied to the outcome-onset locked ERPs in the 200-1000 ms time window. The PCA factors that approximated classical ERP components (P2, feedback-related negativity, P3a, and P3b) in terms of time course and scalp distribution were tested for their association with subsequent decision-making strategies. Our results revealed that a fronto-central PCA factor approximating the classical P3a was related to changes of decision-making strategies on subsequent trials. The decision to switch between high- and low-risk options resulted in a larger P3a relative to the decision to retain the same choice. According to the results, we suggest that the amplitude of the fronto-central P3a is an electrophysiological index of the influence of current outcome on subsequent risk decision-making. Furthermore, the ERP source analysis indicated that the activations of the frontopolar cortex and sensorimotor cortex were involved in subsequent changes of strategies, which enriches our understanding of the neural mechanisms of adjusting decision-making strategies based on previous experience. Copyright © 2013 Elsevier Ltd. All rights reserved.

An electrophysiological index of changes in risk decision-making strategies

PubMed Central

Zhang, Dandan; Gu, Ruolei; Wu, Tingting; Broster, Lucas S.; Luo, Yi; Jiang, Yang; Luo, Yue-jia

2014-01-01

Human decision-making is significantly modulated by previously experienced outcomes. Using event-related potentials (ERPs), we examined whether ERP components evoked by outcome feedbacks could serve as biomarkers to signal the influence of current outcome evaluation on subsequent decision-making. In this study, eighteen adult volunteers participated in a simple monetary gambling task, in which they were asked to choose between two options that differed in risk. Their decisions were immediately followed by outcome presentation. Temporospatial principle component analysis (PCA) was applied to the outcome-onset locked ERPs in the -200 – 1000 ms time window. The PCA factors that approximated classical ERP components (P2, feedback-related negativity, P3a, & P3b) in terms of time course and scalp distribution were tested for their association with subsequent decision-making strategies. Our results revealed that a fronto-central PCA factor approximating the classical P3a was related to changes of decision-making strategies on subsequent trials. The decision to switch between high- and low-risk options resulted in a larger P3a relative to the decision to retain the same choice. According to the results, we suggest the amplitude of the fronto-central P3a is an electrophysiological index of the influence of current outcome on subsequent risk decision-making. Furthermore, the ERP source analysis indicated that the activations of the frontopolar cortex and sensorimotor cortex were involved in subsequent changes of strategies, which enriches our understanding of the neural mechanisms of adjusting decision-making strategies based on previous experience. PMID:23643796

Site-specific radical formation in DNA induced by Cu(II)-H2O2 oxidizing system, using ESR, Immuno-spin trapping, LC/MS and MS/MS

PubMed Central

Bhattacharjee, Suchandra; Deterding, Leesa J.; Chatterjee, Saurabh; Jiang, JinJie; Ehrenshaft, Marilyn; Lardinois, Olivier; Ramirez, Dario C.; Tomer, Kenneth B.; Mason, Ronald P.

2011-01-01

Oxidative stress-related damage to the DNA macromolecule produces a multitude of lesions that are implicated in mutagenesis, carcinogenesis, reproductive cell death and aging. Many of these lesions have been studied and characterized by various techniques. Of the techniques that are available, the comet assay, HPLC-EC, GC-MS, HPLC-MS and especially HPLC-MS/MS remain the most widely used and have provided invaluable information on these lesions. However, accurate measurement of DNA damage has been a matter of debate. In particular, there have been reports of artifactual oxidation leading to erroneously high damage estimates. Further, most of these techniques measure the end product of a sequence of events and thus provide only limited information on the initial radical mechanism. We report here a qualitative measurement of DNA damage induced by a Cu(II)-H2O2 oxidizing system using immuno spin-trapping (IST) with EPR, MS and MS/MS. The radical generated is trapped by DMPO immediately upon formation. The DMPO adduct formed is initially EPR active but subsequently is oxidized to the stable nitrone, which can then be detected by IST and further characterized by MS and MS/MS. PMID:21382477

Direct and indirect organogenesis of Alpinia galanga and the phytochemical analysis.

PubMed

Rao, Kiranmayee; Chodisetti, Bhuvaneswari; Gandi, Suryakala; Mangamoori, Lakshmi Narasu; Giri, Archana

2011-11-01

Alpinia galanga is a rhizomatous herb rich in essential oils and various other significant phytoconstituents. Rapid direct regeneration was obtained from the rhizome explants (15.66 ± 0.57 shoots) on MS media supplemented with zeatin at a concentration of 2 mg/l. The callus cultures of A. galanga were initiated from the rhizome explants on MS media supplemented with 2 mg/l each of BAP, 2,4-D, and NAA. The callus was analyzed for the presence of a vital phytoconstituent--acetoxychavicol acetate (ACA) associated with various biological properties. ACA was detected in the young friable callus as well as the stationary phase callus. Moreover, the induction of morphogenetic response in callus resulted in higher accumulation of ACA. The phytohormone withdrawal from the propagation media and the subsequent transfer of callus to BAP (2 mg/l) containing MS media has resulted in multiple shoot induction. The regenerated (indirect) plants have shown 1.6-fold higher ACA content (1.253%) when compared to the control plant (0.783%). Micropropagation of such conventionally propagated plants is very essential to meet the commercial demand as well as to ensure easy storage and transportation of disease free stocks.

An automatic quantification system for MS lesions with integrated DICOM structured reporting (DICOM-SR) for implementation within a clinical environment

NASA Astrophysics Data System (ADS)

Jacobs, Colin; Ma, Kevin; Moin, Paymann; Liu, Brent

2010-03-01

Multiple Sclerosis (MS) is a common neurological disease affecting the central nervous system characterized by pathologic changes including demyelination and axonal injury. MR imaging has become the most important tool to evaluate the disease progression of MS which is characterized by the occurrence of white matter lesions. Currently, radiologists evaluate and assess the multiple sclerosis lesions manually by estimating the lesion volume and amount of lesions. This process is extremely time-consuming and sensitive to intra- and inter-observer variability. Therefore, there is a need for automatic segmentation of the MS lesions followed by lesion quantification. We have developed a fully automatic segmentation algorithm to identify the MS lesions. The segmentation algorithm is accelerated by parallel computing using Graphics Processing Units (GPU) for practical implementation into a clinical environment. Subsequently, characterized quantification of the lesions is performed. The quantification results, which include lesion volume and amount of lesions, are stored in a structured report together with the lesion location in the brain to establish a standardized representation of the disease progression of the patient. The development of this structured report in collaboration with radiologists aims to facilitate outcome analysis and treatment assessment of the disease and will be standardized based on DICOM-SR. The results can be distributed to other DICOM-compliant clinical systems that support DICOM-SR such as PACS. In addition, the implementation of a fully automatic segmentation and quantification system together with a method for storing, distributing, and visualizing key imaging and informatics data in DICOM-SR for MS lesions improves the clinical workflow of radiologists and visualizations of the lesion segmentations and will provide 3-D insight into the distribution of lesions in the brain.

Ultra-high performance liquid chromatography coupled with quadrupole/time of flight mass spectrometry based chemical profiling approach for the holistic quality control of complex Kang-Jing formula preparations.

PubMed

Yang, Xiao-Huan; Cheng, Xiao-Lan; Qin, Bing; Cai, Zhuo-Ya; Cai, Xiong; Liu, Shao; Wang, Qi; Qin, Yong

2016-05-30

The Kang-Jing (KJ) formula is a compound preparation made from 12 kinds of herbs. So far, four different methods (M1-M4) have been documented for KJ preparation, but the influence of preparation methods on the holistic quality of KJ have remained unknown. In this study, a strategy was proposed to investigate the influence of different preparation methods on the holistic quality of KJ using ultra-high performance liquid chromatography coupled with quadrupole/time of flight mass spectrometry (UHPLC-QTOF-MS/MS) based chemical profiling. A total of 101 compounds mainly belonging to flavonoids, tanshinones, monoterpene glycosides, triterpenoid saponins, alkaloids, phenolic acids and volatile oils, were identified. Among these compounds, glaucine was detected only in M3/M4 samples, while two dehydrocorydaline isomers merely detected in M2/M3/M4 samples. Tetrahydrocolumbamine, ethylic lithospermic acid, salvianolic acid E and rosmarimic acid were only detected in M1/M3/M4 samples. In the subsequent quantitative analysis, 12 major compounds were determined by UHPLC-MS/MS. The proposed method was validated with respect to linearity, accuracy, precision and recovery. It was found that the contents of marker compounds varied significantly in samples prepared by different methods. These results demonstrated that preparation method does significantly affect the holistic quality of KJ. UHPLC-QTOF-MS/MS based chemical profiling approach is efficient and reliable for comprehensive quality evaluation of KJ. Collectively, this study provide the chemical evidence for revealing the material basis of KJ, and establish a simple and accurate chemical profiling method for its quality control. Copyright © 2016 Elsevier B.V. All rights reserved.

Microcystin-LR Detected in a Low Molecular Weight Fraction from a Crude Extract of Zoanthus sociatus

PubMed Central

Domínguez-Pérez, Dany; Alexei Rodríguez, Armando; Osorio, Hugo; Azevedo, Joana; Castañeda, Olga; Vasconcelos, Vítor; Antunes, Agostinho

2017-01-01

Cnidarian constitutes a great source of bioactive compounds. However, research involving peptides from organisms belonging to the order Zoanthidea has received very little attention, contrasting to the numerous studies of the order Actiniaria, from which hundreds of toxic peptides and proteins have been reported. In this work, we performed a mass spectrometry analysis of a low molecular weight (LMW) fraction previously reported as lethal to mice. The low molecular weight (LMW) fraction was obtained by gel filtration of a Zoanthus sociatus (order Zoanthidea) crude extract with a Sephadex G-50, and then analyzed by matrix-assisted laser desorption/ionization time-of-flight/time-of-flight (MALDI-TOF/TOF) mass spectrometry (MS) in positive ion reflector mode from m/z 700 to m/z 4000. Afterwards, some of the most intense and representative MS ions were fragmented by MS/MS with no significant results obtained by Protein Pilot protein identification software and the Mascot algorithm search. However, microcystin masses were detected by mass-matching against libraries of non-ribosomal peptide database (NORINE). Subsequent reversed-phase C18 HPLC (in isocratic elution mode) and mass spectrometry analyses corroborated the presence of the cyanotoxin Microcystin-LR (MC-LR). To the best of our knowledge, this finding constitutes the first report of MC-LR in Z. sociatus, and one of the few evidences of such cyanotoxin in cnidarians. PMID:28257074

Metabolomic analysis-Addressing NMR and LC-MS related problems in human feces sample preparation.

PubMed

Moosmang, Simon; Pitscheider, Maria; Sturm, Sonja; Seger, Christoph; Tilg, Herbert; Halabalaki, Maria; Stuppner, Hermann

2017-10-31

Metabolomics is a well-established field in fundamental clinical research with applications in different human body fluids. However, metabolomic investigations in feces are currently an emerging field. Fecal sample preparation is a demanding task due to high complexity and heterogeneity of the matrix. To gain access to the information enclosed in human feces it is necessary to extract the metabolites and make them accessible to analytical platforms like NMR or LC-MS. In this study different pre-analytical parameters and factors were investigated i.e. water content, different extraction solvents, influence of freeze-drying and homogenization, ratios of sample weight to extraction solvent, and their respective impact on metabolite profiles acquired by NMR and LC-MS. The results indicate that profiles are strongly biased by selection of extraction solvent or drying of samples, which causes different metabolites to be lost, under- or overstated. Additionally signal intensity and reproducibility of the measurement were found to be strongly dependent on sample pre-treatment steps: freeze-drying and homogenization lead to improved release of metabolites and thus increased signals, but at the same time induced variations and thus deteriorated reproducibility. We established the first protocol for extraction of human fecal samples and subsequent measurement with both complementary techniques NMR and LC-MS. Copyright © 2017 Elsevier B.V. All rights reserved.

Post-translational modification of human heat shock factors and their functions: a recent update by proteomic approach.

PubMed

Xu, Yan-Ming; Huang, Dong-Yang; Chiu, Jen-Fu; Lau, Andy T Y

2012-05-04

Heat shock factors (HSFs) are vital for modulating stress and heat shock-related gene expression in cells. The activity of HSFs is controlled largely by post-translational modifications (PTMs). For example, basal phosphorylation of HSF1 on three serine sites suppresses the heat shock response, and hyperphosphorylation of HSF1 on several other serine and threonine sites by stress-activated kinases results in its activation, while acetylation on K80 inhibits its DNA-binding ability. Sumoylation of HSF2 on K82 regulates its DNA-binding ability, whereas sumoylation of HSF4B on K293 represses its transcriptional activity. With the advancement of proteomic technology, novel PTM sites on various HSFs have been identified with the use of tandem mass spectrometry (MS/MS), but the functions of many of these PTMs are still unclear. Yet, it should be noted that the discovery of these novel PTM sites provided the necessary evidence for the existence of these PTM marks in vivo. Followed by subsequent functional analysis, this would ultimately lead to a better understanding of these PTM marks. MS/MS-based proteomic approach is becoming a gold standard in PTM validation in the field of life science. Here, the recent literature of all known PTMs reported on human HSFs and the resulting functions will be discussed.

The "Gut Feeling": Breaking Down the Role of Gut Microbiome in Multiple Sclerosis.

PubMed

Freedman, Samantha N; Shahi, Shailesh K; Mangalam, Ashutosh K

2018-01-01

Multiple sclerosis (MS) is a chronic neuroinflammatory disease of the central nervous system with unknown etiology. Recently, the gut microbiota has emerged as a potential factor in the development of MS, with a number of studies having shown that patients with MS exhibit gut dysbiosis. The gut microbiota helps the host remain healthy by regulating various functions, including food metabolism, energy homeostasis, maintenance of the intestinal barrier, inhibition of colonization by pathogenic organisms, and shaping of both mucosal and systemic immune responses. Alteration of the gut microbiota, and subsequent changes in its metabolic network that perturb this homeostasis, may lead to intestinal and systemic disorders such as MS. Here we discuss the findings of recent MS microbiome studies and potential mechanisms through which gut microbiota can predispose to, or protect against, MS. These findings highlight the need of an improved understanding of the interactions between the microbiota and host for developing therapies based on gut commensals with which to treat MS.

A comparison of sample preparation strategies for biological tissues and subsequent trace element analysis using LA-ICP-MS.

PubMed

Bonta, Maximilian; Török, Szilvia; Hegedus, Balazs; Döme, Balazs; Limbeck, Andreas

2017-03-01

Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) is one of the most commonly applied methods for lateral trace element distribution analysis in medical studies. Many improvements of the technique regarding quantification and achievable lateral resolution have been achieved in the last years. Nevertheless, sample preparation is also of major importance and the optimal sample preparation strategy still has not been defined. While conventional histology knows a number of sample pre-treatment strategies, little is known about the effect of these approaches on the lateral distributions of elements and/or their quantities in tissues. The technique of formalin fixation and paraffin embedding (FFPE) has emerged as the gold standard in tissue preparation. However, the potential use for elemental distribution studies is questionable due to a large number of sample preparation steps. In this work, LA-ICP-MS was used to examine the applicability of the FFPE sample preparation approach for elemental distribution studies. Qualitative elemental distributions as well as quantitative concentrations in cryo-cut tissues as well as FFPE samples were compared. Results showed that some metals (especially Na and K) are severely affected by the FFPE process, whereas others (e.g., Mn, Ni) are less influenced. Based on these results, a general recommendation can be given: FFPE samples are completely unsuitable for the analysis of alkaline metals. When analyzing transition metals, FFPE samples can give comparable results to snap-frozen tissues. Graphical abstract Sample preparation strategies for biological tissues are compared with regard to the elemental distributions and average trace element concentrations.

Proteomics and Metabolomics Analyses to Elucidate the Desulfurization Pathway of Chelatococcus sp.

PubMed Central

Chaudhuri, Mihir K.

2016-01-01

Desulfurization of dibenzothiophene (DBT) and alkylated DBT derivatives present in transport fuel through specific cleavage of carbon-sulfur (C-S) bonds by a newly isolated bacterium Chelatococcus sp. is reported for the first time. Gas chromatography-mass spectrometry (GC-MS) analysis of the products of DBT degradation by Chelatococcus sp. showed the transient formation of 2-hydroxybiphenyl (2-HBP) which was subsequently converted to 2-methoxybiphenyl (2-MBP) by methylation at the hydroxyl group of 2-HBP. The relative ratio of 2-HBP and 2-MBP formed after 96 h of bacterial growth was determined at 4:1 suggesting partial conversion of 2-HBP or rapid degradation of 2-MBP. Nevertheless, the enzyme involved in this conversion process remains to be identified. This production of 2-MBP rather than 2-HBP from DBT desulfurization has a significant metabolic advantage for enhancing the growth and sulfur utilization from DBT by Chelatococcus sp. and it also reduces the environmental pollution by 2-HBP. Furthermore, desulfurization of DBT derivatives such as 4-M-DBT and 4, 6-DM-DBT by Chelatococcus sp. resulted in formation of 2-hydroxy-3-methyl-biphenyl and 2-hydroxy –3, 3/- dimethyl-biphenyl, respectively as end product. The GC and X-ray fluorescence studies revealed that Chelatococcus sp. after 24 h of treatment at 37°C reduced the total sulfur content of diesel fuel by 12% by per gram resting cells, without compromising the quality of fuel. The LC-MS/MS analysis of tryptic digested intracellular proteins of Chelatococcus sp. when grown in DBT demonstrated the biosynthesis of 4S pathway desulfurizing enzymes viz. monoxygenases (DszC, DszA), desulfinase (DszB), and an NADH-dependent flavin reductase (DszD). Besides, several other intracellular proteins of Chelatococcus sp. having diverse biological functions were also identified by LC-MS/MS analysis. Many of these enzymes are directly involved with desulfurization process whereas the other enzymes/proteins support growth of bacteria at an expense of DBT. These combined results suggest that Chelatococcus sp. prefers sulfur-specific extended 4S pathway for deep-desulphurization which may have an advantage for its intended future application as a promising biodesulfurizing agent. PMID:27100386

Inventory of File gfs.t06z.pgrb2.0p25.anl

Science.gov Websites

UGRD analysis U-Component of Wind [m/s] 005 10 mb VGRD analysis V-Component of Wind [m/s] 006 10 mb -Component of Wind [m/s] 011 20 mb VGRD analysis V-Component of Wind [m/s] 012 20 mb ABSV analysis Absolute UGRD analysis U-Component of Wind [m/s] 018 30 mb VGRD analysis V-Component of Wind [m/s] 019 30 mb

Inventory of File gfs.t06z.pgrb2.0p50.anl

Science.gov Websites

UGRD analysis U-Component of Wind [m/s] 005 10 mb VGRD analysis V-Component of Wind [m/s] 006 10 mb -Component of Wind [m/s] 011 20 mb VGRD analysis V-Component of Wind [m/s] 012 20 mb ABSV analysis Absolute UGRD analysis U-Component of Wind [m/s] 018 30 mb VGRD analysis V-Component of Wind [m/s] 019 30 mb

Comprehensive Proteoform Characterization of Plasma Complement Component C8αβγ by Hybrid Mass Spectrometry Approaches

NASA Astrophysics Data System (ADS)

Franc, Vojtech; Zhu, Jing; Heck, Albert J. R.

2018-03-01

The human complement hetero-trimeric C8αβγ (C8) protein assembly ( 150 kDa) is an important component of the membrane attack complex (MAC). C8 initiates membrane penetration and coordinates MAC pore formation. Here, we charted in detail the structural micro-heterogeneity within C8, purified from human plasma, combining high-resolution native mass spectrometry and (glyco)peptide-centric proteomics. The intact C8 proteoform profile revealed at least 20 co-occurring MS signals. Additionally, we employed ion exchange chromatography to separate purified C8 into four distinct fractions. Their native MS analysis revealed even more detailed structural micro-heterogeneity on C8. Subsequent peptide-centric analysis, by proteolytic digestion of C8 and LC-MS/MS, provided site-specific quantitative profiles of different types of C8 glycosylation. Combining all this data provides a detailed specification of co-occurring C8 proteoforms, including experimental evidence on N-glycosylation, C-mannosylation, and O-glycosylation. In addition to the known N-glycosylation sites, two more N-glycosylation sites were detected on C8. Additionally, we elucidated the stoichiometry of all C-mannosylation sites in all the thrombospondin-like (TSP) domains of C8α and C8β. Lastly, our data contain the first experimental evidence of O-linked glycans located on C8γ. Albeit low abundant, these O-glycans are the first PTMs ever detected on this subunit. By placing the observed PTMs in structural models of free C8 and C8 embedded in the MAC, it may be speculated that some of the newly identified modifications may play a role in the MAC formation. [Figure not available: see fulltext.

Residue analysis of four diacylhydrazine insecticides in fruits and vegetables by Quick, Easy, Cheap, Effective, Rugged, and Safe (QuEChERS) method using ultra-performance liquid chromatography coupled to tandem mass spectrometry.

PubMed

Liu, Xingang; Xu, Jun; Dong, Fengshou; Li, Yuanbo; Song, Wenchen; Zheng, Yongquan

2011-08-01

The new analytical method using Quick, Easy, Cheap, Effective, Rugged, and Safe (QuEChERS) procedure for simultaneous determination of diacylhydrazine insecticide residues in fruits and vegetables was developed using ultra-performance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS/MS). The four insecticides (tebufenozide, methoxfenozide, chromafenozide, and halofenozide) were extracted from six fruit and vegetable matrices using acetonitrile and subsequently cleaned up using primary secondary amine (PSA) or octadecylsilane (C18) as sorbent prior to UPLC-MS/MS analysis. The determination of the target compounds was achieved in less than 3.0 min using an electrospray ionization source in positive mode (ESI+) for tebufenozide, methoxfenozide, and halofenozide and in negative mode (ESI-) for chromafenozide. The limits of detection were below 0.6 μg kg(-1), while the limit of quantification did not exceed 2 μg kg(-1) in different matrices. The QuEChERS procedure by using two sorbents (PSA and C18) and the matrix-matched standards gave satisfactory recoveries and relative standard deviation (RSD) values in different matrices at four spiked levels (0.01, 0.05, 0.1, and 1 mg kg(-1)). The overall average recoveries for this method in apple, grape, cucumber, tomato, cabbage, and spinach at four levels ranged from 74.2% to 112.5% with RSDs in the range of 1.4-13.8% (n = 5) for all analytes. This study provides a theoretical basis for China to draw up maximum residue limits and analytical method for diacylhydrazine insecticide in vegetables and fruits.

Development and validation of a method for determination of corticosteroids in pig fat using liquid chromatography-tandem mass spectrometry.

PubMed

Tölgyesi, Adám; Sharma, Virender K; Fekete, Jeno

2011-02-15

A new method was developed to determine five corticosteroids (prednisolone, methylprednisone, flumethasone, dexamethasone, and methylprednisolone) in pig fat samples by liquid chromatography-tandem mass spectrometry (LC-MS/MS) utilizing an optimized liquid-liquid extraction (LLE) and subsequent solid-phase extraction (SPE) for sample clean-up. In the sample preparation, a pig fat sample was dissolved in n-hexane and then extracted into the methanol-water (50/50, v/v) mixture that enabled extraction of only medium polar corticosteroids and not the non-polar components of matrices. This extract was cleaned-up and concentrated on polymeric Oasis HLB SPE cartridge. Separation involved isocratic solvent (methanol-acetate buffer, pH 5.4) and Ascentis Express Fused-Core type HLPC column; reduced the analysis time to 7.5 min, which is at least two times lower than time required for separation using conventional techniques. Other advantage of the developed method is the minimized ion suppression of LC-MS/MS analysis, which allowed detection of corticosteroids in sub μg/kg. Method was validated according to European Union (EU) Commission Decision 2002/657/EC. Measured parameters such as selectivity, linearity, recovery, within-laboratory reproducibility, decision limit, and detection capability satisfied the EU Directive. Ranges of mean recoveries and within-laboratory reproducibility were 81-100% and 8.0-20.5%, respectively. Decision limits were calculated in the range from 4.5 to 11.9 μg/kg for MRL compounds and varied from 0.1 to 0.2 μg/kg for banned substances. Limit of detections (LODs), calculated as three time signal-to-noise ratio, were in the range of 0.1-0.3 μg/kg. Copyright © 2010 Elsevier B.V. All rights reserved.

Impact of expanded newborn screening--United States, 2006.

PubMed

2008-09-19

Universal newborn screening for selected metabolic, endocrine, hematologic, and functional disorders is a well-established practice of state public health programs. Recent developments in tandem mass spectrometry (MS/MS), which is now capable of multi-analyte analysis in a high throughput capacity, has enabled newborn screening to include many more disorders detectable from a newborn blood spot. In 2006, to address the substantial variation that existed from state to state in the number of disorders included in newborn screening panels, the American College of Medical Genetics (ACMG), under guidance from the Health Resources and Services Administration, recommended a uniform panel of 29 disorders, which was subsequently endorsed by the federal Advisory Committee on Heritable Disorders in Newborns and Children. After 2006, most states began to expand their panels to include all 29 disorders; currently, 21 states and the District of Columbia have fully implemented the ACMG panel. To estimate the burden to state newborn screening programs resulting from this expansion, CDC used 2001-2006 data from those states with well-established MS/MS screening programs to estimate the number of children in the United States who would have been identified with disorders in 2006 if all 50 states and the District of Columbia had been using the ACMG panel. This report describes the results of that analysis, which indicated that, although such an expansion would have increased the number of children identified by only 32% (from 4,370 to 6,439), these children would have had many rare disorders that require local or regional capacity to deliver expertise in screening, diagnosis, and management. The findings underscore the need for public health and health-care delivery systems to build or expand the programs required to manage the rare disorders detected through expanded newborn screening, while also continuing programs to address more common disorders.

A new method for the noninvasive determination of abdominal muscle feedforward activity based on tissue velocity information from tissue Doppler imaging.

PubMed

Mannion, A F; Pulkovski, N; Schenk, P; Hodges, P W; Gerber, H; Loupas, T; Gorelick, M; Sprott, H

2008-04-01

Rapid arm movements elicit anticipatory activation of the deep-lying abdominal muscles; this appears modified in back pain, but the invasive technique used for its assessment [fine-wire electromyography (EMG)] has precluded its widespread investigation. We examined whether tissue-velocity changes recorded with ultrasound (M-mode) tissue Doppler imaging (TDI) provided a viable noninvasive alternative. Fourteen healthy subjects rapidly flexed, extended, and abducted the shoulder; recordings were made of medial deltoid (MD) surface EMG and of fine-wire EMG and TDI tissue-velocity changes of the contralateral transversus abdominis, obliquus internus, and obliquus externus. Muscle onsets were determined by blinded visual analysis of EMG and TDI data. TDI could not distinguish between the relative activation of the three muscles, so in subsequent analyses only the onset of the earliest abdominal muscle activity was used. The latter occurred <50 ms after the onset of medial deltoid EMG (i.e., was feedforward) and correlated with the corresponding EMG onsets (r = 0.47, P < 0.0001). The mean difference between methods was 20 ms and was likely explained by electromechanical delay; limits of agreement were wide (-40 to +80 ms) but no greater than those typical of repeated measurements using either technique. The between-day standard error of measurement of the TDI onsets (examined in 16 further subjects) was 16 ms. TDI yielded reliable and valid measures of the earliest onset of feedforward activity within the anterolateral abdominal muscle group. The method can be used to assess muscle dysfunction in large groups of back-pain patients and may also be suitable for the noninvasive analysis of other deep-lying or small/thin muscles.

Method development for the analysis of ionophore antimicrobials in dairy manure to assess removal within a membrane-based treatment system.

PubMed

Hurst, Jerod J; Wallace, Josh S; Aga, Diana S

2018-04-01

Ionophore antimicrobials are heavily used in the livestock industries, both for preventing animal infection by coccidia protozoa and for increasing feed efficiency. Ionophores are excreted mostly unmetabolized and are released into the environment when manure is land-applied to fertilize croplands. Here, an analytical method was optimized to study the occurrences of five ionophore residues (monensin, lasalocid, maduramycin, salinomycin, and narasin) in dairy manure after solid-liquid separation and further treatment of the liquid manure by a membrane-based treatment system. Ionophore residues from the separated solid manure (dewatered manure) and suspended solids of manure slurry samples were extracted using ultrasonication with methanol, followed by sample clean-up using solid phase extraction (SPE) and subsequent analysis via liquid chromatography-tandem mass spectrometry (LC-MS/MS). The use of an ethyl acetate and methanol (1:1 v:v) mixture as an SPE eluent resulted in higher recoveries and lower method quantitation limits (MQL), when compared to using methanol. Overall recoveries from separated solid manure ranged from 73 to 134%. Liquid manure fractions were diluted with Nanopure™ water and cleaned up using SPE, where recoveries ranged from 51 to 100%. The developed extraction and LC-MS/MS methods were applied to analyze dairy manure samples subjected to an advanced manure treatment process involving a membrane-based filtration step (reverse osmosis). Monensin and lasalocid were detected at higher concentrations in the suspended solid fractions (4.40-420 ng/g for lasalocid and 85-1950 ng/g for monensin) compared to the liquid fractions (

Predicting sorption of pharmaceuticals and personal care products onto soil and digested sludge using artificial neural networks.

PubMed

Barron, Leon; Havel, Josef; Purcell, Martha; Szpak, Michal; Kelleher, Brian; Paull, Brett

2009-04-01

A comprehensive analytical investigation of the sorption behaviour of a large selection of over-the-counter, prescribed pharmaceuticals and illicit drugs to agricultural soils and freeze-dried digested sludges is presented. Batch sorption experiments were carried out to identify which compounds could potentially concentrate in soils as a result of biosolid enrichment. Analysis of aqueous samples was carried out directly using liquid chromatography-tandem mass spectrometry (LC-MS/MS). For solids analysis, combined pressurised liquid extraction and solid phase extraction methods were used prior to LC-MS/MS. Solid-water distribution coefficients (K(d)) were calculated based on slopes of sorption isotherms over a defined concentration range. Molecular descriptors such as log P, pK(a), molar refractivity, aromatic ratio, hydrophilic factor and topological surface area were collected for all solutes and, along with generated K(d) data, were incorporated as a training set within a developed artificial neural network to predict K(d) for all solutes within both sample types. Therefore, this work represents a novel approach using combined and cross-validated analytical and computational techniques to confidently study sorption modes within the environment. The logarithm plots of predicted versus experimentally determined K(d) are presented which showed excellent correlation (R(2) > 0.88), highlighting that artificial neural networks could be used as a predictive tool for this application. To evaluate the developed model, it was used to predict K(d) for meclofenamic acid, mefenamic acid, ibuprofen and furosemide and subsequently compared to experimentally determined values in soil. Ratios of experimental/predicted K(d) values were found to be 1.00, 1.00, 1.75 and 1.65, respectively.

Reproductive performance of donor mares subsequent to eFSH treatment in early vernal transition: Comparison between the first, second, and mid-season estrous cycles of the breeding season.

PubMed

Raz, Tal; Hunter, Barbara; Carley, Sylvia; Card, Claire

2009-11-01

The objective was to compare the reproductive performances associated with the first (Cycle-1), second (Cycle-2), and mid-season (MS-Cycle) ovulations of the breeding season in donor mares that were treated with equine-FSH (eFSH) in the early vernal transition. Mares (n=15) kept under ambient light were examined ultrasonographically per-rectum starting January 30. When an ovarian follicle > or =25mm in diameter was detected, twice daily eFSH treatments were initiated. The eFSH treatments ceased when a follicle > or =35mm was detected, and 36h later hCG was administered. Thereafter, mares were artificially inseminated every 48h until ovulation (Day 0). Trans-cervical embryo recovery attempts were performed on Day 8, and subsequently PGF2alpha was administered. Equine FSH was not administered in the subsequent estrous cycles. In Cycle-2 and in the MS-Cycle, hCG was administered when a follicle > or =35mm was detected; breeding, embryo recovery, and PGF2alpha administration, were similar to Cycle-1. Mares had an untreated estrous cycle (no treatment or breeding) between Cycle-2 and the MS-Cycle. All mares developed follicle(s) > or =35mm after 4.9+/-0.6 days of eFSH treatment, and subsequently ovulations occurred; mean (95% CI) interval from treatment initiation to ovulation was 7.9 (6.5-9.3) days. The number of preovulatory follicles (> or =30mm) at the time of hCG administration (Cycle-1: 2.2+/-0.3 compared with Cycle-2: 1.0+/-0 compared with MS-Cycle: 1.1+/-0.1 follicles), and the number of ovulations (2.5+/-0.4 compared with 1.0+/-0 compared with 1.1+/-0.1 ovulations) were greater (p<0.05) in Cycle-1. Nevertheless, mean embryo numbers did not differ among cycles (0.8+/-0.2 compared with 0.5+/-0.1 compared with 0.5+/-0.1 embryo/mare). On average, embryo morphology grade was less (p<0.05) in Cycle-1 as compared to non-eFSH cycles (combined Cycle-2 and MS-Cycle). This impaired embryo quality could be due to a seasonal effect, or negative effect of the eFSH treatment, which was possibly related to alterations in the hormonal environment (estradiol-17beta and progesterone). A prolonged IOI (>21 days) was recorded in 7 of 15 mares following the Cycle-1 ovulation, but not subsequently. In conclusion, eFSH treatment of vernal transitional donor mares stimulated ovulation within only few days of treatment, and the following embryo recovery rate was at least as good as in the subsequent estrous cycles; however, on average, embryos were morphologically impaired. In subsequent estrous cycles in the breeding season, ovulations, embryo recovery rates, and embryo variables did not appear to be negatively affected; however, the first inter-ovulatory interval of the breeding season was prolonged in approximately half of the mares.

Neural Responses in Parietal and Occipital Areas in Response to Visual Events Are Modulated by Prior Multisensory Stimuli

PubMed Central

Innes-Brown, Hamish; Barutchu, Ayla; Crewther, David P.

2013-01-01

The effect of multi-modal vs uni-modal prior stimuli on the subsequent processing of a simple flash stimulus was studied in the context of the audio-visual ‘flash-beep’ illusion, in which the number of flashes a person sees is influenced by accompanying beep stimuli. EEG recordings were made while combinations of simple visual and audio-visual stimuli were presented. The experiments found that the electric field strength related to a flash stimulus was stronger when it was preceded by a multi-modal flash/beep stimulus, compared to when it was preceded by another uni-modal flash stimulus. This difference was found to be significant in two distinct timeframes – an early timeframe, from 130–160 ms, and a late timeframe, from 300–320 ms. Source localisation analysis found that the increased activity in the early interval was localised to an area centred on the inferior and superior parietal lobes, whereas the later increase was associated with stronger activity in an area centred on primary and secondary visual cortex, in the occipital lobe. The results suggest that processing of a visual stimulus can be affected by the presence of an immediately prior multisensory event. Relatively long-lasting interactions generated by the initial auditory and visual stimuli altered the processing of a subsequent visual stimulus. PMID:24391939

Hypothalamic demyelination causing panhypopituitarism.

PubMed

Dixon-Douglas, Julia; Burgess, John; Dreyer, Michael

2018-05-01

Hypothalamic involvement in multiple sclerosis (MS) and neuromyelitis optica spectrum disorder (NMOSD) is rare and endocrinopathies involving the hypothalamic-pituitary axis in patients with demyelinating conditions have rarely been reported. We present two cases of MS/NMOSD with associated hypothalamic-pituitary involvement and subsequent hypopituitarism, including the first report of a patient with hypothalamic demyelination causing panhypopituitarism. Differential diagnoses, including alemtuzumab-related and primary pituitary pathology are discussed. © 2018 Royal Australasian College of Physicians.

Outcome Prediction in Pneumonia Induced ALI/ARDS by Clinical Features and Peptide Patterns of BALF Determined by Mass Spectrometry

PubMed Central

Frenzel, Jochen; Gessner, Christian; Sandvoss, Torsten; Hammerschmidt, Stefan; Schellenberger, Wolfgang; Sack, Ulrich; Eschrich, Klaus; Wirtz, Hubert

2011-01-01

Background Peptide patterns of bronchoalveolar lavage fluid (BALF) were assumed to reflect the complex pathology of acute lung injury (ALI)/acute respiratory distress syndrome (ARDS) better than clinical and inflammatory parameters and may be superior for outcome prediction. Methodology/Principal Findings A training group of patients suffering from ALI/ARDS was compiled from equal numbers of survivors and nonsurvivors. Clinical history, ventilation parameters, Murray's lung injury severity score (Murray's LISS) and interleukins in BALF were gathered. In addition, samples of bronchoalveolar lavage fluid were analyzed by means of hydrophobic chromatography and MALDI-ToF mass spectrometry (MALDI-ToF MS). Receiver operating characteristic (ROC) analysis for each clinical and cytokine parameter revealed interleukin-6>interleukin-8>diabetes mellitus>Murray's LISS as the best outcome predictors. Outcome predicted on the basis of BALF levels of interleukin-6 resulted in 79.4% accuracy, 82.7% sensitivity and 76.1% specificity (area under the ROC curve, AUC, 0.853). Both clinical parameters and cytokines as well as peptide patterns determined by MALDI-ToF MS were analyzed by classification and regression tree (CART) analysis and support vector machine (SVM) algorithms. CART analysis including Murray's LISS, interleukin-6 and interleukin-8 in combination was correct in 78.0%. MALDI-ToF MS of BALF peptides did not reveal a single identifiable biomarker for ARDS. However, classification of patients was successfully achieved based on the entire peptide pattern analyzed using SVM. This method resulted in 90% accuracy, 93.3% sensitivity and 86.7% specificity following a 10-fold cross validation (AUC = 0.953). Subsequent validation of the optimized SVM algorithm with a test group of patients with unknown prognosis yielded 87.5% accuracy, 83.3% sensitivity and 90.0% specificity. Conclusions/Significance MALDI-ToF MS peptide patterns of BALF, evaluated by appropriate mathematical methods can be of value in predicting outcome in pneumonia induced ALI/ARDS. PMID:21991318

Outcome prediction in pneumonia induced ALI/ARDS by clinical features and peptide patterns of BALF determined by mass spectrometry.

PubMed

Frenzel, Jochen; Gessner, Christian; Sandvoss, Torsten; Hammerschmidt, Stefan; Schellenberger, Wolfgang; Sack, Ulrich; Eschrich, Klaus; Wirtz, Hubert

2011-01-01

Peptide patterns of bronchoalveolar lavage fluid (BALF) were assumed to reflect the complex pathology of acute lung injury (ALI)/acute respiratory distress syndrome (ARDS) better than clinical and inflammatory parameters and may be superior for outcome prediction. A training group of patients suffering from ALI/ARDS was compiled from equal numbers of survivors and nonsurvivors. Clinical history, ventilation parameters, Murray's lung injury severity score (Murray's LISS) and interleukins in BALF were gathered. In addition, samples of bronchoalveolar lavage fluid were analyzed by means of hydrophobic chromatography and MALDI-ToF mass spectrometry (MALDI-ToF MS). Receiver operating characteristic (ROC) analysis for each clinical and cytokine parameter revealed interleukin-6>interleukin-8>diabetes mellitus>Murray's LISS as the best outcome predictors. Outcome predicted on the basis of BALF levels of interleukin-6 resulted in 79.4% accuracy, 82.7% sensitivity and 76.1% specificity (area under the ROC curve, AUC, 0.853). Both clinical parameters and cytokines as well as peptide patterns determined by MALDI-ToF MS were analyzed by classification and regression tree (CART) analysis and support vector machine (SVM) algorithms. CART analysis including Murray's LISS, interleukin-6 and interleukin-8 in combination was correct in 78.0%. MALDI-ToF MS of BALF peptides did not reveal a single identifiable biomarker for ARDS. However, classification of patients was successfully achieved based on the entire peptide pattern analyzed using SVM. This method resulted in 90% accuracy, 93.3% sensitivity and 86.7% specificity following a 10-fold cross validation (AUC = 0.953). Subsequent validation of the optimized SVM algorithm with a test group of patients with unknown prognosis yielded 87.5% accuracy, 83.3% sensitivity and 90.0% specificity. MALDI-ToF MS peptide patterns of BALF, evaluated by appropriate mathematical methods can be of value in predicting outcome in pneumonia induced ALI/ARDS.

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.

Molecular Mechanism of Photoactivation and Structural Location of the Cyanobacterial Orange Carotenoid Protein

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

Zhang, Hao; Liu, Haijun; Niedzwiedzki, Dariusz M.

The orange carotenoid protein (OCP) plays a photoprotective role in cyanobacterial photosynthesis similar to that of nonphotochemical quenching in higher plants. Under high-light conditions, the OCP binds to the phycobilisome (PBS) and reduces the extent of transfer of energy to the photosystems. The protective cycle starts from a light-induced activation of the OCP. Detailed information about the molecular mechanism of this process as well as the subsequent recruitment of the active OCP to the phycobilisome are not known. We report here our investigation on the OCP photoactivation from the cyanobacterium Synechocystis sp. PCC 6803 by using a combination of nativemore » electrospray mass spectrometry (MS) and protein cross-linking. We demonstrate that native MS can capture the OCP with its intact pigment and further reveal that the OCP undergoes a dimer-to-monomer transition upon light illumination. The reversion of the activated form of the OCP to the inactive, dark form was also observed by using native MS. Furthermore, in vitro reconstitution of the OCP and PBS allowed us to perform protein chemical cross-linking experiments. Liquid chromatography–MS/MS analysis identified cross-linking species between the OCP and the PBS core components. Our result indicates that the N-terminal domain of the OCP is closely involved in the association with a site formed by two allophycocyanin trimers in the basal cylinders of the phycobilisome core. This report improves our understanding of the activation mechanism of the OCP and the structural binding site of the OCP during the cyanobacterial nonphotochemical quenching process.« less

Software ion scan functions in analysis of glycomic and lipidomic MS/MS datasets.

PubMed

Haramija, Marko

2018-03-01

Hardware ion scan functions unique to tandem mass spectrometry (MS/MS) mode of data acquisition, such as precursor ion scan (PIS) and neutral loss scan (NLS), are important for selective extraction of key structural data from complex MS/MS spectra. However, their software counterparts, software ion scan (SIS) functions, are still not regularly available. Software ion scan functions can be easily coded for additional functionalities, such as software multiple precursor ion scan, software no ion scan, and software variable ion scan functions. These are often necessary, since they allow more efficient analysis of complex MS/MS datasets, often encountered in glycomics and lipidomics. Software ion scan functions can be easily coded by using modern script languages and can be independent of instrument manufacturer. Here we demonstrate the utility of SIS functions on a medium-size glycomic MS/MS dataset. Knowledge of sample properties, as well as of diagnostic and conditional diagnostic ions crucial for data analysis, was needed. Based on the tables constructed with the output data from the SIS functions performed, a detailed analysis of a complex MS/MS glycomic dataset could be carried out in a quick, accurate, and efficient manner. Glycomic research is progressing slowly, and with respect to the MS experiments, one of the key obstacles for moving forward is the lack of appropriate bioinformatic tools necessary for fast analysis of glycomic MS/MS datasets. Adding novel SIS functionalities to the glycomic MS/MS toolbox has a potential to significantly speed up the glycomic data analysis process. Similar tools are useful for analysis of lipidomic MS/MS datasets as well, as will be discussed briefly. Copyright © 2017 John Wiley & Sons, Ltd.

Inflammation: an important parameter in the search of prostate cancer biomarkers

PubMed Central

2014-01-01

Background A more specific and early diagnostics for prostate cancer (PCa) is highly desirable. In this study, being inflammation the focus of our effort, serum protein profiles were analyzed in order to investigate if this parameter could interfere with the search of discriminating proteins between PCa and benign prostatic hyperplasia (BPH). Methods Patients with clinical suspect of PCa and candidates for trans-rectal ultrasound guided prostate biopsy (TRUS) were enrolled. Histological specimens were examined in order to grade and classify the tumor, identify BPH and detect inflammation. Surface Enhanced Laser Desorption/Ionization-Time of Flight-Mass Spectrometry (SELDI-ToF-MS) and two-dimensional gel electrophoresis (2-DE) coupled with Liquid Chromatography-MS/MS (LC-MS/MS) were used to analyze immuno-depleted serum samples from patients with PCa and BPH. Results The comparison between PCa (with and without inflammation) and BPH (with and without inflammation) serum samples by SELDI-ToF-MS analysis did not show differences in protein expression, while changes were only observed when the concomitant presence of inflammation was taken into consideration. In fact, when samples with histological sign of inflammation were excluded, 20 significantly different protein peaks were detected. Subsequent comparisons (PCa with inflammation vs PCa without inflammation, and BPH with inflammation vs BPH without inflammation) showed that 16 proteins appeared to be modified in the presence of inflammation, while 4 protein peaks were not modified. With 2-DE analysis, comparing PCa without inflammation vs PCa with inflammation, and BPH without inflammation vs the same condition in the presence of inflammation, were identified 29 and 25 differentially expressed protein spots, respectively. Excluding samples with inflammation the comparison between PCa vs BPH showed 9 unique PCa proteins, 4 of which overlapped with those previously identified in the presence of inflammation, while other 2 were new proteins, not identified in our previous comparisons. Conclusions The present study indicates that inflammation might be a confounding parameter during the proteomic research of candidate biomarkers of PCa. These results indicate that some possible biomarker-candidate proteins are strongly influenced by the presence of inflammation, hence only a well-selected protein pattern should be considered for potential marker of PCa. PMID:24944525

Determination of N-nitrosodimethylamine in drinking water by UPLC-MS/MS.

PubMed

Wang, Wanfeng; Hu, Jianying; Yu, Jianwei; Yang, Min

2010-01-01

The method for detecting N-nitrosodimethylamine (NDMA) in drinking water using ultra performance liquid chromatography (UPLC) coupled with tandem mass spectrometry (MS/MS) was improved by optimizing the clean-up procedure to remove the matrix interference in pretreatment process, and was then applied to a survey of NDMA in both raw and finished water samples from five water treatment plants in South China. The NDMA concentrations ranged from 4.7 to 15.1 ng/L in raw water samples, and from 4.68 to 46.9 ng/L in finished water. The NDMA concentration in raw water was found to be related with nitrite concentration, and during the treatment, the NDMA concentration increased following ozonation but decreased after subsequent activated carbon treatment.

Synthesis of Mesoporous Metal Oxides by Structure Replication: Thermal Analysis of Metal Nitrates in Porous Carbon Matrices

PubMed Central

Weinberger, Christian; Roggenbuck, Jan; Hanss, Jan; Tiemann, Michael

2015-01-01

A variety of metal nitrates were filled into the pores of an ordered mesoporous CMK-3 carbon matrix by solution-based impregnation. Thermal conversion of the metal nitrates into the respective metal oxides, and subsequent removal of the carbon matrix by thermal combustion, provides a versatile means to prepare mesoporous metal oxides (so-called nanocasting). This study aims to monitor the thermally induced processes by thermogravimetric analysis (TGA), coupled with mass ion detection (MS). The highly dispersed metal nitrates in the pores of the carbon matrix tend to react to the respective metal oxides at lower temperature than reported in the literature for pure, i.e., carbon-free, metal nitrates. The subsequent thermal combustion of the CMK-3 carbon matrix also occurs at lower temperature, which is explained by a catalytic effect of the metal oxides present in the pores. This catalytic effect is particularly strong for oxides of redox active metals, such as transition group VII and VIII metals (Mn, Fe, Co, Ni), Cu, and Ce. PMID:28347073

1,1-dimethylhydrazine as a high purity nitrogen source for MOVPE-water reduction and quantification using nuclear magnetic resonance, gas chromatography-atomic emission detection spectroscopy and cryogenic-mass spectroscopy analytical techniques

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

Odedra, R.; Smith, L.M.; Rushworth, S.A.

2000-01-01

Hydrazine derivatives are attractive low temperature nitrogen sources for use in MOVPE due to their low thermal stability. However their purification and subsequent analysis has not previously been investigated in depth for this application. A detailed study on 1,1-dimethylhydrazine {l{underscore}brace}(CH{sub 3}){sub 2}N-NH{sub 2}{r{underscore}brace} purified by eight different methods and the subsequent quantitative measurements of water present in the samples obtained is reported here. A correlation between {sup 1}H nuclear magnetic resonance spectroscopy (NMR), gas chromatography-atomic emission detection (GC-AED) and cryogenic mass spectroscopy (Cryogenic-MS) has been performed. All three analysis techniques can be used to measure water in the samples andmore » with the best purification the water content can be lowered well below 100 ppm. The high purity of this material has been demonstrated by growth results and the state-of-the-art performance of laser diodes.« less

Increased Bisecting N-Acetylglucosamine and Decreased Branched Chain Glycans of N-linked Glycoproteins in Expressed Prostatic Secretions Associated with Prostate Cancer Progression

PubMed Central

Nyalwidhe, Julius O.; Betesh, Lucy R.; Powers, Thomas W.; Jones, E. Ellen; White, Krista Y.; Burch, Tanya C.; Brooks, Jasmin; Watson, Megan T.; Lance, Raymond S.; Troyer, Dean A.; Semmes, O. John; Mehta, Anand; Drake, Richard R.

2013-01-01

Purpose Using prostatic fluids rich in glycoproteins like prostate specific antigen (PSA) and prostatic acid phosphatase (PAP) , the goal of this study was to identify the structural types and relative abundance of glycans associated with prostate cancer status for subsequent use in emerging mass spectrometry-based glycopeptide analysis platforms. Experimental Design A series of pooled samples of expressed prostatic secretions (EPS) and exosomes reflecting different stages of prostate cancer disease were used for N-linked glycan profiling by three complementary methods, MALDI-TOF profiling, normal-phase HPLC separation, and triple quadropole MS analysis of PAP glycopeptides. Results Glycan profiling of N-linked glycans from different EPS fluids indicated a global decrease in larger branched tri- and tetra-antennary glycans. Differential exoglycosidase treatments indicated a substantial increase in bisecting N-acetylglucosamines correlated with disease severity. A triple quadrupole MS analysis of the N-linked glycopeptides sites from PAP in aggressive prostate cancer pools was done to cross-reference with the glycan profiling data. Conclusion and clinical relevance Changes in glycosylation as detected in EPS fluids reflect the clinical status of prostate cancer. Defining these molecular signatures at the glycopeptide level in individual samples could improve current approaches of diagnosis and prognosis. PMID:23775902

DIGE Proteome Analysis Reveals Suitability of Ischemic Cardiac In Vitro Model for Studying Cellular Response to Acute Ischemia and Regeneration

PubMed Central

Haas, Sina; Jahnke, Heinz-Georg; Moerbt, Nora; von Bergen, Martin; Aharinejad, Seyedhossein; Andrukhova, Olena; Robitzki, Andrea A.

2012-01-01

Proteomic analysis of myocardial tissue from patient population is suited to yield insights into cellular and molecular mechanisms taking place in cardiovascular diseases. However, it has been limited by small sized biopsies and complicated by high variances between patients. Therefore, there is a high demand for suitable model systems with the capability to simulate ischemic and cardiotoxic effects in vitro, under defined conditions. In this context, we established an in vitro ischemia/reperfusion cardiac disease model based on the contractile HL-1 cell line. To identify pathways involved in the cellular alterations induced by ischemia and thereby defining disease-specific biomarkers and potential target structures for new drug candidates we used fluorescence 2D-difference gel electrophoresis. By comparing spot density changes in ischemic and reperfusion samples we detected several protein spots that were differentially abundant. Using MALDI-TOF/TOF-MS and ESI-MS the proteins were identified and subsequently grouped by functionality. Most prominent were changes in apoptosis signalling, cell structure and energy-metabolism. Alterations were confirmed by analysis of human biopsies from patients with ischemic cardiomyopathy. With the establishment of our in vitro disease model for ischemia injury target identification via proteomic research becomes independent from rare human material and will create new possibilities in cardiac research. PMID:22384053

Late-onset multiple sclerosis presenting with cognitive dysfunction and severe cortical/infratentorial atrophy.

PubMed

Calabrese, Massimiliano; Gajofatto, Alberto; Gobbin, Francesca; Turri, Giulia; Richelli, Silvia; Matinella, Angela; Oliboni, Eugenio Simone; Benedetti, Maria Donata; Monaco, Salvatore

2015-04-01

Although cognitive dysfunction is a relevant aspect of multiple sclerosis (MS) from the earliest disease phase, cognitive onset is unusual thus jeopardizing early and accurate diagnosis. Here we describe 12 patients presenting with cognitive dysfunction as primary manifestation of MS with either mild or no impairment in non-cognitive neurological domains. Twelve patients with cognitive onset who were subsequently diagnosed with MS (CI-MS) were included in this retrospective study. Twelve cognitively normal MS patients (CN-MS), 12 healthy controls and four patients having progressive supranuclear palsy (PSP) served as the reference population. Ten CI-MS patients had progressive clinical course and all patients had late disease onset (median age = 49 years; range = 40-58 years). Among cognitive functions, frontal domains were the most involved. Compared to CN-MS and healthy controls, significant cortical and infratentorial atrophy characterized CI-MS patients. Selective atrophy of midbrain tegmentum with relative sparing of pons, known as "The Hummingbird sign," was observed in eight CI-MS and in three PSP patients. Our observation suggests that MS diagnosis should be taken into consideration in case of cognitive dysfunction, particularly when associated with slowly progressive disease course and severe cortical, cerebellar and brainstem atrophy even in the absence of other major neurological symptoms and signs. © The Author(s), 2014.

Single hair analysis of small molecules using MALDI-triple quadrupole MS imaging and LC-MS/MS: investigations on opportunities and pitfalls.

PubMed

Poetzsch, Michael; Steuer, Andrea E; Roemmelt, Andreas T; Baumgartner, Markus R; Kraemer, Thomas

2014-12-02

Single hair analysis normally requires extensive sample preparation microscale protocols including time-consuming steps like segmentation and extraction. Matrix assisted laser desorption and ionization mass spectrometric imaging (MALDI-MSI) was shown to be an alternative tool in single hair analysis, but still, questions remain. Therefore, an investigation of MALDI-MSI in single hair analysis concerning the extraction process, usage of internal standard (IS), and influences on the ionization processes were systematically investigated to enable the reliable application to hair analysis. Furthermore, single dose detection, quantitative correlation to a single hair, and hair strand LC-MS/MS results were performed, and the performance was compared to LC-MS/MS single hair monitoring. The MALDI process was shown to be independent from natural hair color and not influenced by the presence of melanin. Ionization was shown to be reproducible along and in between different hair samples. MALDI image intensities in single hair and hair snippets showed good semiquantitative correlation to zolpidem hair concentrations obtained from validated routine LC-MS/MS methods. MALDI-MSI is superior to LC-MS/MS analysis when a fast, easy, and cheap sample preparation is necessary, whereas LC-MS/MS showed higher sensitivity with the ability of single dose detection for zolpidem. MALDI-MSI and LC-MS/MS segmental single hair analysis showed good correlation, and both are suitable for consumption monitoring of drugs of abuse with a high time resolution.

Comparative proteomic analysis in children with idiopathic short stature (ISS) before and after short-term recombinant human growth hormone (rhGH) therapy.

PubMed

Heo, Sun Hee; Choi, Jin-Ho; Kim, Yoo-Mi; Jung, Chang-Woo; Lee, Jin; Jin, Hye Young; Kim, Gu-Hwan; Lee, Beom Hee; Shin, Choong Ho; Yoo, Han-Wook

2013-04-01

This study was undertaken to identify growth hormone (GH) responsive proteins and protein expression patterns by short-term recombinant human growth hormone (rhGH) therapy in patients with idiopathic short stature (ISS) using proteomic analysis. Seventeen children (14 males and three females) with ISS were included. They were treated with rhGH at a dose of 0.31 ± 0.078 mg/kg/week for 3 months. Immunodepletion of six highly-abundant serum proteins followed by 2D DIGE analysis, and subsequent MALDI TOF MS, were employed to generate a panel of proteins differentially expressed after short-term rhGH therapy and verify the differences in serum levels of specific proteins by rhGH therapy. Fourteen spots were differentially expressed after rhGH treatment. Among them, apo E and apo L-1 expression were consistently enhanced, whereas serum amyloid A was reduced after rhGH therapy. The differential expressions of these proteins were subsequently verified by Western blot analysis using sera of the before and after rhGH treatment. This study suggests that rhGH therapy influences lipoprotein metabolism and enhances apo L-1 protein expression in ISS patients. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

UV Lamp as a Facile Ozone Source for Structural Analysis of Unsaturated Lipids Via Electrospray Ionization-Mass Spectrometry.

PubMed

Stinson, Craig A; Zhang, Wenpeng; Xia, Yu

2018-03-01

Ozonolysis of alkene functional groups is a type of highly specific and effective chemical reaction, which has found increasing applications in structural analysis of unsaturated lipids via coupling with mass spectrometry (MS). In this work, we utilized a low-pressure mercury lamp (6 W) to initiate ozonolysis inside electrospray ionization (ESI) sources. By placing the lamp near a nanoESI emitter that partially transmits 185 nm ultraviolet (UV) emission from the lamp, dissolved dioxygen in the spray solution was converted into ozone, which subsequently cleaved the double bonds within fatty acyls of lipids. Solvent conditions, such as presence of water and acid solution pH, were found to be critical in optimizing ozonolysis yields. Fast (on seconds time scale) and efficient (50%-100% yield) ozonolysis was achieved for model unsaturated phospholipids and fatty acids with UV lamp-induced ozonolysis incorporated on a static and an infusion nanoESI source. The method was able to differentiate double bond location isomers and identify the geometry of the double bond based on yield. The analytical utility of UV lamp-induced ozonolysis was further demonstrated by implementation on a liquid chromatography (LC)-MS platform. Ozonolysis was effected in a flow microreactor that was made from ozone permeable tubing, so that ambient ozone produced by the lamp irradiation could diffuse into the reactor and induce online ozonolysis post-LC separation and before ESI-MS. Graphical Abstract ᅟ.

UV Lamp as a Facile Ozone Source for Structural Analysis of Unsaturated Lipids Via Electrospray Ionization-Mass Spectrometry

NASA Astrophysics Data System (ADS)

Stinson, Craig A.; Zhang, Wenpeng; Xia, Yu

2018-03-01

Ozonolysis of alkene functional groups is a type of highly specific and effective chemical reaction, which has found increasing applications in structural analysis of unsaturated lipids via coupling with mass spectrometry (MS). In this work, we utilized a low-pressure mercury lamp (6 W) to initiate ozonolysis inside electrospray ionization (ESI) sources. By placing the lamp near a nanoESI emitter that partially transmits 185 nm ultraviolet (UV) emission from the lamp, dissolved dioxygen in the spray solution was converted into ozone, which subsequently cleaved the double bonds within fatty acyls of lipids. Solvent conditions, such as presence of water and acid solution pH, were found to be critical in optimizing ozonolysis yields. Fast (on seconds time scale) and efficient (50%-100% yield) ozonolysis was achieved for model unsaturated phospholipids and fatty acids with UV lamp-induced ozonolysis incorporated on a static and an infusion nanoESI source. The method was able to differentiate double bond location isomers and identify the geometry of the double bond based on yield. The analytical utility of UV lamp-induced ozonolysis was further demonstrated by implementation on a liquid chromatography (LC)-MS platform. Ozonolysis was effected in a flow microreactor that was made from ozone permeable tubing, so that ambient ozone produced by the lamp irradiation could diffuse into the reactor and induce online ozonolysis post-LC separation and before ESI-MS. [Figure not available: see fulltext.

Halogenated solvent interactions with N,N-dimethyltryptamine: formation of quaternary ammonium salts and their artificially induced rearrangements during analysis.

PubMed

Brandt, Simon D; Martins, Cláudia P B; Freeman, Sally; Dempster, Nicola; Riby, Philip G; Gartz, Jochen; Alder, John F

2008-07-04

The psychoactive properties of N,N-dimethyltryptamine (DMT) 1a are known to induce altered states of consciousness in humans. This particular attribute attracts great interest from a variety of scientific and also clandestine communities. Our recent research has confirmed that DMT reacts with dichloromethane (DCM), either as a result of work-up or storage to give a quaternary N-chloromethyl ammonium salt 2a. Furthermore, this was observed to undergo rearrangement during analysis using gas chromatography-mass spectrometry (GC-MS) with products including 3-(2-chloroethyl)indole 3 and 2-methyltetrahydro-beta-carboline 4 (2-Me-THBC). This study further investigates this so far unexplored area of solvent interactions by the exposure of DMT to other halogenated solvents including dibromomethane and 1,2-dichloroethane (DCE). The N-bromomethyl- and N-chloroethyl quaternary ammonium derivatives were subsequently characterised by ion trap GC-MS in electron and chemical ionisation tandem MS mode and by NMR spectroscopy. The DCE-derived derivative formed at least six rearrangement products in the total ion chromatogram. Identification of mass spectrometry generated by-products was verified by conventional or microwave-accelerated synthesis. The use of deuterated DCM and deuterated DMT 1b provided insights into the mechanism of the rearrangements. The presence of potentially characteristic marker molecules may allow the identification of solvents used during the manufacture of controlled substances, which is often neglected since these are considered inert.

Application of proteomics in the discovery of candidate protein biomarkers in a Diabetes Autoantibody Standardization Program (DASP) sample subset

PubMed Central

Metz, Thomas O.; Qian, Wei-Jun; Jacobs, Jon M.; Gritsenko, Marina A.; Moore, Ronald J.; Polpitiya, Ashoka D.; Monroe, Matthew E.; Camp, David G.; Mueller, Patricia W.; Smith, Richard D.

2009-01-01

Novel biomarkers of type 1 diabetes must be identified and validated in initial, exploratory studies before they can be assessed in proficiency evaluations. Currently, untargeted “-omics” approaches are under-utilized in profiling studies of clinical samples. This report describes the evaluation of capillary liquid chromatography (LC) coupled with mass spectrometry (MS) in a pilot proteomic analysis of human plasma and serum from a subset of control and type 1 diabetic individuals enrolled in the Diabetes Autoantibody Standardization Program with the goal of identifying candidate biomarkers of type 1 diabetes. Initial high-resolution capillary LC-MS/MS experiments were performed to augment an existing plasma peptide database, while subsequent LC-FTICR studies identified quantitative differences in the abundance of plasma proteins. Analysis of LC-FTICR proteomic data identified five candidate protein biomarkers of type 1 diabetes. Alpha-2-glycoprotein 1 (zinc), corticosteroid-binding globulin, and lumican were 2-fold up-regulated in type 1 diabetic samples relative to control samples, whereas clusterin and serotransferrin were 2-fold up-regulated in control samples relative to type 1 diabetic samples. Observed perturbations in the levels of all five proteins are consistent with the metabolic aberrations found in type 1 diabetes. While the discovery of these candidate protein biomarkers of type 1 diabetes is encouraging, follow up studies are required for validation in a larger population of individuals and for determination of laboratory-defined sensitivity and specificity values using blinded samples. PMID:18092746

Application of proteomics in the discovery of candidate protein biomarkers in a diabetes autoantibody standardization program sample subset.

PubMed

Metz, Thomas O; Qian, Wei-Jun; Jacobs, Jon M; Gritsenko, Marina A; Moore, Ronald J; Polpitiya, Ashoka D; Monroe, Matthew E; Camp, David G; Mueller, Patricia W; Smith, Richard D

2008-02-01

Novel biomarkers of type 1 diabetes must be identified and validated in initial, exploratory studies before they can be assessed in proficiency evaluations. Currently, untargeted "-omics" approaches are underutilized in profiling studies of clinical samples. This report describes the evaluation of capillary liquid chromatography (LC) coupled with mass spectrometry (MS) in a pilot proteomic analysis of human plasma and serum from a subset of control and type 1 diabetic individuals enrolled in the Diabetes Autoantibody Standardization Program, with the goal of identifying candidate biomarkers of type 1 diabetes. Initial high-resolution capillary LC-MS/MS experiments were performed to augment an existing plasma peptide database, while subsequent LC-FTICR studies identified quantitative differences in the abundance of plasma proteins. Analysis of LC-FTICR proteomic data identified five candidate protein biomarkers of type 1 diabetes. alpha-2-Glycoprotein 1 (zinc), corticosteroid-binding globulin, and lumican were 2-fold up-regulated in type 1 diabetic samples relative to control samples, whereas clusterin and serotransferrin were 2-fold up-regulated in control samples relative to type 1 diabetic samples. Observed perturbations in the levels of all five proteins are consistent with the metabolic aberrations found in type 1 diabetes. While the discovery of these candidate protein biomarkers of type 1 diabetes is encouraging, follow up studies are required for validation in a larger population of individuals and for determination of laboratory-defined sensitivity and specificity values using blinded samples.

Loss of H2 and CO from protonated aldehydes in electrospray ionization mass spectrometry.

PubMed

Neta, Pedatsur; Simón-Manso, Yamil; Liang, Yuxue; Stein, Stephen E

2014-09-15

Electrospray ionization mass spectrometry (ESI-MS) of many protonated aldehydes shows loss of CO as a major fragmentation pathway. However, we find that certain aldehydes undergo loss of H2 followed by reaction with water in the collision cell. This complicates interpretation of tandem mass (MS/MS) spectra and affects multiple reaction monitoring (MRM) results. 3-Formylchromone and other aldehydes were dissolved in acetonitrile/water/formic acid and studied by ESI-MS to record their MS(2) and MS(n) spectra in several mass spectrometers (QqQ, QTOF, ion trap (IT), and Orbitrap HCD). Certain product ions were found to react with water and the rate of reaction was determined in the IT instrument using zero collision energy and variable activation times. Theoretical calculations were performed to help with the interpretation of the fragmentation mechanism. Protonated 3-formylchromones and 3-formylcoumarins undergo loss of H2 as a major fragmentation route to yield a ketene cation, which reacts with water to form a protonated carboxylic acid. In general, protonated aldehydes which contain a vicinal group that forms a hydrogen bridge with the formyl group undergo significant loss of H2. Subsequent losses of CO and C3O are also observed. Theoretical calculations suggest mechanistic details for these losses. Loss of H2 is a major fragmentation channel for protonated 3-formychromones and certain other aldehydes and it is followed by reaction with water to produce a protonated carboxylic acid, which undergoes subsequent fragmentation. This presents a problem for reference libraries and raises concerns about MRM results. Published in 2014. This article is a U.S. Government work and is in the public domain in the USA.

Verification of propofol sulfate as a further human propofol metabolite using LC-ESI-QQQ-MS and LC-ESI-QTOF-MS analysis.

PubMed

Maas, Alexandra; Maier, Christoph; Michel-Lauter, Beate; Broecker, Sebastian; Madea, Burkhard; Hess, Cornelius

2017-03-01

Propofol (2,6-diisopropylphenol) is a water-insoluble, intravenous anesthetic that is widely used for the induction and maintenance of anesthesia as well as for endoscopic and pediatric sedation. After admission, propofol undergoes extensive hepatic and extrahepatic metabolism, including direct conjugation to propofol glucuronide and hydroxylation to 2,6-diisopropyl-1,4-quinol. The latter substance subsequently undergoes phase II metabolism, resulting in the formation of further metabolites (1quinolglucuronide, 4quinolglucuronide and 4quinol-sulfate). Further minor phase I propofol metabolites (2-(ω-propanol)-6-isopropylphenol and 2-(ω-propanol)-6-isopropyl-1,4-quinol)) are also described. Due to its chemical structure with the phenolic hydroxyl group, propofol is also an appropriate substrate for sulfation by sulfotransferases. The existence of propofol sulfate was investigated by liquid chromatography electrospray ionization triple quadrupole mass spectrometry (LCESIQQQ-MS) and liquid chromatography electrospray ionization quadrupole time-of-flight mass spectrometry (LCESI-QTOF-MS). A propofol sulfate reference standard was used for identification and method development, yielding a precursor at m/z 257 (deprotonated propofol sulfate) and product ions at m/z 177 (deprotonated propofol) and m/z 80 ([SO3]-). Propofol sulfate - a further phase II metabolite of propofol - was verified in urine samples by LC-ESI-QQQ-MS and LC-ESI-QTOF-MS. Analyses of urine samples from five volunteers collected before and after propofol-induced sedation verified the presence of propofol sulfate in urine following propofol administration, whereas ascertained concentrations of this metabolite were significantly lower compared with detected propofol glucuronide concentrations. The existence of propofol sulfate as a further phase II propofol metabolite in humans could be verified by two different detection techniques (LCESIQQQ-MS and LC-ESI-QTOFMS) on the basis of a propofol sulfate reference standard. Evaluation of the quantitative analyses of propofol sulfate imply that propofol sulfate represents a minor metabolite of propofol and is only slightly involved in human propofol clearance.

Treatment Effects for Dysphagia in Adults with Multiple Sclerosis: A Systematic Review.

PubMed

Alali, Dalal; Ballard, Kirrie; Bogaardt, Hans

2016-10-01

Dysphagia or swallowing difficulties have been reported to be a concern in adults with multiple sclerosis (MS). This problem can result in several complications including aspiration pneumonia, reduced quality of life and an increase in mortality rate. No previous systematic reviews on treatment effects for dysphagia in MS have been published. The main objective of this study is to summarise and qualitatively analyse published studies on treatment effects for dysphagia in MS. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines were applied to conduct a systematic search of seven databases, using relevant key words, and subsequent analysis of the identified studies. The studies were required to meet all three inclusion criteria of including a statement on intention to treat, or measure the effects of treatment for dysphagia in adults with MS and data on treatment outcomes for at least one adult diagnosed with MS. Retained studies were evaluated by two independent reviewers using a critical appraisal tool. This study has not been registered. A total of 563 studies were identified from the database searches. After screening and assessment of full articles for eligibility, five studies were included in the review. Three examined electrical stimulation and two examined the use of botulinum toxin. One study testing electrical stimulation was a randomised controlled trial, two were well-designed case series and two were case series lacking experimental control. All studies reported some positive effects on dysphagia; however, treatments that involved the use of electrical stimulation showed larger effect sizes. There is a paucity of evidence to guide treatment of dysphagia in MS, with only electrical stimulation and botulinum toxin treatment represented in the literature search conducted here. While both treatments show initial promise for reducing the swallowing impairment, they require further research using well-controlled experimental designs to determine their clinical applicability and long-term treatment effects for dysphagia across different types and severity of MS.

Synchronized Survey Scan Approach Allows for Efficient Discrimination of Isomeric and Isobaric Compounds during LC-MS/MS Analyses

PubMed Central

Masike, Keabetswe

2018-01-01

Liquid chromatography-mass spectrometry- (LC-MS-) based multiple reaction monitoring (MRM) methods have been used to detect and quantify metabolites for years. These approaches rely on the monitoring of various fragmentation pathways of multiple precursors and the subsequent corresponding product ions. However, MRM methods are incapable of confidently discriminating between isomeric and isobaric molecules and, as such, the development of methods capable of overcoming this challenge has become imperative. Due to increasing scanning rates of recent MS instruments, it is now possible to operate MS instruments both in the static and dynamic modes. One such method is known as synchronized survey scan (SSS), which is capable of acquiring a product ion scan (PIS) during MRM analysis. The current study shows, for the first time, the use of SSS-based PIS approach as a feasible identification feature of MRM. To achieve the above, five positional isomers of dicaffeoylquinic acids (diCQAs) were studied with the aid of SSS-based PIS method. Here, the MRM transitions were automatically optimized using a 3,5-diCQA isomer by monitoring fragmentation transitions common to all five isomers. Using the mixture of these isomers, fragmentation spectra of the five isomers achieved with SSS-based PIS were used to identify each isomer based on previously published hierarchical fragmentation keys. The optimized method was also used to detect and distinguish between diCQA components found in Bidens pilosa and their isobaric counterparts found in Moringa oleifera plants. Thus, the method was shown to distinguish (by differences in fragmentation patterns) between diCQA and their isobars, caffeoylquinic acid (CQA) glycosides. In conclusion, SSS allowed the detection and discrimination of isomeric and isobaric compounds in a single chromatographic run by producing a PIS spectrum, triggered in the automatic MS/MS synchronized survey scan mode. PMID:29805830

Urine Multi-drug Screening with GC-MS or LC-MS-MS Using SALLE-hybrid PPT/SPE.

PubMed

Lee, Junhui; Park, Jiwon; Go, Ahra; Moon, Heesung; Kim, Sujin; Jung, Sohee; Jeong, Wonjoon; Chung, Heesun

2018-05-14

To intoxicated patients in the emergency room, toxicological analysis can be considerably helpful for identifying the involved toxicants. In order to develop a urine multi-drug screening (UmDS) method, gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-tandem mass spectrometry (LC-MS-MS) were used to determine targeted and unknown toxicants in urine. A GC-MS method in scan mode was validated for selectivity, limit of detection (LOD) and recovery. An LC-MS-MS multiple reaction monitoring (MRM) method was validated for lower LOD, recovery and matrix effect. The results of the screening analysis were compared with patient medical records to check the reliability of the screen. Urine samples collected from an emergency room were extracted through a combination of salting-out assisted liquid-liquid extraction (SALLE) and hybrid protein precipitation/solid phase extraction (hybrid PPT/SPE) plates and examined by GC-MS and LC-MS-MS. GC-MS analysis was performed as unknown drug screen and LC-MS-MS analysis was conducted as targeted drug screen. After analysis by GC-MS, a library search was conducted using an in-house library established with the automated mass spectral deconvolution and identification system (AMDISTM). LC-MS-MS used Cliquid®2.0 software for data processing and acquisition in MRM mode. An UmDS method by GC-MS and LC-MS-MS was developed by using a SALLE-hybrid PPT/SPE and in-house library. The results of UmDS by GC-MS and LC-MS-MS showed that toxicants could be identified from 185 emergency room patient samples containing unknown toxicants. Zolpidem, acetaminophen and citalopram were the most frequently encountered drugs in emergency room patients. The UmDS analysis developed in this study can be used effectively to detect toxic substances in a short time. Hence, it could be utilized in clinical and forensic toxicology practices.

Inventory of File sref_em.t03z.pgrb212.ctl.grib2

Science.gov Websites

UGRD analysis U-Component of Wind [m/s] 006 10 m above ground VGRD analysis V-Component of Wind [m/s of Wind [m/s] 018 250 mb VGRD analysis V-Component of Wind [m/s] 019 500 mb HGT analysis Geopotential Height [gpm] 020 500 mb UGRD analysis U-Component of Wind [m/s] 021 500 mb VGRD analysis V-Component of

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UGRD analysis U-Component of Wind [m/s] 006 10 m above ground VGRD analysis V-Component of Wind [m/s of Wind [m/s] 018 250 mb VGRD analysis V-Component of Wind [m/s] 019 500 mb HGT analysis Geopotential Height [gpm] 020 500 mb UGRD analysis U-Component of Wind [m/s] 021 500 mb VGRD analysis V-Component of

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UGRD analysis U-Component of Wind [m/s] 006 10 m above ground VGRD analysis V-Component of Wind [m/s of Wind [m/s] 018 250 mb VGRD analysis V-Component of Wind [m/s] 019 500 mb HGT analysis Geopotential Height [gpm] 020 500 mb UGRD analysis U-Component of Wind [m/s] 021 500 mb VGRD analysis V-Component of

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UGRD analysis U-Component of Wind [m/s] 006 10 m above ground VGRD analysis V-Component of Wind [m/s of Wind [m/s] 018 250 mb VGRD analysis V-Component of Wind [m/s] 019 500 mb HGT analysis Geopotential Height [gpm] 020 500 mb UGRD analysis U-Component of Wind [m/s] 021 500 mb VGRD analysis V-Component of

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UGRD analysis U-Component of Wind [m/s] 006 10 m above ground VGRD analysis V-Component of Wind [m/s of Wind [m/s] 018 250 mb VGRD analysis V-Component of Wind [m/s] 019 500 mb HGT analysis Geopotential Height [gpm] 020 500 mb UGRD analysis U-Component of Wind [m/s] 021 500 mb VGRD analysis V-Component of

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UGRD analysis U-Component of Wind [m/s] 006 10 m above ground VGRD analysis V-Component of Wind [m/s of Wind [m/s] 018 250 mb VGRD analysis V-Component of Wind [m/s] 019 500 mb HGT analysis Geopotential Height [gpm] 020 500 mb UGRD analysis U-Component of Wind [m/s] 021 500 mb VGRD analysis V-Component of

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UGRD analysis U-Component of Wind [m/s] 006 10 m above ground VGRD analysis V-Component of Wind [m/s of Wind [m/s] 018 250 mb VGRD analysis V-Component of Wind [m/s] 019 500 mb HGT analysis Geopotential Height [gpm] 020 500 mb UGRD analysis U-Component of Wind [m/s] 021 500 mb VGRD analysis V-Component of

Inventory of File sref_nmm.t03z.pgrb212.ctl.grib2

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UGRD analysis U-Component of Wind [m/s] 006 10 m above ground VGRD analysis V-Component of Wind [m/s of Wind [m/s] 018 250 mb VGRD analysis V-Component of Wind [m/s] 019 500 mb HGT analysis Geopotential Height [gpm] 020 500 mb UGRD analysis U-Component of Wind [m/s] 021 500 mb VGRD analysis V-Component of

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Science.gov Websites

UGRD analysis U-Component of Wind [m/s] 006 10 m above ground VGRD analysis V-Component of Wind [m/s of Wind [m/s] 018 250 mb VGRD analysis V-Component of Wind [m/s] 019 500 mb HGT analysis Geopotential Height [gpm] 020 500 mb UGRD analysis U-Component of Wind [m/s] 021 500 mb VGRD analysis V-Component of

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UGRD analysis U-Component of Wind [m/s] 006 10 m above ground VGRD analysis V-Component of Wind [m/s of Wind [m/s] 018 250 mb VGRD analysis V-Component of Wind [m/s] 019 500 mb HGT analysis Geopotential Height [gpm] 020 500 mb UGRD analysis U-Component of Wind [m/s] 021 500 mb VGRD analysis V-Component of

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analysis Pressure Reduced to MSL [Pa] 002 surface GUST analysis Wind Speed (Gust) [m/s] 003 100 mb HGT -Component of Wind [m/s] 007.2 100 mb VGRD analysis V-Component of Wind [m/s] 008 150 mb HGT analysis Wind [m/s] 012.2 150 mb VGRD analysis V-Component of Wind [m/s] 013 200 mb HGT analysis Geopotential

Development and Validation of a Simple and Rapid UPLC-MS Assay for Valproic Acid and Its Comparison With Immunoassay and HPLC Methods.

PubMed

Zhao, Mingming; Li, Guofei; Qiu, Feng; Sun, Yaxin; Xu, Yinghong; Zhao, Limei

2016-04-01

Valproic acid (VPA), a widely used antiepileptic drug, has a narrow therapeutic range of 50-100 mcg/mL and shows large individual variability. It is very important to monitor the trough concentration of VPA using a reliable method. Therefore, the aim of this study was to develop and validate a rapid ultraperformance liquid chromatographic-mass spectrometry (UPLC-MS) method for quantification of VPA in human serum and to compare with fluorescence polarization immunoassay (FPIA), chemiluminescence microparticle immunoassay (CMIA), and high-performance liquid chromatography (HPLC) methods. The method included extraction of VPA in serum by deproteinization with acetonitrile. The analysis was performed using an EC-C18 column (2.7 μm, 4.6 × 50 mm) under isocratic conditions with a mobile phase of acetonitrile/water (containing 0.1% formic acid) (45/55, vol/vol) at a flow rate of 0.6 mL/min. The detection was performed on a triple-quadrupole tandem mass spectrometer using an electrospary probe in the negative ionization mode. The method was validated by studies of selectivity, linearity, lower limit of quantification, accuracy, precision, recovery, matrix effect, and stability. Furthermore, all the 4 methods including FPIA, CMIA, and HPLC were subsequently used to assay the VPA concentration in 498 clinical serum samples collected from patients who received VPA. These methods were compared by Deming regression and Bland-Altman analysis. The retention time of VPA was 2.09 minutes. The calibration curve was linear over the concentration range of 1-200 mcg/mL, with a lower limit of quantification of 1 mcg/mL. The interday and intraday precision (RSD %) was less than 4.6% and 4.5%, respectively, and the accuracy (RE %) was below 7.9%. The recoveries and matrix effect of VPA at concentrations of 2, 50, and 160 mcg/mL met the requirement for the analysis of biological samples. No obvious degradation of VPA was observed under various storage conditions including room temperature for 12 hour, 3 freeze-thaw cycles, and -20°C for 3 months. Regression analysis showed that the correlation coefficients for the UPLC-MS versus FPIA, CMIA, and HPLC were 0.989, 0.988, and 0.987, respectively. The results of agreement tests between UPLC-MS and other methods showed that the mean difference of UPLC-MS and FPIA was -1.4 mcg/mL and 95% confidence interval of -7.7 to 4.9 mcg/mL, and the values for UPLC-MS and CMIA were -0.8 mcg/mL and -7.5 to 5.8 mcg/mL, for UPLC-MS and HPLC were 1.1 mcg/mL and -5.7 to 7.9 mcg/mL. The rapid UPLC-MS method we developed showed a good analytical performance required for therapeutic drug monitoring, leading to potential improvements in patient care and laboratory management. Compared with the FPIA, CMIA, and HPLC methods, the UPLC-MS method correlated well and displayed comparable VPA concentrations.

Tracking oil and gas wastewater-derived organic matter in a hybrid biofilter membrane treatment system: A multi-analytical approach.

PubMed

Riley, Stephanie M; Ahoor, Danika C; Regnery, Julia; Cath, Tzahi Y

2018-02-01

Dissolved organic matter (DOM) present in oil and gas (O&G) produced water and fracturing flowback was characterized and quantified by multiple analytical techniques throughout a hybrid biological-physical treatment process. Quantitative and qualitative analysis of DOM by liquid chromatography - organic carbon detection (LC-OCD), liquid chromatography-high-resolution mass spectrometry (LC-HRMS), gas chromatography-mass spectrometry (GC-MS), and 3D fluorescence spectroscopy, demonstrated increasing removal of all groups of DOM throughout the treatment train, with most removal occurring during biological pretreatment and some subsequent removal achieved during membrane treatment. Parallel factor analysis (PARAFAC) further validated these results and identified five fluorescent components, including DOM described as humic acids, fulvic acids, proteins, and aromatics. Tryptophan-like compounds bound by complexation to humics/fulvics were most difficult to remove biologically, while aromatics (particularly low molecular weight neutrals) were more challenging to remove with membranes. Strong correlation among PARAFAC, LC-OCD, LC-HRMS, and GC-MS suggests that PARAFAC can be a quick, affordable, and accurate tool for evaluating the presence or removal of specific DOM groups in O&G wastewater. Copyright © 2017 Elsevier B.V. All rights reserved.

Naturally Occurring Human Urinary Peptides for Use in Diagnosis of Chronic Kidney Disease*

PubMed Central

Good, David M.; Zürbig, Petra; Argilés, Àngel; Bauer, Hartwig W.; Behrens, Georg; Coon, Joshua J.; Dakna, Mohammed; Decramer, Stéphane; Delles, Christian; Dominiczak, Anna F.; Ehrich, Jochen H. H.; Eitner, Frank; Fliser, Danilo; Frommberger, Moritz; Ganser, Arnold; Girolami, Mark A.; Golovko, Igor; Gwinner, Wilfried; Haubitz, Marion; Herget-Rosenthal, Stefan; Jankowski, Joachim; Jahn, Holger; Jerums, George; Julian, Bruce A.; Kellmann, Markus; Kliem, Volker; Kolch, Walter; Krolewski, Andrzej S.; Luppi, Mario; Massy, Ziad; Melter, Michael; Neusüss, Christian; Novak, Jan; Peter, Karlheinz; Rossing, Kasper; Rupprecht, Harald; Schanstra, Joost P.; Schiffer, Eric; Stolzenburg, Jens-Uwe; Tarnow, Lise; Theodorescu, Dan; Thongboonkerd, Visith; Vanholder, Raymond; Weissinger, Eva M.; Mischak, Harald; Schmitt-Kopplin, Philippe

2010-01-01

Because of its availability, ease of collection, and correlation with physiology and pathology, urine is an attractive source for clinical proteomics/peptidomics. However, the lack of comparable data sets from large cohorts has greatly hindered the development of clinical proteomics. Here, we report the establishment of a reproducible, high resolution method for peptidome analysis of naturally occurring human urinary peptides and proteins, ranging from 800 to 17,000 Da, using samples from 3,600 individuals analyzed by capillary electrophoresis coupled to MS. All processed data were deposited in an Structured Query Language (SQL) database. This database currently contains 5,010 relevant unique urinary peptides that serve as a pool of potential classifiers for diagnosis and monitoring of various diseases. As an example, by using this source of information, we were able to define urinary peptide biomarkers for chronic kidney diseases, allowing diagnosis of these diseases with high accuracy. Application of the chronic kidney disease-specific biomarker set to an independent test cohort in the subsequent replication phase resulted in 85.5% sensitivity and 100% specificity. These results indicate the potential usefulness of capillary electrophoresis coupled to MS for clinical applications in the analysis of naturally occurring urinary peptides. PMID:20616184

Discrimination and chemical characterization of different Paeonia lactifloras (Radix Paeoniae Alba and Radix Paeoniae Rubra) by infrared macro-fingerprint analysis-through-separation

NASA Astrophysics Data System (ADS)

Wang, Yang; Wang, Ping; Xu, Changhua; Sun, Suqin; Zhou, Qun; Shi, Zhe; Li, Jin; Chen, Tao; Li, Zheng; Cui, Weili

2015-11-01

Paeonia lactiflora, a commonly used herbal medicine (HM) in Traditional Chinese Medicine (TCM), mainly has two species, Radix Paeoniae Alba (RPA) and Radix Paeoniae Rubra (RPR), for different clinical applications in TCM. For expounding the chemical profile of RPA and RPR and ensuring the clinical efficacy and safety, an infrared macro-fingerprint analysis-through-separation method integrated with statistical pattern recognition was developed to analyze and discriminate the two Paeonia lactifloras. In IR spectra, the major difference between the two was in the range of 1200-900 cm-1: the strongest peak of RPA was at 1024 cm-1, while that of RPR was 1049 cm-1. The difference was magnified in second derivative spectra. The findings were further verified by investigating the separation process of total glucosides, stepwisely monitored by both of IR and UPLC-MS/MS. Simultaneously, the aqueous extracts of RPA and RPR had been separated continuously to acquire the comprehensively hierarchical chemical characteristics for undoubtedly identification and subsequently discrimination of the two herbs. Moreover, 60 batches of the two HMs (30 for each) were objectively classified by principal component regression (PCR) model based on IR macro-fingerprints.

Investigation of the stallion sperm proteome by mass spectrometry.

PubMed

Swegen, Aleona; Curry, Benjamin J; Gibb, Zamira; Lambourne, Sarah R; Smith, Nathan D; Aitken, R John

2015-03-01

Stallion spermatozoa continue to present scientific and clinical challenges with regard to the biological mechanisms responsible for their survival and function. In particular, deeper understanding of sperm energy metabolism, defence against oxidative damage and cell-cell interactions should improve fertility assessment and the application of advanced reproductive technologies in the equine species. In this study, we used highly sensitive LC-MS/MS technology and sequence database analysis to identify and characterise the proteome of Percoll-isolated ejaculated equine spermatozoa, with the aim of furthering our understanding of this cell's complex biological machinery. We were able to identify 9883 peptides comprising 1030 proteins, which were subsequently attributed to 975 gene products. Gene ontology analysis for molecular and cellular processes revealed new information about the metabolism, antioxidant defences and receptors of stallion spermatozoa. Mitochondrial proteins and those involved in catabolic processes constituted dominant categories. Several enzymes specific to β-oxidation of fatty acids were identified, and further experiments were carried out to ascertain their functional significance. Inhibition of carnitine palmitoyl transferase 1, a rate-limiting enzyme of β-oxidation, reduced motility parameters, indicating that β-oxidation contributes to maintenance of motility in stallion spermatozoa. © 2015 Society for Reproduction and Fertility.

Layer chromatography-bioassays directed screening and identification of antibacterial compounds from Scotch thistle.

PubMed

Móricz, Ágnes M; Krüzselyi, Dániel; Alberti, Ágnes; Darcsi, András; Horváth, Györgyi; Csontos, Péter; Béni, Szabolcs; Ott, Péter G

2017-11-17

The antibacterial profiling of Onopordum acanthium L. leaf extract and subsequent targeted identification of active compounds is demonstrated. Thin-layer chromatography (TLC) and off-line overpressured layer chromatography (OPLC) coupled with direct bioautography were utilized for investigation of the extract against eight bacterial strains including two plant and three human pathogens and a soil, a marine and a probiotic human gut bacteria. Antibacterial fractions obtaining infusion-transfusion OPLC were transferred to HPLC-MS/MS analysis that resulted in the characterization of three active compounds and two of them were identified as, linoleic and linolenic acid. OPLC method was adopted to preparative-scale flash chromatography for the isolation of the third active compound, which was identified after a further semi-preparative HPLC purification as the germacranolide sesquiterpene lactone onopordopicrin. Pure onopordopicrin exhibited antibacterial activity that was specified as minimal inhibitory concentration in the liquid phase as well. Copyright © 2017 Elsevier B.V. All rights reserved.

Autism and urinary exogenous neuropeptides: development of an on-line SPE-HPLC-tandem mass spectrometry method to test the opioid excess theory.

PubMed

Dettmer, K; Hanna, D; Whetstone, P; Hansen, R; Hammock, B D

2007-08-01

Autism is a complex neurodevelopmental disorder with unknown etiology. One hypothesis regarding etiology in autism is the "opioid peptide excess" theory that postulates that excessive amounts of exogenous opioid-like peptides derived from dietary proteins are detectable in urine and that these compounds may be pathophysiologically important in autism. A selective LC-MS/MS method was developed to analyze gliadinomorphin, beta-casomorphin, deltorphin 1, and deltorphin 2 in urine. The method is based on on-line SPE extraction of the neuropeptides from urine, column switching, and subsequent HPLC analysis. A limit of detection of 0.25 ng/mL was achieved for all analytes. Analyte recovery rates from urine ranged between 78% and 94%, with relative standard deviations of 0.2-6.8%. The method was used to screen 69 urine samples from children with and without autism spectrum disorders for the occurrence of neuropeptides. The target neuropeptides were not detected above the detection limit in either sample set.

Enantioselective extraction of (+)-(S)-citalopram and its main metabolites using a tailor-made stir bar chiral imprinted polymer for their LC-ESI-MS/MS quantitation in urine samples.

PubMed

Unceta, Nora; Gómez-Caballero, Alberto; García, Deiene; Díaz, Goretti; Guerreiro, Antonio; Piletsky, Sergey; Goicolea, M Aránzazu; Barrio, Ramón J

2013-11-15

This paper reports the application of a chiral imprinted polymer (CIP)-coated stir bar for the selective extraction of (+)-(S)-citalopram (SCIT) and its main metabolites, (+)-(S)-desmethylcitalopram (SDCIT) and (+)-(S)-didesmethylcitalopram (SDDCIT), from urine samples. The developed device has been demonstrated to be capable of selectively extracting the three target analytes from urine samples without saturating the imprinted sites. A CIP-coated stir bar sorptive extraction procedure (CIP-SBSE) is proposed for the isolation of SCIT, SDCIT and SDDCIT followed by their subsequent analysis using liquid chromatography ion trap mass spectrometry (LC-ITMS). Deuterated SCIT-d6 was used as an internal standard. The method was validated using a standard procedure, which revealed that a quantification of 5 ng mL(-1) was obtained in urine samples and that the accuracy and precision were within the established values while no matrix effect was observed. Copyright © 2013 Elsevier B.V. All rights reserved.

Effect of fermentation and subsequent pasteurization processes on amino acids composition of orange juice.

PubMed

Cerrillo, I; Fernández-Pachón, M S; Collado-González, J; Escudero-López, B; Berná, G; Herrero-Martín, G; Martín, F; Ferreres, F; Gil-Izquierdo, A

2015-06-01

The fermentation of fruit produces significant changes in their nutritional composition. An orange beverage has been obtained from the controlled alcoholic fermentation and thermal pasteurization of orange juice. A study was performed to determine the influence of both processes on its amino acid profile. UHPLC-QqQ-MS/MS was used for the first time for analysis of orange juice samples. Out of 29 amino acids and derivatives identified, eight (ethanolamine, ornithine, phosphoethanolamine, α-amino-n-butyric acid, hydroxyproline, methylhistidine, citrulline, and cystathionine) have not previously been detected in orange juice. The amino acid profile of the orange juice was not modified by its processing, but total amino acid content of the juice (8194 mg/L) was significantly increased at 9 days of fermentation (13,324 mg/L). Although the pasteurization process produced partial amino acid degradation, the total amino acid content was higher in the final product (9265 mg/L) than in the original juice, enhancing its nutritional value.

Resilience Mediates the Longitudinal Relationships Between Social Support and Mental Health Outcomes in Multiple Sclerosis.

PubMed

Koelmel, Emily; Hughes, Abbey J; Alschuler, Kevin N; Ehde, Dawn M

2017-06-01

To investigate the longitudinal relationships between social support and subsequent mental health outcomes in individuals with multiple sclerosis (MS), and to examine resilience as a mediator between social support and subsequent mental health outcomes in this population. Observational, longitudinal cohort study. Participants were assessed at 4 time points over 12 months in the context of a previously reported randomized controlled trial. Telephone-based measures administered to community-based participants. Individuals (N=163) with MS and 1 or more of the following symptoms: depression, fatigue, and pain. Not applicable. Mental health outcomes included (1) depressive symptomatology, assessed using the Patient Health Questionnaire-9; (2) anxious symptomatology, assessed using the short form of the Emotional Distress-Anxiety Scale from the Patient-Reported Outcomes Measurement Information System; and (3) general mental health status, assessed using the Mental Component Summary score from the Short Form-8 Health Survey. Resilience was assessed using the Connor-Davidson Resilience Scale. At any given time, social support from significant others, family members, and friends was significantly associated with subsequent mental health outcomes for all 3 measures assessed (all P values <.05). Resilience measured concomitantly with social support significantly mediated the relationships between social support and subsequent mental health outcomes. After controlling for resilience, most of the direct relationships between social support and mental health outcomes were no longer significant. There are significant longitudinal relationships between social support, resilience, and mental health outcomes for people with MS. Given the mediating role of resilience in supporting better mental health outcomes, future clinical research and practice may benefit from an emphasis on resilience-focused psychological interventions. Copyright © 2016 American Congress of Rehabilitation Medicine. All rights reserved.

Magneto-Seebeck effect in spin valves

NASA Astrophysics Data System (ADS)

Zhang, X. M.; Wan, C. H.; Wu, H.; Tang, P.; Yuan, Z. H.; Zhang, Q. T.; Zhang, X.; Tao, B. S.; Fang, C.; Han, X. F.

2017-10-01

The magneto-Seebeck (MS) effect, which is also called magneto-thermo-power, was observed in Co/Cu/Co and NiFe/Cu/Co spin valves. Their Seebeck coefficients in the parallel state were larger than those in the antiparallel state, and the MS ratio defined as (SAP -SP)/SP could reach -9% in our case. The MS effect originated not only from trivial giant magnetoresistance but also from spin current generated due to spin-polarized thermoelectric conductivity of ferromagnetic materials and subsequent modulation of the spin current by different spin configurations in spin valves. A simple Mott two-channel model reproduced a -11% MS effect for the Co/Cu/Co spin valves, qualitatively consistent with our observations. The MS effect could be applied for simultaneously sensing the temperature gradient and the magnetic field and also be possibly applied to determine spin polarization of thermoelectric conductivity and the Seebeck coefficient of ferromagnetic thin films.

Metabolic profiling and systematic identification of flavonoids and isoflavonoids in roots and cell suspension cultures of Medicago truncatula using HPLC-UV-ESI-MS and GC-MS.

PubMed

Farag, Mohamed A; Huhman, David V; Lei, Zhentian; Sumner, Lloyd W

2007-02-01

An integrated approach utilizing HPLC-UV-ESI-MS and GC-MS was used for the large-scale and systematic identification of polyphenols in Medicago truncatula root and cell culture. Under optimized conditions, we were able to simultaneously quantify and identify 35 polyphenols including 26 isoflavones, 3 flavones, 2 flavanones, 2 aurones and a chalcone. All identifications were based upon UV spectra, mass spectral characteristics of protonated molecules, tandem mass spectral data, mass measurements obtained using a quadrupole time-of-flight mass spectrometer (QtofMS), and confirmed through the co-characterization of authentic compounds. In specific instances where the stereochemistry of sugar conjugates was uncertain, subsequent enzymatic hydrolysis of the conjugate followed by GC-MS was used to assign the sugar stereochemical configuration. Comparative metabolic profiling of Medicago truncatula root and cell cultures was then performed and revealed significant differences in the isoflavonoid composition of these two tissues.

MagR Alone Is Insufficient to Confer Cellular Calcium Responses to Magnetic Stimulation

PubMed Central

Pang, Keliang; You, He; Chen, Yanbo; Chu, Pengcheng; Hu, Meiqin; Shen, Jianying; Guo, Wei; Xie, Can; Lu, Bai

2017-01-01

Magnetic manipulation of cell activity offers advantages over optical manipulation but an ideal tool remains elusive. The MagR protein was found through its interaction with cryptochrome (Cry) and the protein in solution appeared to respond to magnetic stimulation (MS). After we initiated an investigation on the specific role of MagR in cellular response to MS, a subsequent study claimed that MagR expression alone could achieve cellular activation by MS. Here we report that despite systematically testing different ways of measuring intracellular calcium and different MS protocols, it was not possible to detect any cellular or neuronal responses to MS in MagR-expressing HEK cells or primary neurons from the dorsal root ganglion and the hippocampus. By contrast, in neurons co-expressing MagR and channelrhodopin, optical but not MS increased calcium influx in hippocampal neurons. Our results indicate that MagR alone is not sufficient to confer cellular magnetic responses. PMID:28360843

Data reduction of isotope-resolved LC-MS spectra.

PubMed

Du, Peicheng; Sudha, Rajagopalan; Prystowsky, Michael B; Angeletti, Ruth Hogue

2007-06-01

Data reduction of liquid chromatography-mass spectrometry (LC-MS) spectra can be a challenge due to the inherent complexity of biological samples, noise and non-flat baseline. We present a new algorithm, LCMS-2D, for reliable data reduction of LC-MS proteomics data. LCMS-2D can reliably reduce LC-MS spectra with multiple scans to a list of elution peaks, and subsequently to a list of peptide masses. It is capable of noise removal, and deconvoluting peaks that overlap in m/z, in retention time, or both, by using a novel iterative peak-picking step, a 'rescue' step, and a modified variable selection method. LCMS-2D performs well with three sets of annotated LC-MS spectra, yielding results that are better than those from PepList, msInspect and the vendor software BioAnalyst. The software LCMS-2D is available under the GNU general public license from http://www.bioc.aecom.yu.edu/labs/angellab/as a standalone C program running on LINUX.

Effects of maternal separation on nicotine-induced conditioned place preference and subsequent learning and memory in adolescent female rats.

PubMed

Dalaveri, Fatemeh; Nakhaee, Nouzar; Esmaeilpour, Khadijeh; Mahani, Saeed Esmaeili; Sheibani, Vahid

2017-02-03

Adverse early life experiences can potentially increase risk for drug abuse later in life. However, little research has been conducted studying the effects of maternal separation (MS), an experimental model for early life stress, on the rewarding effects of nicotine. Cognitive function may be affected by MS. So, we also investigated whether nicotine administration affect spatial learning and memory in MS adolescent female rats. Rat pups were subjected to daily MS for 15min (MS15) or 180min (MS180) during the first 2 weeks of life or reared under normal animal facility rearing (AFR) conditions. The place preference test was performed with nicotine (0.6mg/kg,s.c.) or vehicle over a period of 6 conditioning trials during adolescence. Spatial learning and memory performance was evaluated by using Morris water maze (MWM). In our study, adolescent female rats exposed to MS180 shown a significantly greater preference for a nicotine-paired compartment during the testing phase than the MS15 group. Nicotine altered the MS-induced spatial learning defects in the MS180 group. These findings suggest that MS may increase sensitivity to the rewarding effects of nicotine and also it is possible to suggest that nicotine administration may influence learning dysfunction induced by MS in adolescent female rats. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

High-throughput analysis of amphetamines in blood and urine with online solid-phase extraction-liquid chromatography-tandem mass spectrometry.

PubMed

Fernández, María del Mar Ramírez; Wille, Sarah M R; Samyn, Nele; Wood, Michelle; López-Rivadulla, Manuel; De Boeck, Gert

2009-01-01

An automated online solid-phase extraction-liquid chromatography-tandem mass spectrometry (SPE-LC-MS-MS) method for the analysis of amphetamines in blood and urine was developed and validated. Chromatographic separation was achieved on a Nucleodur Sphinx RP column with an LC gradient (a mixture of 10 mM ammonium formate buffer and acetonitrile), ensuring the elution of amphetamine, methamphetamine, MDMA, MDA, MDEA, PMA, and ephedrine within 11 min. The method was fully validated, according to international guidelines, using only 100 and 50 microL of blood and urine, respectively. The method showed an excellent intra- and interassay precision (relative standard deviation < 11.2% and bias < 13%) for two external quality control samples (QC) for both matrices and three and two 'in house' QCs for blood and urine, respectively. Responses were linear over the investigated range (r(2) > 0.99, 2.5-400 microg/L for blood and 25-1000 microg/L for urine). Limits of quantification were determined to be 2.5 and 25 microg/L for blood and urine, respectively. Limits of detection ranged from 0.05 to 0.5 microg/L for blood and 0.25 to 2.5 microg/L for urine, depending on the compound. Furthermore, the analytes and the processed samples were demonstrated to be stable (in the autosampler for at least 72 h and after three freeze/thaw cycles), and no disturbing matrix effects were observed for all compounds. Moreover, no carryover was observed after the analysis of high concentration samples (15,000 microg/L). The method was subsequently applied to authentic blood and urine samples obtained from forensic cases, which covered a broad range of concentrations. The validation results and actual sample analyses demonstrated that this method is rugged, precise, accurate, and well-suited for routine analysis as more than 72 samples are analyzed non-stop in 24 h with minimum sample handling. The combination of the high-throughput online SPE and the well-known sensitivity and selectivity assured by MS-MS resulted in the elimination of the bottleneck associated with the sample preparation requirements and provided increased sensitivity, accuracy, and precision.

Attribution of the discrepancy between ELISA and LC-MS/MS assay results of a PEGylated scaffold protein in post-dose monkey plasma samples due to the presence of anti-drug antibodies.

PubMed

Wang, Shujie J; Wu, Steven T; Gokemeijer, Jochem; Fura, Aberra; Krishna, Murli; Morin, Paul; Chen, Guodong; Price, Karen; Wang-Iverson, David; Olah, Timothy; Weiner, Russell; Tymiak, Adrienne; Jemal, Mohammed

2012-01-01

High-performance liquid chromatography-tandem mass spectrometry (LC-MS/MS) and enzyme-linked immunosorbent assay (ELISA) methods were developed for the quantification of a PEGylated scaffold protein drug in monkey plasma samples. The LC-MS/MS method was based on the extraction of the therapeutic protein with a water-miscible organic solvent and the subsequent trypsin digestion of the extract followed by the detection of a surrogate peptide. The assay was linear over a range of 10-3,000 ng/mL. The ELISA method utilized a therapeutic target-binding format in which the recombinant target antigen was used to capture the drug in the sample, followed by detection with an anti-PEG monoclonal antibody. The assay range was 30-2,000 ng/mL. A correlation study between the two methods was performed by measuring the drug concentrations in plasma samples from a single-dose pharmacokinetic (PK) study in cynomolgus monkeys following a 5-mg/kg subcutaneous administration (n = 4). In the early time points of the PK profile, the drug concentrations obtained by the LC-MS/MS method agreed very well with those obtained by the ELISA method. However, at later time points, the drug concentrations measured by the LC-MS/MS method were consistently higher than those measured by the ELISA method. The PK parameters calculated based on the concentration data showed that the two methods gave equivalent peak exposure (C(max)) at 24-48 h. However, the LC-MS/MS results exhibited about 1.53-fold higher total exposure (AUC(tot)) than the ELISA results. The discrepancy between the LC-MS/MS and ELISA results was investigated by conducting immunogenicity testing, anti-drug antibody (ADA) epitope mapping, and Western blot analysis of the drug concentrations coupled with Protein G separation. The results demonstrated the presence of ADA specific to the engineered antigen-binding region of the scaffold protein drug that interfered with the ability of the drug to bind to the target antigen used in the ELISA method. In the presence of the ADAs, the ELISA method measured only the active circulating drug (target-binding), while the LC-MS/MS method measured the total circulating drug. The work presented here indicates that the bioanalysis of protein drugs may be complicated owing to the presence of drug-binding endogenous components or ADAs in the post-dose (incurred) samples. The clear understanding of the behavior of different bioanalytical techniques vis-à-vis the potentially interfering components found in incurred samples is critical in selecting bioanalytical strategies for measuring protein drugs.

Quantitative proteome analysis of barley seeds using ruthenium(II)-tris-(bathophenanthroline-disulphonate) staining.

PubMed

Witzel, Katja; Surabhi, Giridara-Kumar; Jyothsnakumari, Gottimukkala; Sudhakar, Chinta; Matros, Andrea; Mock, Hans-Peter

2007-04-01

This paper describes the application of the recently introduced fluorescence stain Ruthenium(II)-tris-(bathophenanthroline-disulphonate) (RuBP) on a comparative proteome analysis of two phenotypically different barley lines. We carried out an analysis of protein patterns from 2-D gels of the parental lines of the Oregon Wolfe Barley mapping population DOM and REC and stained with either the conventional colloidal Coomassie Brilliant Blue (cCBB) or with the novel RuBP solution. We wished to experimentally verify the usefulness of such a stain in evaluating the complex pattern of a seed proteome, in comparison to the previously used cCBB staining technique. To validate the efficiency of visualization by both stains, we first compared the overall number of detected protein spots. On average, 790 spots were visible by cCBB staining and 1200 spots by RuBP staining. Then, the intensity of a set of spots was assessed, and changes in relative abundance were determined using image analysis software. As expected, staining with RuBP performed better in quantitation in terms of sensitivity and dynamic range. Furthermore, spots from a cultivar-specific region in the protein map were chosen for identification to asses the gain of biological information due to the staining procedure. From this particular region, eight spots were visualized exclusively by RuBP and identification was successful for all spots, proving the ability to identify even very low abundant proteins. Performance in MS analysis was comparable for both protein stains. Proteins were identified by MALDI-TOF MS peptide mass fingerprinting. This approach was not successful for all spots, due to the restricted entry number for barley in the database. Therefore, we subsequently used LC-ESI-Q-TOF MS/MS and de novo sequencing for identification. Because only an insufficient number of proteins from barley is annotated, an EST-based identification strategy was chosen for our experiment. We wished to test whether under these limitations the application of a more sensitive stain would lead to a more advanced proteome approach. In summary, we demonstrate here that the application of RuBP as an economical but reliable and sensitive fluorescence stain is highly suitable for quantitative proteome analysis of plant seeds.

Characterization of Differential Cocaine Metabolism in Mouse and Rat through Metabolomics-Guided Metabolite Profiling

PubMed Central

Yao, Dan; Shi, Xiaolei; Wang, Lei; Gosnell, Blake A.

2013-01-01

Rodent animal models have been widely used for studying neurologic and toxicological events associated with cocaine abuse. It is known that the mouse is more susceptible to cocaine-induced hepatotoxicity (CIH) than the rat. However, the causes behind this species-dependent sensitivity to cocaine have not been elucidated. In this study, cocaine metabolism in the mouse and rat was characterized through LC-MS-based metabolomic analysis of urine samples and were further compared through calculating the relative abundance of individual cocaine metabolites. The results showed that the levels of benzoylecgonine, a major cocaine metabolite from ester hydrolysis, were comparable in the urine from the mice and rats treated with the same dose of cocaine. However, the levels of the cocaine metabolites from oxidative metabolism, such as N-hydroxybenzoylnorecgonine and hydroxybenzoylecgonine, differed dramatically between the two species, indicating species-dependent cocaine metabolism. Subsequent structural analysis through accurate mass analysis and LC-MS/MS fragmentation revealed that N-oxidation reactions, including N-demethylation and N-hydroxylation, are preferred metabolic routes in the mouse, while extensive aryl hydroxylation reactions occur in the rat. Through stable isotope tracing and in vitro enzyme reactions, a mouse-specific α-glucoside of N-hydroxybenzoylnorecgonine and a group of aryl hydroxy glucuronides high in the rat were identified and structurally elucidated. The differences in the in vivo oxidative metabolism of cocaine between the two rodent species were confirmed by the in vitro microsomal incubations. Chemical inhibition of P450 enzymes further revealed that different P450-mediated oxidative reactions in the ecgonine and benzoic acid moieties of cocaine contribute to the species-dependent biotransformation of cocaine. PMID:23034697

Fusion Bead Procedure for Nuclear Forensics Employing Synthetic Enstatite to Dissolve Uraniferous and Other Challenging Materials Prior to Laser Ablation Inductively Coupled Plasma Mass Spectrometry.

PubMed

Reading, David G; Croudace, Ian W; Warwick, Phillip E

2017-06-06

There is an increasing demand for rapid and effective analytical tools to support nuclear forensic investigations of seized or suspect materials. Some methods are simply adapted from other scientific disciplines and can effectively be used to rapidly prepare complex materials for subsequent analysis. A novel sample fusion method is developed, tested, and validated to produce homogeneous, flux-free glass beads of geochemical reference materials (GRMs), uranium ores, and uranium ore concentrates (UOC) prior to the analysis of 14 rare earth elements (REE) via laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). The novelty of the procedure is the production of glass beads using 9 parts high purity synthetic enstatite (MgSiO 3 ) as the glass former with 1 part of sample (sample mass ∼1.5 mg). The beads are rapidly prepared (∼10 min overall time) by fusing the blended mixture on an iridium strip resistance heater in an argon-purged chamber. Many elements can be measured in the glass bead, but the rare earth group in particular is a valuable series in nuclear forensic studies and is well-determined using LA-ICP-MS. The REE data obtained from the GRMs, presented as chondrite normalized patterns, are in very good agreement with consensus patterns. The UOCs have comparable patterns to solution ICP-MS methods and published data. The attractions of the current development are its conservation of sample, speed of preparation, and suitability for microbeam analysis, all of which are favorable for nuclear forensics practitioners and geochemists requiring REE patterns from scarce or valuable samples.

An electroglottographical analysis-based discriminant function model differentiating multiple sclerosis patients from healthy controls.

PubMed

Vavougios, George D; Doskas, Triantafyllos; Konstantopoulos, Kostas

2018-05-01

Dysarthrophonia is a predominant symptom in many neurological diseases, affecting the quality of life of the patients. In this study, we produced a discriminant function equation that can differentiate MS patients from healthy controls, using electroglottographic variables not analyzed in a previous study. We applied stepwise linear discriminant function analysis in order to produce a function and score derived from electroglottographic variables extracted from a previous study. The derived discriminant function's statistical significance was determined via Wilk's λ test (and the associated p value). Finally, a 2 × 2 confusion matrix was used to determine the function's predictive accuracy, whereas the cross-validated predictive accuracy is estimated via the "leave-one-out" classification process. Discriminant function analysis (DFA) was used to create a linear function of continuous predictors. DFA produced the following model (Wilk's λ = 0.043, χ2 = 388.588, p < 0.0001, Tables 3 and 4): D (MS vs controls) = 0.728*DQx1 mean monologue + 0.325*CQx monologue + 0.298*DFx1 90% range monologue + 0.443*DQx1 90% range reading - 1.490*DQx1 90% range monologue. The derived discriminant score (S1) was used subsequently in order to form the coordinates of a ROC curve. Thus, a cutoff score of - 0.788 for S1 corresponded to a perfect classification (100% sensitivity and 100% specificity, p = 1.67e -22 ). Consistent with previous findings, electroglottographic evaluation represents an easy to implement and potentially important assessment in MS patients, achieving adequate classification accuracy. Further evaluation is needed to determine its use as a biomarker.

Serum biomarkers of Burkholderia mallei infection elucidated by proteomic imaging of skin and lung abscesses.

PubMed

Glaros, Trevor G; Blancett, Candace D; Bell, Todd M; Natesan, Mohan; Ulrich, Robert G

2015-01-01

The bacterium Burkholderia mallei is the etiological agent of glanders, a highly contagious, often fatal zoonotic infectious disease that is also a biodefense concern. Clinical laboratory assays that analyze blood or other biological fluids are the highest priority because these specimens can be collected with minimal risk to the patient. However, progress in developing sensitive assays for monitoring B. mallei infection is hampered by a shortage of useful biomarkers. Reasoning that there should be a strong correlation between the proteomes of infected tissues and circulating serum, we employed imaging mass spectrometry (IMS) of thin-sectioned tissues from Chlorocebus aethiops (African green) monkeys infected with B. mallei to localize host and pathogen proteins that were associated with abscesses. Using laser-capture microdissection of specific regions identified by IMS and histology within the tissue sections, a more extensive proteomic analysis was performed by a technique that combined the physical separation capabilities of liquid chromatography (LC) with the sensitive mass analysis capabilities of mass spectrometry (LC-MS/MS). By examining standard formalin-fixed, paraffin-embedded tissue sections, this strategy resulted in the identification of several proteins that were associated with lung and skin abscesses, including the host protein calprotectin and the pathogen protein GroEL. Elevated levels of calprotectin detected by ELISA and antibody responses to GroEL, measured by a microarray of the bacterial proteome, were subsequently detected in the sera of C. aethiops, Macaca mulatta, and Macaca fascicularis primates infected with B. mallei. Our results demonstrate that a combination of multidimensional MS analysis of traditional histology specimens with high-content protein microarrays can be used to discover lead pairs of host-pathogen biomarkers of infection that are identifiable in biological fluids.

Identification of multiple sclerosis patients at highest risk of cognitive impairment using an integrated brain magnetic resonance imaging assessment approach.

PubMed

Uher, T; Vaneckova, M; Sormani, M P; Krasensky, J; Sobisek, L; Dusankova, J Blahova; Seidl, Z; Havrdova, E; Kalincik, T; Benedict, R H B; Horakova, D

2017-02-01

While impaired cognitive performance is common in multiple sclerosis (MS), it has been largely underdiagnosed. Here a magnetic resonance imaging (MRI) screening algorithm is proposed to identify patients at highest risk of cognitive impairment. The objective was to examine whether assessment of lesion burden together with whole brain atrophy on MRI improves our ability to identify cognitively impaired MS patients. Of the 1253 patients enrolled in the study, 1052 patients with all cognitive, volumetric MRI and clinical data available were included in the analysis. Brain MRI and neuropsychological assessment with the Brief International Cognitive Assessment for Multiple Sclerosis were performed. Multivariable logistic regression and individual prediction analysis were used to investigate the associations between MRI markers and cognitive impairment. The results of the primary analysis were validated at two subsequent time points (months 12 and 24). The prevalence of cognitive impairment was greater in patients with low brain parenchymal fraction (BPF) (<0.85) and high T2 lesion volume (T2-LV) (>3.5 ml) than in patients with high BPF (>0.85) and low T2-LV (<3.5 ml), with an odds ratio (OR) of 6.5 (95% CI 4.4-9.5). Low BPF together with high T2-LV identified in 270 (25.7%) patients predicted cognitive impairment with 83% specificity, 82% negative predictive value, 51% sensitivity and 75% overall accuracy. The risk of confirmed cognitive decline over the follow-up was greater in patients with high T2-LV (OR 2.1; 95% CI 1.1-3.8) and low BPF (OR 2.6; 95% CI 1.4-4.7). The integrated MRI assessment of lesion burden and brain atrophy may improve the stratification of MS patients who may benefit from cognitive assessment. © 2016 EAN.

A new strategy for statistical analysis-based fingerprint establishment: Application to quality assessment of Semen sojae praeparatum.

PubMed

Guo, Hui; Zhang, Zhen; Yao, Yuan; Liu, Jialin; Chang, Ruirui; Liu, Zhao; Hao, Hongyuan; Huang, Taohong; Wen, Jun; Zhou, Tingting

2018-08-30

Semen sojae praeparatum with homology of medicine and food is a famous traditional Chinese medicine. A simple and effective quality fingerprint analysis, coupled with chemometrics methods, was developed for quality assessment of Semen sojae praeparatum. First, similarity analysis (SA) and hierarchical clusting analysis (HCA) were applied to select the qualitative markers, which obviously influence the quality of Semen sojae praeparatum. 21 chemicals were selected and characterized by high resolution ion trap/time-of-flight mass spectrometry (LC-IT-TOF-MS). Subsequently, principal components analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA) were conducted to select the quantitative markers of Semen sojae praeparatum samples from different origins. Moreover, 11 compounds with statistical significance were determined quantitatively, which provided an accurate and informative data for quality evaluation. This study proposes a new strategy for "statistic analysis-based fingerprint establishment", which would be a valuable reference for further study. Copyright © 2018 Elsevier Ltd. All rights reserved.

Detecting a wide range of environmental contaminants in human blood samples--combining QuEChERS with LC-MS and GC-MS methods.

PubMed

Plassmann, Merle M; Schmidt, Magdalena; Brack, Werner; Krauss, Martin

2015-09-01

Exposure to environmental pollution and consumer products may result in an uptake of chemicals into human tissues. Several studies have reported the presence of diverse environmental contaminants in human blood samples. However, previously developed multi-target methods for the analysis of human blood include a fairly limited amount of compounds stemming from one or two related compound groups. Thus, the sample preparation method QuEChERS (quick easy cheap effective rugged and safe) was tested for the extraction of 64 analytes covering a broad compound domain followed by detection using liquid and gas chromatography coupled to mass spectrometry (LC- and GC-MS). Forty-seven analytes showed absolute recoveries above 70% in the first QuEChERS step, being a simple liquid-liquid extraction (LLE) using acetonitrile and salt. The second QuEChERS step, being a dispersive solid phase extraction, did not result in an overall improvement of recoveries or removal of background signals. Using solely the LLE step, eight analytes could subsequently be detected in human blood samples from the German Environmental Specimen Bank. Using a LC-multiple reaction monitoring (MRM) method with a triple quadrupole instrument, better recoveries were achieved than with an older LC-high-resolution (HR) MS full scan orbitrap instrument, which required a higher concentration factor of the extracts. However, the application of HRMS full scan methods could be used for the detection of additional compounds retrospectively.

Microcystin-LR Detected in a Low Molecular Weight  Fraction from a Crude Extract of Zoanthus sociatus.

PubMed

Domínguez-Pérez, Dany; Rodríguez, Armando Alexei; Osorio, Hugo; Azevedo, Joana; Castañeda, Olga; Vasconcelos, Vítor; Antunes, Agostinho

2017-03-01

Cnidarian constitutes a great source of bioactive compounds. However, research involving peptides from organisms belonging to the order Zoanthidea has received very little attention, contrasting to the numerous studies of the order Actiniaria, from which hundreds of toxic peptides and proteins have been reported. In this work, we performed a mass spectrometry analysis of a low molecular weight (LMW) fraction previously reported as lethal to mice. The low molecular weight (LMW) fraction was obtained by gel filtration of a Zoanthus sociatus (order Zoanthidea) crude extract with a Sephadex G-50, and then analyzed by matrix-assisted laser desorption/ionization time-of-flight/time-of-flight (MALDI-TOF/TOF) mass spectrometry (MS) in positive ion reflector mode from m/z 700 to m/z 4000. Afterwards, some of the most intense and representative MS ions were fragmented by MS/MS with no significant results obtained by Protein Pilot protein identification software and the Mascot algorithm search. However, microcystin masses were detected by mass-matching against libraries of non-ribosomal peptide database (NORINE). Subsequent reversed-phase C18 HPLC (in isocratic elution mode) and mass spectrometry analyses corroborated the presence of the cyanotoxin Microcystin-LR (MC-LR). To the best of our knowledge, this finding constitutes the first report of MC-LR in Z. sociatus, and one of the few evidences of such cyanotoxin in cnidarians.

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

Comparative shotgun proteomics using spectral count data and quasi-likelihood modeling.

PubMed

Li, Ming; Gray, William; Zhang, Haixia; Chung, Christine H; Billheimer, Dean; Yarbrough, Wendell G; Liebler, Daniel C; Shyr, Yu; Slebos, Robbert J C

2010-08-06

Shotgun proteomics provides the most powerful analytical platform for global inventory of complex proteomes using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and allows a global analysis of protein changes. Nevertheless, sampling of complex proteomes by current shotgun proteomics platforms is incomplete, and this contributes to variability in assessment of peptide and protein inventories by spectral counting approaches. Thus, shotgun proteomics data pose challenges in comparing proteomes from different biological states. We developed an analysis strategy using quasi-likelihood Generalized Linear Modeling (GLM), included in a graphical interface software package (QuasiTel) that reads standard output from protein assemblies created by IDPicker, an HTML-based user interface to query shotgun proteomic data sets. This approach was compared to four other statistical analysis strategies: Student t test, Wilcoxon rank test, Fisher's Exact test, and Poisson-based GLM. We analyzed the performance of these tests to identify differences in protein levels based on spectral counts in a shotgun data set in which equimolar amounts of 48 human proteins were spiked at different levels into whole yeast lysates. Both GLM approaches and the Fisher Exact test performed adequately, each with their unique limitations. We subsequently compared the proteomes of normal tonsil epithelium and HNSCC using this approach and identified 86 proteins with differential spectral counts between normal tonsil epithelium and HNSCC. We selected 18 proteins from this comparison for verification of protein levels between the individual normal and tumor tissues using liquid chromatography-multiple reaction monitoring mass spectrometry (LC-MRM-MS). This analysis confirmed the magnitude and direction of the protein expression differences in all 6 proteins for which reliable data could be obtained. Our analysis demonstrates that shotgun proteomic data sets from different tissue phenotypes are sufficiently rich in quantitative information and that statistically significant differences in proteins spectral counts reflect the underlying biology of the samples.

Urea free and more efficient sample preparation method for mass spectrometry based protein identification via combining the formic acid-assisted chemical cleavage and trypsin digestion.

PubMed

Wu, Shuaibin; Yang, Kaiguang; Liang, Zhen; Zhang, Lihua; Zhang, Yukui

2011-10-30

A formic acid (FA)-assisted sample preparation method was presented for protein identification via mass spectrometry (MS). Detailedly, an aqueous solution containing 2% FA and dithiothreitol was selected to perform protein denaturation, aspartic acid (D) sites cleavage and disulfide linkages reduction simultaneously at 108°C for 2h. Subsequently, FA wiped off via vacuum concentration. Finally, iodoacetamide (IAA) alkylation and trypsin digestion could be performed ordinally. A series of model proteins (BSA, β-lactoglobulin and apo-Transferrin) were treated respectively using such method, followed by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) analysis. The identified peptide number was increased by ∼ 80% in comparison with the conventional urea-assisted sample preparation method. Moreover, BSA identification was achieved efficiently down to femtomole (25 ± 0 sequence coverage and 16 ± 1 peptides) via such method. In contrast, there were not peptides identified confidently via the urea-assisted method before desalination via the C18 zip tip. The absence of urea in this sample preparation method was an advantage for the more favorable digestion and MALDI-TOF MS analysis. The performances of two methods for the real sample (rat liver proteome) were also compared, followed by a nanoflow reversed-phase liquid chromatography with electrospray ionization tandem mass spectrometry system analysis. As a result, 1335 ± 43 peptides were identified confidently (false discovery rate <1%) via FA-assisted method, corresponding to 295 ± 12 proteins (of top match=1 and requiring 2 unique peptides at least). In contrast, there were only 1107 ± 16 peptides (corresponding to 231 ± 10 proteins) obtained from the conventional urea-assisted method. It was serving as a more efficient protein sample preparation method for researching specific proteomes better, and providing assistance to develop other proteomics analysis methods, such as, peptide quantitative analysis. Copyright © 2011 Elsevier B.V. All rights reserved.

Comparative Shotgun Proteomics Using Spectral Count Data and Quasi-Likelihood Modeling

PubMed Central

2010-01-01

Shotgun proteomics provides the most powerful analytical platform for global inventory of complex proteomes using liquid chromatography−tandem mass spectrometry (LC−MS/MS) and allows a global analysis of protein changes. Nevertheless, sampling of complex proteomes by current shotgun proteomics platforms is incomplete, and this contributes to variability in assessment of peptide and protein inventories by spectral counting approaches. Thus, shotgun proteomics data pose challenges in comparing proteomes from different biological states. We developed an analysis strategy using quasi-likelihood Generalized Linear Modeling (GLM), included in a graphical interface software package (QuasiTel) that reads standard output from protein assemblies created by IDPicker, an HTML-based user interface to query shotgun proteomic data sets. This approach was compared to four other statistical analysis strategies: Student t test, Wilcoxon rank test, Fisher’s Exact test, and Poisson-based GLM. We analyzed the performance of these tests to identify differences in protein levels based on spectral counts in a shotgun data set in which equimolar amounts of 48 human proteins were spiked at different levels into whole yeast lysates. Both GLM approaches and the Fisher Exact test performed adequately, each with their unique limitations. We subsequently compared the proteomes of normal tonsil epithelium and HNSCC using this approach and identified 86 proteins with differential spectral counts between normal tonsil epithelium and HNSCC. We selected 18 proteins from this comparison for verification of protein levels between the individual normal and tumor tissues using liquid chromatography−multiple reaction monitoring mass spectrometry (LC−MRM-MS). This analysis confirmed the magnitude and direction of the protein expression differences in all 6 proteins for which reliable data could be obtained. Our analysis demonstrates that shotgun proteomic data sets from different tissue phenotypes are sufficiently rich in quantitative information and that statistically significant differences in proteins spectral counts reflect the underlying biology of the samples. PMID:20586475

A comparison between DART-MS and DSA-MS in the forensic analysis of writing inks.

PubMed

Drury, Nicholas; Ramotowski, Robert; Moini, Mehdi

2018-05-23

Ambient ionization mass spectrometry is gaining momentum in forensic science laboratories because of its high speed of analysis, minimal sample preparation, and information-rich results. One such application of ambient ionization methodology includes the analysis of writing inks from questioned documents where colorants of interest may not be soluble in common solvents, rendering thin layer chromatography (TLC) and separation-mass spectrometry methods such as LC/MS (-MS) impractical. Ambient ionization mass spectrometry uses a variety of ionization techniques such as penning ionization in Direct Analysis in Real Time (DART), and atmospheric pressure chemical ionization in Direct Sample Analysis (DSA), and electrospray ionization in Desorption Electrospray Ionization (DESI). In this manuscript, two of the commonly used ambient ionization techniques are compared: Perkin Elmer DSA-MS and IonSense DART in conjunction with a JEOL AccuTOF MS. Both technologies were equally successful in analyzing writing inks and produced similar spectra. DSA-MS produced less background signal likely because of its closed source configuration; however, the open source configuration of DART-MS provided more flexibility for sample positioning for optimum sensitivity and thereby allowing smaller piece of paper containing writing ink to be analyzed. Under these conditions, the minimum sample required for DART-MS was 1mm strokes of ink on paper, whereas DSA-MS required a minimum of 3mm. Moreover, both techniques showed comparable repeatability. Evaluation of the analytical figures of merit, including sensitivity, linear dynamic range, and repeatability, for DSA-MS and DART-MS analysis is provided. To the forensic context of the technique, DART-MS was applied to the analysis of United States Secret Service ink samples directly on a sampling mesh, and the results were compared with DSA-MS of the same inks on paper. Unlike analysis using separation mass spectrometry, which requires sample preparation, both DART-MS and DSA-MS successfully analyzed writing inks with minimal sample preparation. Copyright © 2018 Elsevier B.V. All rights reserved.

The fine temporal structure of the rat licking pattern: what causes the variabiliy in the interlick intervals and how is it affected by the drinking solution?

PubMed

Lin, Xiong Bin; Pierce, Dwight R; Light, Kim Edward; Hayar, Abdallah

2013-10-01

Licking is a repetitive behavior controlled by a central pattern generator. Even though interlick intervals (ILIs) within bursts of licks are considered fairly regular, the conditions that affect their variability are unknown. We analyzed the licking pattern in rats that licked water, 10% sucrose solution, or 10% ethanol solution, in 90-min recording sessions after 4h of water deprivation. The histograms of ILIs indicate that licking typically occurred at a preferred ILI of about 130-140ms with evidence of bimodal or multimodal distributions due to occasional licking failures. We found that the longer the pause between bursts of licks, the shorter was the first ILI of the burst. When bursts of licks were preceded by a pause >4 s, the ILI was the shortest (~110ms) at the beginning of the burst, and then it increased rapidly in the first few licks and slowly in subsequent licks. Interestingly, the first ILI of a burst of licks was not significantly different when licking any of the 3 solutions, but subsequent licks exhibited a temporal pattern characteristic of each solution. The rapid deceleration in intraburst licking rate was due to an increase from ~27ms to ~56ms in the tongue-spout contact duration while the intercontact interval was only slightly changed (80-90ms). Therefore, the contact duration seems to be the major factor that increases the variability in the ILIs and could be another means for the rat to adjust the amount of fluid ingested in each individual lick.

Inventory of File sref.t03z.pgrb216.mean_3hrly.grib2

Science.gov Websites

UGRD analysis U-Component of Wind [m/s] wt ens-mean 002 10 m above ground VGRD analysis V-Component of Wind [m/s] wt ens-mean 003 1000 mb UGRD analysis U-Component of Wind [m/s] wt ens-mean 004 850 mb UGRD analysis U-Component of Wind [m/s] wt ens-mean 005 700 mb UGRD analysis U-Component of Wind [m/s] wt ens

Inventory of File sref.t03z.pgrb212.spread_3hrly.grib2

Science.gov Websites

ground UGRD analysis U-Component of Wind [m/s] std dev 002 10 m above ground VGRD analysis V-Component of Wind [m/s] std dev 003 1000 mb UGRD analysis U-Component of Wind [m/s] std dev 004 850 mb UGRD analysis U-Component of Wind [m/s] std dev 005 700 mb UGRD analysis U-Component of Wind [m/s] std dev 006 600

Inventory of File sref.t03z.pgrb243.mean_3hrly.grib2

Science.gov Websites

UGRD analysis U-Component of Wind [m/s] wt ens-mean 002 10 m above ground VGRD analysis V-Component of Wind [m/s] wt ens-mean 003 1000 mb UGRD analysis U-Component of Wind [m/s] wt ens-mean 004 850 mb UGRD analysis U-Component of Wind [m/s] wt ens-mean 005 700 mb UGRD analysis U-Component of Wind [m/s] wt ens

Inventory of File sref.t03z.pgrb216.spread_3hrly.grib2

Science.gov Websites

ground UGRD analysis U-Component of Wind [m/s] std dev 002 10 m above ground VGRD analysis V-Component of Wind [m/s] std dev 003 1000 mb UGRD analysis U-Component of Wind [m/s] std dev 004 850 mb UGRD analysis U-Component of Wind [m/s] std dev 005 700 mb UGRD analysis U-Component of Wind [m/s] std dev 006 600

Inventory of File sref.t03z.pgrb243.spread_3hrly.grib2

Science.gov Websites

ground UGRD analysis U-Component of Wind [m/s] std dev 002 10 m above ground VGRD analysis V-Component of Wind [m/s] std dev 003 1000 mb UGRD analysis U-Component of Wind [m/s] std dev 004 850 mb UGRD analysis U-Component of Wind [m/s] std dev 005 700 mb UGRD analysis U-Component of Wind [m/s] std dev 006 600

Inventory of File sref.t03z.pgrb212.mean_3hrly.grib2

Science.gov Websites

UGRD analysis U-Component of Wind [m/s] wt ens-mean 002 10 m above ground VGRD analysis V-Component of Wind [m/s] wt ens-mean 003 1000 mb UGRD analysis U-Component of Wind [m/s] wt ens-mean 004 850 mb UGRD analysis U-Component of Wind [m/s] wt ens-mean 005 700 mb UGRD analysis U-Component of Wind [m/s] wt ens

Inventory of File sref.t03z.pgrb132.spread_3hrly.grib2

Science.gov Websites

ground UGRD analysis U-Component of Wind [m/s] std dev 002 10 m above ground VGRD analysis V-Component of Wind [m/s] std dev 003 1000 mb UGRD analysis U-Component of Wind [m/s] std dev 004 850 mb UGRD analysis U-Component of Wind [m/s] std dev 005 700 mb UGRD analysis U-Component of Wind [m/s] std dev 006 600

Inventory of File sref.t03z.pgrb132.mean_3hrly.grib2

Science.gov Websites

UGRD analysis U-Component of Wind [m/s] wt ens-mean 002 10 m above ground VGRD analysis V-Component of Wind [m/s] wt ens-mean 003 1000 mb UGRD analysis U-Component of Wind [m/s] wt ens-mean 004 850 mb UGRD analysis U-Component of Wind [m/s] wt ens-mean 005 700 mb UGRD analysis U-Component of Wind [m/s] wt ens

Testing primary-school children's understanding of the nature of science.

PubMed

Koerber, Susanne; Osterhaus, Christopher; Sodian, Beate

2015-03-01

Understanding the nature of science (NOS) is a critical aspect of scientific reasoning, yet few studies have investigated its developmental beginnings and initial structure. One contributing reason is the lack of an adequate instrument. Two studies assessed NOS understanding among third graders using a multiple-select (MS) paper-and-pencil test. Study 1 investigated the validity of the MS test by presenting the items to 68 third graders (9-year-olds) and subsequently interviewing them on their underlying NOS conception of the items. All items were significantly related between formats, indicating that the test was valid. Study 2 applied the same instrument to a larger sample of 243 third graders, and their performance was compared to a multiple-choice (MC) version of the test. Although the MC format inflated the guessing probability, there was a significant relation between the two formats. In summary, the MS format was a valid method revealing third graders' NOS understanding, thereby representing an economical test instrument. A latent class analysis identified three groups of children with expertise in qualitatively different aspects of NOS, suggesting that there is not a single common starting point for the development of NOS understanding; instead, multiple developmental pathways may exist. © 2014 The British Psychological Society.

Capturing the worlds of multiple sclerosis: Hannah Laycock's photography.

PubMed

Bolaki, Stella

2017-03-01

This essay explores UK photographer Hannah Laycock's Awakenings and, to a lesser extent, Perceiving Identity that were created in 2015, following her diagnosis with multiple sclerosis (MS) in 2013. It draws on scholarship by people with chronic illness while situating these two MS projects in the context of Laycock's earlier art and portrait photography dealing with fragility, image and desire, and power relations between subject and observer. The analysis illustrates how her evocative photography captures the lived or subjective experience of an invisible and often misunderstood condition by initially focusing on the tension between transparency and opacity in her work. It further shows how her images counter dominant didactic metaphors such as, 'the body as machine', that perpetuate the dehumanising and objectifying aspects of medical care. Subsequent sections trace the influence that Oliver Sacks has had on Laycock's practice, and reflect on other metaphors and tropes in Awakenings that illuminate the relationship between body and self in MS. The essay concludes by acknowledging the therapeutic power of art and calling upon health professionals to make more use of such artistic work in clinical practice. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Metabolomic Fingerprinting in Various Body Fluids of a Diet-Controlled Clinical Smoking Cessation Study Using a Validated GC-TOF-MS Metabolomics Platform.

PubMed

Goettel, Michael; Niessner, Reinhard; Mueller, Daniel; Scherer, Max; Scherer, Gerhard; Pluym, Nikola

2017-10-06

Untargeted GC-TOF-MS analysis proved to be a suitable analytical platform to determine alterations in the metabolic profile. Several metabolic pathways were found to be altered in a first clinical study comparing smokers against nonsmokers. Subsequently, we conducted a clinical diet-controlled study to investigate alterations in the metabolic profile during the course of 3 months of smoking cessation. Sixty male subjects were included in the study, and plasma, saliva, and urine samples were collected during four 24 h stationary visits: at baseline, while still smoking, after 1 week, after 1 month, and after 3 months of cessation. Additionally, subjects were monitored for their compliance by measurements of CO in exhaled breath and salivary cotinine throughout the study. GC-TOF-MS fingerprinting was applied to plasma, saliva, and urine samples derived from 39 compliant subjects. In total, 52 metabolites were found to be significantly altered including 26 in plasma, 20 in saliva, and 12 in urine, respectively. In agreement with a previous study comparing smokers and nonsmokers, the fatty acid and amino acid metabolism showed significant alterations upon 3 months of smoking cessation. Thus these results may indicate a partial recovery of metabolic pathway perturbations, even after a relatively short period of smoking cessation.

Multiplatform Mass Spectrometry-Based Approach Identifies Extracellular Glycolipids of the Yeast Rhodotorula babjevae UCDFST 04-877.

PubMed

Cajka, Tomas; Garay, Luis A; Sitepu, Irnayuli R; Boundy-Mills, Kyria L; Fiehn, Oliver

2016-10-28

A multiplatform mass spectrometry-based approach was used for elucidating extracellular lipids with biosurfactant properties produced by the oleaginous yeast Rhodotorula babjevae UCDFST 04-877. This strain secreted 8.6 ± 0.1 g/L extracellular lipids when grown in a benchtop bioreactor fed with 100 g/L glucose in medium without addition of hydrophobic substrate, such as oleic acid. Untargeted reversed-phase liquid chromatography-quadrupole/time-of-flight mass spectrometry (QTOFMS) detected native glycolipid molecules with masses of 574-716 Da. After hydrolysis into the fatty acid and sugar components and hydrophilic interaction chromatography-QTOFMS analysis, the extracellular lipids were found to consist of hydroxy fatty acids and sugar alcohols. Derivatization and chiral separation gas chromatography-mass spectrometry (GC-MS) identified these components as d-arabitol, d-mannitol, (R)-3-hydroxymyristate, (R)-3-hydroxypalmitate, and (R)-3-hydroxystearate. In order to assemble these substructures back into intact glycolipids that were detected in the initial screen, potential structures were in-silico acetylated to match the observed molar masses and subsequently characterized by matching predicted and observed MS/MS fragmentation using the Mass Frontier software program. Eleven species of acetylated sugar alcohol esters of hydroxy fatty acids were characterized for this yeast strain.

Mass Spectrometric Quantification of N-Linked Glycans by Reference to Exogenous Standards.

PubMed

Mehta, Nickita; Porterfield, Mindy; Struwe, Weston B; Heiss, Christian; Azadi, Parastoo; Rudd, Pauline M; Tiemeyer, Michael; Aoki, Kazuhiro

2016-09-02

Environmental and metabolic processes shape the profile of glycoprotein glycans expressed by cells, whether in culture, developing tissues, or mature organisms. Quantitative characterization of glycomic changes associated with these conditions has been achieved historically by reductive coupling of oligosaccharides to various fluorophores following release from glycoprotein and subsequent HPLC or capillary electrophoretic separation. Such labeling-based approaches provide a robust means of quantifying glycan amount based on fluorescence yield. Mass spectrometry, on the other hand, has generally been limited to relative quantification in which the contribution of the signal intensity for an individual glycan is expressed as a percent of the signal intensity summed over the total profile. Relative quantification has been valuable for highlighting changes in glycan expression between samples; sensitivity is high, and structural information can be derived by fragmentation. We have investigated whether MS-based glycomics is amenable to absolute quantification by referencing signal intensities to well-characterized oligosaccharide standards. We report the qualification of a set of N-linked oligosaccharide standards by NMR, HPLC, and MS. We also demonstrate the dynamic range, sensitivity, and recovery from complex biological matrices for these standards in their permethylated form. Our results indicate that absolute quantification for MS-based glycomic analysis is reproducible and robust utilizing currently available glycan standards.

EPA CRL MS014: Analysis of Aldicarb, Bromadiolone, Carbofuran, Oxamyl and Methomyl in Water by Multiple Reaction Monitoring Liquid Chromatography / Tandem Mass Spectrometry (LC/MS/MS)

EPA Pesticide Factsheets

Method MS014 describes procedures for solvent extraction of aldicarb, bromadiolone, carbofuran, oxamyl and methomyl from water samples, followed by analysis using liquid chromatography tandem mass spectrometry (LC-MS-MS).

A new approach in sample treatment combined with UHPLC-MS/MS for the determination of multiclass mycotoxins in edible nuts and seeds.

PubMed

Arroyo-Manzanares, Natalia; Huertas-Pérez, José F; Gámiz-Gracia, Laura; García-Campaña, Ana M

2013-10-15

A sensitive, simple and rapid method for the determination of fourteen mycotoxins in nuts and seeds (including almonds, peanuts, sunflower seeds, pumpkin seeds, walnuts, macadamia nuts, pistachios, hazelnuts and pine nuts) has been developed using ultra-high performance liquid chromatography coupled with tandem mass spectrometry (UHPLC-MS/MS). The sample treatment comprises a first step based on QuEChERS procedure for the determination of fumonisin B1, fumonisin B2, deoxynivalenol, fusarenon-X, T-2 and HT-2 toxin, citrinin, sterigmatocystin, zearalenone and ochratoxin A. A subsequent clean-up step based on the dispersive liquid-liquid microextraction (DLLME) was necessary for the determination of aflatoxins (B1, B2, G1 and G2), since their determination was not possible applying only the QuEChERS-based extraction. The method was validated for peanuts as representative matrix and was subsequently evaluated for the other eight matrices. Quantification limits obtained for aflatoxins, the unique mycotoxins legislated on these matrices, were lower than the maximum levels allowed by the current legislation, while quantification limits obtained for the other mycotoxins were lower than the limits usually permitted by the legislation in other food matrices. Precision of the method was always lower than 11%, and recoveries ranged between 60.7% and 104.3%. © 2013 Elsevier B.V. All rights reserved.

Estimation of Vs30 Soil Profile Structure of Singapore from Microtremor Records

NASA Astrophysics Data System (ADS)

Walling, M. Y.; Megawati, K.; Zhu, C.

2012-04-01

Singapore lies at the southern tip of the Malay Peninsula, covering a land area of 600 km2 and with a population exceeding 5 million. Array microtremor recording were carried out in Singapore for 40 sites that encompasses the sites of all the major geological formations. The Spatial Autocorrelation (SPAC) method is employed to determine the phase velocity dispersion curves and subsequently inverted to determine the shallow shear-wave velocity (V s) and soil stratigraphy. The depth of penetration is generally about 30 m - 40 m for most of the sites. For the present study, the V s estimation is restricted to the upper 30 m of the soil (V s30), confirming with the IBC (2006). The Reclaimed Land and the young Quaternary soft soil deposit of Kallang Formation show low V s30 values ranging from 207 m/s - 247 m/s, belonging to site E and at the boundary of site E and D. The Old Alluvium formation shows higher V s30 values ranging from 362 m/s - 563 m/s and can be classified under site C. The estimated V s30 for the sedimentary sequence of Jurong Formation reveal site C classification, with the V s30 range from 317 m/s - 712 m/s. On the other hand, the Bukit Timah Granite body shows low V s30 ranging from 225 m/s - 387 m/s, with most of the sites concentrated under site D classification and few sites at the boundary of sites D and C, for the upper 30 m. This low V s30 value of the granitic body can be explained in the light of intense weathering that the granite body has undergone for the upper layer, which is also supported from borehole records. The SPAC results are compared with nearby borehole data and they show a good correlation for sites that have soft soil formation and for the weathered granite body. The correlation confirms the reliability of SPAC method that can be applied for highly populated urbanized places like Singapore. The present research finding will be useful for further studies of site response analysis, site characterization and ground motion simulation.

Qualitative analysis of tackifier resins in pressure sensitive adhesives using direct analysis in real time time-of-flight mass spectrometry.

PubMed

Mess, Aylin; Vietzke, Jens-Peter; Rapp, Claudius; Francke, Wittko

2011-10-01

Tackifier resins play an important role as additives in pressure sensitive adhesives (PSAs) to modulate their desired properties. With dependence on their origin and processing, tackifier resins can be multicomponent mixtures. Once they have been incorporated in a polymer matrix, conventional chemical analysis of tackifiers usually tends to be challenging because a suitable sample pretreatment and/or separation is necessary and all characteristic components have to be detected for an unequivocal identification of the resin additive. Nevertheless, a reliable analysis of tackifiers is essential for product quality and safety reasons. A promising approach for the examination of tackifier resins in PSAs is the novel direct analysis in real time mass spectrometry (DART-MS) technique, which enables screening analysis without time-consuming sample preparation. In the present work, four key classes of tackifier resins were studied (rosin, terpene phenolic, polyterpene, and hydrocarbon resins). Their corresponding complex mass spectra were interpreted and used as reference spectra for subsequent analyses. These data were used to analyze tackifier additives in synthetic rubber and acrylic adhesive matrixes. To prove the efficiency of the developed method, complete PSA products containing two or three different tackifiers were analyzed. The tackifier resins were successfully identified, while measurement time and interpretation took less than 10 mins per sample. Determination of resin additives in PSAs can be performed down to 0.1% (w/w, limit of detection) using the three most abundant signals for each tackifier. In summary, DART-MS is a rapid and efficient screening method for the analysis of various tackifiers in PSAs.

Analytical variables affecting analysis of F2-isoprostanes and F4-neuroprostanes in human cerebrospinal fluid by gas chromatography/mass spectrometry.

PubMed

Yen, Hsiu-Chuan; Wei, Hsing-Ju; Chen, Ting-Wei

2013-01-01

F2-isoprostanes (F2-IsoPs) are a gold marker of lipid peroxidation in vivo, whereas F4-neuroprostanes (F4-NPs) measured in cerebrospinal fluid (CSF) or brain tissue selectively indicate neuronal oxidative damage. Gas chromatography/negative-ion chemical-ionization mass spectrometry (GC/NICI-MS) is the most sensitive and robust method for quantifying these compounds, which is essential for CSF samples because abundance of these compounds in CSF is very low. The present study revealed potential interferences on the analysis of F2-IsoPs and F4-NPs in CSF by GC/NICI-MS due to the use of improper analytical methods that have been employed in the literature. First, simultaneous quantification of F2-IsoPs and F4-NPs in CSF samples processed for F4-NPs analysis could cause poor chromatographic separation and falsely higher F2-IsoPs values for CSF samples with high levels of F2-IsoPs and F4-NPs. Second, retention of unknown substances in GC columns from CSF samples during F4-NPs analysis and from plasma samples during F2-IsoPs analysis might interfere with F4-NPs analysis of subsequent runs, which could be solved by holding columns at a high temperature for a period of time after data acquisition. Therefore, these special issues should be taken into consideration when performing analysis of F2-IsoPs and F4-NPs in CSF to avoid misleading results.

Analytical Variables Affecting Analysis of F2-Isoprostanes and F4-Neuroprostanes in Human Cerebrospinal Fluid by Gas Chromatography/Mass Spectrometry

PubMed Central

Yen, Hsiu-Chuan; Wei, Hsing-Ju; Chen, Ting-Wei

2013-01-01

F2-isoprostanes (F2-IsoPs) are a gold marker of lipid peroxidation in vivo, whereas F4-neuroprostanes (F4-NPs) measured in cerebrospinal fluid (CSF) or brain tissue selectively indicate neuronal oxidative damage. Gas chromatography/negative-ion chemical-ionization mass spectrometry (GC/NICI-MS) is the most sensitive and robust method for quantifying these compounds, which is essential for CSF samples because abundance of these compounds in CSF is very low. The present study revealed potential interferences on the analysis of F2-IsoPs and F4-NPs in CSF by GC/NICI-MS due to the use of improper analytical methods that have been employed in the literature. First, simultaneous quantification of F2-IsoPs and F4-NPs in CSF samples processed for F4-NPs analysis could cause poor chromatographic separation and falsely higher F2-IsoPs values for CSF samples with high levels of F2-IsoPs and F4-NPs. Second, retention of unknown substances in GC columns from CSF samples during F4-NPs analysis and from plasma samples during F2-IsoPs analysis might interfere with F4-NPs analysis of subsequent runs, which could be solved by holding columns at a high temperature for a period of time after data acquisition. Therefore, these special issues should be taken into consideration when performing analysis of F2-IsoPs and F4-NPs in CSF to avoid misleading results. PMID:23957004

DIGE compatible labelling of surface proteins on vital cells in vitro and in vivo.

PubMed

Mayrhofer, Corina; Krieger, Sigurd; Allmaier, Günter; Kerjaschki, Dontscho

2006-01-01

Efficient methods for profiling of the cell surface proteome are desirable to get a deeper insight in basic biological processes, to localise proteins and to uncover proteins differentially expressed in diseases. Here we present a strategy to target cell surface exposed proteins via fluorescence labelling using CyDye DIGE fluors. This method has been applied to human cell lines in vitro as well as to a complex biological system in vivo. It allows detection of fluorophore-tagged cell surface proteins and visualisation of the accessible proteome within a single 2-D gel, simplifying subsequent UV MALDI-MS analysis.

Insight into Identification of Acinetobacter Species by Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) in the Clinical Laboratory

NASA Astrophysics Data System (ADS)

Li, Xiuyuan; Tang, Yanyan; Lu, Xinxin

2018-04-01

Currently, the capability of identification for Acinetobacter species using MALDI-TOF MS still remains unclear in clinical laboratories due to certain elusory phenomena. Thus, we conducted this research to evaluate this technique and reveal the causes of misidentification. Briefly, a total of 788 Acinetobacter strains were collected and confirmed at the species level by 16S rDNA and rpoB sequencing, and subsequently compared to the identification by MALDI-TOF MS using direct smear and bacterial extraction pretreatments. Cluster analysis was performed based on the mass spectra and 16S rDNA to reflect the diversity among different species. Eventually, 19 Acinetobacter species were confirmed, including 6 species unavailable in Biotyper 3.0 database. Another novel species was observed, temporarily named A. corallinus. The accuracy of identification for Acinetobacter species using MALDI-TOF MS was 97.08% (765/788), regardless of which pretreatment was applied. The misidentification only occurred on 3 A. parvus strains and 20 strains of species unavailable in the database. The proportions of strains with identification score ≥ 2.000 using direct smear and bacterial extraction pretreatments were 86.04% (678/788) and 95.43% (752/788), χ 2 = 41.336, P < 0.001. The species similar in 16 rDNA were discriminative from the mass spectra, such as A. baumannii & A. junii, A. pittii & A. calcoaceticus, and A. nosocomialis & A. seifertii. Therefore, using MALDI-TOF MS to identify Acinetobacter strains isolated from clinical samples was deemed reliable. Misidentification occurred occasionally due to the insufficiency of the database rather than sample extraction failure. We suggest gene sequencing should be performed when the identification score is under 2.000 even when using bacterial extraction pretreatment. [Figure not available: see fulltext.

Gestational diabetes mellitus and the risk of metabolic syndrome: a population-based study in Lausanne, Switzerland.

PubMed

Noussitou, P; Monbaron, D; Vial, Y; Gaillard, R C; Ruiz, J

2005-09-01

To investigate the relationships between gestational diabetes mellitus (GDM) and the metabolic syndrome (MS), as it was suggested that insulin resistance was the hallmark of both conditions. To analyse post-partum screening in order to identify risk factors for the subsequent development of type 2 diabetes mellitus (DM). A retrospective analysis of all singleton pregnancies diagnosed with GDM at the Lausanne University Hospital for 3 consecutive years. Pre-pregnancy obesity, hypertension and dyslipidaemia were recorded as constituents of the MS. For 5788 deliveries, 159 women (2.7%) with GDM were identified. Constituents of the MS were present before GDM pregnancy in 26% (n = 37/144): 84% (n = 31/37) were obese, 38% (n = 14/37) had hypertension and 22% (n = 8/37) had dyslipidaemia. Gestational hypertension was associated with obesity (OR = 3.2, P = 0.02) and dyslipidaemia (OR = 5.4, P=0.002). Seventy-four women (47%) returned for post-partum OGTT, which was abnormal in 20 women (27%): 11% (n = 8) had type 2 diabetes and 16% (n = 12) had impaired glucose tolerance. Independent predictors of abnormal glucose tolerance in the post-partum were: having > 2 abnormal values on the diagnostic OGTT during pregnancy and presenting MS constituents (OR = 5.2, CI 1.8-23.2 and OR = 5.3, CI 1.3-22.2). In one fourth of GDM pregnancies, metabolic abnormalities precede the appearance of glucose intolerance. These women have a high risk of developing the MS and type 2 diabetes in later years. Where GDM screening is not universal, practitioners should be aware of those metabolic risks in every pregnant woman presenting with obesity, hypertension or dyslipidaemia, in order to achieve better diagnosis and especially better post-partum follow-up and treatment.

Insight into Identification of Acinetobacter Species by Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) in the Clinical Laboratory.

PubMed

Li, Xiuyuan; Tang, Yanyan; Lu, Xinxin

2018-04-09

Currently, the capability of identification for Acinetobacter species using MALDI-TOF MS still remains unclear in clinical laboratories due to certain elusory phenomena. Thus, we conducted this research to evaluate this technique and reveal the causes of misidentification. Briefly, a total of 788 Acinetobacter strains were collected and confirmed at the species level by 16S rDNA and rpoB sequencing, and subsequently compared to the identification by MALDI-TOF MS using direct smear and bacterial extraction pretreatments. Cluster analysis was performed based on the mass spectra and 16S rDNA to reflect the diversity among different species. Eventually, 19 Acinetobacter species were confirmed, including 6 species unavailable in Biotyper 3.0 database. Another novel species was observed, temporarily named A. corallinus. The accuracy of identification for Acinetobacter species using MALDI-TOF MS was 97.08% (765/788), regardless of which pretreatment was applied. The misidentification only occurred on 3 A. parvus strains and 20 strains of species unavailable in the database. The proportions of strains with identification score ≥ 2.000 using direct smear and bacterial extraction pretreatments were 86.04% (678/788) and 95.43% (752/788), χ 2  = 41.336, P < 0.001. The species similar in 16 rDNA were discriminative from the mass spectra, such as A. baumannii & A. junii, A. pittii & A. calcoaceticus, and A. nosocomialis & A. seifertii. Therefore, using MALDI-TOF MS to identify Acinetobacter strains isolated from clinical samples was deemed reliable. Misidentification occurred occasionally due to the insufficiency of the database rather than sample extraction failure. We suggest gene sequencing should be performed when the identification score is under 2.000 even when using bacterial extraction pretreatment. Graphical Abstract ᅟ.

Complete automation of solid-phase extraction with subsequent liquid chromatography-tandem mass spectrometry for the quantification of benzoylecgonine, m-hydroxybenzoylecgonine, p-hydroxybenzoylecgonine, and norbenzoylecgonine in urine--application to a high-throughput urine analysis laboratory.

PubMed

Robandt, Paul P; Reda, Louis J; Klette, Kevin L

2008-10-01

A fully automated system utilizing a liquid handler and an online solid-phase extraction (SPE) device coupled with liquid chromatography-tandem mass spectrometry (LC-MS-MS) was designed to process, detect, and quantify benzoylecgonine (BZE), meta-hydroxybenzoylecgonine (m-OH BZE), para-hydroxybenzoylecgonine (p-OH BZE), and norbenzoylecgonine (nor-BZE) metabolites in human urine. The method was linear for BZE, m-OH BZE, and p-OH BZE from 1.2 to 10,000 ng/mL with limits of detection (LOD) and quantification (LOQ) of 1.2 ng/mL. Nor-BZE was linear from 5 to 10,000 ng/mL with an LOD and LOQ of 1.2 and 5 ng/mL, respectively. The intrarun precision measured as the coefficient of variation of 10 replicates of a 100 ng/mL control was less than 2.6%, and the interrun precision for 5 replicates of the same control across 8 batches was less than 4.8% for all analytes. No assay interference was noted from controls containing cocaine, cocaethylene, and ecgonine methyl ester. Excellent data concordance (R2 > 0.994) was found for direct comparison of the automated SPE-LC-MS-MS procedure and an existing gas chromatography-MS procedure using 94 human urine samples previously determined to be positive for BZE. The automated specimen handling and SPE procedure, when compared to the traditional extraction schema, eliminates the human factors of specimen handling, processing, extraction, and derivatization, thereby reducing labor costs and rework resulting from batch handling issues, and may reduce the number of fume hoods required in the laboratory.

Treadmill Training or Progressive Strength Training to Improve Walking in People with Multiple Sclerosis? A Randomized Parallel Group Trial.

PubMed

Braendvik, Siri Merete; Koret, Teija; Helbostad, Jorunn L; Lorås, Håvard; Bråthen, Geir; Hovdal, Harald Olav; Aamot, Inger Lise

2016-12-01

The most effective treatment approach to improve walking in people with multiple sclerosis (MS) is not known. The aim of this trial was to assess the efficacy of treadmill training and progressive strength training on walking in people with MS. A single blinded randomized parallel group trial was carried out. Eligible participants were adults with MS with Expanded Disability Status Scale score ≤6. A total of 29 participants were randomized and 28 received the allocated exercise intervention, treadmill (n = 13) or strength training (n = 15). Both groups exercised 30 minutes, three times a week for 8 weeks. Primary outcome was The Functional Ambulation Profile evaluated by the GAITRite walkway. Secondary outcomes were walking work economy and balance control during walking, measured by a small lightweight accelerometer connected to the lower back. Testing was performed at baseline and the subsequent week after completion of training. Two participants were lost to follow-up, and 11 (treadmill) and 15 (strength training) were left for analysis. The treadmill group increased their Functional Ambulation Profile score significantly compared with the strength training group (p = .037). A significant improvement in walking work economy (p = .024) and a reduction of root mean square of vertical acceleration (p = .047) also favoured the treadmill group. The results indicate that task-specific training by treadmill walking is a favourable approach compared with strength training to improve walking in persons with mild and moderate MS. Implications for Physiotherapy practice, this study adds knowledge for the decision of optimal treatment approaches in people with MS. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 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.

Pericardial Fat is Associated With Atrial Conduction: The Framingham Heart Study

PubMed Central

Friedman, Daniel J.; Wang, Na; Meigs, James B.; Hoffmann, Udo; Massaro, Joseph M.; Fox, Caroline S.; Magnani, Jared W.

2014-01-01

Background Obesity is associated with altered atrial electrophysiology and a prominent risk factor for atrial fibrillation. Body mass index, the most widely used adiposity measure, has been related to atrial electrical remodeling. We tested the hypothesis that pericardial fat is independently associated with electrocardiographic measures of atrial conduction. Methods and Results We performed a cross‐sectional analysis of 1946 Framingham Heart Study participants (45% women) to determine the relation between pericardial fat and atrial conduction as measured by P wave indices (PWI): PR interval, P wave duration (P‐duration), P wave amplitude (P‐amplitude), P wave area (P‐area), and P wave terminal force (P‐terminal). We performed sex‐stratified linear regression analyses adjusted for relevant clinical variables and ectopic fat depots. Each 1‐SD increase in pericardial fat was significantly associated with PR interval (β=1.7 ms, P=0.049), P‐duration (β=2.3 ms, P<0.001), and P‐terminal (β=297 μV·ms, P<0.001) among women; and P‐duration (β=1.2 ms, P=0.002), P‐amplitude (β=−2.5 μV, P<0. 001), and P‐terminal (β=160 μV·ms, P=0.002) among men. Among both sexes, pericardial fat was significantly associated with P‐duration in analyses additionally adjusting for visceral fat or intrathoracic fat; a similar but non‐significant trend existed with P‐terminal. Among women, pericardial fat was significantly associated with P wave area after adjustment for visceral and intrathoracic fat. Conclusions Pericardial fat is associated with atrial conduction as quantified by PWI, even with adjustment for extracardiac fat depots. Further studies are warranted to identify the mechanisms through which pericardial fat may modify atrial electrophysiology and promote subsequent risk for arrhythmogenesis. PMID:24595189

Relationship between improvement in left ventricular dyssynchrony and contractile function and clinical outcome with cardiac resynchronization therapy: the MADIT-CRT trial.

PubMed

Pouleur, Anne-Catherine; Knappe, Dorit; Shah, Amil M; Uno, Hajime; Bourgoun, Mikhail; Foster, Elyse; McNitt, Scott; Hall, W Jackson; Zareba, Wojciech; Goldenberg, Ilan; Moss, Arthur J; Pfeffer, Marc A; Solomon, Scott D

2011-07-01

To assess long-term effects of cardiac resynchronization therapy (CRT) on left ventricular (LV) dyssynchrony and contractile function, by two-dimensional speckle-tracking echocardiography, compared with implantable cardioverter defibrillator (ICD) only in MADIT-CRT. We studied 761 patients in New York Heart Association I/II, ejection fraction ≤30%, and QRS ≥130 ms [n = 434, CRT-defibrillator (CRT-D), n = 327, ICD] with echocardiographic studies available at baseline and 12 months. Dyssynchrony was determined as the standard deviation of time to peak transverse strain between 12 segments of apical four- and two-chamber views, and contractile function as global longitudinal strain (GLS) by averaging longitudinal strain over these 12 segments. We compared changes in LV dyssynchrony and contractile function between treatment groups and assessed relationships between these changes over the first year and subsequent outcomes (median post 1-year follow-up = 14.9 months). Mean changes in LV dyssynchrony and contractile function measured by GLS in the overall population were, respectively, -29 ± 83 ms and -1 ± 2.9%. However, both LV dyssynchrony (CRT-D: -47 ± 83 ms vs. ICD: -6 ± 76 ms, P < 0.001) and contractile function (CRT-D: -1.4 ± 3.1% vs. ICD: -0.4 ± 2.5%, P < 0.001) improved to a greater extent in the CRT-D group compared with the ICD-only group. A greater improvement in dyssynchrony and contractile function at 1 year was associated with lower rates of the subsequent primary outcome of death or heart failure, adjusting for baseline dyssynchrony and contractile function, treatment arm, ischaemic status, and change in LV end-systolic volume. Each 20 ms decrease in LV dyssynchrony was associated with a 7% reduction in the primary outcome (P = 0.047); each 1% improvement in GLS over the 12-month period was associated with a 24% reduction in the primary outcome (P < 0.001). Cardiac resynchronization therapy resulted in a significant improvement in both LV dyssynchrony and contractile function measured by GLS compared with ICD only and these improvements were associated with better subsequent outcomes.

Recovery of peripheral muscle function from fatiguing exercise and daily physical activity level in patients with multiple sclerosis: a case-control study.

PubMed

Ickmans, Kelly; Simoens, Fauve; Nijs, Jo; Kos, Daphne; Cras, Patrick; Willekens, Barbara; Meeus, Mira

2014-07-01

Delayed recovery of muscle function following exercise has been demonstrated in the lower limbs of patients with multiple sclerosis (MS). However, studies examining this in the upper limbs are currently lacking. This study compared physical activity level (PAL) and recovery of upper limb muscle function following exercise between MS patients and healthy inactive controls. Furthermore, the relationship between PAL and muscle recovery was examined. PAL of 19 MS patients and 32 controls was measured using an accelerometer for 7 consecutive days. Afterwards, recovery of muscle function was assessed by performing a fatiguing upper limb exercise test with subsequent recovery measures. Muscle recovery of the upper limb muscles was similar in both groups. Average activity counts were significantly lower in MS patients than in the control group. MS patients spent significantly more time being sedentary and less time on activities of moderate intensity compared with the control group. No significant correlation between PAL and recovery of muscle function was found in MS patients. Recovery of upper limb muscle function following exercise is normal in MS patients. MS patients are less physically active than healthy inactive controls. PAL and recovery of upper limb muscle function appear unrelated in MS patients. Copyright © 2014 Elsevier B.V. All rights reserved.

Comparison of HPLC and CE for the analysis of dichlorprop in a case of intoxication.

PubMed

West, A; Frost, M; Köhler, H

1997-01-01

A 49-year-old white male was found lying unconscious at home. He had vomited, his mouth was filled with a white foam and a pungent odour filled the room. After emergency treatment blood, urine and stomach contents were screened for drugs after acid and alkaline extraction with subsequent derivatisation and GC-MS analysis. Large quantites of 2,4-dichlorophenoxypropionic acid (dichlorprop, 2,4-DP) were found in all acid extracts. The man died 3 h later in hospital. Body fluids and tissues obtained at autopsy were analysed for 2,4-DP by high-performance liquid chromatography and capillary electrophoresis. The concentrations of 2,4-DP in cardiac blood, stomach contents, bile, liver, spleen, kidney and brain found by both methods were very similar.

An Optimized Informatics Pipeline for Mass Spectrometry-Based Peptidomics

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

Wu, Chaochao; Monroe, Matthew E.; Xu, Zhe

2015-12-26

Comprehensive MS analysis of peptidome, the intracellular and intercellular products of protein degradation, has the potential to provide novel insights on endogenous proteolytic processing and their utility in disease diagnosis and prognosis. Along with the advances in MS instrumentation, a plethora of proteomics data analysis tools have been applied for direct use in peptidomics; however an evaluation of the currently available informatics pipelines for peptidomics data analysis has yet to be reported. In this study, we set off by evaluating the results of several popular MS/MS database search engines including MS-GF+, SEQUEST and MS-Align+ for peptidomics data analysis, followed bymore » identification and label-free quantification using the well-established accurate mass and time (AMT) tag and newly developed informed quantification (IQ) approaches, both based on direct LC-MS analysis. Our result demonstrated that MS-GF+ outperformed both SEQUEST and MS-Align+ in identifying peptidome peptides. Using a database established from the MS-GF+ peptide identifications, both the AMT tag and IQ approaches provided significantly deeper peptidome coverage and less missing value for each individual data set than the MS/MS methods, while achieving robust label-free quantification. Besides having an excellent correlation with the AMT tag quantification results, IQ also provided slightly higher peptidome coverage than AMT. Taken together, we propose an optimal informatics pipeline combining MS-GF+ for initial database searching with IQ (or AMT) for identification and label-free quantification for high-throughput, comprehensive and quantitative peptidomics analysis.« less

Unassigned MS/MS Spectra: Who Am I?

PubMed

Pathan, Mohashin; Samuel, Monisha; Keerthikumar, Shivakumar; Mathivanan, Suresh

2017-01-01

Recent advances in high resolution tandem mass spectrometry (MS) has resulted in the accumulation of high quality data. Paralleled with these advances in instrumentation, bioinformatics software have been developed to analyze such quality datasets. In spite of these advances, data analysis in mass spectrometry still remains critical for protein identification. In addition, the complexity of the generated MS/MS spectra, unpredictable nature of peptide fragmentation, sequence annotation errors, and posttranslational modifications has impeded the protein identification process. In a typical MS data analysis, about 60 % of the MS/MS spectra remains unassigned. While some of these could attribute to the low quality of the MS/MS spectra, a proportion can be classified as high quality. Further analysis may reveal how much of the unassigned MS spectra attribute to search space, sequence annotation errors, mutations, and/or posttranslational modifications. In this chapter, the tools used to identify proteins and ways to assign unassigned tandem MS spectra are discussed.

Healthcare resource utilization following switch or discontinuation in multiple sclerosis patients on disease modifying drugs.

PubMed

Reynolds, Matthew W; Stephen, Reejis; Seaman, Chris; Rajagopalan, Kitty

2010-03-01

The objective of this study was to explore the cost and utilization in the period following discontinuations or switches of disease modifying drugs (DMDs) for patients with multiple sclerosis (MS). Secondary objectives included an assessment of the time to switch or discontinuation from index DMD treatment. Cases were defined as a billed MS diagnosis in continuously enrolled patients initiated with interferon-beta1a IM, interferon-beta1b SC, glatiramer acetate, and interferon-beta1a SC found in the PharMetrics Patient-Centric Database. Information on patient demographics, diagnoses, procedures, pharmacy-dispensed drugs, and costs was extracted; reasons for discontinuation and expenses outside of the healthcare system were not available. Treatment discontinuations and switches between study drugs were defined using pharmacy prescription patterns and analyzed by descriptive and regression methods. The non-pharmacy medical costs in the 18 months following switching or discontinuation were compared to the costs in a randomly selected similar period for those patients who did not switch or discontinue these agents. A total of 5,772 MS patients were continuously enrolled and were treated with one or more of the four drugs of interest, and about half of these patients switched drugs or discontinued treatment for at least 90 days. Patients initiated with interferon-beta1b SC were more likely to discontinue treatment compared to interferon-beta1a IM users. Non-pharmaceutical medical costs were highest for those switching treatments followed by those discontinuing DMDs in the 18 months following a switch or discontinuation, compared to persistent users of these drugs. Interferon beta1b SC initiators had higher costs following changes or discontinuations, while glatiramer acetate and interferon-beta1a SC users had lower subsequent costs compared to interferon-beta1a IM users. Unfortunately, the reasons for stopping the initial treatment cannot be determined from analysis of an administrative claims database. Also, the MS cases followed in this analysis are billing diagnostic events unconfirmed through a review of medical records or other data sources. The results are unstratified in terms of severity and thus while treatment patterns may vary for patients with different types of MS (e.g., progressive vs. relapsing-remitting), this cannot be examined in this analysis. Changing or discontinuing DMDs is common among MS patients and is associated with higher non-pharmaceutical medical costs that vary based on the initiating drug and other demographics characteristics.

Mental stress-induced ischemia in patients with coronary artery disease: echocardiographic characteristics and relation to exercise-induced ischemia.

PubMed

Stepanovic, Jelena; Ostojic, Miodrag; Beleslin, Branko; Vukovic, Olivera; Djordjevic-Dikic, Ana; Dikic, Ana Djordjevic; Giga, Vojislav; Nedeljkovic, Ivana; Nedeljkovic, Milan; Stojkovic, Sinisa; Vukcevic, Vladan; Dobric, Milan; Petrasinovic, Zorica; Marinkovic, Jelena; Lecic-Tosevski, Dusica

2012-09-01

The aims of this study were to investigate the incidence and parameters associated with myocardial ischemia during mental stress (MS) as measured by echocardiography and to evaluate the relation between MS-induced and exercise-induced myocardial ischemia. Study participants were 79 patients (63 men; mean [M] [standard deviation {SD}] age = 52 [8] years) with angiographically confirmed coronary artery disease and previous positive exercise test result. The MS protocol consisted of mental arithmetic and anger recall task. The patients performed a treadmill exercise test 15 to 20 minutes after the MS task. Data of post-MS exercise were compared with previous exercise stress test results. The frequency of echocardiographic abnormalities was 35% in response to the mental arithmetic task, compared with 61% with anger recall and 96% with exercise (p < .001, exercise versus MS). Electrocardiogram abnormalities and chest pain were substantially less common during MS than were echocardiographic abnormalities. Independent predictors of MS-induced myocardial ischemia were: wall motion score index at rest (p = .02), peak systolic blood pressure (p = .005), and increase in rate-pressure product (p = .004) during MS. The duration of exercise stress test was significantly shorter (p < .001) when MS preceded the exercise and in the case of earlier exercise (M [SD] = 4.4 [1.9] versus 6.7 [2.2] minutes for patients positive on MS and 5.7 [1.9] versus 8.0 [2.3] minutes for patients negative on MS). Echocardiography can be successfully used to document myocardial ischemia induced by MS. MS-induced ischemia was associated with an increase in hemodynamic parameters during MS and worse function of the left ventricle. MS may shorten the duration of subsequent exercise stress testing and can potentiate exercise-induced ischemia in susceptible patients with coronary artery disease.

LC-MS/MS strategies for therapeutic antibodies and investigation into the quantitative impact of antidrug-antibodies.

PubMed

Ewles, Matthew; Mannu, Ranbir; Fox, Chris; Stanta, Johannes; Evans, Graeme; Goodwin, Lee; Duffy, James; Bell, Len; Estdale, Sian; Firth, David

2016-12-01

We aimed to establish novel, high-throughput LC-MS/MS strategies for quantification of monoclonal antibodies in human serum and examine the potential impact of antidrug antibodies. We present two strategies using a thermally stable immobilized trypsin. The first strategy uses whole serum digestion and the second introduces Protein G enrichment to improve the selectivity. The impact of anti-trastuzumab antibodies on the methods was tested. Whole serum digestion has been validated for trastuzumab (LLOQ 0.25 µg/ml). Protein G enrichment has been validated for trastuzumab (LLOQ 0.1 µg/ml), bevacizumab (LLOQ 0.1 µg/ml) and adalimumab (LLOQ 0.25 µg/ml). We have shown the potential for anti-drug antibodies to impact on the quantification and we have subsequently established a strategy to overcome this impact where total quantification is desired.

A new calibrant for MALDI-TOF-TOF-PSD-MS/MS of non-digested proteins for top-down proteomic analysis

USDA-ARS?s Scientific Manuscript database

RATIONALE: Matrix-assisted laser desorption/ionization (MALDI) time-of-flight-time-of-flight (TOF-TOF) tandem mass spectrometry (MS/MS) has seen increasing use for post-source decay (PSD)-MS/MS analysis of non-digested protein ions for top-down proteomic identification. However, there is no commonl...

Quality evaluation of LC-MS/MS-based E. coli H antigen typing (MS-H) through label-free quantitative data analysis in a clinical sample setup.

PubMed

Cheng, Keding; Sloan, Angela; McCorrister, Stuart; Peterson, Lorea; Chui, Huixia; Drebot, Mike; Nadon, Celine; Knox, J David; Wang, Gehua

2014-12-01

The need for rapid and accurate H typing is evident during Escherichia coli outbreak situations. This study explores the transition of MS-H, a method originally developed for rapid H antigen typing of E. coli using LC-MS/MS of flagella digest of reference strains and some clinical strains, to E. coli isolates in clinical scenario through quantitative analysis and method validation. Motile and nonmotile strains were examined in batches to simulate clinical sample scenario. Various LC-MS/MS batch run procedures and MS-H typing rules were compared and summarized through quantitative analysis of MS-H data output for a standard method development. Label-free quantitative data analysis of MS-H typing was proven very useful for examining the quality of MS-H result and the effects of some sample carryovers from motile E. coli isolates. Based on this, a refined procedure and protein identification rule specific for clinical MS-H typing was established and validated. With LC-MS/MS batch run procedure and database search parameter unique for E. coli MS-H typing, the standard procedure maintained high accuracy and specificity in clinical situations, and its potential to be used in a clinical setting was clearly established. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The influence of different hormone concentration and combination on callus induction and regeneration of Rauwolfia serpentina L. Benth.

PubMed

Salma, U; Rahman, M S M; Islam, S; Haque, N; Jubair, T A; Haque, A K M F; Mukti, I J

2008-06-15

The influence of media composition on callus induction and subsequent regeneration of Rauwolfia serpentina L. Benth has been studied. High frequency (96.43%) callus induction was obtained when nodal segments from in vitro raised shoots were cultured on MS medium supplemented with 0.5 mg L(-1) BA and 2.0 mg L(-1) NAA. The callus differentiated into adventitious shoots when it was subcultured on MS medium supplemented with 2.0 mg L(-1) BA with 0.2 mg L(-1) NAA. Regenerated shoots were best rooted on half-strength MS medium with 1.0 mg L(-1) each of IBA and IAA.

Evaluating the capabilities of aerosol-to-liquid particle extraction system (ALPXS)/ICP-MS for monitoring trace metals in indoor air.

PubMed

Jayawardene, Innocent; Rasmussen, Pat E; Chenier, Marc; Gardner, H David

2014-09-01

This study investigates the application of the Aerosol-to-Liquid Particle Extraction System (ALPXS), which uses wet electrostatic precipitation to collect airborne particles, for multi-element indoor stationary monitoring. Optimum conditions are determined for capturing airborne particles for metal determination by inductively coupled plasma-mass spectrometry (ICP-MS), for measuring field blanks, and for calculating limits of detection (LOD) and quantification (LOQ). Due to the relatively high flow rate (300 L min(-1)), a sampling duration of 1 hr to 2 hr was adequate to capture airborne particle-bound metals under the investigated experimental conditions. The performance of the ALPXS during a building renovation demonstrated signal-to-noise ratios appropriate for sampling airborne particles in environments with elevated metal concentrations, such as workplace settings. The ALPXS shows promise as a research tool for providing useful information on short-term variations (transient signals) and for trapping particles into aqueous solutions where needed for subsequent characterization. As the ALPXS does not provide size-specific samples, and its efficiency at different flow rates has yet to be quantified, the ALPXS would not replace standard filter-based protocols accepted for regulatory applications (e.g., exposure measurements), but rather would provide additional information if used in conjunction with filter based methods. Implications: This study investigates the capability of the Aerosol-to-Liquid Particle Extraction System (ALPXS) for stationary sampling of airborne metals in indoor workplace environments, with subsequent analysis by ICP-MS. The high flow rate (300 L/min) permits a short sampling duration (< 2 hr). Results indicated that the ALPXS was capable of monitoring short-term changes in metal emissions during a renovation activity. This portable instrument may prove to be advantageous in occupational settings as a qualitative indicator of elevated concentrations of airborne metals at short time scales.

Microwave-assisted wet digestion with H2O2 at high temperature and pressure using single reaction chamber for elemental determination in milk powder by ICP-OES and ICP-MS.

PubMed

Muller, Edson I; Souza, Juliana P; Muller, Cristiano C; Muller, Aline L H; Mello, Paola A; Bizzi, Cezar A

2016-08-15

In this work a green digestion method which only used H2O2 as an oxidant and high temperature and pressure in the single reaction chamber system (SRC-UltraWave™) was applied for subsequent elemental determination by inductively coupled plasma-based techniques. Milk powder was chosen to demonstrate the feasibility and advantages of the proposed method. Samples masses up to 500mg were efficiently digested, and the determination of Ca, Fe, K, Mg and Na was performed by inductively coupled plasma optical emission spectrometry (ICP-OES), while trace elements (B, Ba, Cd, Cu, Mn, Mo, Pb, Sr and Zn) were determined by inductively coupled plasma mass spectrometry (ICP-MS). Residual carbon (RC) lower than 918mgL(-1) of C was obtained for digests which contributed to minimizing interferences in determination by ICP-OES and ICP-MS. Accuracy was evaluated using certified reference materials NIST 1549 (non-fat milk powder certified reference material) and NIST 8435 (whole milk powder reference material). The results obtained by the proposed method were in agreement with the certified reference values (t-test, 95% confidence level). In addition, no significant difference was observed between results obtained by the proposed method and conventional wet digestion using concentrated HNO3. As digestion was performed without using any kind of acid, the characteristics of final digests were in agreement with green chemistry principles when compared to digests obtained using conventional wet digestion method with concentrated HNO3. Additionally, H2O2 digests were more suitable for subsequent analysis by ICP-based techniques due to of water being the main product of organic matrix oxidation. The proposed method was suitable for quality control of major components and trace elements present in milk powder in consonance with green sample preparation. Copyright © 2016 Elsevier B.V. All rights reserved.

Toward artifact-free data in Hadamard transform-based double multiplexing of ion mobility-Orbitrap mass spectrometry

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

Tummalacherla, Meghasyam; Garimella, Sandilya V. B.; Prost, Spencer A.

The integration of ion mobility spectrometry (IMS) with trap-based mass spectrometer (MS) such as Orbitrap using the dual gate approach suffers from low duty cycle. Efforts to improve the duty cycle involve the utilization of Hadamard transform based double multiplexing which significantly improve the signal to noise ratio and duty cycle of the ion mobility – Orbitrap mass spectrometry (IM – Orbitrap MS) platform. However, significant fluctuations in ion intensity and the temporal shifts in the encoded data give rise to artifacts and noise in the demultiplexed data which significantly reduce the data quality and negate the benefits of multiplexing.more » We propose a new approach that identifies the true IM peaks and helps in eliminating the artifacts in the demultiplexed data leading to a decrease in false positives in subsequent data processing. The algorithm takes an analytical approach to first identify the position of the IM peak in the temporal domain, and then demultiplex and identify the true data making it easier for subsequent data processing. After the application of the algorithm, the quality of the IM-Orbitrap MS measurements was greatly improved because of the reduction in artifacts.« less

Successful adaption of a forensic toxicological screening workflow employing nontargeted liquid chromatography-tandem mass spectrometry to water analysis.

PubMed

Steger, Julia; Arnhard, Kathrin; Haslacher, Sandra; Geiger, Klemens; Singer, Klaus; Schlapp, Michael; Pitterl, Florian; Oberacher, Herbert

2016-04-01

Forensic toxicology and environmental water analysis share the common interest and responsibility in ensuring comprehensive and reliable confirmation of drugs and pharmaceutical compounds in samples analyzed. Dealing with similar analytes, detection and identification techniques should be exchangeable between scientific disciplines. Herein, we demonstrate the successful adaption of a forensic toxicological screening workflow employing nontargeted LC/MS/MS under data-dependent acquisition control and subsequent database search to water analysis. The main modification involved processing of an increased sample volume with SPE (500 mL vs. 1-10 mL) to reach LODs in the low ng/L range. Tandem mass spectra acquired with a qTOF instrument were submitted to database search. The targeted data mining strategy was found to be sensitive and specific; automated search produced hardly any false results. To demonstrate the applicability of the adapted workflow to complex samples, 14 wastewater effluent samples collected on seven consecutive days at the local wastewater-treatment plant were analyzed. Of the 88,970 fragment ion mass spectra produced, 8.8% of spectra were successfully assigned to one of the 1040 reference compounds included in the database, and this enabled the identification of 51 compounds representing important illegal drugs, members of various pharmaceutical compound classes, and metabolites thereof. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Calcium oxalate crystals increased enolase-1 secretion from renal tubular cells that subsequently enhanced crystal and monocyte invasion through renal interstitium.

PubMed

Chiangjong, Wararat; Thongboonkerd, Visith

2016-04-05

Calcium oxalate monohydrate (COM) crystals cause kidney stone disease by still unclear mechanisms. The present study aimed to characterize changes in secretion of proteins from basolateral compartment of renal tubular epithelial cells after exposure to COM crystals and then correlated them with the stone pathogenesis. Polarized MDCK cells were cultivated in serum-free medium with or without 100 μg/ml COM crystals for 20 h. Secreted proteins collected from the lower chamber (basolateral compartment) were then resolved in 2-D gels and visualized by Deep Purple stain (n = 5 gels/group). Spot matching and intensity analysis revealed six protein spots with significantly altered levels in COM-treated samples. These proteins were then identified by tandem mass spectrometry (Q-TOF MS/MS), including enolase-1, phosphoglycerate mutase-1, actinin, 14-3-3 protein epsilon, alpha-tubulin 2, and ubiquitin-activating enzyme E1. The increased enolase-1 level was confirmed by Western blot analysis. Functional analysis revealed that enolase-1 dramatically induced COM crystal invasion through ECM migrating chamber in a dose-dependent manner. Moreover, enolase-1 bound onto U937 monocytic cell surface markedly enhanced cell migration through the ECM migrating chamber. In summary, our data indicated that the increased secretory enolase-1 induced by COM crystals played an important role in crystal invasion and inflammatory process in renal interstitium.

Building blocks for the development of an interface for high-throughput thin layer chromatography/ambient mass spectrometric analysis: a green methodology.

PubMed

Cheng, Sy-Chyi; Huang, Min-Zong; Wu, Li-Chieh; Chou, Chih-Chiang; Cheng, Chu-Nian; Jhang, Siou-Sian; Shiea, Jentaie

2012-07-17

Interfacing thin layer chromatography (TLC) with ambient mass spectrometry (AMS) has been an important area of analytical chemistry because of its capability to rapidly separate and characterize the chemical compounds. In this study, we have developed a high-throughput TLC-AMS system using building blocks to deal, deliver, and collect the TLC plate through an electrospray-assisted laser desorption ionization (ELDI) source. This is the first demonstration of the use of building blocks to construct and test the TLC-MS interfacing system. With the advantages of being readily available, cheap, reusable, and extremely easy to modify without consuming any material or reagent, the use of building blocks to develop the TLC-AMS interface is undoubtedly a green methodology. The TLC plate delivery system consists of a storage box, plate dealing component, conveyer, light sensor, and plate collecting box. During a TLC-AMS analysis, the TLC plate was sent to the conveyer from a stack of TLC plates placed in the storage box. As the TLC plate passed through the ELDI source, the chemical compounds separated on the plate would be desorbed by laser desorption and subsequently postionized by electrospray ionization. The samples, including a mixture of synthetic dyes and extracts of pharmaceutical drugs, were analyzed to demonstrate the capability of this TLC-ELDI/MS system for high-throughput analysis.

More than 170 polyunsaturated tocopherol-related compounds in a vitamin E capsule: Countercurrent chromatographic enrichment, gas chromatography/mass spectrometry analysis and preliminary identification of the potential artefacts.

PubMed

Hammann, Simon; Kröpfl, Alexander; Vetter, Walter

2016-12-09

Tocopherols and tocotrienols (usually summed up as vitamin E) are a class of structurally related natural antioxidants. Commonly, only some of the eight classic representatives (four tocopherols and four tocotrienols) are found with varied composition in food. In this study we fractionated 230mg oil from commercial vitamin E supplement capsules by countercurrent chromatography (CCC) and subsequent analysis by gas chromatography with mass spectrometry (GC/MS) of silylated CCC fractions showed that these eight isomers represented only about 70% of total tocopherol compounds. Detailed analysis enabled the detection of 161T 3 isomers (α-, γ- and δ-T 3 ) along with 18 tetra- and several penta-unsaturated isomers (tocools), two tocomonoenol isomers, and several degradation products with shorter isoprenoid side chain (apo-tocools). Altogether, over 170 tocool compounds, most likely artefacts which originated from an inappropriate oil refining process were described in this study. Silver ion high performance liquid chromatography (Ag + -HPLC) was used to separate one fraction rich in γ-T 3 into four peaks each consisting of at least five peaks according to GC/MS. About ten γ-T 3 isomers were also detected in rice bran oils from one producer bought retail in Germany. Copyright © 2016 Elsevier B.V. All rights reserved.

Applications of HPLC/MS in the analysis of traditional Chinese medicines

PubMed Central

Li, Miao; Hou, Xiao-Fang; Zhang, Jie; Wang, Si-Cen; Fu, Qiang; He, Lang-Chong

2012-01-01

In China, traditional Chinese medicines (TCMs) have been used in clinical applications for thousands of years. The successful hyphenation of high-Performance liquid chromatography (HPLC) and mass spectrometry (MS) has been applied widely in TCMs and biological samples analysis. Undoubtedly, HPLC/MS technique has facilitated the understanding of the treatment mechanism of TCMs. We reviewed more than 350 published papers within the last 5 years on HPLC/MS in the analysis of TCMs. The present review focused on the applications of HPLC/MS in the component analysis, metabolites analysis, and pharmacokinetics of TCMs etc. 50% of the literature is related to the component analysis of TCMs, which show that this field is the most populär type of research. In the metabolites analysis, HPLC coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry has been demonstrated to be the powerful tool for the characterization of structural features and fragmentation behavior patterns. This paper presented a brief overview of the applications of HPLC/MS in the analysis of TCMs. HPLC/MS in the fingerprint analysis is reviewed elsewhere. PMID:29403684

QEMSCAN+LA-ICP-MS: a 'big data' generator for sedimentary provenance analysis

NASA Astrophysics Data System (ADS)

Vermeesch, Pieter; Rittner, Martin; Garzanti, Eduardo

2017-04-01

Sedimentary provenance may be traced by 'fingerprinting' sediments with chemical, mineralogical or isotopic means. Normally, each of these provenance proxies is characterised on a separate aliquot of the same sample. For example, the chemical composition of the bulk sample may be analysed by X-ray fluorescence (XRF) on one aliquot, framework petrography on another, heavy mineral analysis on a density separate of a third split, and zircon U-Pb dating on a further density separate of the heavy mineral fraction. The labour intensity of this procedure holds back the widespread application of multi-method provenance studies. We here present a new method to solve this problem and avoid mineral separation by coupling a QEMSCAN electron microscope to an LA-ICP-MS instrument and thereby generate all four aforementioned provenance datasets as part of the same workflow. Given a polished hand specimen, a petrographic thin section, or a grain mount, the QEMSCAN+LA-ICP-MS method produces chemical and mineralogical maps from which the X-Y coordinates of the datable mineral are extracted. These coordinates are subsequently passed on to the laser ablation system for isotopic and, hence, geochronological analysis. In the process of finding all the zircons in a sediment grain mount, the QEMSCAN yields the compositional and mineralogical compositions as byproducts. We have applied the new QEMSCAN+LA-ICP-MS instrument suite to over 100 samples from three large sediment routing systems: (1) the Tigris-Euphrates river catchments and Rub' Al Khali desert in Arabia; (2) the Nile catchment in northeast Africa and (3) desert and beach sands between the Orange and Congo rivers in southwest Africa. These studies reveal (1) that Rub' Al Khali sand is predominantly derived from the Arabian Shield and not from Mesopotamia; (2) that the Blue Nile is the principal source of Nile sand; and (3) that Orange River sand is carried northward by longshore drift nearly 1,800km from South Africa to southern Angola. In addition to these geological findings, the first applications of QEMSCAN+LA-ICP-MS highlight some key advantages of the new workflow over traditional provenance analysis: (a) the new method not only increases sample throughput but also improves data quality by reducing significant biases associated with mineral separation and grain selection; (b) the three case studies highlight the importance of zircon 'fertility' for interpreting detrital zircon U-Pb datasets, and the ability of QEMSCAN to quantify this crucial parameter semi-automatically; (c) QEMSCAN+LA-ICP-MS provides an opportunity to add textural information to detrital geochronology and, for example, quantify possible grain-size dependence of U-Pb age distributions. But besides these advantages, the three case studies also reveal a number of limitations: (a) mineral identification by QEMSCAN is not as reliable as commonly achieved by human observers; (b) heavy mineral compositions obtained by QEMSCAN cannot easily be compared with conventional point counting data; and (c) apparent grain sizes can be greatly affected by polishing artefacts. In conclusion, QEMSCAN+LA-ICP-MS is a transformational new technique for provenance analysis but should be used with caution, in combination with conventional petrographic and heavy mineral techniques.

Techniques for quantitative LC-MS/MS analysis of protein therapeutics: advances in enzyme digestion and immunocapture.

PubMed

Fung, Eliza N; Bryan, Peter; Kozhich, Alexander

2016-04-01

LC-MS/MS has been investigated to quantify protein therapeutics in biological matrices. The protein therapeutics is digested by an enzyme to generate surrogate peptide(s) before LC-MS/MS analysis. One challenge is isolating protein therapeutics in the presence of large number of endogenous proteins in biological matrices. Immunocapture, in which a capture agent is used to preferentially bind the protein therapeutics over other proteins, is gaining traction. The protein therapeutics is eluted for digestion and LC-MS/MS analysis. One area of tremendous potential for immunocapture-LC-MS/MS is to obtain quantitative data where ligand-binding assay alone is not sufficient, for example, quantitation of antidrug antibody complexes. Herein, we present an overview of recent advance in enzyme digestion and immunocapture applicable to protein quantitation.

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).

A novel deletion of SNURF/SNRPN exon 1 in a patient with Prader-Willi-like phenotype.

PubMed

Cao, Yang; AlHumaidi, Susan S; Faqeih, Eissa A; Pitel, Beth A; Lundquist, Patrick; Aypar, Umut

2017-08-01

Here we report the smallest deletion involving SNURF/SNRPN that causes major symptoms of Prader-Willi syndrome (PWS), including hypotonia, dysmorphic features, intellectual disability, and obesity. A female patient with the aforementioned and additional features was referred to the Mayo Clinic Cytogenetics laboratory for genetic testing. Chromosomal microarray analysis and subsequent Sanger sequencing identified a de novo 6.4 kb deletion at 15q11.2, containing exon 1 of the SNURF gene and exon 1 of the shortest isoform of the SNRPN gene. SNURF/SNRPN exon 1, which is methylated on the silent maternal allele, is associated with acetylated histones on the expressed paternal allele. This region also overlaps with the PWS-imprinting center (IC). Subsequent molecular methylation analysis was performed using methylation-specific MLPA (MS-MLPA), which characterized that the deletion of SNURF/SNRPN exon 1 was paternal in origin, consistent with the PWS-like phenotype. Since SNURF/SNRPN gene and the PWS-IC are known to regulate snoRNAs, it is likely that the PWS-like phenotype observed in patients with paternal SNURF/SNRPN deletion is due to the disrupted expression of SNORD116 snoRNAs. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

A Guideline to Univariate Statistical Analysis for LC/MS-Based Untargeted Metabolomics-Derived Data

PubMed Central

Vinaixa, Maria; Samino, Sara; Saez, Isabel; Duran, Jordi; Guinovart, Joan J.; Yanes, Oscar

2012-01-01

Several metabolomic software programs provide methods for peak picking, retention time alignment and quantification of metabolite features in LC/MS-based metabolomics. Statistical analysis, however, is needed in order to discover those features significantly altered between samples. By comparing the retention time and MS/MS data of a model compound to that from the altered feature of interest in the research sample, metabolites can be then unequivocally identified. This paper reports on a comprehensive overview of a workflow for statistical analysis to rank relevant metabolite features that will be selected for further MS/MS experiments. We focus on univariate data analysis applied in parallel on all detected features. Characteristics and challenges of this analysis are discussed and illustrated using four different real LC/MS untargeted metabolomic datasets. We demonstrate the influence of considering or violating mathematical assumptions on which univariate statistical test rely, using high-dimensional LC/MS datasets. Issues in data analysis such as determination of sample size, analytical variation, assumption of normality and homocedasticity, or correction for multiple testing are discussed and illustrated in the context of our four untargeted LC/MS working examples. PMID:24957762

A Guideline to Univariate Statistical Analysis for LC/MS-Based Untargeted Metabolomics-Derived Data.

PubMed

Vinaixa, Maria; Samino, Sara; Saez, Isabel; Duran, Jordi; Guinovart, Joan J; Yanes, Oscar

2012-10-18

Several metabolomic software programs provide methods for peak picking, retention time alignment and quantification of metabolite features in LC/MS-based metabolomics. Statistical analysis, however, is needed in order to discover those features significantly altered between samples. By comparing the retention time and MS/MS data of a model compound to that from the altered feature of interest in the research sample, metabolites can be then unequivocally identified. This paper reports on a comprehensive overview of a workflow for statistical analysis to rank relevant metabolite features that will be selected for further MS/MS experiments. We focus on univariate data analysis applied in parallel on all detected features. Characteristics and challenges of this analysis are discussed and illustrated using four different real LC/MS untargeted metabolomic datasets. We demonstrate the influence of considering or violating mathematical assumptions on which univariate statistical test rely, using high-dimensional LC/MS datasets. Issues in data analysis such as determination of sample size, analytical variation, assumption of normality and homocedasticity, or correction for multiple testing are discussed and illustrated in the context of our four untargeted LC/MS working examples.

Targeted Feature Detection for Data-Dependent Shotgun Proteomics

PubMed Central

2017-01-01

Label-free quantification of shotgun LC–MS/MS data is the prevailing approach in quantitative proteomics but remains computationally nontrivial. The central data analysis step is the detection of peptide-specific signal patterns, called features. Peptide quantification is facilitated by associating signal intensities in features with peptide sequences derived from MS2 spectra; however, missing values due to imperfect feature detection are a common problem. A feature detection approach that directly targets identified peptides (minimizing missing values) but also offers robustness against false-positive features (by assigning meaningful confidence scores) would thus be highly desirable. We developed a new feature detection algorithm within the OpenMS software framework, leveraging ideas and algorithms from the OpenSWATH toolset for DIA/SRM data analysis. Our software, FeatureFinderIdentification (“FFId”), implements a targeted approach to feature detection based on information from identified peptides. This information is encoded in an MS1 assay library, based on which ion chromatogram extraction and detection of feature candidates are carried out. Significantly, when analyzing data from experiments comprising multiple samples, our approach distinguishes between “internal” and “external” (inferred) peptide identifications (IDs) for each sample. On the basis of internal IDs, two sets of positive (true) and negative (decoy) feature candidates are defined. A support vector machine (SVM) classifier is then trained to discriminate between the sets and is subsequently applied to the “uncertain” feature candidates from external IDs, facilitating selection and confidence scoring of the best feature candidate for each peptide. This approach also enables our algorithm to estimate the false discovery rate (FDR) of the feature selection step. We validated FFId based on a public benchmark data set, comprising a yeast cell lysate spiked with protein standards that provide a known ground-truth. The algorithm reached almost complete (>99%) quantification coverage for the full set of peptides identified at 1% FDR (PSM level). Compared with other software solutions for label-free quantification, this is an outstanding result, which was achieved at competitive quantification accuracy and reproducibility across replicates. The FDR for the feature selection was estimated at a low 1.5% on average per sample (3% for features inferred from external peptide IDs). The FFId software is open-source and freely available as part of OpenMS (www.openms.org). PMID:28673088

An interlaboratory comparison of bone lead measurements via K-shell X-ray fluorescence spectrometry: validation against inductively coupled plasma mass spectrometry

PubMed Central

Bellis, David J.; Todd, Andrew C.

2012-01-01

109Cd-based K-shell X-ray fluorescence spectrometry (hereafter, for brevity, XRF) is used, often in epidemiological studies, to perform non-invasive, in vivo measurements of lead in bone. We conducted the first interlaboratory study of XRF via the circulation of nine goat tibiæ in which the mean lead value ranged from 4.0 µg g−1 to 55.3 µg g−1 bone mineral. The test tibiæ were subsequently analyzed via nitric acid digestion followed by lead determination by inductively coupled plasma mass spectrometry (ICP-MS) – along with certified reference materials for bone lead – thus providing measurement traceability to SI units. Analysis of dried bone for lead via nitric acid digestion and ICP-MS yields mass fraction data in units of µg g−1 dry weight. The mean bone lead value based on ICP-MS analysis ranged from 1.8 µg g−1 to 35.8 µg g−1 dry weight. For comparison purposes, XRF-measured Pb values (µg g−1 bone mineral) were converted into the ICP-MS-measured units (µg g−1dry weight bone) by multiplying the former by the average ash fraction from the nine tibiæ. Eight of the XRF systems did not yield a significant bias for any of the nine tibiæ; one system was biased for one of the tibiæ; two systems were biased for two tibiæ; one system was biased for four tibiæ; two systems (813-1 and 804-2) were biased for five tibiæ and one system (801-1) was biased for six of the nine tibiæ. Average bias for the systems (under those particular operating conditions) that were biased for the majority of samples ranged from −2.6 µg g−1 (−15.7%) to 5.1 µg g−1 (30.7%) dry weight bone. All participants now have the ICP-MS data, allowing any corrective actions deemed necessary to be implemented. The ICP-MS data, however, indicated that the lead mass fraction varied considerably with the sampling location within the tibiæ, to the extent of exceeding XRF variability for the higher lead values. Material heterogeneity is an unavoidable reality of measuring lead in bone. PMID:22468015

Targeted Feature Detection for Data-Dependent Shotgun Proteomics.

PubMed

Weisser, Hendrik; Choudhary, Jyoti S

2017-08-04

Label-free quantification of shotgun LC-MS/MS data is the prevailing approach in quantitative proteomics but remains computationally nontrivial. The central data analysis step is the detection of peptide-specific signal patterns, called features. Peptide quantification is facilitated by associating signal intensities in features with peptide sequences derived from MS2 spectra; however, missing values due to imperfect feature detection are a common problem. A feature detection approach that directly targets identified peptides (minimizing missing values) but also offers robustness against false-positive features (by assigning meaningful confidence scores) would thus be highly desirable. We developed a new feature detection algorithm within the OpenMS software framework, leveraging ideas and algorithms from the OpenSWATH toolset for DIA/SRM data analysis. Our software, FeatureFinderIdentification ("FFId"), implements a targeted approach to feature detection based on information from identified peptides. This information is encoded in an MS1 assay library, based on which ion chromatogram extraction and detection of feature candidates are carried out. Significantly, when analyzing data from experiments comprising multiple samples, our approach distinguishes between "internal" and "external" (inferred) peptide identifications (IDs) for each sample. On the basis of internal IDs, two sets of positive (true) and negative (decoy) feature candidates are defined. A support vector machine (SVM) classifier is then trained to discriminate between the sets and is subsequently applied to the "uncertain" feature candidates from external IDs, facilitating selection and confidence scoring of the best feature candidate for each peptide. This approach also enables our algorithm to estimate the false discovery rate (FDR) of the feature selection step. We validated FFId based on a public benchmark data set, comprising a yeast cell lysate spiked with protein standards that provide a known ground-truth. The algorithm reached almost complete (>99%) quantification coverage for the full set of peptides identified at 1% FDR (PSM level). Compared with other software solutions for label-free quantification, this is an outstanding result, which was achieved at competitive quantification accuracy and reproducibility across replicates. The FDR for the feature selection was estimated at a low 1.5% on average per sample (3% for features inferred from external peptide IDs). The FFId software is open-source and freely available as part of OpenMS ( www.openms.org ).

Metabolomic and elemental analysis of camel and bovine urine by GC-MS and ICP-MS.

PubMed

Ahamad, Syed Rizwan; Alhaider, Abdul Qader; Raish, Mohammad; Shakeel, Faiyaz

2017-01-01

Recent studies from the author's laboratory indicated that camel urine possesses antiplatelet activity and anti-cancer activity which is not present in bovine urine. The objective of this study is to compare the volatile and elemental components of bovine and camel urine using GC-MS and ICP-MS analysis. We are interested to know the component that performs these biological activities. The freeze dried urine was dissolved in dichloromethane and then derivatization process followed by using BSTFA for GC-MS analysis. Thirty different compounds were analyzed by the derivatization process in full scan mode. For ICP-MS analysis twenty eight important elements were analyzed in both bovine and camel urine. The results of GC-MS and ICP-MS analysis showed marked difference in the urinary metabolites. GC-MS evaluation of camel urine finds a lot of products of metabolism like benzene propanoic acid derivatives, fatty acid derivatives, amino acid derivatives, sugars, prostaglandins and canavanine. Several research reports reveal the metabolomics studies on camel urine but none of them completely reported the pharmacology related metabolomics. The present data of GC-MS suggest and support the previous studies and activities related to camel urine.

Piper nigrum: micropropagation, antioxidative enzyme activities, and chromatographic fingerprint analysis for quality control.

PubMed

Ahmad, Nisar; Abbasi, Bilal Haider; Rahman, Inayat ur; Fazal, Hina

2013-04-01

A reliable in vitro regeneration system for the economical and medicinally important Piper nigrum L. has been established. Callus and shoot regeneration was encouraged from leaf portions on Murashige and Skoog (MS) medium augmented with varied concentrations of plant growth regulators. A higher callus production (90 %) was observed in explants incubated on MS medium incorporated with 1.0 mg L(-1) 6-benzyladenine (BA) along with 0.5 mg L(-1) gibberellic acid after 4 weeks of culture. Moreover, a callogenic response of 85 % was also recorded for 1.0 mg L(-1) BA in combination with 0.25 mg L(-1) α-naphthalene acetic acid (NAA) and 0.25 mg L(-1) 2,4-dichlorophenoxyacetic acid or 0.5 mg L(-1) indole butyric acid (IBA) along with 0.25 mg L(-1) NAA and indole acetic acid. Subsequent sub-culturing of callus after 4 weeks of culture onto MS medium supplemented with 1.5 mg L(-1) thiodiazoran or 1.5 mg L(-1) IBA induced 100 % shoot response. Rooted plantlets were achieved on medium containing varied concentrations of auxins. The antioxidative enzyme activities [superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX)] revealed that significantly higher SOD was observed in regenerated plantlets than in other tissues. However, POD, CAT, and APX were higher in callus than in other tissues. A high-performance liquid chromatography (HPLC) fingerprint analysis protocol was established for quality control in different in vitro-regenerated tissues of P. nigrum L. During analysis, most of the common peaks represent the active principle "piperine." The chemical contents, especially piperine, showed variation from callus culture to whole plantlet regeneration. Based on the deviation in chromatographic peaks, the in vitro-regenerated plantlets exhibit a nearly similar piperine profile to acclimated plantlets. The in vitro regeneration system and HPLC fingerprint analysis established here brought a novel approach to the quality control of in vitro plantlets, producing metabolites of interest with substantial applications for the conservation of germplasm.

Gas Chromatography-Tandem Mass Spectrometry of Lignin Pyrolyzates with Dopant-Assisted Atmospheric Pressure Chemical Ionization and Molecular Structure Search with CSI:FingerID

NASA Astrophysics Data System (ADS)

Larson, Evan A.; Hutchinson, Carolyn P.; Lee, Young Jin

2018-06-01

Dopant-assisted atmospheric pressure chemical ionization (dAPCI) is a soft ionization method rarely used for gas chromatography-mass spectrometry (GC-MS). The current study combines GC-dAPCI with tandem mass spectrometry (MS/MS) for analysis of a complex mixture such as lignin pyrolysis analysis. To identify the structures of volatile lignin pyrolysis products, collision-induced dissociation (CID) MS/MS using a quadrupole time-of-flight mass spectrometer (QTOFMS) and pseudo MS/MS through in-source collision-induced dissociation (ISCID) using a single stage TOFMS are utilized. To overcome the lack of MS/MS database, Compound Structure Identification (CSI):FingerID is used to interpret CID spectra and predict best matched structures from PubChem library. With this approach, a total of 59 compounds were positively identified in comparison to only 22 in NIST database search of GC-EI-MS dataset. This study demonstrates the effectiveness of GC-dAPCI-MS/MS to overcome the limitations of traditional GC-EI-MS analysis when EI-MS database is not sufficient. [Figure not available: see fulltext.

Sulfonium Ion Derivatization, Isobaric Stable Isotope Labeling and Data Dependent CID- and ETD-MS/MS for Enhanced Phosphopeptide Quantitation, Identification and Phosphorylation Site Characterization

PubMed Central

Lu, Yali; Zhou, Xiao; Stemmer, Paul M.; Reid, Gavin E.

2014-01-01

An amine specific peptide derivatization strategy involving the use of novel isobaric stable isotope encoded ‘fixed charge’ sulfonium ion reagents, coupled with an analysis strategy employing capillary HPLC, ESI-MS, and automated data dependent ion trap CID-MS/MS, -MS3, and/or ETD-MS/MS, has been developed for the improved quantitative analysis of protein phosphorylation, and for identification and characterization of their site(s) of modification. Derivatization of 50 synthetic phosphopeptides with S,S′-dimethylthiobutanoylhydroxysuccinimide ester iodide (DMBNHS), followed by analysis using capillary HPLC-ESI-MS, yielded an average 2.5-fold increase in ionization efficiencies and a significant increase in the presence and/or abundance of higher charge state precursor ions compared to the non-derivatized phosphopeptides. Notably, 44% of the phosphopeptides (22 of 50) in their underivatized states yielded precursor ions whose maximum charge states corresponded to +2, while only 8% (4 of 50) remained at this maximum charge state following DMBNHS derivatization. Quantitative analysis was achieved by measuring the abundances of the diagnostic product ions corresponding to the neutral losses of ‘light’ (S(CH3)2) and ‘heavy’ (S(CD3)2) dimethylsulfide exclusively formed upon CID-MS/MS of isobaric stable isotope labeled forms of the DMBNHS derivatized phosphopeptides. Under these conditions, the phosphate group stayed intact. Access for a greater number of peptides to provide enhanced phosphopeptide sequence identification and phosphorylation site characterization was achieved via automated data-dependent CID-MS3 or ETD-MS/MS analysis due to the formation of the higher charge state precursor ions. Importantly, improved sequence coverage was observed using ETD-MS/MS following introduction of the sulfonium ion fixed charge, but with no detrimental effects on ETD fragmentation efficiency. PMID:21952753

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.

High pressure stopped-flow apparatus for the rapid mixing and subsequent study of two fluids under high hydrostatic pressures

NASA Astrophysics Data System (ADS)

Karan, Daniel M.; Macey, Robert I.

1980-08-01

A stopped-flow apparatus is described for the rapid mixing and subsequent study of two dissimilar fluids under pressures up to 1200 bar. The device consists of two identical pressure chambers which contain the two fluids, a third pressure chamber which contains gas to maintain the pressure in the system, an optical port for photometric observation, and various connections. The device has been used to measure reaction times on the order of a hundred milliseconds to tens of seconds, using a maximum of 2 ml of each reagent per experimental determination. The dead time is found to be 5-25 ms with minium average flow velocities of 2.0 m/s. The construction and operation of the device are described and examples of water transport data in red blood cells and the bromophenolblue indicated chemical reaction of NaHCO3 and HCl under pressure are presented.

Development of fast cooling pulsed magnets at the Wuhan National High Magnetic Field Center.

PubMed

Peng, Tao; Sun, Quqin; Zhao, Jianlong; Jiang, Fan; Li, Liang; Xu, Qiang; Herlach, Fritz

2013-12-01

Pulsed magnets with fast cooling channels have been developed at the Wuhan National High Magnetic Field Center. Between the inner and outer sections of a coil wound with a continuous length of CuNb wire, G10 rods with cross section 4 mm × 5 mm were inserted as spacers around the entire circumference, parallel to the coil axis. The free space between adjacent rods is 6 mm. The liquid nitrogen flows freely in the channels between these rods, and in the direction perpendicular to the rods through grooves provided in the rods. For a typical 60 T pulsed magnetic field with pulse duration of 40 ms, the cooling time between subsequent pulses is reduced from 160 min to 35 min. Subsequently, the same technology was applied to a 50 T magnet with 300 ms pulse duration. The cooling time of this magnet was reduced from 480 min to 65 min.

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.

The Fine Temporal Structure of the Rat Licking Pattern: What Causes the Variabiliy in the Interlick Intervals and How is it Affected by the Drinking Solution?

PubMed Central

2013-01-01

Licking is a repetitive behavior controlled by a central pattern generator. Even though interlick intervals (ILIs) within bursts of licks are considered fairly regular, the conditions that affect their variability are unknown. We analyzed the licking pattern in rats that licked water, 10% sucrose solution, or 10% ethanol solution, in 90-min recording sessions after 4h of water deprivation. The histograms of ILIs indicate that licking typically occurred at a preferred ILI of about 130−140ms with evidence of bimodal or multimodal distributions due to occasional licking failures. We found that the longer the pause between bursts of licks, the shorter was the first ILI of the burst. When bursts of licks were preceded by a pause >4 s, the ILI was the shortest (~110ms) at the beginning of the burst, and then it increased rapidly in the first few licks and slowly in subsequent licks. Interestingly, the first ILI of a burst of licks was not significantly different when licking any of the 3 solutions, but subsequent licks exhibited a temporal pattern characteristic of each solution. The rapid deceleration in intraburst licking rate was due to an increase from ~27ms to ~56ms in the tongue-spout contact duration while the intercontact interval was only slightly changed (80−90ms). Therefore, the contact duration seems to be the major factor that increases the variability in the ILIs and could be another means for the rat to adjust the amount of fluid ingested in each individual lick. PMID:23902635

Inventory of File gfs.t06z.pgrb2b.0p25.f000

Science.gov Websites

UGRD analysis U-Component of Wind [m/s] 005 1 mb VGRD analysis V-Component of Wind [m/s] 006 1 mb ABSV Temperature [K] 011 2 mb RH analysis Relative Humidity [%] 012 2 mb UGRD analysis U-Component of Wind [m/s ] 013 2 mb VGRD analysis V-Component of Wind [m/s] 014 2 mb ABSV analysis Absolute Vorticity [1/s] 015 2

Inventory of File gfs.t06z.pgrb2b.1p00.f000

Science.gov Websites

UGRD analysis U-Component of Wind [m/s] 005 1 mb VGRD analysis V-Component of Wind [m/s] 006 1 mb ABSV Temperature [K] 011 2 mb RH analysis Relative Humidity [%] 012 2 mb UGRD analysis U-Component of Wind [m/s ] 013 2 mb VGRD analysis V-Component of Wind [m/s] 014 2 mb ABSV analysis Absolute Vorticity [1/s] 015 2

Inventory of File gfs.t06z.pgrb2b.0p50.f000

Science.gov Websites

UGRD analysis U-Component of Wind [m/s] 005 1 mb VGRD analysis V-Component of Wind [m/s] 006 1 mb ABSV Temperature [K] 011 2 mb RH analysis Relative Humidity [%] 012 2 mb UGRD analysis U-Component of Wind [m/s ] 013 2 mb VGRD analysis V-Component of Wind [m/s] 014 2 mb ABSV analysis Absolute Vorticity [1/s] 015 2

Identification and quantification of six major α-dicarbonyl process contaminants in high-fructose corn syrup.

PubMed

Gensberger, Sabrina; Mittelmaier, Stefan; Glomb, Marcus A; Pischetsrieder, Monika

2012-07-01

High-fructose corn syrup (HFCS) is a widely used liquid sweetener produced from corn starch by hydrolysis and partial isomerization of glucose to fructose. During these processing steps, sugars can be considerably degraded, leading, for example, to the formation of reactive α-dicarbonyl compounds (α-DCs). The present study performed targeted screening to identify the major α-DCs in HFCS. For this purpose, α-DCs were selectively converted with o-phenylendiamine to the corresponding quinoxaline derivatives, which were analyzed by liquid chromatography with hyphenated diode array-tandem mass spectrometry (LC-DAD-MS/MS) detection. 3-Deoxy-D-erythro-hexos-2-ulose (3-deoxyglucosone), D-lyxo-hexos-2-ulose (glucosone), 3-deoxy-D-threo-hexos-2-ulose (3-deoxygalactosone), 1-deoxy-D-erythro-hexos-2,3-diulose (1-deoxyglucosone), 3,4-dideoxyglucosone-3-ene, methylglyoxal, and glyoxal were identified by enhanced mass spectra as well as MS/MS product ion spectra using the synthesized standards as reference. Addition of diethylene triamine pentaacetic acid and adjustment of the derivatization conditions ensured complete derivatization without de novo formation for all identified α-DCs in HFCS matrix except for glyoxal. Subsequently, a ultra-high performance LC-DAD-MS/MS method was established to quantify 3-deoxyglucosone, glucosone, 3-deoxygalactosone, 1-deoxyglucosone, 3,4-dideoxyglucosone-3-ene, and methylglyoxal in HFCS. Depending on the α-DC compound and concentration, the recovery ranged between 89.2% and 105.8% with a relative standard deviation between 1.9% and 6.5%. Subsequently, the α-DC profiles of 14 commercial HFCS samples were recorded. 3-Deoxyglucosone was identified as the major α-DC with concentrations up to 730 μg/mL HFCS. The total α-DC content ranged from 293 μg/mL to 1,130 μg/mL HFCS. Significantly different α-DC levels were not detected between different HFCS specifications, but between samples of various manufacturers indicating that the α-DC load is influenced by the production procedures.

Identification and quantification of astaxanthin esters in shrimp (Pandalus borealis) and in a microalga (Haematococcus pluvialis) by liquid chromatography-mass spectrometry using negative ion atmospheric pressure chemical ionization.

PubMed

Breithaupt, Dietmar E

2004-06-16

Negative ion liquid chromatography-atmospheric pressure chemical ionization mass spectrometry [negative ion LC-(APCI)MS] was used for the identification of astaxanthin esters in extracts of commercial shrimp (Pandalus borealis) and dried microalga (Haematococcus pluvialis) samples. A cleanup step using a normal phase solid phase extraction (SPE) cartridge was applied prior to analysis. Recovery experiments with astaxanthin oleate as model compound proved the applicability of this step (98.5 +/- 7.6%; n = 4). The assignment of astaxanthin esters in negative ion LC-(APCI)MS was based on the detection of the molecular ion (M*-) and the formation of characteristic fragment ions, resulting from the loss of one or two fatty acids. Quantification of individual astaxanthin esters was performed using an astaxanthin calibration curve, which was found to be linear over the required range (1-51 micromol/L; r2 = 0.9996). Detection limits, based on the intensity of M*-, a signal-to-noise ratio of 3:1, and an injection volume of 20 microL, were estimated to be 0.05 microg/mL (free astaxanthin), 0.28 microg/mL (astaxanthin-C16:0), and 0.78 microg/mL (astaxanthin-C16:0/C16:0), respectively. This LC-(APCI)MS method allows for the first time the characterization of native astaxanthin esters in P. borealis and H. pluvialis without using time-consuming isolation steps with subsequent gas chromatographic analyses of fatty acid methyl esters. The results suggest that the pattern of astaxanthin-bound polyunsaturated fatty acids of P. borealis does not reflect the respective fatty acid pattern found in triacylglycerides. Application of the presented LC-(APCI)MS technique in common astaxanthin ester analysis will forestall erroneous xanthophyll ester assignment in natural sources.

Small explosive volcanic plume dynamics: insights from feature tracking velocimetry at Santiaguito lava dome

NASA Astrophysics Data System (ADS)

Benage, M. C.; Andrews, B. J.

2016-12-01

Volcanic explosions eject turbulent, transient jets of hot volcanic gas and particles into the atmosphere. Though the jet of hot material is initially negatively buoyant, the jet can become buoyant through entrainment and subsequent thermal expansion of entrained air that allows the eruptive plume to rise several kilometers. Although basic plume structure is qualitatively well known, the velocity field and dynamic structure of volcanic plumes are not well quantified. An accurate and quantitative description of volcanic plumes is essential for hazard assessments, such as if the eruption will form a buoyant plume that will affect aviation or produce dangerous pyroclastic density currents. Santa Maria volcano, in Guatemala, provides the rare opportunity to safely capture video of Santiaguito lava dome explosions and small eruptive plumes. In January 2016, two small explosions (< 2 km) that lasted several minutes and with little cloud obstruction were recorded for image analysis. The volcanic plume structure is analyzed through sequential image frames from the video where specific features are tracked using a feature tracking velocimetry (FTV) algorithm. The FTV algorithm quantifies the 2D apparent velocity fields along the surface of the plume throughout the duration of the explosion. Image analysis of small volcanic explosions allows us to examine the maximum apparent velocities at two heights above the dome surface, 0-25 meters, where the explosions first appear, and 100-125 meters. Explosions begin with maximum apparent velocities of <15 m/s. We find at heights near the dome surface and 10 seconds after explosion initiation, the maximum apparent velocities transition to sustained velocities of 5-15 m/s. At heights 100-125 meters above the dome surface, the apparent velocities transition to sustained velocities of 5-15 m/s after 25 seconds. Throughout the explosion, transient velocity maximums can exceed 40 m/s at both heights. Here, we provide novel quantification and description of turbulent surface velocity fields of explosive volcanic eruptions at active lava domes.

Extraction efficiency and implications for absolute quantitation of propranolol in mouse brain, liver and kidney thin tissue sections using droplet-based liquid microjunction surface sampling-HPLC ESI-MS/MS

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

Kertesz, Vilmos; Weiskittel, Taylor M.; Vavek, Marissa

Currently, absolute quantitation aspects of droplet-based surface sampling for thin tissue analysis using a fully automated autosampler/HPLC-ESI-MS/MS system are not fully evaluated. Knowledge of extraction efficiency and its reproducibility is required to judge the potential of the method for absolute quantitation of analytes from thin tissue sections. Methods: Adjacent thin tissue sections of propranolol dosed mouse brain (10- μm-thick), kidney (10- μm-thick) and liver (8-, 10-, 16- and 24- μm-thick) were obtained. Absolute concentration of propranolol was determined in tissue punches from serial sections using standard bulk tissue extraction protocols and subsequent HPLC separations and tandem mass spectrometric analysis. Thesemore » values were used to determine propranolol extraction efficiency from the tissues with the droplet-based surface sampling approach. Results: Extraction efficiency of propranolol using 10- μm-thick brain, kidney and liver thin tissues using droplet-based surface sampling varied between ~45-63%. Extraction efficiency decreased from ~65% to ~36% with liver thickness increasing from 8 μm to 24 μm. Randomly selecting half of the samples as standards, precision and accuracy of propranolol concentrations obtained for the other half of samples as quality control metrics were determined. Resulting precision ( ±15%) and accuracy ( ±3%) values, respectively, were within acceptable limits. In conclusion, comparative quantitation of adjacent mouse thin tissue sections of different organs and of various thicknesses by droplet-based surface sampling and by bulk extraction of tissue punches showed that extraction efficiency was incomplete using the former method, and that it depended on the organ and tissue thickness. However, once extraction efficiency was determined and applied, the droplet-based approach provided the required quantitation accuracy and precision for assay validations. Furthermore, this means that once the extraction efficiency was calibrated for a given tissue type and drug, the droplet-based approach provides a non-labor intensive and high-throughput means to acquire spatially resolved quantitative analysis of multiple samples of the same type.« less

Method development and validation for total haloxyfop analysis in infant formulas and related ingredient matrices using liquid chromatography-tandem mass spectrometry.

PubMed

Koesukwiwat, Urairat; Vaclavik, Lukas; Mastovska, Katerina

2018-05-08

According to the European Commission directive 2006/141/EC, haloxyfop residue levels should not exceed 0.003 mg/kg in ready-to-feed infant formula, and the residue definition includes sum of haloxyfop, its esters, salts, and conjugates expressed as haloxyfop. A simple method for total haloxyfop analysis in infant formula and related ingredient matrices was developed and validated using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The sample preparation consisted of an alkaline hydrolysis with methanolic sodium hydroxide to release haloxyfop (parent acid) from its bound forms prior to the extraction with acetonitrile. A mixture of magnesium sulfate (MgSO 4 ) and sodium chloride (NaCl) (4:1, w/w) was added to the extract to induce phase separation and force the analyte into the upper acetonitrile-methanol layer and then a 1-mL aliquot was subsequently cleaned up by dispersive solid phase extraction with 150 mg of MgSO 4 and 50 mg of octadecyl (C 18 ) sorbent. The analytical procedure was developed and carefully optimized to enable low-level, total haloxyfop analysis in a variety of challenging matrices, including infant formulas and their important high-carbohydrate, high-protein, high-fat, and emulsifier ingredients. The final method was validated in two different laboratories by fortifying samples with haloxyfop and haloxyfop-methyl, which was used as a model compound simulating bound forms of the analyte. Mean recoveries of haloxyfop across all fortification levels and evaluated matrices ranged between 92.2 and 114% with repeatability, within-lab reproducibility, and reproducibility RSDs ≤ 14%. Based on the validation results, this method was capable to convert the haloxyfop ester into the parent acid in a wide range of sample types and to reliably identify and quantify total haloxyfop at the target 0.003 mg/kg level in infant formulas (both powdered and ready-to-feed liquid forms). Graphical abstract LC-MS/MS-based workflow for the determination of the total haloxyfop in infant formula and related ingredients.

Fast determination of pesticides and other contaminants of emerging concern in treated wastewater using direct injection coupled to highly sensitive ultra-high performance liquid chromatography-tandem mass spectrometry.

PubMed

Campos-Mañas, Marina Celia; Plaza-Bolaños, Patricia; Sánchez-Pérez, José Antonio; Malato, Sixto; Agüera, Ana

2017-07-21

It is well known that wastewater treatment plant (WWTP) effluents usually contain micropollutants such as pharmaceuticals (or their transformation products, TPs) or pesticides, which is a major issue when evaluating their possible reuse (e.g. for irrigation in agriculture). In search for an improved accuracy and simplicity, methods based on the direct injection of the sample (DI) represent a recent trend taking advantage of the increasing sensitivity of new mass spectrometry (MS) instruments. Thus, the present study shows the development and validation of a DI-based method by ultra-high-performance liquid chromatography quadrupole-linear ion trap analyser (UHPLC-QqLIT-MS/MS). The proposed method was applied to the monitoring of 115 organic microcontaminants (including pharmaceuticals, TPs and pesticides) at the ngL -1 /μgL -1 level in wastewater effluents from urban WWTPs. Sample pre-treatment was reduced to acetonitrile addition and filtration of the mixture previous to LC-MS analysis. Total analysis time was <15min. A subsequent validation protocol was carried out in treated WW (TWW), following indications of SANTE and Eurachem Guidelines. Linearity and matrix effect were evaluated in the range of 10-1000ngL -1 . 70% of the analytes showed a moderate matrix effect (≤25%). Trueness (expressed as recovery) and precision (calculated as relative standard deviation, RSD) were evaluated at four concentration levels (20, 50, 500 and 1000ngL -1 ) in TWW samples. The LODs ranged from 1 to 357ngL -1 and the LOQs from 10 to 500ngL -1 . 92% of the compounds showed limits of quantification ≤100ngL -1 . In most cases, mean recoveries were in the range 70-120%, and RSD values were ≤20%. The validated method was successfully applied to the analysis of 10 TWW samples, demonstrating the occurrence of 67 target compounds at concentration levels from 26705ngL -1 (4-aminoantipyrine) to 10ngL -1 (tebuconazole and bezafibrate). Copyright © 2017 Elsevier B.V. All rights reserved.

Extraction efficiency and implications for absolute quantitation of propranolol in mouse brain, liver and kidney thin tissue sections using droplet-based liquid microjunction surface sampling-HPLC ESI-MS/MS

DOE PAGES

Kertesz, Vilmos; Weiskittel, Taylor M.; Vavek, Marissa; ...

2016-06-22

Currently, absolute quantitation aspects of droplet-based surface sampling for thin tissue analysis using a fully automated autosampler/HPLC-ESI-MS/MS system are not fully evaluated. Knowledge of extraction efficiency and its reproducibility is required to judge the potential of the method for absolute quantitation of analytes from thin tissue sections. Methods: Adjacent thin tissue sections of propranolol dosed mouse brain (10- μm-thick), kidney (10- μm-thick) and liver (8-, 10-, 16- and 24- μm-thick) were obtained. Absolute concentration of propranolol was determined in tissue punches from serial sections using standard bulk tissue extraction protocols and subsequent HPLC separations and tandem mass spectrometric analysis. Thesemore » values were used to determine propranolol extraction efficiency from the tissues with the droplet-based surface sampling approach. Results: Extraction efficiency of propranolol using 10- μm-thick brain, kidney and liver thin tissues using droplet-based surface sampling varied between ~45-63%. Extraction efficiency decreased from ~65% to ~36% with liver thickness increasing from 8 μm to 24 μm. Randomly selecting half of the samples as standards, precision and accuracy of propranolol concentrations obtained for the other half of samples as quality control metrics were determined. Resulting precision ( ±15%) and accuracy ( ±3%) values, respectively, were within acceptable limits. In conclusion, comparative quantitation of adjacent mouse thin tissue sections of different organs and of various thicknesses by droplet-based surface sampling and by bulk extraction of tissue punches showed that extraction efficiency was incomplete using the former method, and that it depended on the organ and tissue thickness. However, once extraction efficiency was determined and applied, the droplet-based approach provided the required quantitation accuracy and precision for assay validations. Furthermore, this means that once the extraction efficiency was calibrated for a given tissue type and drug, the droplet-based approach provides a non-labor intensive and high-throughput means to acquire spatially resolved quantitative analysis of multiple samples of the same type.« less

Extracellular proteome analysis of Leptospira interrogans serovar Lai.

PubMed

Zeng, Lingbing; Zhang, Yunyi; Zhu, Yongzhang; Yin, Haidi; Zhuang, Xuran; Zhu, Weinan; Guo, Xiaokui; Qin, Jinhong

2013-10-01

Abstract Leptospirosis is one of the most important zoonoses. Leptospira interrogans serovar Lai is a pathogenic spirochete that is responsible for leptospirosis. Extracellular proteins play an important role in the pathogenicity of this bacterium. In this study, L. interrogans serovar Lai was grown in protein-free medium; the supernatant was collected and subsequently analyzed as the extracellular proteome. A total of 66 proteins with more than two unique peptides were detected by MS/MS, and 33 of these were predicted to be extracellular proteins by a combination of bioinformatics analyses, including Psortb, cello, SoSuiGramN and SignalP. Comparisons of the transcriptional levels of these 33 genes between in vivo and in vitro conditions revealed that 15 genes were upregulated and two genes were downregulated in vivo compared to in vitro. A BLAST search for the components of secretion system at the genomic and proteomic levels revealed the presence of the complete type I secretion system and type II secretion system in this strain. Moreover, this strain also exhibits complete Sec translocase and Tat translocase systems. The extracellular proteome analysis of L. interrogans will supplement the previously generated whole proteome data and provide more information for studying the functions of specific proteins in the infection process and for selecting candidate molecules for vaccines or diagnostic tools for leptospirosis.

Interdisciplinary Project-Based Learning through an Environmental Water Quality Study

NASA Astrophysics Data System (ADS)

Juhl, Lorie; Yearsley, Kaye; Silva, Andrew J.

1997-12-01

An interdisciplinary environmental water quality study was designed and conducted to enhance training and employability of chemical and environmental technician students in associate degree programs. Four project objectives were identified as a means to enhance the educational experience and employability of our students: provide experience on analytical instrumentation for organic compounds (gas chromatography/mass spectrometry, GC/MS), require interdisciplinary group interactions and problem solving, provide experience with Environmental Protection Agency (EPA) procedures, and require cooperation with state agencies/private organizations. Students worked in groups that included representatives from both programs to develop project objectives and a Sampling and Analysis Plan (SAP) following EPA standards. Input from personnel at Idaho's Department of Environmental Quality and Bureau of Laboratories and from volunteers in an environmental "watch dog" organization called the Henry's Fork Foundation aided students in the development and implementation of their SAP. Subsequently, groups sampled sections of the Henry's Fork River and analyzed for organic, inorganic, and fecal contaminants. Analysis included EPA method 525.2 for pesticides using GC/MS. Data from all river segments was shared and each group submitted a final report analyzing results. Surveys completed by students and instructors indicate that the project is a successful teaching method allowing introduction of new skills as well as review of important technical and employability skills.

Evaluation of peak picking quality in LC-MS metabolomics data.

PubMed

Brodsky, Leonid; Moussaieff, Arieh; Shahaf, Nir; Aharoni, Asaph; Rogachev, Ilana

2010-11-15

The output of LC-MS metabolomics experiments consists of mass-peak intensities identified through a peak-picking/alignment procedure. Besides imperfections in biological samples and instrumentation, data accuracy is highly dependent on the applied algorithms and their parameters. Consequently, quality control (QC) is essential for further data analysis. Here, we present a QC approach that is based on discrepancies between replicate samples. First, the quantile normalization of per-sample log-signal distributions is applied to each group of biologically homogeneous samples. Next, the overall quality of each replicate group is characterized by the Z-transformed correlation coefficients between samples. This general QC allows a tuning of the procedure's parameters which minimizes the inter-replicate discrepancies in the generated output. Subsequently, an in-depth QC measure detects local neighborhoods on a template of aligned chromatograms that are enriched by divergences between intensity profiles of replicate samples. These neighborhoods are determined through a segmentation algorithm. The retention time (RT)-m/z positions of the neighborhoods with local divergences are indicative of either: incorrect alignment of chromatographic features, technical problems in the chromatograms, or to a true biological discrepancy between replicates for particular metabolites. We expect this method to aid in the accurate analysis of metabolomics data and in the development of new peak-picking/alignment procedures.

Carbon based sample supports and matrices for laser desorption/ ionization mass spectrometry.

PubMed

Rainer, Matthias; Najam-ul-Haq, Muhammad; Huck, Christian W; Vallant, Rainer M; Heigl, Nico; Hahn, Hans; Bakry, Rania; Bonn, Günther K

2007-01-01

Laser desorption/ionization mass spectrometry (LDI-MS) is a widespread and powerful technique for mass analysis allowing the soft ionization of molecules such as peptides, proteins and carbohydrates. In many applications, an energy absorbing matrix has to be added to the analytes in order to protect them from being fragmented by direct laser beam. LDI-MS in conjunction with matrix is commonly referred as matrix-assisted LDI (MALDI). One of the striking disadvantages of this method is the desorption of matrix molecules, which causes interferences originating from matrix background ions in lower mass range (< 1000 Da). This has been led to the development of a variety of different carbon based LDI sample supports, which are capable of absorbing laser light and simultaneously transfering energy to the analytes for desorption. Furthermore carbon containing sample supports are used as carrier materials for the specific binding and preconcentration of molecules out of complex samples. Their subsequent analysis with MALDI mass spectrometry allows performing studies in metabolomics and proteomics. Finally a thin layer of carbon significantly improves sensitivity concerning detection limit. Analytes in low femtomole and attomole range can be detected in this regard. In the present article, these aspects are reviewed from patents where nano-based carbon materials are comprehensively utilized.

Probing Protein Glycation by Chromatography and Mass Spectrometry: Analysis of Glycation Adducts

PubMed Central

Soboleva, Alena; Vikhnina, Maria; Grishina, Tatiana; Frolov, Andrej

2017-01-01

Glycation is a non-enzymatic post-translational modification of proteins, formed by the reaction of reducing sugars and α-dicarbonyl products of their degradation with amino and guanidino groups of proteins. Resulted early glycation products are readily involved in further transformation, yielding a heterogeneous group of advanced glycation end products (AGEs). Their formation is associated with ageing, metabolic diseases, and thermal processing of foods. Therefore, individual glycation adducts are often considered as the markers of related pathologies and food quality. In this context, their quantification in biological and food matrices is required for diagnostics and establishment of food preparation technologies. For this, exhaustive protein hydrolysis with subsequent amino acid analysis is the strategy of choice. Thereby, multi-step enzymatic digestion procedures ensure good recoveries for the most of AGEs, whereas tandem mass spectrometry (MS/MS) in the multiple reaction monitoring (MRM) mode with stable isotope dilution or standard addition represents “a gold standard” for their quantification. Although the spectrum of quantitatively assessed AGE structures is continuously increases, application of untargeted profiling techniques for identification of new products is desired, especially for in vivo characterization of anti-glycative systems. Thereby, due to a high glycative potential of plant metabolites, more attention needs to be paid on plant-derived AGEs. PMID:29182540

Combining Laser Ablation/Liquid Phase Collection Surface Sampling and High-Performance Liquid Chromatography Electrospray Ionization Mass Spectrometry

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

Ovchinnikova, Olga S; Kertesz, Vilmos; Van Berkel, Gary J

This paper describes the coupling of ambient pressure transmission geometry laser ablation with a liquid phase sample collection method for surface sampling and ionization with subsequent mass spectral analysis. A commercially available autosampler was adapted to produce a liquid droplet at the end of the syringe injection needle while in close proximity to the surface to collect the sample plume produced by laser ablation. The sample collection was followed by either flow injection or a high performance liquid chromatography (HPLC) separation of the extracted components and detection with electrospray ionization mass spectrometry (ESI-MS). To illustrate the analytical utility of thismore » coupling, thin films of a commercial ink sample containing rhodamine 6G and of mixed isobaric rhodamine B and 6G dyes on glass microscope slides were analyzed. The flow injection and HPLC/ESI-MS analysis revealed successful laser ablation, capture and, with HPLC, the separation of the two compounds. The ablated circular area was about 70 m in diameter for these experiments. The spatial sampling resolution afforded by the laser ablation, as well as the ability to use sample processing methods like HPLC between the sample collection and ionization steps, makes this combined surface sampling/ionization technique a highly versatile analytical tool.« less

Lysine Succinylation Contributes to Aflatoxin Production and Pathogenicity in Aspergillus flavus*

PubMed Central

Ren, Silin; Yang, Mingkun; Yue, Yuewei; Ge, Feng; Li, Yu; Guo, Xiaodong; Zhang, Jia; Zhang, Feng; Nie, Xinyi; Wang, Shihua

2018-01-01

Aspergillus flavus (A. flavus) is a ubiquitous saprophytic and pathogenic fungus that produces the aflatoxin carcinogen, and A. flavus can have tremendous economic and health impacts worldwide. Increasing evidence demonstrates that lysine succinylation plays an important regulatory role in metabolic processes in both bacterial and human cells. However, little is known about the extent and function of lysine succinylation in A. flavus. Here, we performed a global succinylome analysis of A. flavus using high accuracy nano-LC-MS/MS in combination with the enrichment of succinylated peptides from digested cell lysates and subsequent peptide identification. In total, 985 succinylation sites on 349 succinylated proteins were identified in this pathogen. Bioinformatics analysis revealed that the succinylated proteins were involved in various biological processes and were particularly enriched in the aflatoxin biosynthesis process. Site-specific mutagenesis and biochemical studies showed that lysine succinylation on the norsolorinic acid reductase NorA (AflE), a key enzyme in aflatoxins biosynthesis, can affect the production of sclerotia and aflatoxins biosynthesis in A. flavus. Together, our findings reveal widespread roles for lysine succinylation in regulating metabolism and aflatoxins biosynthesis in A. flavus. Our data provide a rich resource for functional analyses of lysine succinylation and facilitate the dissection of metabolic networks in this pathogen. PMID:29298838

A UPLC-MS/MS method for analysis of vancomycin in human cerebrospinal fluid and comparison with the chemiluminescence immunoassay.

PubMed

Mei, Shenghui; Wang, Jiaqing; Zhu, Leting; Chen, Ruiling; Li, Xingang; Chen, Kai; Chen, Guangqiang; Zhou, Jianxin; Wang, Qiang; Zhao, Zhigang

2017-08-01

Vancomycin (VCM) is clinically used in treating patients with postoperative intracranial infections. The cerebrospinal fluid (CSF) concentration of VCM varies greatly among patients. To guide the dosage regimens, monitoring of VCM in CSF is needed. However a method for analysis of VCM in human CSF is lacking. An ultraperformance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) was developed and validated for analysis of VCM in human CSF, and the agreement of UPLC-MS/MS and chemiluminescence immunoassay (CLIA) in the analysis of CSF VCM was evaluated. The ion transitions were m/z 725.5 > 144.1 for VCM and m/z 455.2 > 308.2 for methotrexate (internal standard). The agreement between UPLC-MS/MS and CLIA was evaluated by Bland-Altman plot in 179 samples. The calibration range of the UPLC-MS/MS method was 1-400 mg/L. The inaccuracy and imprecision were -0.69-10.80% and <4.95%. The internal standard normalized recovery and matrix factor were 86.14-99.31 and 85.84-92.07%, respectively. The measurements of CLIA and UPLC-MS/MS were strongly correlated (r > 0.98). The 95% limit of agreement of the ratio of CLIA to UPLC-MS/MS was 61.66-107.40%. Further studies are warranted to confirm the results. Copyright © 2017 John Wiley & Sons, Ltd.

Status of selected ion flow tube MS: accomplishments and challenges in breath analysis and other areas.

PubMed

Smith, David; Španěl, Patrik

2016-06-01

This article reflects our observations of recent accomplishments made using selected ion flow tube MS (SIFT-MS). Only brief descriptions are given of SIFT-MS as an analytical method and of the recent extensions to the underpinning analytical ion chemistry required to realize more robust analyses. The challenge of breath analysis is given special attention because, when achieved, it renders analysis of other air media relatively straightforward. Brief overviews are given of recent SIFT-MS breath analyses by leading research groups, noting the desirability of detection and quantification of single volatile biomarkers rather than reliance on statistical analyses, if breath analysis is to be accepted into clinical practice. A 'strengths, weaknesses, opportunities and threats' analysis of SIFT-MS is made, which should help to increase its utility for trace gas analysis.

Toxicokinetics of new psychoactive substances: plasma protein binding, metabolic stability, and human phase I metabolism of the synthetic cannabinoid WIN 55,212-2 studied using in vitro tools and LC-HR-MS/MS.

PubMed

Mardal, Marie; Gracia-Lor, Emma; Leibnitz, Svenja; Castiglioni, Sara; Meyer, Markus R

2016-10-01

The new psychoactive substance WIN 55,212-2 ((R)-(+)-[2,3-dihydro-5-methyl-3-(4-morpholinylmethyl)pyrrolo-[1,2,3-de]-1,4-benzoxazin-6-yl]-1-napthalenylmethanone) is a potent synthetic cannabinoid receptor agonist. The metabolism of WIN 55,212-2 in man has never been reported. Therefore, the aim of this study was to identify the human in vitro metabolites of WIN 55,212-2 using pooled human liver microsomes and liquid chromatography-high resolution-tandem mass spectrometry (LC-HR-MS/MS) to provide targets for toxicological, doping, and environmental screening procedures. Moreover, a metabolic stability study in pooled human liver microsomes (pHLM) was carried out. In total, 19 metabolites were identified and the following partly overlapping metabolic steps were deduced: degradation of the morpholine ring via hydroxylation, N- and O-dealkylation, and oxidative deamination, hydroxylations on either the naphthalene or morpholine ring or the alkyl spacer with subsequent oxidation, epoxide formation with subsequent hydrolysis, or combinations. In conclusion, WIN 55,212-2 was extensively metabolized in human liver microsomes incubations and the calculated hepatic clearance was comparably high, indicating a fast and nearly complete metabolism in vivo. This is in line with previous findings on other synthetic cannabinoids. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Assigning Peptide Disulfide Linkage Pattern Among Regio-Isomers via Methoxy Addition to Disulfide and Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Durand, Kirt L.; Tan, Lei; Stinson, Craig A.; Love-Nkansah, Chasity B.; Ma, Xiaoxiao; Xia, Yu

2017-06-01

Pinpointing disulfide linkage pattern is critical in the characterization of proteins and peptides consisting of multiple disulfide bonds. Herein, we report a method based on coupling online disulfide modification and tandem mass spectrometry (MS/MS) to distinguish peptide disulfide regio-isomers. Such a method relies on a new disulfide bond cleavage reaction in solution, involving methanol as a reactant and 254 nm ultraviolet (UV) irradiation. This reaction leads to selective cleavage of a disulfide bond and formation of sulfenic methyl ester (-SOCH3) at one cysteine residue and a thiol (-SH) at the other. Under low energy collision-induced dissociation (CID), cysteine sulfenic methyl ester motif produces a signature methanol loss (-32 Da), allowing its identification from other possible isomeric structures such as S-hydroxylmethyl (-SCH2OH) and methyl sulfoxide (-S(O)-CH3). Since disulfide bond can be selectively cleaved and modified upon methoxy addition, subsequent MS2 CID of the methoxy addition product provides enhanced sequence coverage as demonstrated by the analysis of bovine insulin. More importantly, this reaction does not induce disulfide scrambling, likely due to the fact that radical intermediates are not involved in the process. An approach based on methoxy addition followed by MS3 CID has been developed for assigning disulfide linkage patterns in peptide disulfide regio-isomers. This methodology was successfully applied to characterizing peptide systems having two disulfide bonds and three disulfide linkage isomers: side-by-side, overlapped, and looped-within-a-loop configurations. [Figure not available: see fulltext.

A novel sample preparation and on-line HPLC-DAD-MS/MS-BCD analysis for rapid screening and characterization of specific enzyme inhibitors in herbal extracts: case study of α-glucosidase.

PubMed

Li, D Q; Zhao, J; Xie, J; Li, S P

2014-01-01

Drug discovery from complex mixture like Chinese herbs is a challenge and extensive false positives make the obtainment of specific bioactive compounds difficult. In the present study, a novel sample preparation method was proposed to rapidly reveal the specific bioactive compounds from complex mixtures using α-glucosidase as a case. Firstly, aqueous and methanol extracts of 500 traditional Chinese medicines were carried out with the aim of finding new sources of α-glucosidase inhibitors. As a result, the extracts of fruit of Terminalia chebula (FTC), flowers of Rosa rugosa (FRR) and Eugenia caryophyllata (FEC) as well as husk of Punica granatum (HPG) showed high inhibition on α-glucosidase. On-line liquid chromatography-diode array detection-tandem mass spectrometry and biochemical detection (HPLC-DAD-MS/MS-BCD) was performed to rapidly screen and characterize α-glucosidase inhibitors in these four extracts. After tentative identification, most of compounds with inhibitory activity in the investigated crude extracts were found to be tannins commonly recognized as non-specific enzyme inhibitors in vitro. Subsequently, the four extracts were treated with gelatin to improve specificity of the on-line system. Finally, two compounds with specific α-glucosidase inhibition were identified as corilagin and ellagic acid. The developed method could discover specific α-glucosidase inhibitors in complex mixtures such as plant extracts, which could also be used for discovery of specific inhibitors of other enzymes. Copyright © 2013 Elsevier B.V. All rights reserved.

Antagonism of corticotrophin-releasing factor receptors in the fourth ventricle modifies responses to mild but not restraint stress.

PubMed

Miragaya, Joanna R; Harris, Ruth B S

2008-08-01

Repeated restraint stress (RRS; 3 h of restraint on 3 consecutive days) in rodents produces temporary hypophagia, but a long-term downregulation of body weight. The mild stress (MS) of an intraperitoneal injection of saline and housing in a novel room for 2 h also inhibits food intake and weight gain, but the effects are smaller than for RRS. Previous exposure to RRS exaggerates hypophagia, glucocorticoid release, and anxiety-type behavior caused by MS. Here we tested the involvement of brain stem corticotrophin-releasing factor receptors (CRFR) in mediating energetic and glucocorticoid responses to RRS or MS and in promoting stress hyperresponsiveness in RRS rats. Administration of 1.3 nmol alphahCRF(9-41), a nonspecific CRFR antagonist, exaggerated hypophagia and weight loss in both RRS and MS rats, whereas 0.26 nmol had no effect in RRS or MS rats. In contrast, 2 nmol of the nonspecific antagonist astressin had no effect on weight loss or hypersensitivity to subsequent MS in RRS rats, but blocked weight loss and inhibition of food intake caused by MS alone. MS rats infused with 3 nmol antisauvagine-30, a CRFR2 antagonist, did not lose weight in the 48 h after MS, but 0.3 nmol did not prevent weight loss in MS rats. These data suggest that inhibition of food intake and weight loss induced by RRS or by MS involve different pathways, with hindbrain CRFR mediating the effect of MS on body weight and food intake. Hindbrain CRFR do not appear to influence stress-induced corticosterone release in RRS rats.

Study of chlordecone desorption from activated carbons and subsequent dechlorination by reduced cobalamin.

PubMed

Ranguin, Ronald; Durimel, Axelle; Karioua, Reeka; Gaspard, Sarra

2017-11-01

Since 1972, the French departments of Guadeloupe and Martinique have intensively used organochlorinated pesticides such as chlordecone (CLD) and hexachlorocyclohexane (HCH) isomers to prevent the proliferation of banana weevil (Cosmopolite sordidus). These molecules are stable in the environment, leading to a continuous contamination of soils, water, and food chain in the banana-producing areas. In these polluted areas, water treatment plants are equipped with activated carbon (AC) filters. In order to improve treatment of CLD-contaminated waters by AC, CLD adsorption and desorption kinetic studies are carried out using different ACs produced from sugar cane bagasse as adsorbents and subsequent CLD degradation is performed using reduced vitamin B12 (VB12). A GC-MS method for CLD quantification is as well optimized. This study shows that bagasse ACs are able to capture the pollutant, leading to a CLD concentration decrease from 1 to 73 μg L -1 , with an adsorption capacity of 162 μg mg -1 . Adsorption capacity increase with the temperature indicates an endothermic process. Polar solvents favor CLD desorption from ACs, suggesting hydrogen bonding between CLD and surface groups of ACs, the best solvent for chemical desorption being ethanol. Subsequent degradation of CLD in ethanol is performed using vitamin B12 reduced by either 1,4-dithiotreitol (DTT) or zerovalent zinc, leading to 90% of CLD removal and to the molecule cage structure opening for formation of a pentachloroindene intermediate product, characterized by GC MS/MS. A pathway for pentachloroindene formation from CLD is proposed.

Could transformation mechanisms of acetylase-harboring pMdT1 plasmid be evaluated through proteomic tools in Escherichia coli?

PubMed

Magalhães, Pedro; Pinto, Luís; Gonçalves, Alexandre; Araújo, José Eduardo; Santos, Hugo M; Capelo, José Luis; Saénz, Yolanda; de Toro, María; Torres, Carmen; Chambon, Christophe; Hébraud, Michel; Poeta, Patrícia; Igrejas, Gilberto

2016-08-11

Escherichia coli is a commensal microorganism of the gastrointestinal tract of animals and humans and it is an excellent model organism for the study of antibiotic resistance mechanisms. The resistance transmission and other characteristics of bacteria are based on different types of gene transfer occurring throughout the bacterial evolution. One of which is horizontal gene transfer that allows us to understand the ability of bacteria to acquire new genes. One dimensional and two dimensional electrophoresis (2-DE) techniques were performed in order to identify and characterize the proteome of two E. coli strains: Electromax DH10B, a transformation-ready strain; and TF-Se20, the Electromax DH10B that contains the aac(6')-Ib-cr4-harboring pMdT1 plasmid. After 2-DE and subsequent analysis by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), it was possible to identify 76 distinct proteins on the TF-Se20 strain, whereas 71 had a known function. From Electromax DH10B strain, 72 different proteins were identified of which 71 were associated with a biological process. The protein of interest, aminoglycoside N-(6')-acetyltransferase type 1, was identified by MALDI-TOF MS. The liquid chromatography-tandem mass spectrometry (LC-MS/MS) technique was performed to determine its sequence. Seventy six percent of the acetylase sequence was reconstructed only in the TF-Se20 strain, representing the single protein associated to antibiotic resistance. MALDI-TOF MS and LC-MS/MS approaches allowed us to determine the total proteome of both strains, as well as the acetylase sequence. Both of them enhance the ability to obtain more accurate information about the mechanisms of antimicrobial resistance. The pMdT1 plasmid brings a new perspective in understanding the metabolic processes that lead to antibiotic resistance. This study highlights the importance of proteomics and bioinformatics in understanding mechanisms of gene transfer and antibiotic resistance. These two approaches allow to compare the protein expression in different samples, as well as different biological processes related to each protein. Copyright © 2016 Elsevier B.V. All rights reserved.

Metabolism and bioactivation of the tricyclic antidepressant amitriptyline in human liver microsomes and human urine.

PubMed

Zhou, Xin; Chen, Chang; Zhang, Fangrong; Zhang, Yang; Feng, Yuling; Ouyang, Hui; Xu, Yong; Jiang, Hongliang

2016-07-01

Amitriptyline is a widely used tricyclic antidepressant, but the metabolic studies were conducted almost 20 years ago using high-performance liquid chromatography coupled with ultraviolet detector or radiolabeled methods. First, multiple ion monitoring (MIM)- enhanced product ion (EPI) scan was used to obtain the diagnostic ions or neutral losses in human liver microsome incubations with amitriptyline. Subsequently, predicted multiple reaction monitoring (MRM)-EPI scan was used to identify the metabolites in human urine with the diagnostic ions or neutral losses. Finally, product ion filtering and neutral loss filtering were used as the data mining tools to screen metabolites. Consequently, a total of 28 metabolites were identified in human urine after an oral administration using LC-MS/MS. An integrated workflow using LC-MS/MS was developed to comprehensively profile the metabolites of amitriptyline in human urine, in which five N-acetyl-l-cysteine conjugates were characterized as tentative biomarkers for idiosyncratic toxicity.

A new method for stable lead isotope extraction from seawater.

PubMed

Zurbrick, Cheryl M; Gallon, Céline; Flegal, A Russell

2013-10-24

A new technique for stable lead (Pb) isotope extraction from seawater is established using Toyopearl AF-Chelate 650M(®) resin (Tosoh Bioscience LLC). This new method is advantageous because it is semi-automated and relatively fast; in addition it introduces a relatively low blank by minimizing the volume of chemicals used in the extraction. Subsequent analyses by HR ICP-MS have a good relative external precision (2σ) of 3.5‰ for (206)Pb/(207)Pb, while analyses by MC-ICP-MS have a better relative external precision of 0.6‰. However, Pb sample concentrations limit MC-ICP-MS analyses to (206)Pb, (207)Pb, and (208)Pb. The method was validated by processing the common Pb isotope reference material NIST SRM-981 and several GEOTRACES intercalibration samples, followed by analyses by HR ICP-MS, all of which showed good agreement with previously reported values. Copyright © 2013 Elsevier B.V. All rights reserved.

Fluorescence-labeled methylation-sensitive amplified fragment length polymorphism (FL-MS-AFLP) analysis for quantitative determination of DNA methylation and demethylation status.

PubMed

Kageyama, Shinji; Shinmura, Kazuya; Yamamoto, Hiroko; Goto, Masanori; Suzuki, Koichi; Tanioka, Fumihiko; Tsuneyoshi, Toshihiro; Sugimura, Haruhiko

2008-04-01

The PCR-based DNA fingerprinting method called the methylation-sensitive amplified fragment length polymorphism (MS-AFLP) analysis is used for genome-wide scanning of methylation status. In this study, we developed a method of fluorescence-labeled MS-AFLP (FL-MS-AFLP) analysis by applying a fluorescence-labeled primer and fluorescence-detecting electrophoresis apparatus to the existing method of MS-AFLP analysis. The FL-MS-AFLP analysis enables quantitative evaluation of more than 350 random CpG loci per run. It was shown to allow evaluation of the differences in methylation level of blood DNA of gastric cancer patients and evaluation of hypermethylation and hypomethylation in DNA from gastric cancer tissue in comparison with adjacent non-cancerous tissue.

Integrating genome-wide association studies and gene expression data highlights dysregulated multiple sclerosis risk pathways.

PubMed

Liu, Guiyou; Zhang, Fang; Jiang, Yongshuai; Hu, Yang; Gong, Zhongying; Liu, Shoufeng; Chen, Xiuju; Jiang, Qinghua; Hao, Junwei

2017-02-01

Much effort has been expended on identifying the genetic determinants of multiple sclerosis (MS). Existing large-scale genome-wide association study (GWAS) datasets provide strong support for using pathway and network-based analysis methods to investigate the mechanisms underlying MS. However, no shared genetic pathways have been identified to date. We hypothesize that shared genetic pathways may indeed exist in different MS-GWAS datasets. Here, we report results from a three-stage analysis of GWAS and expression datasets. In stage 1, we conducted multiple pathway analyses of two MS-GWAS datasets. In stage 2, we performed a candidate pathway analysis of the large-scale MS-GWAS dataset. In stage 3, we performed a pathway analysis using the dysregulated MS gene list from seven human MS case-control expression datasets. In stage 1, we identified 15 shared pathways. In stage 2, we successfully replicated 14 of these 15 significant pathways. In stage 3, we found that dysregulated MS genes were significantly enriched in 10 of 15 MS risk pathways identified in stages 1 and 2. We report shared genetic pathways in different MS-GWAS datasets and highlight some new MS risk pathways. Our findings provide new insights on the genetic determinants of MS.

Impact of a transposon insertion in phzF2 on the specialized metabolite production and interkingdom interactions of Pseudomonas aeruginosa.

PubMed

Phelan, Vanessa V; Moree, Wilna J; Aguilar, Julieta; Cornett, Dale S; Koumoutsi, Alexandra; Noble, Suzanne M; Pogliano, Kit; Guerrero, Carlos A; Dorrestein, Pieter C

2014-05-01

In microbiology, gene disruption and subsequent experiments often center on phenotypic changes caused by one class of specialized metabolites (quorum sensors, virulence factors, or natural products), disregarding global downstream metabolic effects. With the recent development of mass spectrometry-based methods and technologies for microbial metabolomics investigations, it is now possible to visualize global production of diverse classes of microbial specialized metabolites simultaneously. Using imaging mass spectrometry (IMS) applied to the analysis of microbiology experiments, we can observe the effects of mutations, knockouts, insertions, and complementation on the interactive metabolome. In this study, a combination of IMS and liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to visualize the impact on specialized metabolite production of a transposon insertion into a Pseudomonas aeruginosa phenazine biosynthetic gene, phzF2. The disruption of phenazine biosynthesis led to broad changes in specialized metabolite production, including loss of pyoverdine production. This shift in specialized metabolite production significantly alters the metabolic outcome of an interaction with Aspergillus fumigatus by influencing triacetylfusarinine production.

Fragmentation study of iridoid glycosides including epimers by liquid chromatography-diode array detection/electrospray ionization mass spectrometry and its application in metabolic fingerprint analysis of Gardenia jasminoides Ellis.

PubMed

Zhou, Tingting; Liu, Hua; Wen, Jun; Fan, Guorong; Chai, Yifeng; Wu, Yutian

2010-09-15

A high-performance liquid chromatography-diode array detection/electrospray ionization mass spectrometry (HPLC-DAD/ESI-MS) method was applied to the characterization of ten iridoid glycosides in Gardenia jasminoides Ellis, a traditional Chinese medicine. During the process of structural elucidation, two groups of isomers including two epimers were structurally characterized and differentiated according to their distinctive fragmentation patterns which were closely related to their isomeric differentiations. Subsequently, the major compounds were purified by multi-dimensional chromatography and semi-preparative HPLC and the structure identification was confirmed with NMR techniques. The major fragmentation pathways of iridoid glycosides in Gardenia jasminoides Ellis obtained through the MS data were schemed systematically, which provided the best sensitivity and specificity for characterization of the iridoid glycosides especially the isomers so far. Based on the fragmentation patterns of iridoid glycosides concluded, seven major iridoid glycosides were characterized in rat plasma after intravenous administration of Gardenia jasminoides Ellis. Copyright 2010 John Wiley & Sons, Ltd.

Use of GC/MS and Microtome Techniques as Methods to Evaluate ODC Free Cleaner Diffusion and Evaporation in Insulation and Phenolic Case Material

NASA Technical Reports Server (NTRS)

Biegert, L. L.

2001-01-01

Because of the 1990 Clean Air Act Amendment (CAAA) many chlorinated solvents used in the aerospace industry are being phased out. Replacement of the ODC (ozone-depleting chemicals) with less volatile, non-ozone depleting cleaners has been extensively studied over the past seven years at Thiokol Propulsion, a Division of Cordant Technologies, Inc. The down selection of ODC replacement cleaners has been based on several factors including the diffusion evaporation of the cleaners in selected substrates. Methodologies were developed to evaluate the cleaner content in substrates. Methods of cutting thin slices of material (microtoming) were combined with GC/MS (gas chromatography/mass spectroscopy) analysis. Substrates evaluated in this study include potential solid rocket motor materials: ASNBR (asbestos-filled nitrile butadiene rubber) and CFEPDM (carbon-filled ethylene propylene dimonomer) insulation and glass (GCP), carbon (CCP) and silica (SCP) cloth phenolic substrates with fibers either parallel (0 deg) or perpendicular (90 deg) to the surface. Residue profiles indicate both cleaner and substrate composition affect the diffusion and subsequent evaporation of the cleaner from the substrate surface.

Liquid-phase-based separation systems for depletion, prefractionation and enrichment of proteins in biological fluids and matrices for in-depth proteomics analysis – An update covering the period 2011-2014

PubMed Central

Puangpila, Chanida; Mayadunne, Erandi; Rassi, Ziad El

2015-01-01

This review article expands on the previous one (S. Selvaraju and Z. El Rassi, Electrophoresis 2012, 33, 74-88) by reviewing pertinent literature in the period extending from early 2011 to present. As the previous review article, the present one is concerned with proteomic sample preparation (e.g., depletion of high abundance proteins, reduction of the protein dynamic concentration range, enrichment of a particular sub-proteome), and the subsequent chromatographic and/or electrophoretic pre-fractionation prior to peptide separation and identification by LC-MS/MS. This review article is distinguished from its second version published in Electrophoresis 2012, 33, 74-88 by expanding on capturing/enriching sub-phosphoproteomes by immobilized metal affinity chromatography and metal oxide affinity chromatography. Seventy-seven papers published in the period extending from mid 2011 to the present have been reviewed. By no means this review article is exhaustive, given the fact that its aim is to give a concise treatment of the latest developments in the field. PMID:25287967

Liquid chromatography-tandem mass spectrometric assay for the simultaneous determination of the irreversible BTK inhibitor ibrutinib and its dihydrodiol-metabolite in plasma and its application in mouse pharmacokinetic studies.

PubMed

Rood, Johannes J M; van Hoppe, Stephanie; Schinkel, Alfred H; Schellens, Jan H M; Beijnen, Jos H; Sparidans, Rolf W

2016-01-25

A validated simple, fast and sensitive bio-analytical assay for ibrutinib and its dihydrodiol metabolite in human and mouse plasma was set up. Sample preparation was performed by protein precipitation, and addition of the respective deuterated internal standards, followed by LC-MS/MS analysis. Separation was performed on a 3.5 μm particle-size, bridged ethylene hybrid column with gradient elution by 0.1% v/v formic acid and acetonitrile. The full eluate was transferred to an electrospray interface in positive ionization mode, and subsequently analyzed by a triple quadrupole mass spectrometer by selected reaction monitoring. The assay was validated in a 5-5000 ng/ml calibration range. Both ibrutinib and dihydrodiol-ibrutinib were deemed stable under refrigerated or frozen storage conditions. At room temperature, ibrutinib showed a not earlier described instability, and revealed rapid degradation at 37 °C. Finally, the assay was used for a pharmacokinetic study of plasma levels in treated FVB mice. Copyright © 2015 Elsevier B.V. All rights reserved.

Production of ⁶¹Cu by the natZn(p,α) reaction: Improved separation and specific activity determination by titration with three chelators

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

Asad, Ali H.; Smith, Suzanne V.; Morandeau, Laurence M.

In this study, the cyclotron-based production of position-emitting ⁶¹Cu using the (p,α) reaction at 11.7 MeV was investigated starting from natural-zinc ( natZn) and enriched ⁶⁴Zn-foil targets, as well as its subsequent purification. For natZn, a combination of three resins were assessed to separate ⁶¹Cu from contaminating 66,67,68Ga and natZn. The specific activity of the purified ⁶¹Cu determined using ICP-MS analysis ranged from 143.3±14.3(SD) to 506.2±50.6 MBq/μg while the titration method using p-SCN-Bn-DOTA, p-SCN-Bn-NOTA and diamsar gave variable results (4.7±0.2 to 412.5±15.3 MBq/μg), with diamsar lying closest to the ICP-MS values. Results suggest that the p-SCN-Bn-DOTA and p-SCN-Bn-NOTA titration methodsmore » are significantly affected by the presence of trace-metal contaminants.« less

Analysis of the lightning-attractive radius for wind turbines considering the developing process of positive attachment leader

NASA Astrophysics Data System (ADS)

Yang, Ning; Zhang, Qilin; Hou, Wenhao; Wen, Ying

2017-03-01

In this paper, we have presented the upward leader propagation model, considering the transition of stream leader process by the finite element method and analyzing the inception and subsequent physical processes of upward leader and the attractive radius for large wind turbines. For validating our model, the comparison of simulated results with the optically high-speed video observation shows that the model can predict an accepted result of upward leader from a 163 m tall tower, the simulated upward leader velocity and length before final jump are 2.3 × 105 m/s and 187.67 m presented by Warner (2010), which are very similar to the observed results of 2.8 × 105 m/s and 184 m, respectively. At the same time, we find that the assumed constant speed ratio of downward/upward leader is improper and cannot accurately predict the attractive radius by lightning strike. Also, the simulated results are compared with the widely used EGM (electro geometric model), and it is found that the EGM has an obvious underestimation of attractive radius more than 50%.

[PROTEOMIC ANALYSIS OF ADAPTIVE MECHANISMS TO SALINITY STRESS IN MARINE GASTROPODS LITTORINA SAXATILIS].

PubMed

Muraeva, O A; Maltseva, A L; Mikhailova, N A; Granovitch, A I

2015-01-01

Salinity is one of the most important abiotic environmental factors affecting marine animals. If salinity deviate from optimum, adaptive mechanisms switch on to maintain organism's physiological activity. In this study, the reaction of the snails Littorina saxatilis from natural habitats and in response to experimental salinity decreasing was analyzed on proteomic level. The isolation of all snails inside their shells and gradually declining mortality was observed under acute experimental salinity decrease (down to 10 per hundred). Proteomic changes were evaluated in the surviving experimental mollusks compared to control individual using differential 2D gel-electrophoresis (DIGE) and subsequent LC-MS/MS-identification of proteins. Approximately 10% of analyzed proteins underwent up- or down regulation during the experiment. Proteins of folding, antioxidant response, intercellular matrix, cell adhesion, cell signaling and metabolic enzymes were identified among them. Proteome changes observed in experimental hypoosmotic stress partially reproduced in the proteomes of mollusks that live in conditions of natural freshening (estuaries). Possible mechanisms involved in the adaptation process of L. saxatilis individuals to hypo-osmotic stress are discussed.

Arsenic Speciation in Fish Products and Seafood as a Prerequisite for Proper Risk Assessment

PubMed Central

Orletti, Roberta; Chessa, Giannina; Carloni, Cristiano; Griffoni, Francesco; Palombo, Paolo; Velieri, Francesco

2015-01-01

The Boi Cerbus lagoon, facing a mining and industrial site in Sardinia (Italy), is an important fishing area for the local population. Previous studies showed high concentrations of total arsenic (Astot) in fish, molluscs and crustaceans sampled in the lagoon, and a possible exceeding of the provisional tolerable weekly intake set by the Joint FAO/WHO Expert Committee on Food Additives by some local consumer groups. However, the percentage of inorganic As (Asinorg) should be known for a correct assessment of potential risk, as its toxicity is much higher than that of the organic forms. Eighty samples of 14 different species of fish, molluscs and crustaceans, sampled in the Boi Cerbus lagoon in 3 different seasons (winter, spring and summer), were analysed for Astot by inductively coupled plasma mass spectrometry (ICP-MS) and Asinorg by high performance liquid chromatography-ICP-MS. All the data obtained from the analysis were statistically processed to evaluate significant differences based on season, taxon and habitat, in preparation for a subsequent risk assessment. PMID:27800381

Analysis of hazardous organic residues from sodium hydrosulfite industry and utilization as raw materials in a novel solid lubricant production.

PubMed

Shang, Jiwu; Zhang, Yihe; Zhou, Fengshan; Lv, Fengzhu; Han, Feng; Lu, Jinbo; Meng, Xianghai; Chu, Paul K; Ye, Zhengfang; Xing, Jing

2011-12-30

The hazardous organic residual wastes produced by the sodium hydrosulfite industry are demonstrated to be convertible into a novel solid lubricant. Identification and isolation of the organic residues are achieved by Fourier transform infrared (FTIR) spectroscopy, gas chromatography-mass spectrometry (GC-MS), and nuclear magnetic resonance (NMR). FTIR and GC-MS provide important information about the residues and the two main components obtained by column chromatography are further analyzed by NMR. The main organic residues are found to be thiodiglycol and 2,2'-dithiodiethanol which have potential applications in petroleum drilling because of their S-S and/or C-S functional groups. The lubricity of the organic residues is subsequently studied and the influence of different adsorbents on the lubricity is investigated and discussed. This homemade lubricant is observed to have good lubricity and by increasing the concentration of the commercial solid lubricant M, the lubricity diminishes. The process is expected to not only have commercial impact but also help to reduce environmental pollution. Copyright © 2011 Elsevier B.V. All rights reserved.

Synchronized Regulation of Different Zwitterionic Metabolites in the Osmoadaption of Phytoplankton

PubMed Central

Gebser, Björn; Pohnert, Georg

2013-01-01

The ability to adapt to different seawater salinities is essential for cosmopolitan marine phytoplankton living in very diverse habitats. In this study, we examined the role of small zwitterionic metabolites in the osmoadaption of two common microalgae species Emiliania huxleyi and Prorocentrum minimum. By cultivation of the algae under salinities between 16‰ and 38‰ and subsequent analysis of dimethylsulfoniopropionate (DMSP), glycine betaine (GBT), gonyol, homarine, trigonelline, dimethylsulfonioacetate, trimethylammonium propionate, and trimethylammonium butyrate using HPLC-MS, we could reveal two fundamentally different osmoadaption mechanisms. While E. huxleyi responded with cell size reduction and a nearly constant ratio between the major metabolites DMSP, GBT and homarine to increasing salinity, osmolyte composition of P. minimum changed dramatically. In this alga DMSP concentration remained nearly constant at 18.6 mM between 20‰ and 32‰ but the amount of GBT and dimethylsulfonioacetate increased from 4% to 30% of total investigated osmolytes. Direct quantification of zwitterionic metabolites via LC-MS is a powerful tool to unravel the complex osmoadaption and regulation mechanisms of marine phytoplankton. PMID:23774888

Impact of a Transposon Insertion in phzF2 on the Specialized Metabolite Production and Interkingdom Interactions of Pseudomonas aeruginosa

PubMed Central

Phelan, Vanessa V.; Moree, Wilna J.; Aguilar, Julieta; Cornett, Dale S.; Koumoutsi, Alexandra; Noble, Suzanne M.; Pogliano, Kit; Guerrero, Carlos A.

2014-01-01

In microbiology, gene disruption and subsequent experiments often center on phenotypic changes caused by one class of specialized metabolites (quorum sensors, virulence factors, or natural products), disregarding global downstream metabolic effects. With the recent development of mass spectrometry-based methods and technologies for microbial metabolomics investigations, it is now possible to visualize global production of diverse classes of microbial specialized metabolites simultaneously. Using imaging mass spectrometry (IMS) applied to the analysis of microbiology experiments, we can observe the effects of mutations, knockouts, insertions, and complementation on the interactive metabolome. In this study, a combination of IMS and liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to visualize the impact on specialized metabolite production of a transposon insertion into a Pseudomonas aeruginosa phenazine biosynthetic gene, phzF2. The disruption of phenazine biosynthesis led to broad changes in specialized metabolite production, including loss of pyoverdine production. This shift in specialized metabolite production significantly alters the metabolic outcome of an interaction with Aspergillus fumigatus by influencing triacetylfusarinine production. PMID:24532776

Production of ⁶¹Cu by the natZn(p,α) reaction: Improved separation and specific activity determination by titration with three chelators

DOE PAGES

Asad, Ali H.; Smith, Suzanne V.; Morandeau, Laurence M.; ...

2015-09-01

In this study, the cyclotron-based production of position-emitting ⁶¹Cu using the (p,α) reaction at 11.7 MeV was investigated starting from natural-zinc ( natZn) and enriched ⁶⁴Zn-foil targets, as well as its subsequent purification. For natZn, a combination of three resins were assessed to separate ⁶¹Cu from contaminating 66,67,68Ga and natZn. The specific activity of the purified ⁶¹Cu determined using ICP-MS analysis ranged from 143.3±14.3(SD) to 506.2±50.6 MBq/μg while the titration method using p-SCN-Bn-DOTA, p-SCN-Bn-NOTA and diamsar gave variable results (4.7±0.2 to 412.5±15.3 MBq/μg), with diamsar lying closest to the ICP-MS values. Results suggest that the p-SCN-Bn-DOTA and p-SCN-Bn-NOTA titration methodsmore » are significantly affected by the presence of trace-metal contaminants.« less

Lanthanides determination in red wine using ultrasound assisted extraction, flow injection, aerosol desolvation and ICP-MS.

PubMed

Bentlin, Fabrina R S; dos Santos, Clarissa M M; Flores, Erico M M; Pozebon, Dirce

2012-01-13

This paper deals with the determination of the fourteen naturally occurring elements of the lanthanide series in red wine. Ultrasound (US) was used for sample preparation prior lanthanides determination using ICP-MS. Flow injection (FI) and pneumatic nebulization/aerosol desolvation were used for nebulization of aliquots of 50 μL of sample and its subsequent transportation to plasma. Sample preparation procedures, matrix interference and time of sonication were evaluated. Better results for lanthanides in red wine were obtained by sonication with US probe for 90 s and sample 10-fold diluted. The limits of detection of La, Ce, Nd, Sm, Gd, Pr, Eu, Tb, Dy, Ho, Er, Tm, Lu and Yb were 6.57, 10.8, 9.97, 9.38, 2.71, 1.29, 1.22, 0.52, 2.35, 0.96, 2.30, 0.45, 0.24 and 1.35 ng L(-1), respectively. Red wines of different varieties from three countries of South America were discriminated according to the country of origin by means of multivariate analysis of lanthanides concentration. Copyright © 2011 Elsevier B.V. All rights reserved.

Rapid detection of peptide markers for authentication purposes in raw and cooked meat using ambient liquid extraction surface analysis mass spectrometry.

PubMed

Montowska, Magdalena; Alexander, Morgan R; Tucker, Gregory A; Barrett, David A

2014-10-21

In this Article, our previously developed ambient LESA-MS methodology is implemented to analyze five types of thermally treated meat species, namely, beef, pork, horse, chicken, and turkey meat, to select and identify heat-stable and species-specific peptide markers. In-solution tryptic digests of cooked meats were deposited onto a polymer surface, followed by LESA-MS analysis and evaluation using multivariate data analysis and tandem electrospray MS. The five types of cooked meat were clearly discriminated using principal component analysis and orthogonal partial least-squares discriminant analysis. 23 heat stable peptide markers unique to species and muscle protein were identified following data-dependent tandem LESA-MS analysis. Surface extraction and direct ambient MS analysis of mixtures of cooked meat species was performed for the first time and enabled detection of 10% (w/w) of pork, horse, and turkey meat and 5% (w/w) of chicken meat in beef, using the developed LESA-MS/MS analysis. The study shows, for the first time, that ambient LESA-MS methodology displays specificity sufficient to be implemented effectively for the analysis of processed and complex peptide digests. The proposed approach is much faster and simpler than other measurement tools for meat speciation; it has potential for application in other areas of meat science or food production.

Analysis of iodinated X-ray contrast agents in water samples by ion chromatography and inductively-coupled plasma mass spectrometry.

PubMed

Sacher, Frank; Raue, Brigitte; Brauch, Heinz-Jürgen

2005-08-26

In this paper, an analytical method for the determination of six iodinated X-ray contrast agents (amidotrizoic acid, iohexol, iomeprol, iopamidol, iopromide, and ioxitalamic acid), iodide, and iodate in water samples is presented. The method is based on a separation of the analytes by ion chromatography (IC) and a subsequent detection by inductively-coupled plasma mass spectrometry (ICP-MS). The method was optimised with respect to separation conditions (column type and eluent composition) and extensively validated. Without pre-concentration of the samples, limits of detection below 0.2 microg/l could be achieved whereby reproducibility was below 6% for all compounds under investigation.

Prevalence of QT interval prolongation in patients admitted to cardiac care units and frequency of subsequent administration of QT interval-prolonging drugs: a prospective, observational study in a large urban academic medical center in the US.

PubMed

Tisdale, James E; Wroblewski, Heather A; Overholser, Brian R; Kingery, Joanna R; Trujillo, Tate N; Kovacs, Richard J

2012-06-01

Cardiac arrest due to torsades de pointes (TdP) is a rare but catastrophic event in hospitals. Patients admitted to cardiac units are at higher risk of drug-induced QT interval prolongation and TdP, due to a preponderance of risk factors. Few data exist regarding the prevalence of QT interval prolongation in patients admitted to cardiac units or the frequency of administering QT interval-prolonging drugs to patients presenting with QT interval prolongation. The aim of this study was to determine the prevalence of Bazett's-corrected QT (QT(c)) interval prolongation upon admission to cardiac units and the proportion of patients presenting with QT(c) interval prolongation who are subsequently administered QT interval-prolonging drugs during hospitalization. This was a prospective, observational study conducted over a 1-year period (October 2008-October 2009) in 1159 consecutive patients admitted to two cardiac units in a large urban academic medical centre located in Indianapolis, IN, USA. Patients were enrolled into the study at the time of admission to the hospital and were followed daily during hospitalization. Exclusion criteria were age <18 years, ECG rhythm of complete ventricular pacing, and patient designation as 'outpatient' in a bed and/or duration of stay <24 hours. Data collected included demographic information, past medical history, daily progress notes, medication administration records, laboratory data, ECGs, telemetry monitoring strips and diagnostic reports. All patients underwent continuous cardiac telemetry monitoring and/or had a baseline 12-lead ECG obtained within 4 hours of admission. QT intervals were determined manually from lead II of 12-lead ECGs or from continuous lead II telemetry monitoring strips. QT(c) interval prolongation was defined as ≥470 ms for males and ≥480 ms for females. In both males and females, QT(c) interval >500 ms was considered abnormally high. A medication was classified as QT interval-prolonging if there were published data indicating that the drug causes QT interval prolongation and/or TdP. Study endpoints were (i) prevalence of QT(c) interval prolongation upon admission to the Cardiac Medical Critical Care Unit (CMCCU) or an Advanced Heart Care Unit (AHCU); (ii) proportion of patients admitted to the CMCCU/AHCU with QT(c) interval prolongation who subsequently were administered QT interval-prolonging drugs during hospitalization; (iii) the proportion of these higher-risk patients in whom TdP risk factor monitoring was performed; (iv) proportion of patients with QT(c) interval prolongation who subsequently received QT-prolonging drugs and who experienced further QT(c) interval prolongation. Of 1159 patients enrolled, 259 patients met exclusion criteria, resulting in a final sample size of 900 patients. mean (± SD) age, 65 ± 15 years; female, 47%; Caucasian, 70%. Admitting diagnoses: heart failure (22%), myocardial infarction (16%), atrial fibrillation (9%), sudden cardiac arrest (3%). QT(c) interval prolongation was present in 27.9% of patients on admission; 18.2% had QT(c) interval >500 ms. Of 251 patients admitted with QT(c) interval prolongation, 87 (34.7%) were subsequently administered QT interval-prolonging drugs. Of 166 patients admitted with QT(c) interval >500 ms, 70 (42.2%) were subsequently administered QT interval-prolonging drugs; additional QT(c) interval prolongation ≥60 ms occurred in 57.1% of these patients. QT(c) interval prolongation is common among patients admitted to cardiac units. QT interval-prolonging drugs are commonly prescribed to patients presenting with QT(c) interval prolongation.

Comparison of Ti-Based Coatings on Silicon Nanowires for Phosphopeptide Enrichment and Their Laser Assisted Desorption/Ionization Mass Spectrometry Detection

PubMed Central

Kurylo, Ievgen; Hamdi, Abderrahmane; Addad, Ahmed; Coffinier, Yannick

2017-01-01

We created different TiO2-based coatings on silicon nanowires (SiNWs) by using either thermal metallization or atomic layer deposition (ALD). The fabricated surfaces were characterized by X-ray photoelectron spectroscopy (XPS), energy dispersive X-ray spectroscopy (EDX), and reflectivity measurements. Surfaces with different TiO2 based coating thicknesses were then used for phosphopeptide enrichment and subsequent detection by laser desorption/ionization mass spectrometry (LDI-MS). Results showed that the best enrichment and LDI-MS detection were obtained using the silicon nanowires covered with 10 nm of oxidized Ti deposited by means of thermal evaporation. This sample was also able to perform phosphopeptide enrichment and MS detection from serum. PMID:28914806

Rapid and reliable species identification of wild mushrooms by matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS).

PubMed

Sugawara, Ryota; Yamada, Sayumi; Tu, Zhihao; Sugawara, Akiko; Suzuki, Kousuke; Hoshiba, Toshihiro; Eisaka, Sadao; Yamaguchi, Akihiro

2016-08-31

Mushrooms are a favourite natural food in many countries. However, some wild species cause food poisoning, sometimes lethal, due to misidentification caused by confusing fruiting bodies similar to those of edible species. The morphological inspection of mycelia, spores and fruiting bodies have been traditionally used for the identification of mushrooms. More recently, DNA sequencing analysis has been successfully applied to mushrooms and to many other species. This study focuses on a simpler and more rapid methodology for the identification of wild mushrooms via protein profiling based on matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS). A preliminary study using 6 commercially available cultivated mushrooms suggested that a more reproducible spectrum was obtained from a portion of the cap than from the stem of a fruiting body by the extraction of proteins with a formic acid-acetonitrile mixture (1 + 1). We used 157 wild mushroom-fruiting bodies collected in the centre of Hokkaido from June to November 2014. Sequencing analysis of a portion of the ribosomal RNA gene provided 134 identifications of mushrooms by genus or species, however 23 samples containing 10 unknown species that had lower concordance rate of the nucleotide sequences in a BLAST search (less than 97%) and 13 samples that had unidentifiable poor or mixed sequencing signals remained unknown. MALDI-TOF MS analysis yielded a reproducible spectrum (frequency of matching score ≥ 2.0 was ≥6 spectra from 12 spectra measurements) for 114 of 157 samples. Profiling scores that matched each other within the database gave correct species identification (with scores of ≥2.0) for 110 samples (96%). An in-house prepared database was constructed from 106 independent species, except for overlapping identifications. We used 48 wild mushrooms that were collected in autumn 2015 to validate the in-house database. As a result, 21 mushrooms were identified at the species level with scores ≥2.0 and 5 mushrooms at the genus level with scores ≥1.7, although the signals of 2 mushrooms were insufficient for analysis. The remaining 20 samples were recognized as "unreliable identification" with scores <1.7. Subsequent DNA analysis confirmed that the correct species or genus identifications were achieved by MALDI-TOF MS for the 26 former samples, whereas the 18 mushrooms with poorly matched scores were species that were not included in the database. Thus, the proposed MALDI-TOF MS coupled with our database could be a powerful tool for the rapid and reliable identification of mushrooms; however, continuous updating of the database is necessary to enrich it with more abundant species. Copyright © 2016 Elsevier B.V. All rights reserved.

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.

Combined Atomic Force Microscope-Based Topographical Imaging and Nanometer Scale Resolved Proximal Probe Thermal Desorption/Electrospray Ionization-Mass Spectrometry

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

Ovchinnikova, Olga S; Nikiforov, Maxim; Bradshaw, James A

2011-01-01

Nanometer scale proximal probe thermal desorption/electrospray ionization mass spectrometry (TD/ESI-MS) was demonstrated for molecular surface sampling of caffeine from a thin film using a 30 nm diameter nano-thermal analysis (nano-TA) probe tip in an atomic force microscope (AFM) coupled via a vapor transfer line and ESI interface to a MS detection platform. Using a probe temperature of 350 C and a spot sampling time of 30 s, conical desorption craters 250 nm in diameter and 100 nm deep were created as shown through subsequent topographical imaging of the surface within the same system. Automated sampling of a 5 x 2more » array of spots, with 2 m spacing between spots, and real time selective detection of the desorbed caffeine using tandem mass spectrometry was also demonstrated. Estimated from the crater volume (~2x106 nm3), only about 10 amol (2 fg) of caffeine was liberated from each thermal desorption crater in the thin film. These results illustrate a relatively simple experimental setup and means to acquire in automated fashion sub-micrometer scale spatial sampling resolution and mass spectral detection of materials amenable to TD. The ability to achieve MS-based chemical imaging with 250 nm scale spatial resolution with this system is anticipated.« less

Spatiotemporal commonalities of fronto-parietal activation in attentional orienting triggered by supraliminal and subliminal gaze cues: An event-related potential study.

PubMed

Uono, Shota; Sato, Wataru; Sawada, Reiko; Kochiyama, Takanori; Toichi, Motomi

2018-05-04

Eye gaze triggers attentional shifts with and without conscious awareness. It remains unclear whether the spatiotemporal patterns of electric neural activity are the same for conscious and unconscious attentional shifts. Thus, the present study recorded event-related potentials (ERPs) and evaluated the neural activation involved in attentional orienting induced by subliminal and supraliminal gaze cues. Nonpredictive gaze cues were presented in the central field of vision, and participants were asked to detect a subsequent peripheral target. The mean reaction time was shorter for congruent gaze cues than for incongruent gaze cues under both presentation conditions, indicating that both types of cues reliably trigger attentional orienting. The ERP analysis revealed that averted versus straight gaze induced greater negative deflection in the bilateral fronto-central and temporal regions between 278 and 344 ms under both supraliminal and subliminal presentation conditions. Supraliminal cues, irrespective of gaze direction, induced a greater negative amplitude than did subliminal cues at the right posterior cortices at a peak of approximately 170 ms and in the 200-300 ms. These results suggest that similar spatial and temporal fronto-parietal activity is involved in attentional orienting triggered by both supraliminal and subliminal gaze cues, although inputs from different visual processing routes (cortical and subcortical regions) may trigger activity in the attentional network. Copyright © 2018 Elsevier B.V. All rights reserved.

Reduced event-related current density in the anterior cingulate cortex in schizophrenia.

PubMed

Mulert, C; Gallinat, J; Pascual-Marqui, R; Dorn, H; Frick, K; Schlattmann, P; Mientus, S; Herrmann, W M; Winterer, G

2001-04-01

There is good evidence from neuroanatomic postmortem and functional imaging studies that dysfunction of the anterior cingulate cortex plays a prominent role in the pathophysiology of schizophrenia. So far, no electrophysiological localization study has been performed to investigate this deficit. We investigated 18 drug-free schizophrenic patients and 25 normal subjects with an auditory choice reaction task and measured event-related activity with 19 electrodes. Estimation of the current source density distribution in Talairach space was performed with low-resolution electromagnetic tomography (LORETA). In normals, we could differentiate between an early event-related potential peak of the N1 (90-100 ms) and a later N1 peak (120-130 ms). Subsequent current-density LORETA analysis in Talairach space showed increased activity in the auditory cortex area during the first N1 peak and increased activity in the anterior cingulate gyrus during the second N1 peak. No activation difference was observed in the auditory cortex between normals and patients with schizophrenia. However, schizophrenics showed significantly less anterior cingulate gyrus activation and slowed reaction times. Our results confirm previous findings of an electrical source in the anterior cingulate and an anterior cingulate dysfunction in schizophrenics. Our data also suggest that anterior cingulate function in schizophrenics is disturbed at a relatively early time point in the information-processing stream (100-140 ms poststimulus). Copyright 2001 Academic Press.

Rapid determination of anti-estrogens by gas chromatography/mass spectrometry in urine: Method validation and application to real samples.

PubMed

Gerace, E; Salomone, A; Abbadessa, G; Racca, S; Vincenti, M

2012-02-01

A fast screening protocol was developed for the simultaneous determination of nine anti-estrogenic agents (aminoglutethimide, anastrozole, clomiphene, drostanolone, formestane, letrozole, mesterolone, tamoxifen, testolactone) plus five of their metabolites in human urine. After an enzymatic hydrolysis, these compounds can be extracted simultaneously from urine with a simple liquid-liquid extraction at alkaline conditions. The analytes were subsequently analyzed by fast-gas chromatography/mass spectrometry (fast-GC/MS) after derivatization. The use of a short column, high-flow carrier gas velocity and fast temperature ramping produced an efficient separation of all analytes in about 4 min, allowing a processing rate of 10 samples/h. The present analytical method was validated according to UNI EN ISO/IEC 17025 guidelines for qualitative methods. The range of investigated parameters included the limit of detection, selectivity, linearity, repeatability, robustness and extraction efficiency. High MS-sampling rate, using a benchtop quadrupole mass analyzer, resulted in accurate peak shape definition under both scan and selected ion monitoring modes, and high sensitivity in the latter mode. Therefore, the performances of the method are comparable to the ones obtainable from traditional GC/MS analysis. The method was successfully tested on real samples arising from clinical treatments of hospitalized patients and could profitably be used for clinical studies on anti-estrogenic drug administration.

Rapid determination of anti-estrogens by gas chromatography/mass spectrometry in urine: Method validation and application to real samples

PubMed Central

Gerace, E.; Salomone, A.; Abbadessa, G.; Racca, S.; Vincenti, M.

2011-01-01

A fast screening protocol was developed for the simultaneous determination of nine anti-estrogenic agents (aminoglutethimide, anastrozole, clomiphene, drostanolone, formestane, letrozole, mesterolone, tamoxifen, testolactone) plus five of their metabolites in human urine. After an enzymatic hydrolysis, these compounds can be extracted simultaneously from urine with a simple liquid–liquid extraction at alkaline conditions. The analytes were subsequently analyzed by fast-gas chromatography/mass spectrometry (fast-GC/MS) after derivatization. The use of a short column, high-flow carrier gas velocity and fast temperature ramping produced an efficient separation of all analytes in about 4 min, allowing a processing rate of 10 samples/h. The present analytical method was validated according to UNI EN ISO/IEC 17025 guidelines for qualitative methods. The range of investigated parameters included the limit of detection, selectivity, linearity, repeatability, robustness and extraction efficiency. High MS-sampling rate, using a benchtop quadrupole mass analyzer, resulted in accurate peak shape definition under both scan and selected ion monitoring modes, and high sensitivity in the latter mode. Therefore, the performances of the method are comparable to the ones obtainable from traditional GC/MS analysis. The method was successfully tested on real samples arising from clinical treatments of hospitalized patients and could profitably be used for clinical studies on anti-estrogenic drug administration. PMID:29403714

A Study on the Reliability of an On-Site Oral Fluid Drug Test in a Recreational Context

PubMed Central

Gentili, Stefano; Tittarelli, Roberta; Mannocchi, Giulio

2016-01-01

The reliability of DrugWipe 5A on site test for principal drugs of abuse (cannabis, amphetamines, cocaine, and opiates) detection in oral fluid was assessed by comparing the on-site results with headspace solid-phase microextraction (HS-SPME) gas chromatography-mass spectrometry (GC-MS) analysis on samples extracted by the device collection pad. Oral fluid samples were collected at recreational settings (e.g., discos, pubs, and music bars) of Rome metropolitan area. Eighty-three club goers underwent the on-site drug screening test with one device. Independently from the result obtained, a second device was used just to collect another oral fluid sample subsequently extracted and analyzed in the laboratory following HS-SPME procedure, gas chromatographic separation by a capillary column, and MS detection by electron impact ionization. DrugWipe 5A on-site test showed 54 samples (65.1%) positive to one or more drugs of abuse, whereas 75 samples (90.4%) tested positive for one or more substances following GC-MS assay. Comparing the obtained results, the device showed sensitivity, specificity, and accuracy around 80% for amphetamines class. Sensitivity (67 and 50%) was obtained for cocaine and opiates, while both sensitivity and accuracy were unsuccessful (29 and 53%, resp.) for cannabis, underlying the limitation of the device for this latter drug class. PMID:27610266

Aggregation of MBP in chronic demyelination

PubMed Central

Frid, Kati; Einstein, Ofira; Friedman-Levi, Yael; Binyamin, Orli; Ben-Hur, Tamir; Gabizon, Ruth

2015-01-01

Objectives Misfolding of key disease proteins to an insoluble state is associated with most neurodegenerative conditions, such as prion, Parkinson, and Alzheimer’s diseases. In this work, and by studying animal models of multiple sclerosis, we asked whether this is also the case for myelin basic protein (MBP) in the late and neurodegenerative phases of demyelinating diseases. Methods To this effect, we tested whether MBP, an essential myelin component, present prion-like properties in animal models of MS, as is the case for Cuprizone-induced chronic demyelination or chronic phases of Experimental Autoimmune Encephalomyelitis (EAE). Results We show here that while total levels of MBP were not reduced following extensive demyelination, part of these molecules accumulated thereafter as aggregates inside oligodendrocytes or around neuronal cells. In chronic EAE, MBP precipitated concomitantly with Tau, a marker of diverse neurodegenerative conditions, including MS. Most important, analysis of fractions from Triton X-100 floatation gradients suggest that the lipid composition of brain membranes in chronic EAE differs significantly from that of naïve mice, an effect which may relate to oxidative insults and subsequently prevent the appropriate insertion and compaction of new MBP in the myelin sheath, thereby causing its misfolding and aggregation. Interpretation Prion-like aggregation of MBP following chronic demyelination may result from an aberrant lipid composition accompanying this pathological status. Such aggregation of MBP may contribute to neuronal damage that occurs in the progressive phase of MS. PMID:26273684

Urinary Amino Acid Analysis: A Comparison of iTRAQ®-LC-MS/MS, GC-MS, and Amino Acid Analyzer

PubMed Central

Kaspar, Hannelore; Dettmer, Katja; Chan, Queenie; Daniels, Scott; Nimkar, Subodh; Daviglus, Martha L.; Stamler, Jeremiah; Elliott, Paul; Oefner, Peter J.

2009-01-01

Urinary amino acid analysis is typically done by cation-exchange chromatography followed by post-column derivatization with ninhydrin and UV detection. This method lacks throughput and specificity. Two recently introduced stable isotope ratio mass spectrometric methods promise to overcome those shortcomings. Using two blinded sets of urine replicates and a certified amino acid standard, we compared the precision and accuracy of gas chromatography/mass spectrometry (GC-MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) of propyl chloroformate and iTRAQ® derivatized amino acids, respectively, to conventional amino acid analysis. The GC-MS method builds on the direct derivatization of amino acids in diluted urine with propyl chloroformate, GC separation and mass spectrometric quantification of derivatives using stable isotope labeled standards. The LC-MS/MS method requires prior urinary protein precipitation followed by labeling of urinary and standard amino acids with iTRAQ® tags containing different cleavable reporter ions distinguishable by MS/MS fragmentation. Means and standard deviations of percent technical error (%TE) computed for 20 amino acids determined by amino acid analyzer, GC-MS, and iTRAQ®-LC-MS/MS analyses of 33 duplicate and triplicate urine specimens were 7.27±5.22, 21.18±10.94, and 18.34±14.67, respectively. Corresponding values for 13 amino acids determined in a second batch of 144 urine specimens measured in duplicate or triplicate were 8.39±5.35, 6.23±3.84, and 35.37±29.42. Both GC-MS and iTRAQ®-LC-MS/MS are suited for high-throughput amino acid analysis, with the former offering at present higher reproducibility and completely automated sample pretreatment, while the latter covers more amino acids and related amines. PMID:19481989

Urinary amino acid analysis: a comparison of iTRAQ-LC-MS/MS, GC-MS, and amino acid analyzer.

PubMed

Kaspar, Hannelore; Dettmer, Katja; Chan, Queenie; Daniels, Scott; Nimkar, Subodh; Daviglus, Martha L; Stamler, Jeremiah; Elliott, Paul; Oefner, Peter J

2009-07-01

Urinary amino acid analysis is typically done by cation-exchange chromatography followed by post-column derivatization with ninhydrin and UV detection. This method lacks throughput and specificity. Two recently introduced stable isotope ratio mass spectrometric methods promise to overcome those shortcomings. Using two blinded sets of urine replicates and a certified amino acid standard, we compared the precision and accuracy of gas chromatography/mass spectrometry (GC-MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) of propyl chloroformate and iTRAQ derivatized amino acids, respectively, to conventional amino acid analysis. The GC-MS method builds on the direct derivatization of amino acids in diluted urine with propyl chloroformate, GC separation and mass spectrometric quantification of derivatives using stable isotope labeled standards. The LC-MS/MS method requires prior urinary protein precipitation followed by labeling of urinary and standard amino acids with iTRAQ tags containing different cleavable reporter ions distinguishable by MS/MS fragmentation. Means and standard deviations of percent technical error (%TE) computed for 20 amino acids determined by amino acid analyzer, GC-MS, and iTRAQ-LC-MS/MS analyses of 33 duplicate and triplicate urine specimens were 7.27+/-5.22, 21.18+/-10.94, and 18.34+/-14.67, respectively. Corresponding values for 13 amino acids determined in a second batch of 144 urine specimens measured in duplicate or triplicate were 8.39+/-5.35, 6.23+/-3.84, and 35.37+/-29.42. Both GC-MS and iTRAQ-LC-MS/MS are suited for high-throughput amino acid analysis, with the former offering at present higher reproducibility and completely automated sample pretreatment, while the latter covers more amino acids and related amines.

Quantitation of Mycotoxins Using Direct Analysis in Real Time Mass Spectrometry (DART-MS).

PubMed

Busman, Mark

2018-05-01

Ambient ionization represents a new generation of MS ion sources and is used for the rapid ionization of small molecules under ambient conditions. The combination of ambient ionization and MS allows the analysis of multiple food samples with simple or no sample treatment or in conjunction with prevailing sample preparation methods. Two ambient ionization methods, desorptive electrospray ionization (DESI) and direct analysis in real time (DART) have been adapted for food safety application. Both ionization techniques provide unique advantages and capabilities. DART has been used for a variety of qualitative and quantitative applications. In particular, mycotoxin contamination of food and feed materials has been addressed by DART-MS. Applications to mycotoxin analysis by ambient ionization MS and particularly DART-MS are summarized.

Limitations of Using Microsoft Excel Version 2016 (MS Excel 2016) for Statistical Analysis for Medical Research.

PubMed

Tanavalee, Chotetawan; Luksanapruksa, Panya; Singhatanadgige, Weerasak

2016-06-01

Microsoft Excel (MS Excel) is a commonly used program for data collection and statistical analysis in biomedical research. However, this program has many limitations, including fewer functions that can be used for analysis and a limited number of total cells compared with dedicated statistical programs. MS Excel cannot complete analyses with blank cells, and cells must be selected manually for analysis. In addition, it requires multiple steps of data transformation and formulas to plot survival analysis graphs, among others. The Megastat add-on program, which will be supported by MS Excel 2016 soon, would eliminate some limitations of using statistic formulas within MS Excel.

Ratiometric analysis of in vivo retinal layer thicknesses in multiple sclerosis

NASA Astrophysics Data System (ADS)

Bhaduri, Basanta; Nolan, Ryan M.; Shelton, Ryan L.; Pilutti, Lara A.; Motl, Robert W.; Boppart, Stephen A.

2016-09-01

We performed ratiometric analysis of retinal optical coherence tomography images for the first time in multiple sclerosis (MS) patients. The ratiometric analysis identified differences in several retinal layer thickness ratios in the cohort of MS subjects without a history of optic neuritis (ON) compared to healthy control (HC) subjects, and there was no difference in standard retinal nerve fiber layer thickness (RNFLT). The difference in such ratios between HC subjects and those with mild MS-disability, without a difference in RNFLT, further suggests the possibility of using layer ratiometric analysis for detecting early retinal changes in MS. Ratiometric analysis may be useful and potentially more sensitive for detecting disease changes in MS.

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.

Development and comparison of HPLC-MS/MS and UPLC-MS/MS methods for determining eight coccidiostats in beef.

PubMed

Zhao, Xia; Wang, Bo; Xie, Kaizhou; Liu, Jianyu; Zhang, Yangyang; Wang, Yajuan; Guo, Yawen; Zhang, Genxi; Dai, Guojun; Wang, Jinyu

2018-06-15

A high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) method and an ultraperformance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method for determining eight coccidiostat (halofuginone, lasalocid, maduramicin, monensin, narasin, nigericin, robenidine and salinomycin) residues in beef were developed and compared. Samples were extracted with a mixture of acetic acid, acetonitrile and ethyl acetate and were then purified on a C 18 solid-phase extraction (SPE) column. The purified samples were analyzed by HPLC-MS/MS and UPLC-MS/MS, using 0.1% formic acid-water solution (A) and pure methanol (B) as the mobile phase. The samples were fractionated on a C 18 column using different gradient elution procedures, followed by qualitative analysis using a mass spectrometer operated in multiple reaction monitoring (MRM) mode with positive electrospray ionization; the external standard method was used for quantitation. At spiked levels that ranged from the limit of quantification (LOQ) to 100 μg/kg, the average recoveries were 71.96%-100.32% and 71.24%-89.24%, with relative standard deviations (RSDs) of 2.65%-12.38% and 2.98%-14.86% for UPLC-MS/MS and HPLC-MS/MS, respectively. The limits of detection (LODs) and LOQs of the eight coccidiostats were 0.14-0.32 μg/kg and 0.43-1.21 μg/kg, respectively, for UPLC-MS/MS analysis and 0.16-0.58 μg/kg and 0.53-1.92 μg/kg, respectively, for HPLC-MS/MS analysis. Both methods had good accuracy and precision, but UPLC-MS/MS had higher sensitivity than HPLC-MS/MS. Copyright © 2018 Elsevier B.V. All rights reserved.

Inventory of File sref_nmb.t03z.pgrb221.ctl.grib2

Science.gov Websites

006 10 m above ground UGRD analysis U-Component of Wind [m/s] ENS=low-res ctl 007 10 m above ground VGRD analysis V-Component of Wind [m/s] ENS=low-res ctl 008 surface WEASD analysis Water Equivalent of -Component of Wind [m/s] ENS=low-res ctl 021 250 mb VGRD analysis V-Component of Wind [m/s] ENS=low-res ctl

Inventory of File sref_nmb.t03z.pgrb132.ctl.grib2

Science.gov Websites

006 10 m above ground UGRD analysis U-Component of Wind [m/s] ENS=low-res ctl 007 10 m above ground VGRD analysis V-Component of Wind [m/s] ENS=low-res ctl 008 surface WEASD analysis Water Equivalent of -Component of Wind [m/s] ENS=low-res ctl 021 250 mb VGRD analysis V-Component of Wind [m/s] ENS=low-res ctl

Inventory of File sref_nmb.t03z.pgrb243.ctl.grib2

Science.gov Websites

006 10 m above ground UGRD analysis U-Component of Wind [m/s] ENS=low-res ctl 007 10 m above ground VGRD analysis V-Component of Wind [m/s] ENS=low-res ctl 008 surface WEASD analysis Water Equivalent of -Component of Wind [m/s] ENS=low-res ctl 021 250 mb VGRD analysis V-Component of Wind [m/s] ENS=low-res ctl

Inventory of File sref_em.t03z.pgrb212.p1.f00.grib2

Science.gov Websites

Relative Humidity [%] 014.1 10 m above ground UGRD analysis U-Component of Wind [m/s] 014.2 10 m above ground VGRD analysis V-Component of Wind [m/s] 015 surface WEASD analysis Water Equivalent of Accumulated Wind [m/s] 032.2 30-0 mb above ground VGRD analysis V-Component of Wind [m/s] 033 30-0 mb above ground

Inventory of File sref_em.t03z.pgrb221.p1.f00.grib2

Science.gov Websites

Relative Humidity [%] 014.1 10 m above ground UGRD analysis U-Component of Wind [m/s] 014.2 10 m above ground VGRD analysis V-Component of Wind [m/s] 015 surface WEASD analysis Water Equivalent of Accumulated Wind [m/s] 032.2 30-0 mb above ground VGRD analysis V-Component of Wind [m/s] 033 30-0 mb above ground

Inventory of File sref_nmb.t03z.pgrb216.ctl.grib2

Science.gov Websites

006 10 m above ground UGRD analysis U-Component of Wind [m/s] ENS=low-res ctl 007 10 m above ground VGRD analysis V-Component of Wind [m/s] ENS=low-res ctl 008 surface WEASD analysis Water Equivalent of -Component of Wind [m/s] ENS=low-res ctl 021 250 mb VGRD analysis V-Component of Wind [m/s] ENS=low-res ctl

Quantitative proteomics analysis using 2D-PAGE to investigate the effects of cigarette smoke and aerosol of a prototypic modified risk tobacco product on the lung proteome in C57BL/6 mice.

PubMed

Elamin, Ashraf; Titz, Bjoern; Dijon, Sophie; Merg, Celine; Geertz, Marcel; Schneider, Thomas; Martin, Florian; Schlage, Walter K; Frentzel, Stefan; Talamo, Fabio; Phillips, Blaine; Veljkovic, Emilija; Ivanov, Nikolai V; Vanscheeuwijck, Patrick; Peitsch, Manuel C; Hoeng, Julia

2016-08-11

Smoking is associated with several serious diseases, such as lung cancer and chronic obstructive pulmonary disease (COPD). Within our systems toxicology framework, we are assessing whether potential modified risk tobacco products (MRTP) can reduce smoking-related health risks compared to conventional cigarettes. In this article, we evaluated to what extent 2D-PAGE/MALDI MS/MS (2D-PAGE) can complement the iTRAQ LC-MS/MS results from a previously reported mouse inhalation study, in which we assessed a prototypic MRTP (pMRTP). Selected differentially expressed proteins identified by both LC-MS/MS and 2D-PAGE approaches were further verified using reverse-phase protein microarrays. LC-MS/MS captured the effects of cigarette smoke (CS) on the lung proteome more comprehensively than 2D-PAGE. However, an integrated analysis of both proteomics data sets showed that 2D-PAGE data complement the LC-MS/MS results by supporting the overall trend of lower effects of pMRTP aerosol than CS on the lung proteome. Biological effects of CS exposure supported by both methods included increases in immune-related, surfactant metabolism, proteasome, and actin cytoskeleton protein clusters. Overall, while 2D-PAGE has its value, especially as a complementary method for the analysis of effects on intact proteins, LC-MS/MS approaches will likely be the method of choice for proteome analysis in systems toxicology investigations. Quantitative proteomics is anticipated to play a growing role within systems toxicology assessment frameworks in the future. To further understand how different proteomics technologies can contribute to toxicity assessment, we conducted a quantitative proteomics analysis using 2D-PAGE and isobaric tag-based LC-MS/MS approaches and compared the results produced from the 2 approaches. Using a prototypic modified risk tobacco product (pMRTP) as our test item, we show compared with cigarette smoke, how 2D-PAGE results can complement and support LC-MS/MS data, demonstrating the much lower effects of pMRTP aerosol than cigarette smoke on the mouse lung proteome. The combined analysis of 2D-PAGE and LC-MS/MS data identified an effect of cigarette smoke on the proteasome and actin cytoskeleton in the lung. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Metabolomics and Trace Element Analysis of Camel Tear by GC-MS and ICP-MS.

PubMed

Ahamad, Syed Rizwan; Raish, Mohammad; Yaqoob, Syed Hilal; Khan, Altaf; Shakeel, Faiyaz

2017-06-01

Camel tear metabolomics and elemental analysis are useful in getting the information regarding the components responsible for maintaining the protective system that allows living in the desert and dry regions. The aim of this study was to correlate that the camel tears can be used as artificial tears for the evaluation of dryness in the eye. Eye biomarkers of camel tears were analyzed by gas chromatography-mass spectroscopy (GC-MS) and inductively coupled plasma mass spectroscopy (ICP-MS). The major compounds detected in camel tears by GC-MS were alanine, valine, leucine, norvaline, glycine, cadaverine, urea, ribitol, sugars, and higher fatty acids like octadecanoic acid and hexadecanoic acid. GC-MS analysis of camel tears also finds several products of metabolites and its associated metabolic participants. ICP-MS analysis showed the presence of different concentration of elemental composition in the camel tears.

Advanced Mass Spectrometric Methods for the Rapid and Quantitative Characterization of Proteomes

DOE PAGES

Smith, Richard D.

2002-01-01

Progress is reviewedmore » towards the development of a global strategy that aims to extend the sensitivity, dynamic range, comprehensiveness and throughput of proteomic measurements based upon the use of high performance separations and mass spectrometry. The approach uses high accuracy mass measurements from Fourier transform ion cyclotron resonance mass spectrometry (FTICR) to validate peptide ‘accurate mass tags’ (AMTs) produced by global protein enzymatic digestions for a specific organism, tissue or cell type from ‘potential mass tags’ tentatively identified using conventional tandem mass spectrometry (MS/MS). This provides the basis for subsequent measurements without the need for MS/ MS. High resolution capillary liquid chromatography separations combined with high sensitivity, and high resolution accurate FTICR measurements are shown to be capable of characterizing peptide mixtures of more than 10 5 components. The strategy has been initially demonstrated using the microorganisms Saccharomyces cerevisiae and Deinococcus radiodurans. Advantages of the approach include the high confidence of protein identification, its broad proteome coverage, high sensitivity, and the capability for stableisotope labeling methods for precise relative protein abundance measurements. Abbreviations : LC, liquid chromatography; FTICR, Fourier transform ion cyclotron resonance; AMT, accurate mass tag; PMT, potential mass tag; MMA, mass measurement accuracy; MS, mass spectrometry; MS/MS, tandem mass spectrometry; ppm, parts per million.« less

Geometrical families of mechanically stable granular packings

NASA Astrophysics Data System (ADS)

Gao, Guo-Jie; Blawzdziewicz, Jerzy; O'Hern, Corey S.

2009-12-01

We enumerate and classify nearly all of the possible mechanically stable (MS) packings of bidipserse mixtures of frictionless disks in small sheared systems. We find that MS packings form continuous geometrical families, where each family is defined by its particular network of particle contacts. We also monitor the dynamics of MS packings along geometrical families by applying quasistatic simple shear strain at zero pressure. For small numbers of particles (N<16) , we find that the dynamics is deterministic and highly contracting. That is, if the system is initialized in a MS packing at a given shear strain, it will quickly lock into a periodic orbit at subsequent shear strain, and therefore sample only a very small fraction of the possible MS packings in steady state. In studies with N>16 , we observe an increase in the period and random splittings of the trajectories caused by bifurcations in configuration space. We argue that the ratio of the splitting and contraction rates in large systems will determine the distribution of MS-packing geometrical families visited in steady state. This work is part of our long-term research program to develop a master-equation formalism to describe macroscopic slowly driven granular systems in terms of collections of small subsystems.

Multiple Sclerosis and Subsequent Human Immunodeficiency Virus Infection: A Case with the Rare Comorbidity, Focus on Novel Treatment Issues and Review of the Literature.

PubMed

Skarlis, Charalampos; Gontika, Maria; Katsavos, Serafeim; Velonakis, Giorgios; Toulas, Panagiotis; Anagnostouli, Maria

2017-01-01

The comorbidity between Multiple Sclerosis (MS) and Human Immunodeficiency Virus (HIV) infection is particularly rare. Only a few cases of comorbidity of Clinically Definite(CD)-MS and HIV have been documented worldwide, while the potential beneficial role of antiretroviral therapy regarding MS activity has long been an area of debate. We present a 36-year old male, bearing a diagnosis of CD-MS for twelve years. He had been treated for ten years with interferon-beta-1b, when he voluntarily discontinued therapy, claiming clinical stability. One year later he was diagnosed positive for HIV and he started and continued only on efavirenz/emricitabine/tenofovir-disoproxil fumarate (ATRIPLA®), remaining relapse-free until today. This fact, in combination with the unique pharmaceutical composition of the drug, which contains a component similar to a newly-approved agent for MS, dimethyl fumarate, prompted us to review the literature regarding this rare comorbidity and to suggest that the role of the antiretroviral therapy should be further explored in MS. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

Spatio-Temporal Brain Mapping of Motion-Onset VEPs Combined with fMRI and Retinotopic Maps

PubMed Central

Pitzalis, Sabrina; Strappini, Francesca; De Gasperis, Marco; Bultrini, Alessandro; Di Russo, Francesco

2012-01-01

Neuroimaging studies have identified several motion-sensitive visual areas in the human brain, but the time course of their activation cannot be measured with these techniques. In the present study, we combined electrophysiological and neuroimaging methods (including retinotopic brain mapping) to determine the spatio-temporal profile of motion-onset visual evoked potentials for slow and fast motion stimuli and to localize its neural generators. We found that cortical activity initiates in the primary visual area (V1) for slow stimuli, peaking 100 ms after the onset of motion. Subsequently, activity in the mid-temporal motion-sensitive areas, MT+, peaked at 120 ms, followed by peaks in activity in the more dorsal area, V3A, at 160 ms and the lateral occipital complex at 180 ms. Approximately 250 ms after stimulus onset, activity fast motion stimuli was predominant in area V6 along the parieto-occipital sulcus. Finally, at 350 ms (100 ms after the motion offset) brain activity was visible again in area V1. For fast motion stimuli, the spatio-temporal brain pattern was similar, except that the first activity was detected at 70 ms in area MT+. Comparing functional magnetic resonance data for slow vs. fast motion, we found signs of slow-fast motion stimulus topography along the posterior brain in at least three cortical regions (MT+, V3A and LOR). PMID:22558222

Tandem mass spectrometric analysis of novel peptide-modified gemini surfactants used as gene delivery vectors.

PubMed

Al-Dulaymi, M; El-Aneed, A

2017-06-01

Diquaternary ammonium gemini surfactants have emerged as effective gene delivery vectors. A novel series of 11 peptide-modified compounds was synthesized, showing promising results in delivering genetic materials. The purpose of this work is to elucidate the tandem mass spectrometric (MS/MS) dissociation behavior of these novel molecules establishing a generalized MS/MS fingerprint. Exact mass measurements were achieved using a hybrid quadrupole orthogonal time-of-flight mass spectrometer, and a multi-stage MS/MS analysis was conducted using a triple quadrupole-linear ion trap mass spectrometer. Both instruments were operated in the positive ionization mode and are equipped with electrospray ionization. Abundant triply charged [M+H] 3+ species were observed in the single-stage analysis of all the evaluated compounds with mass accuracies of less than 8 ppm in mass error. MS/MS analysis showed that the evaluated gemini surfactants exhibited peptide-related dissociation characteristics because of the presence of amino acids within the compounds' spacer region. In particular, diagnostic product ions were originated from the neutral loss of ammonia from the amino acids' side chain resulting in the formation of pipecolic acid at the N-terminus part of the gemini surfactants. In addition, a charge-directed amide bond cleavage was initiated by the amino acids' side chain producing a protonated α-amino-ε-caprolactam ion and its complimentary C-terminus ion that contains quaternary amines. MS/MS and MS 3 analysis revealed common fragmentation behavior among all tested compounds, resulting in the production of a universal MS/MS fragmentation pathway. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

The Ancient Wood of the Acqualadrone Rostrum: A Materials History Through GC-MS and Sulfur X-ray Absorption Spectroscopy

PubMed Central

Frank, Patrick; Caruso, Francesco; Caponetti, Eugenio

2012-01-01

In 2008 the rostrum from an ancient warship was recovered from the Mediterranean near Acqualadrone, Sicily. To establish its provenance and condition, samples of black and brown rostrum wood were examined using sulfur K-edge x-ray absorption spectroscopy (XAS) and GC-MS. GC-MS of pyrolytic volatiles yielded only guaiacyl derivatives, indicating construction from pinewood. A derivatized extract of black wood yielded forms of abietic acid and sandaracopimaric acid consistent with pine pitch waterproofing. Numerical fits to the sulfur K-edge XAS spectra showed that about 65% of the endogenous sulfur consisted of thiols and disulfides. Elemental sulfur was about 2% and 7% in black and brown wood, respectively, while pyritic sulfur was about 12% and 6%. About 2% of the sulfur in both wood types was modeled as trimethylsulfonium, possibly reflecting biogenic dimethylsulfonio-propionate. High valent sulfur was exclusively represented by sulfate esters, consistent with bacterial sulfotransferase activity. Traces of chloride were detected, but no free sulfate ion. In summary, the rostrum was manufactured of pine wood and subsequently waterproofed with pine pitch. The subsequent 2300 years included battle, foundering, and marine burial followed by anoxia, bacterial colonization, sulfate reduction, and mobilization of transition metals, which produced pyrite and copious appended sulfur functionality. PMID:22545724

Sequential extractions of selenium soils from Stewart Lake: total selenium and speciation measurements with ICP-MS detection.

PubMed

Ponce de León, Claudia A; DeNicola, Katie; Montes Bayón, Maria; Caruso, Joseph A

2003-06-01

Different techniques have been employed in order to evaluate the most efficient procedure for the extraction of selenium from soil as required for speciation. Selenium contaminated sediments from Stewart Lake Wetland, California were used. A strong acid mineralization of the samples gives quantitative total selenium, which is then used to estimate recoveries for the milder extraction methods. The different extraction methodologies involve the sequential use of water, buffer (phosphate, pH 7) and either acid solution (e.g. HNO3 or HCl) or basic solutions (e.g. ammonium acetate, NaOH or TMAH). Pyrophosphate extraction was also evaluated and showed that selenium was not associated with humic acids. The extractants were subsequently analyzed by size exclusion chromatography (SEC) with UV (254 and 400 nm) and on-line ICP-MS detection; anion exchange chromatography, and ion-pair reversed phase chromatography with ICP-MS detection. For sequential extractions the extraction efficiencies showed that the basic extractions were more efficient than the acidic. The difference between the acidic and the basic extraction efficiency is carried to the sulfite extraction, suggesting that whatever is not extracted by the acid is subsequently extracted by the sulfite. The species identified with the different chromatographies were selenate, selenite, elemental selenium and some organic selenium.

Over 2,300 phosphorylated peptide identifications with single-shot capillary zone electrophoresis-tandem mass spectrometry in a 100 min separation

PubMed Central

Ludwig, Katelyn R.; Sun, Liangliang; Zhu, Guijie; Dovichi, Norman J.; Hummon, Amanda B.

2015-01-01

Ultra-performance liquid chromatography (UPLC)-electrospray ionization (ESI)-tandem mass spectrometry (MS/MS) is typically employed for phosphoproteome analysis. Alternatively, capillary zone electrophoresis (CZE) - ESI-MS/MS has great potential for phosphoproteome analysis due to the significantly different migration times of phosphorylated and unphosphorylated forms of peptides. In this work, we systematically compared UPLC-MS/MS and CZE-MS/MS for phosphorylated peptide identifications (IDs) using an enriched phosphoproteome from the MCF-10A cell line. When the sample loading amount of UPLC was 10 times higher than that of CZE (2 μg vs. 200 ng), UPLC generated more phosphorylated peptide IDs than CZE (3,313 vs. 1,783). However, when the same sample loading amounts were used for CZE and UPLC (2–200 ng), CZE-MS/MS consistently and significantly outperformed UPLC-MS/MS in terms of phosphorylated peptide and total peptide IDs. This superior performance is most likely due to the higher peptide intensity generated by CZE-MS/MS. More importantly, compared with UPLC data from 2 μg sample, CZE-MS/MS can identify over 500 unique phosphorylated peptides from 200 ng sample, suggesting that CZE and UPLC are complementary for phosphorylated peptide IDs. With further improved loading capacity via a dynamic pH junction method, 2,313 phosphorylated peptides were identified with single-shot CZE-MS/MS in a 100 min analysis. This number of phosphorylated peptide IDs is over one order of magnitude higher than the number of phosphorylated peptide IDs previously reported by single-shot CZE-MS/MS. PMID:26399161

Determination of red blood cell fatty acid profiles: Rapid and high-confident analysis by chemical ionization-gas chromatography-tandem mass spectrometry.

PubMed

Schober, Yvonne; Wahl, Hans Günther; Renz, Harald; Nockher, Wolfgang Andreas

2017-01-01

Cellular fatty acid (FA) profiles have been acknowledged as biomarkers in various human diseases. Nevertheless, common FA analysis by gas chromatography mass spectrometry (GC-MS) requires long analysis time. Hence, there is a need for feasible methods for high throughput analysis in clinical studies. FA was extracted from red blood cells (RBC) and derivatized to fatty acid methyl esters (FAME). A method using gas chromatography tandem mass spectrometry (GC-MS/MS) with ammonia-induced chemical ionization (CI) was developed for the analysis of FA profiles in human RBC. We compared this method with classical single GC-MS using electron impact ionization (EI). The FA profiles of 703 RBC samples were determined by GC-MS/MS. In contrast to EI ammonia-induced CI resulted in adequate amounts of molecular ions for further fragmentation of FAME. Specific fragments for confident quantification and fragmentation were determined for 45 FA. The GC-MS/MS method has a total run time of 9min compared to typical analysis times of up to 60min in conventional GC-MS. Intra and inter assay variations were <10% for all FA analyzed. Analysis of RBC FA composition revealed an age-dependent increase of the omega-3 eicosapentaenoic and docosahexaenoic acid, and a decline of the omega-6 linoleic acid with a corresponding rise of the omega-3 index. The combination of ammonia-induced CI and tandem mass spectrometry after GC separation allows for high-throughput, robust and confident analysis of FA profiles in the clinical laboratory. Copyright © 2016. Published by Elsevier B.V.

NASA Handbook for Models and Simulations: An Implementation Guide for NASA-STD-7009

NASA Technical Reports Server (NTRS)

Steele, Martin J.

2013-01-01

The purpose of this Handbook is to provide technical information, clarification, examples, processes, and techniques to help institute good modeling and simulation practices in the National Aeronautics and Space Administration (NASA). As a companion guide to NASA-STD- 7009, Standard for Models and Simulations, this Handbook provides a broader scope of information than may be included in a Standard and promotes good practices in the production, use, and consumption of NASA modeling and simulation products. NASA-STD-7009 specifies what a modeling and simulation activity shall or should do (in the requirements) but does not prescribe how the requirements are to be met, which varies with the specific engineering discipline, or who is responsible for complying with the requirements, which depends on the size and type of project. A guidance document, which is not constrained by the requirements of a Standard, is better suited to address these additional aspects and provide necessary clarification. This Handbook stems from the Space Shuttle Columbia Accident Investigation (2003), which called for Agency-wide improvements in the "development, documentation, and operation of models and simulations"' that subsequently elicited additional guidance from the NASA Office of the Chief Engineer to include "a standard method to assess the credibility of the models and simulations."2 General methods applicable across the broad spectrum of model and simulation (M&S) disciplines were sought to help guide the modeling and simulation processes within NASA and to provide for consistent reporting ofM&S activities and analysis results. From this, the standardized process for the M&S activity was developed. The major contents of this Handbook are the implementation details of the general M&S requirements ofNASA-STD-7009, including explanations, examples, and suggestions for improving the credibility assessment of an M&S-based analysis.

Identification of N-glycosylation in prolyl endoprotease from Aspergillus niger and evaluation of the enzyme for its possible application in proteomics.

PubMed

Sebela, Marek; Rehulka, Pavel; Kábrt, Jaromír; Rehulková, Helena; Ozdian, Tomás; Raus, Martin; Franc, Vojtech; Chmelík, Josef

2009-11-01

An acidic prolyl endoprotease from Aspergillus niger was isolated from the commercial product Brewers Clarex to evaluate its possible application in proteomics. The chromatographic purification yielded a single protein band in sodium dodecyl sulfate polyacrylamide gel electrophoresis providing an apparent molecular mass of 63 kDa and a broad peak (m/z 58,061) in linear matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) indicating the glycoprotein nature of the enzyme. Indeed, a colorimetric assessment with phenol and sulfuric acid showed the presence of neutral sugars (9% of weight). The subsequent treatment with N-glycosidase F released a variety of high-mannose type N-glycans, which were successfully detected using MALDI-TOF MS. MALDI-TOF/TOF tandem MS analysis of glycopeptides from a tryptic digest of prolyl endoprotease unraveled the identity of the N-glycosylation site in the primary structure. The data obtained also show that the enzyme is present in its processed form, i.e. without putative signal and propeptide parts. Spectrophotometric measurements demonstrated optimal activity at pH 4.0-4.5 and also high thermostability for the cleavage at the C-terminal part of proline residues. In-solution digestion of standard proteins (12-200 kDa) allowed to evaluate the cleavage specificity. The enzyme acts upon proline and alanine residues, but there is an additional minor cleavage at some other residues like Gly, Leu, Arg, Ser and Tyr. The digestion of a honeybee peptide comprising six proline residues (apidaecin 1A) led to the detection of specific peptides terminated by proline as it was confirmed by MALDI postsource decay analysis. Copyright 2009 John Wiley & Sons, Ltd.

Sleep timing is more important than sleep length or quality for medical school performance.

PubMed

Genzel, L; Ahrberg, K; Roselli, C; Niedermaier, S; Steiger, A; Dresler, M; Roenneberg, T

2013-07-01

Overwhelming evidence supports the importance of sleep for memory consolidation. Medical students are often deprived of sufficient sleep due to large amounts of clinical duties and university load, we therefore investigated how study and sleep habits influence university performance. We performed a questionnaire-based study with 31 medical students of the University of Munich (second and third clinical semesters; surgery and internal medicine). The students kept a diary (in 30-min bins) on their daily schedules (times when they studied by themselves, attended classes, slept, worked on their thesis, or worked to earn money). The project design involved three 2-wk periods (A: during the semester; B: directly before the exam period--pre-exam; C: during the subsequent semester break). Besides the diaries, students completed once questionnaires about their sleep quality (Pittsburgh Sleep Quality Index [PSQI]), their chronotype (Munich Chronotype Questionnaire [MCTQ]), and their academic history (previous grades, including the previously achieved preclinical board exam [PBE]). Analysis revealed significant correlations between the actual sleep behavior during the semester (MS(diary); mid-sleep point averaged from the sleep diaries) during the pre-exam period and the achieved grade (p = 0.002) as well as between the grades of the currently taken exam and the PBE (p = 0.002). A regression analysis with MS(diary) pre-exam and PBE as predictors in a model explained 42.7% of the variance of the exam grade (effect size 0.745). Interestingly, MS(diary)--especially during the pre-exam period-was the strongest predictor for the currently achieved grade, along with the preclinical board exam as a covariate, whereas the chronotype did not significantly influence the exam grade.

Seeing voices: High-density electrical mapping and source-analysis of the multisensory mismatch negativity evoked during the McGurk illusion.

PubMed

Saint-Amour, Dave; De Sanctis, Pierfilippo; Molholm, Sophie; Ritter, Walter; Foxe, John J

2007-02-01

Seeing a speaker's facial articulatory gestures powerfully affects speech perception, helping us overcome noisy acoustical environments. One particularly dramatic illustration of visual influences on speech perception is the "McGurk illusion", where dubbing an auditory phoneme onto video of an incongruent articulatory movement can often lead to illusory auditory percepts. This illusion is so strong that even in the absence of any real change in auditory stimulation, it activates the automatic auditory change-detection system, as indexed by the mismatch negativity (MMN) component of the auditory event-related potential (ERP). We investigated the putative left hemispheric dominance of McGurk-MMN using high-density ERPs in an oddball paradigm. Topographic mapping of the initial McGurk-MMN response showed a highly lateralized left hemisphere distribution, beginning at 175 ms. Subsequently, scalp activity was also observed over bilateral fronto-central scalp with a maximal amplitude at approximately 290 ms, suggesting later recruitment of right temporal cortices. Strong left hemisphere dominance was again observed during the last phase of the McGurk-MMN waveform (350-400 ms). Source analysis indicated bilateral sources in the temporal lobe just posterior to primary auditory cortex. While a single source in the right superior temporal gyrus (STG) accounted for the right hemisphere activity, two separate sources were required, one in the left transverse gyrus and the other in STG, to account for left hemisphere activity. These findings support the notion that visually driven multisensory illusory phonetic percepts produce an auditory-MMN cortical response and that left hemisphere temporal cortex plays a crucial role in this process.

Seeing voices: High-density electrical mapping and source-analysis of the multisensory mismatch negativity evoked during the McGurk illusion

PubMed Central

Saint-Amour, Dave; De Sanctis, Pierfilippo; Molholm, Sophie; Ritter, Walter; Foxe, John J.

2006-01-01

Seeing a speaker’s facial articulatory gestures powerfully affects speech perception, helping us overcome noisy acoustical environments. One particularly dramatic illustration of visual influences on speech perception is the “McGurk illusion”, where dubbing an auditory phoneme onto video of an incongruent articulatory movement can often lead to illusory auditory percepts. This illusion is so strong that even in the absence of any real change in auditory stimulation, it activates the automatic auditory change-detection system, as indexed by the mismatch negativity (MMN) component of the auditory event-related potential (ERP). We investigated the putative left hemispheric dominance of McGurk-MMN using high-density ERPs in an oddball paradigm. Topographic mapping of the initial McGurk-MMN response showed a highly lateralized left hemisphere distribution, beginning at 175 ms. Subsequently, scalp activity was also observed over bilateral fronto-central scalp with a maximal amplitude at ~290 ms, suggesting later recruitment of right temporal cortices. Strong left hemisphere dominance was again observed during the last phase of the McGurk-MMN waveform (350–400 ms). Source analysis indicated bilateral sources in the temporal lobe just posterior to primary auditory cortex. While a single source in the right superior temporal gyrus (STG) accounted for the right hemisphere activity, two separate sources were required, one in the left transverse gyrus and the other in STG, to account for left hemisphere activity. These findings support the notion that visually driven multisensory illusory phonetic percepts produce an auditory-MMN cortical response and that left hemisphere temporal cortex plays a crucial role in this process. PMID:16757004

Isotope-ratio measurements of lead in NIST standard reference materials by multiple-collector inductively coupled plasma mass spectrometry.

PubMed

Platzner, I; Ehrlich, S; Halicz, L

2001-07-01

The capability of a second-generation Nu Instruments multiple collector inductively coupled plasma mass spectrometer (MC-ICP-MS) has been evaluated for precise and accurate isotope-ratio determinations of lead. Essentially the mass spectrometer is a double-focusing instrument of Nier-Johnson analyzer geometry equipped with a newly designed variable-dispersion ion optical device, enabling the measured ion beams to be focused into a fixed array of Faraday collectors and an ion-counting assembly. NIST SRM Pb 981, 982, and 983 isotopic standards were used. Addition of thallium to the lead standards and subsequent simultaneous measurement of the thallium and lead isotopes enabled correction for mass discrimination, by use of the exponential correction law and 205Tl/203Tl = 2.3875. Six measurements of SRM Pb-982 furnished the results 206Pb/204Pb = 36.7326(68), 207Pb/204Pb = 17.1543(30), 208Pb/204Pb = 36.7249(69), 207Pb/206Pb = 0.46700(1), and 208Pb/206Pb = 0.99979(2); the NIST-certified values were 36.738(37), 17.159(25), 36.744(50), 0.46707(20), and 1.00016(36), respectively. Direct isotope lead analysis in silicates can be performed without any chemical separation. NIST SRM 610 glass was dissolved and introduced into the MC-ICP-MS by means of a micro concentric nebulizer. The ratios observed were in excellent agreement with previously reported data obtained by TIMS and laser ablation MC-ICP-MS, despite the high Ca/Pb concentration ratio (200/1) and the presence of many other elements at levels comparable with that of lead. Approximately 0.2 microg lead are sufficient for isotope analysis with ratio uncertainties between 240 and 530 ppm.

Definitive screening design enables optimization of LC-ESI-MS/MS parameters in proteomics.

PubMed

Aburaya, Shunsuke; Aoki, Wataru; Minakuchi, Hiroyoshi; Ueda, Mitsuyoshi

2017-12-01

In proteomics, more than 100,000 peptides are generated from the digestion of human cell lysates. Proteome samples have a broad dynamic range in protein abundance; therefore, it is critical to optimize various parameters of LC-ESI-MS/MS to comprehensively identify these peptides. However, there are many parameters for LC-ESI-MS/MS analysis. In this study, we applied definitive screening design to simultaneously optimize 14 parameters in the operation of monolithic capillary LC-ESI-MS/MS to increase the number of identified proteins and/or the average peak area of MS1. The simultaneous optimization enabled the determination of two-factor interactions between LC and MS. Finally, we found two parameter sets of monolithic capillary LC-ESI-MS/MS that increased the number of identified proteins by 8.1% or the average peak area of MS1 by 67%. The definitive screening design would be highly useful for high-throughput analysis of the best parameter set in LC-ESI-MS/MS systems.

Sulfur analysis by inductively coupled plasma-mass spectrometry: A review

NASA Astrophysics Data System (ADS)

Giner Martínez-Sierra, J.; Galilea San Blas, O.; Marchante Gayón, J. M.; García Alonso, J. I.

2015-06-01

In recent years the number of applications of sulfur (S) analysis using inductively coupled plasma mass spectrometry (ICP-MS) as detector has increased significantly. In this article we describe in some depth the application of ICP-MS for S analysis with emphasis placed on the sulfur-specific detection by hyphenated techniques such as LC, GC, CE and LA coupled on-line to ICP-MS. The different approaches available for sulfur isotope ratio measurements by ICP-MS are also detailed. Particular attention has been paid to the quantification of peptides/proteins and the analysis of metallopeptides/metalloproteins via sulfur by LC-ICP-MS. Likewise, the speciation analysis of metal-based pharmaceuticals and metallodrugs and non-metal selective detection of pharmaceuticals via S are highlighted. Labeling procedures for metabolic applications are also included. Finally, the measurement of natural variations in S isotope composition with multicollector ICP-MS instruments is also covered in this review.

Analysis of Monoclonal Antibodies in Human Serum as a Model for Clinical Monoclonal Gammopathy by Use of 21 Tesla FT-ICR Top-Down and Middle-Down MS/MS

NASA Astrophysics Data System (ADS)

He, Lidong; Anderson, Lissa C.; Barnidge, David R.; Murray, David L.; Hendrickson, Christopher L.; Marshall, Alan G.

2017-05-01

With the rapid growth of therapeutic monoclonal antibodies (mAbs), stringent quality control is needed to ensure clinical safety and efficacy. Monoclonal antibody primary sequence and post-translational modifications (PTM) are conventionally analyzed with labor-intensive, bottom-up tandem mass spectrometry (MS/MS), which is limited by incomplete peptide sequence coverage and introduction of artifacts during the lengthy analysis procedure. Here, we describe top-down and middle-down approaches with the advantages of fast sample preparation with minimal artifacts, ultrahigh mass accuracy, and extensive residue cleavages by use of 21 tesla FT-ICR MS/MS. The ultrahigh mass accuracy yields an RMS error of 0.2-0.4 ppm for antibody light chain, heavy chain, heavy chain Fc/2, and Fd subunits. The corresponding sequence coverages are 81%, 38%, 72%, and 65% with MS/MS RMS error 4 ppm. Extension to a monoclonal antibody in human serum as a monoclonal gammopathy model yielded 53% sequence coverage from two nano-LC MS/MS runs. A blind analysis of five therapeutic monoclonal antibodies at clinically relevant concentrations in human serum resulted in correct identification of all five antibodies. Nano-LC 21 T FT-ICR MS/MS provides nonpareil mass resolution, mass accuracy, and sequence coverage for mAbs, and sets a benchmark for MS/MS analysis of multiple mAbs in serum. This is the first time that extensive cleavages for both variable and constant regions have been achieved for mAbs in a human serum background.