MULTI-DIMENSIONAL MASS SPECTROMETRY-BASED SHOTGUN LIPIDOMICS AND NOVEL STRATEGIES FOR LIPIDOMIC ANALYSES

PubMed Central

Han, Xianlin; Yang, Kui; Gross, Richard W.

2011-01-01

Since our last comprehensive review on multi-dimensional mass spectrometry-based shotgun lipidomics (Mass Spectrom. Rev. 24 (2005), 367), many new developments in the field of lipidomics have occurred. These developments include new strategies and refinements for shotgun lipidomic approaches that use direct infusion, including novel fragmentation strategies, identification of multiple new informative dimensions for mass spectrometric interrogation, and the development of new bioinformatic approaches for enhanced identification and quantitation of the individual molecular constituents that comprise each cell’s lipidome. Concurrently, advances in liquid chromatography-based platforms and novel strategies for quantitative matrix-assisted laser desorption/ionization mass spectrometry for lipidomic analyses have been developed. Through the synergistic use of this repertoire of new mass spectrometric approaches, the power and scope of lipidomics has been greatly expanded to accelerate progress toward the comprehensive understanding of the pleiotropic roles of lipids in biological systems. PMID:21755525

Portable laser synthesizer for high-speed multi-dimensional spectroscopy

DOEpatents

Demos, Stavros G [Livermore, CA; Shverdin, Miroslav Y [Sunnyvale, CA; Shirk, Michael D [Brentwood, CA

2012-05-29

Portable, field-deployable laser synthesizer devices designed for multi-dimensional spectrometry and time-resolved and/or hyperspectral imaging include a coherent light source which simultaneously produces a very broad, energetic, discrete spectrum spanning through or within the ultraviolet, visible, and near infrared wavelengths. The light output is spectrally resolved and each wavelength is delayed with respect to each other. A probe enables light delivery to a target. For multidimensional spectroscopy applications, the probe can collect the resulting emission and deliver this radiation to a time gated spectrometer for temporal and spectral analysis.

Characterizing the Smell of Marijuana by Odor Impact of Volatile Compounds: An Application of Simultaneous Chemical and Sensory Analysis

PubMed Central

2015-01-01

Recent US legislation permitting recreational use of marijuana in certain states brings the use of marijuana odor as probable cause for search and seizure to the forefront of forensic science, once again. This study showed the use of solid-phase microextraction with multidimensional gas chromatography—mass spectrometry and simultaneous human olfaction to characterize the total aroma of marijuana. The application of odor activity analysis offers an explanation as to why high volatile chemical concentration does not equate to most potent odor impact of a certain compound. This suggests that more attention should be focused on highly odorous compounds typically present in low concentrations, such as nonanal, decanol, o-cymene, benzaldehyde, which have more potent odor impact than previously reported marijuana headspace volatiles. PMID:26657499

Analytical Strategies Involved in the Detailed Componential Characterization of Biooil Produced from Lignocellulosic Biomass

PubMed Central

Li, Guo-Sheng; Wei, Xian-Yong

2017-01-01

Elucidation of chemical composition of biooil is essentially important to evaluate the process of lignocellulosic biomass (LCBM) conversion and its upgrading and suggest proper value-added utilization like producing fuel and feedstock for fine chemicals. Although the main components of LCBM are cellulose, hemicelluloses, and lignin, the chemicals derived from LCBM differ significantly due to the various feedstock and methods used for the decomposition. Biooil, produced from pyrolysis of LCBM, contains hundreds of organic chemicals with various classes. This review covers the methodologies used for the componential analysis of biooil, including pretreatments and instrumental analysis techniques. The use of chromatographic and spectrometric methods was highlighted, covering the conventional techniques such as gas chromatography, high performance liquid chromatography, Fourier transform infrared spectroscopy, nuclear magnetic resonance, and mass spectrometry. The combination of preseparation methods and instrumental technologies is a robust pathway for the detailed componential characterization of biooil. The organic species in biooils can be classified into alkanes, alkenes, alkynes, benzene-ring containing hydrocarbons, ethers, alcohols, phenols, aldehydes, ketones, esters, carboxylic acids, and other heteroatomic organic compounds. The recent development of high resolution mass spectrometry and multidimensional hyphenated chromatographic and spectrometric techniques has considerably elucidated the composition of biooils. PMID:29387086

Analysis of Odorants in Marking Fluid of Siberian Tiger (Panthera tigris altaica) Using Simultaneous Sensory and Chemical Analysis with Headspace Solid-Phase Microextraction and Multidimensional Gas Chromatography-Mass Spectrometry-Olfactometry.

PubMed

Soso, Simone B; Koziel, Jacek A

2016-06-25

Scent-marking is the most effective method of communication in the presence or absence of a signaler. These complex mixtures result in a multifaceted interaction triggered by the sense of smell. The objective was to identify volatile organic compound (VOC) composition and odors emitted by total marking fluid (MF) associated with Siberian tigers (Panthera tigris altaica). Siberian tiger, an endangered species, was chosen because its MF had never been analyzed. Solid phase microextraction (SPME) for headspace volatile collection combined with multidimensional gas chromatography-mass spectrometry-olfactometry for simultaneous chemical and sensory analyses were used. Thirty-two VOCs emitted from MF were identified. 2-acetyl-1-pyrroline, the sole previously identified compound responsible for the "characteristic" odor of P. tigris MF, was identified along with two additional compounds confirmed with standards (urea, furfural) and four tentatively identified compounds (3-methylbutanamine, (R)-3-methylcyclopentanone, propanedioic acid, and 3-hydroxybutanal) as being responsible for the characteristic aroma of Siberian tiger MF. Simultaneous chemical and sensory analyses improved characterization of scent-markings and identified compounds not previously reported in MF of other tiger species. This research will assist animal ecologists, behaviorists, and zookeepers in understanding how scents from specific MF compounds impact tiger and wildlife communication and improve management practices related to animal behavior. Simultaneous chemical and sensory analyses is applicable to unlocking scent-marking information for other species.

Characterization of the human submandibular/sublingual saliva glycoproteome using lectin affinity chromatography coupled to Multidimensional Protein Identification Technology

PubMed Central

Gonzalez-Begne, Mireya; Lu, Bingwen; Liao, Lujian; Xu, Tao; Bedi, Gurrinder; Melvin, James E.; Yates, John R.

2011-01-01

In-depth analysis of the salivary proteome is fundamental to understanding the functions of salivary proteins in the oral cavity and to reveal disease biomarkers involved in different pathophysiological conditions, with the ultimate goal of improving patient diagnosis and prognosis. Submandibular and sublingual glands contribute saliva rich in glycoproteins to the total saliva output, making them valuable sources for glycoproteomic analysis. Lectin-affinity chromatography coupled to mass spectrometry-based shotgun proteomics was used to explore the submandibular/sublingual (SM/SL) saliva glycoproteome. A total of 262 N- and O-linked glycoproteins were identified by multidimensional protein identification technology (MudPIT). Only 38 were previously described in SM and SL salivas from the human salivary N-linked glycoproteome, while 224 were unique. Further comparison analysis with SM/SL saliva of the human saliva proteome, revealed 125 glycoproteins not formerly reported in this secretion. KEGG pathway analyses demonstrated that many of these glycoproteins are involved in processes such as complement and coagulation cascades, cell communication, glycosphingolipid biosynthesis neo-lactoseries, O-glycan biosynthesis, glycan structures-biosynthesis 2, starch and sucrose metabolism, peptidoglycan biosynthesis or others pathways. In summary, lectin-affinity chromatography coupled to MudPIT mass spectrometry identified many novel glycoproteins in SM/SL saliva. These new additions to the salivary proteome may prove to be a critical step for providing reliable biomarkers in the diagnosis of a myriad of oral and systemic diseases. PMID:21936497

Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight mass spectrometer: I. How much of the data is theoretically interpretable by search engines?

PubMed

Chalkley, Robert J; Baker, Peter R; Hansen, Kirk C; Medzihradszky, Katalin F; Allen, Nadia P; Rexach, Michael; Burlingame, Alma L

2005-08-01

An in-depth analysis of a multidimensional chromatography-mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight (QqTOF) geometry instrument was carried out. A total of 3269 CID spectra were acquired. Through manual verification of database search results and de novo interpretation of spectra 2368 spectra could be confidently determined as predicted tryptic peptides. A detailed analysis of the non-matching spectra was also carried out, highlighting what the non-matching spectra in a database search typically are composed of. The results of this comprehensive dataset study demonstrate that QqTOF instruments produce information-rich data of which a high percentage of the data is readily interpretable.

Conventional and Advanced Separations in Mass Spectrometry-Based Metabolomics: Methodologies and Applications

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

Heyman, Heino M.; Zhang, Xing; Tang, Keqi

2016-02-16

Metabolomics is the quantitative analysis of all metabolites in a given sample. Due to the chemical complexity of the metabolome, optimal separations are required for comprehensive identification and quantification of sample constituents. This chapter provides an overview of both conventional and advanced separations methods in practice for reducing the complexity of metabolite extracts delivered to the mass spectrometer detector, and covers gas chromatography (GC), liquid chromatography (LC), capillary electrophoresis (CE), supercritical fluid chromatography (SFC) and ion mobility spectrometry (IMS) separation techniques coupled with mass spectrometry (MS) as both uni-dimensional and as multi-dimensional approaches.

LC-IMS-MS Feature Finder

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

2013-03-07

LC-IMS-MS Feature Finder is a command line software application which searches for possible molecular ion signatures in multidimensional liquid chromatography, ion mobility spectrometry, and mass spectrometry data by clustering deisotoped peaks with similar monoisotopic mass values, charge states, elution times, and drift times. The software application includes an algorithm for detecting multiple conformations and co-eluting species in the ion mobility dimension. LC-IMS-MS Feature Finder is designed to create an output file with detected features that includes associated information about the detected features.

Multidimensional proteomics for cell biology.

PubMed

Larance, Mark; Lamond, Angus I

2015-05-01

The proteome is a dynamic system in which each protein has interconnected properties - dimensions - that together contribute to the phenotype of a cell. Measuring these properties has proved challenging owing to their diversity and dynamic nature. Advances in mass spectrometry-based proteomics now enable the measurement of multiple properties for thousands of proteins, including their abundance, isoform expression, turnover rate, subcellular localization, post-translational modifications and interactions. Complementing these experimental developments are new data analysis, integration and visualization tools as well as data-sharing resources. Together, these advances in the multidimensional analysis of the proteome are transforming our understanding of various cellular and physiological processes.

Chemical fingerprinting of naphthenic acids at an oil sands end pit lake by comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry (GC×GC/TOFMS)

NASA Astrophysics Data System (ADS)

Bowman, D. T.; Arriaga, D.; Morris, P.; Risacher, F.; Warren, L. A.; McCarry, B. E.; Slater, G.

2016-12-01

Naphthenic acids (NAs) are naturally occurring in Athabasca oil sands and accumulate in tailings as a result of water-based extraction processes. NAs contribute to the toxicity of tailings and oil sands process-affected water (OSPW). NAs exist as a complex mixture, so the development of an analytical technique to characterize them has been an on-going challenge. The monitoring of individual NAs and their associated isomers through multidimensional chromatography has the potential to provide greater insight into the behavior of NAs in the environment. For NAs whose proportions do not change during environmental processing, NA ratios may provide a means to develop fingerprints characteristic of specific sources. Alternatively, relative changes in the proportions of NAs may provide a tracer of their occurrence and extent of removal. As yet, only a few studies have begun to explore these possibilities. In this study, comprehensive two dimensional gas chromatography/time-of-flight mass spectrometry was used to monitor individual naphthenic acids in an end pit lake in Alberta, Canada. NA profiles from different depths and sampling locations were compared to evaluate the spatial variations at the site.

Characterization of Anthocyanins in Perilla frutescens var. acuta Extract by Advanced UPLC-ESI-IT-TOF-MSn Method and Their Anticancer Bioactivity.

PubMed

He, Yan-Kang; Yao, You-Yuan; Chang, Ya-Ning

2015-05-19

The anthocyanin extract from a domestic Perilla cultivar (Perilla frutescens var. acuta) were isolated and characterized with high mass accuracy and multi-dimensional fragmentation by means of ultra-performance liquid chromatography (UPLC) and electrospray ionization-ion trap-time of flight mass spectrometry analysis (ESI-IT-TOF-MSn). The new developed and applied LC-MS method focused on in-depth screening of anthocyanin compounds with similar structures which also provided a new approach of anthocyanin characterization without the use of external standards. Selective detection of interested anthocyanins was achieved utilizing extracted ion chromatogram (EIC) analysis, while MSn spectra were recorded to allow identification of the anthocyanin based on characteristic fragmentation patterns. Seven anthocyanins including one feruloyl (Cyanidin 3-O-feruloylglucoside-5-O-glucoside), two caffeoyl (Cyanidin 3-O-caffeoylglucoside-5-O-glucoside, Cyanidin 3-O-caffeoylglucoside-5-O-malonylglucoside) and four coumaroyl substituted anthocyanins (Cis-shisonin, Malonyl-cis-shisonin, Shisonin, and Malonyl-shisonin) were identified. Annexin-V FITC/PI flow cytometric assay was performed to analyze the influence of anthocyanin extract of P. frutescens var. acuta on cell apoptosis. The results suggested that Perilla anthocyanins can induce Hela cell apoptosis by a dose dependent manner.

Status quo and future research challenges on organic food quality determination with focus on laboratory methods.

PubMed

Kahl, Johannes; Bodroza-Solarov, Marija; Busscher, Nicolaas; Hajslova, Jana; Kneifel, Wolfgang; Kokornaczyk, Maria Olga; van Ruth, Saskia; Schulzova, Vera; Stolz, Peter

2014-10-01

Organic food quality determination needs multi-dimensional evaluation tools. The main focus is on the authentication as an analytical verification of the certification process. New fingerprinting approaches such as ultra-performance liquid chromatography-mass spectrometry, gas chromatography-mass spectrometry, direct analysis in real time-high-resolution mass spectrometry as well as crystallization with and without the presence of additives seem to be promising methods in terms of time of analysis and detecting organic system-related parameters. For further methodological development, a system approach is recommended, which also takes into account food structure aspects. Furthermore, the authentication of processed organic samples needs more consciousness, hence most of organic food is complex and processed. © 2013 Society of Chemical Industry.

Comprehensive authentication of (E)-alpha(beta)-ionone from raspberries, using constant flow MDGC-C/P-IRMS and enantio-MDGC-MS.

PubMed

Sewenig, Sabine; Bullinger, Dino; Hener, Uwe; Mosandl, Armin

2005-02-23

A new coupling system of GC-GC, connected via a Multi Column Switching Device MCS2 for measuring isotope ratios, is introduced. By means of several standard substances the precise and accurate measurement of isotopic values is proved. First applications concerning the authentication of raspberry aroma compounds are established. Consequently, the combination of constant flow multidimensional gas chromatography-combustion/pyrolysis-isotope ratio mass spectrometry (MDGC-C/P-IRMS) is applied to the authenticity assessment of (E)-alpha(beta)-ionone from six different raspberry cultivars. Furthermore, 12 commercially available raspberry products and samples of (E)-alpha(beta)-ionone, some declared to be natural, are investigated. delta(2)Eta(V)(-)(SMOW) and delta(13)C(V)(-)(PDB) values of (E)-alpha(beta)-ionone are determined, and characteristic authenticity ranges were concluded from raspberries by correlation of both delta(2)Eta(V)(-)(SMOW) and delta(13)C( V)(-)(PDB) values. The results are correlated with the determination of enantiomeric purities of (E)-alpha-ionone, using stir bar sorptive extraction enantio-multidimensional gas chromatography mass spectrometry (SBSE-enantio-MDGC-MS).

Separation and characterization of allergic polymerized impurities in cephalosporins by 2D-HPSEC×LC-IT-TOF MS.

PubMed

Xu, Yu; Wang, DanDan; Tang, Lan; Wang, Jian

2017-10-25

Eleven unknown allergic impurities in cefodizime, cefmenoxime and cefonicid were separated and characterized by a trap-free two-dimensional high performance size exclusion chromatography (HPSEC) and reversed phase liquid chromatography (RP-HPLC) coupled to high resolution ion trap/time-of-flight mass spectrometry (2D-HPSEC×LC-IT-TOF MS) with positive and negative modes of electrospray ionization method. Separation and characterization the allergic polymerized impurities in β-lactam antibiotics were on the basis of column-switching technique which effectively combined the advantages of HPSEC and the ability of RP-HPLC to identify the special impurities. In the first dimension HPSEC, the column was Xtimate SEC-120 analytical column (7.8mm×30cm, 5μm), and the gradient elution used pH 7.0 buffer-acetonitrile as mobile phase And the second dimension analytical column was ZORBAX SB-C18 (4.6×150mm, 3.5μm) with ammonium formate solution (10mM) and ammonium formate (8mM) in [acetonitrile-water (4:1, v/v)] solution as mobile phase. Structures of eleven unknown impurities were deduced based on the high resolution MS n data with both positive and negative modes, in which nine impurities were polymerized impurities. The forming mechanism of β-lactam antibiotic polymerization in cephalosporins was also studied. The question on incompatibility between non-volatile salt mobile phase and mass spectrometry was solved completely by multidimensional heart-cutting approaches and online demineralization technique, which was worthy of widespread use and application for the advantages of stability and repeatability. Copyright © 2017. Published by Elsevier B.V.

Pedagogical Factors Stimulating the Self-Development of Students' Multi-Dimensional Thinking in Terms of Subject-Oriented Teaching

ERIC Educational Resources Information Center

Andreev, Valentin I.

2014-01-01

The main aim of this research is to disclose the essence of students' multi-dimensional thinking, also to reveal the rating of factors which stimulate the raising of effectiveness of self-development of students' multi-dimensional thinking in terms of subject-oriented teaching. Subject-oriented learning is characterized as a type of learning where…

Development of a new ion mobility time-of-flight mass spectrometer

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

Ibrahim, Yehia M.; Baker, Erin S.; Danielson, William F.

2015-02-01

Complex samples require multidimensional measurements with high resolution for full characterization of biological and environmental systems. To address this challenge, we developed a drift tube-based ion mobility spectrometry-Orbitrap mass spectrometry (IMS-Orbitrap MS) platform. To circumvent the timing difference between the fast IMS separation and the slow Orbitrap MS acquisition, we utilized a dual gate and pseudorandom sequence to multiplex ions into the drift tube and Orbitrap. The instrument was designed to operate in signal averaging (SA), single multiplexing (SM) and double multiplexing (DM) IMS modes to fully optimize the signal-to-ratio of the measurements. For the SM measurements, a previously developedmore » algorithm was used to reconstruct the IMS data, while a new algorithm was developed for the DM analyses. The new algorithm is a two-step process that first recovers the SM data from the encoded DM data and then decoded the SM data. The algorithm also performs multiple refining procedures in order to minimize the demultiplexing artifacts traditionally observed in such scheme. The new IMS-Orbitrap MS platform was demonstrated for the analysis of proteomic and petroleum samples, where the integration of IMS and high mass resolution proved essential for accurate assignment of molecular formulae.« less

Femtosecond Multidimensional Imaging - Watching Chemistry from the Molecule's Point of View

NASA Astrophysics Data System (ADS)

Geßner, O.; Lee, A. M. D.; Chrysostom, E. t.-H.; Hayden, C. C.; Stolow, Albert

Using Femtosecond Multidimensional Imaging we disentangle the complex neutral dissociation mechanism of the NO dimer. We characterize all electronic configurations from start to finish and directly observe the evolution of intramolecular vibrational energy redistribution (IVR).

Trends in mass spectrometry instrumentation for proteomics

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

Smith, Richard D.

2002-12-01

Mass spectrometry has become a primary tool for proteomics due to its capabilities for rapid and sensitive protein identification and quantitation. It is now possible to identify thousands of proteins from microgram sample quantities in a single day and to quantify relative protein abundances. However, the needs for increased capabilities for proteome measurements are immense and are now driving both new strategies and instrument advances. These developments include those based on integration with multi-dimensional liquid separations and high accuracy mass measurements, and promise more than order of magnitude improvements in sensitivity, dynamic range, and throughput for proteomic analyses in themore » near future.« less

Characterization of plant polysaccharides from Dendrobium officinale by multiple chromatographic and mass spectrometric techniques.

PubMed

Ma, Huiying; Zhang, Keke; Jiang, Qing; Dai, Diya; Li, Hongli; Bi, Wentao; Chen, David Da Yong

2018-04-27

Plant polysaccharides have numerous medicinal functions. Due to the differences in their origins, regions of production, and cultivation conditions, the quality and the functions of polysaccharides can vary significantly. They are macromolecules with large molecular weight (MW) and complex structure, and pose great challenge for the analytical technology used. Taking Dendrobium officinale (DO) from various origins and locations as model samples. In this investigation, mechanochemical extraction method was used to successfully extract polysaccharides from DO using water as solvent, the process is simple, fast (40 s) and with high yield. The MWs of the intact saccharides from calibration curve and light scattering measurement were determined and compared after separation with size exclusion chromatography (SEC). The large polysaccharide was acid hydrolyzed to oligosaccharides and the products were efficiently separated and identified using liquid chromatography coupled to a high resolution tandem mass spectrometry (LC-MS 2 ). Obvious differences were observed among LC-MS 2 chromatograms of digested products, and the chemical structures for the products were proposed based on accurate mass values. More importantly, isomeric digested carbohydrate compounds were explored and characterized. All the chromatographic and mass spectrometric results in this study provided a multi-dimensional characterization, fingerprint analysis, and molecular structure level assessment of plant polysaccharides. Copyright © 2018 Elsevier B.V. All rights reserved.

A Framework for Dimensionality Assessment for Multidimensional Item Response Models

ERIC Educational Resources Information Center

Svetina, Dubravka; Levy, Roy

2014-01-01

A framework is introduced for considering dimensionality assessment procedures for multidimensional item response models. The framework characterizes procedures in terms of their confirmatory or exploratory approach, parametric or nonparametric assumptions, and applicability to dichotomous, polytomous, and missing data. Popular and emerging…

Identification, synthesis, and characterization of novel sulfur-containing volatile compounds from the in-depth analysis of Lisbon lemon peels (Citrus limon L. Burm. f. cv. Lisbon).

PubMed

Cannon, Robert J; Kazimierski, Arkadiusz; Curto, Nicole L; Li, Jing; Trinnaman, Laurence; Jańczuk, Adam J; Agyemang, David; Da Costa, Neil C; Chen, Michael Z

2015-02-25

Lemons (Citrus limon) are a desirable citrus fruit grown and used globally in a wide range of applications. The main constituents of this sour-tasting fruit have been well quantitated and characterized. However, additional research is still necessary to better understand the trace volatile compounds that may contribute to the overall aroma of the fruit. In this study, Lisbon lemons (C. limon L. Burm. f. cv. Lisbon) were purchased from a grove in California, USA, and extracted by liquid-liquid extraction. Fractionation and multidimensional gas chromatography-mass spectrometry were utilized to separate, focus, and enhance unidentified compounds. In addition, these methods were employed to more accurately assign flavor dilution factors by aroma extract dilution analysis. Numerous compounds were identified for the first time in lemons, including a series of branched aliphatic aldehydes and several novel sulfur-containing structures. Rarely reported in citrus peels, sulfur compounds are known to contribute significantly to the aroma profile of the fruit and were found to be aroma-active in this particular study on lemons. This paper discusses the identification, synthesis, and organoleptic properties of these novel volatile sulfur compounds.

Detection systems for mass spectrometry imaging: a perspective on novel developments with a focus on active pixel detectors.

PubMed

Jungmann, Julia H; Heeren, Ron M A

2013-01-15

Instrumental developments for imaging and individual particle detection for biomolecular mass spectrometry (imaging) and fundamental atomic and molecular physics studies are reviewed. Ion-counting detectors, array detection systems and high mass detectors for mass spectrometry (imaging) are treated. State-of-the-art detection systems for multi-dimensional ion, electron and photon detection are highlighted. Their application and performance in three different imaging modes--integrated, selected and spectral image detection--are described. Electro-optical and microchannel-plate-based systems are contrasted. The analytical capabilities of solid-state pixel detectors--both charge coupled device (CCD) and complementary metal oxide semiconductor (CMOS) chips--are introduced. The Medipix/Timepix detector family is described as an example of a CMOS hybrid active pixel sensor. Alternative imaging methods for particle detection and their potential for future applications are investigated. Copyright © 2012 John Wiley & Sons, Ltd.

Multidimensional Programming Methods for Energy Facility Siting: Alternative Approaches

NASA Technical Reports Server (NTRS)

Solomon, B. D.; Haynes, K. E.

1982-01-01

The use of multidimensional optimization methods in solving power plant siting problems, which are characterized by several conflicting, noncommensurable objectives is addressed. After a discussion of data requirements and exclusionary site screening methods for bounding the decision space, classes of multiobjective and goal programming models are discussed in the context of finite site selection. Advantages and limitations of these approaches are highlighted and the linkage of multidimensional methods with the subjective, behavioral components of the power plant siting process is emphasized.

Avoiding Degeneracy in Multidimensional Unfolding by Penalizing on the Coefficient of Variation

ERIC Educational Resources Information Center

Busing, Frank M. T. A.; Groenen, Patrick J. K.; Heiser, Willem J.

2005-01-01

Multidimensional unfolding methods suffer from the degeneracy problem in almost all circumstances. Most degeneracies are easily recognized: the solutions are perfect but trivial, characterized by approximately equal distances between points from different sets. A definition of an absolutely degenerate solution is proposed, which makes clear that…

Endoplasmic reticulum stress-responsive transcription factor ATF6α directs recruitment of the Mediator of RNA polymerase II transcription and multiple histone acetyltransferase complexes.

PubMed

Sela, Dotan; Chen, Lu; Martin-Brown, Skylar; Washburn, Michael P; Florens, Laurence; Conaway, Joan Weliky; Conaway, Ronald C

2012-06-29

The basic leucine zipper transcription factor ATF6α functions as a master regulator of endoplasmic reticulum (ER) stress response genes. Previous studies have established that, in response to ER stress, ATF6α translocates to the nucleus and activates transcription of ER stress response genes upon binding sequence specifically to ER stress response enhancer elements in their promoters. In this study, we investigate the biochemical mechanism by which ATF6α activates transcription. By exploiting a combination of biochemical and multidimensional protein identification technology-based mass spectrometry approaches, we have obtained evidence that ATF6α functions at least in part by recruiting to the ER stress response enhancer elements of ER stress response genes a collection of RNA polymerase II coregulatory complexes, including the Mediator and multiple histone acetyltransferase complexes, among which are the Spt-Ada-Gcn5 acetyltransferase (SAGA) and Ada-Two-A-containing (ATAC) complexes. Our findings shed new light on the mechanism of action of ATF6α, and they outline a straightforward strategy for applying multidimensional protein identification technology mass spectrometry to determine which RNA polymerase II transcription factors and coregulators are recruited to promoters and other regulatory elements to control transcription.

Five Evils: Multidimensional Poverty and Race in America

ERIC Educational Resources Information Center

Reeves, Richard; Rodrigue, Edward; Kneebone, Elizabeth

2016-01-01

Poverty is about a lack of money, but it's not only about that. As a lived experience, poverty is also characterized by ill health, insecurity, discomfort, isolation, and more. To put it another way: Poverty is multidimensional, and its dimensions often cluster together to intensify the negative effects of being poor. In this first of a two-part…

NMR and MALDI-TOF MS based characterization of exopolysaccharides in anaerobic microbial aggregates from full-scale reactors

PubMed Central

Gonzalez-Gil, Graciela; Thomas, Ludivine; Emwas, Abdul-Hamid; Lens, Piet N. L.; Saikaly, Pascal E.

2015-01-01

Anaerobic granular sludge is composed of multispecies microbial aggregates embedded in a matrix of extracellular polymeric substances (EPS). Here we characterized the chemical fingerprint of the polysaccharide fraction of EPS in anaerobic granules obtained from full-scale reactors treating different types of wastewater. Nuclear magnetic resonance (NMR) signals of the polysaccharide region from the granules were very complex, likely as a result of the diverse microbial population in the granules. Using nonmetric multidimensional scaling (NMDS), the 1H NMR signals of reference polysaccharides (gellan, xanthan, alginate) and those of the anaerobic granules revealed that there were similarities between the polysaccharides extracted from granules and the reference polysaccharide alginate. Further analysis of the exopolysaccharides from anaerobic granules, and reference polysaccharides using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) revealed that exopolysaccharides from two of the anaerobic granular sludges studied exhibited spectra similar to that of alginate. The presence of sequences related to the synthesis of alginate was confirmed in the metagenomes of the granules. Collectively these results suggest that alginate-like exopolysaccharides are constituents of the EPS matrix in anaerobic granular sludge treating different industrial wastewater. This finding expands the engineered environments where alginate has been found as EPS constituent of microbial aggregates. PMID:26391984

Field Air Sampling and Simultaneous Chemical and Sensory Analysis of Livestock Odorants with Sorbent Tube GC-MS/Olfactometry

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

Zhang Shicheng; Department of Environmental Science and Engineering, Fudan University, Shanghai 200433; Cai Lingshuang

2009-05-23

Characterization and quantification of livestock odorants is one of the most challenging analytical tasks because odor-causing gases are very reactive, polar and often present at very low concentrations in a complex matrix of less important or irrelevant gases. The objective of this research was to develop a novel analytical method for characterization of the livestock odorants including their odor character, odor intensity, and hedonic tone and to apply this method for quantitative analysis of the key odorants responsible for livestock odor. Sorbent tubes packed with Tenax TA were used for field sampling. The automated one-step thermal desorption module coupled withmore » multidimensional gas chromatography-mass spectrometry/olfactometry system was used for simultaneous chemical and odor analysis. Fifteen odorous VOCs and semi-VOCs identified from different livestock species operations were quantified. Method detection limits ranges from 40 pg for skatole to 3590 pg for acetic acid. In addition, odor character, odor intensity and hedonic tone associated with each of the target odorants are also analyzed simultaneously. We found that the mass of each VOCs in the sample correlates well with the log stimulus intensity. All of the correlation coefficients (R{sup 2}) are greater than 0.74, and the top 10 correlation coefficients were greater than 0.90.« less

NMR and MALDI-TOF MS based characterization of exopolysaccharides in anaerobic microbial aggregates from full-scale reactors.

PubMed

Gonzalez-Gil, Graciela; Thomas, Ludivine; Emwas, Abdul-Hamid; Lens, Piet N L; Saikaly, Pascal E

2015-09-22

Anaerobic granular sludge is composed of multispecies microbial aggregates embedded in a matrix of extracellular polymeric substances (EPS). Here we characterized the chemical fingerprint of the polysaccharide fraction of EPS in anaerobic granules obtained from full-scale reactors treating different types of wastewater. Nuclear magnetic resonance (NMR) signals of the polysaccharide region from the granules were very complex, likely as a result of the diverse microbial population in the granules. Using nonmetric multidimensional scaling (NMDS), the (1)H NMR signals of reference polysaccharides (gellan, xanthan, alginate) and those of the anaerobic granules revealed that there were similarities between the polysaccharides extracted from granules and the reference polysaccharide alginate. Further analysis of the exopolysaccharides from anaerobic granules, and reference polysaccharides using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) revealed that exopolysaccharides from two of the anaerobic granular sludges studied exhibited spectra similar to that of alginate. The presence of sequences related to the synthesis of alginate was confirmed in the metagenomes of the granules. Collectively these results suggest that alginate-like exopolysaccharides are constituents of the EPS matrix in anaerobic granular sludge treating different industrial wastewater. This finding expands the engineered environments where alginate has been found as EPS constituent of microbial aggregates.

Characterization of factor VIII pharmaceutical preparations by means of MudPIT proteomic approach.

PubMed

Basilico, Fabrizio; Nardini, Ilaria; Mori, Filippo; Brambilla, Elena; Benazzi, Louise; De Palma, Antonella; Rosti, Enrico; Farina, Claudio; Mauri, PierLuigi

2010-09-21

For a good clinical outcome of Haemophilia A substitutive therapy a detailed characterization of factor VIII (FVIII) concentrates is required, in order to disclose the eventual relations between differently composed concentrates and their biological effects. This preliminary work could be a first step towards a deep structural characterization of FVIII concentrates, using the fast and simply manageable MudPIT technology, which enables the identification and characterization of protein mixtures taking advantage of both the high separation capacity of two-dimensional chromatography and the powerful peptide characterization ability of tandem mass spectrometry. The aim of this study was to evaluate the suitability of for the characterization of FVIII molecule in complex mixtures such its commercial concentrates, both plasma-derived and recombinant, and for the determination of the protein composition of different FVIII preparations. By means of Multidimensional Protein Identification Technology (MudPIT) it was possible to assess the presence of factor VIII in its preparations and to identify most of the contaminant proteins without gel separation. In particular, 125 and 42 proteins were identified in plasma-derived and recombinant concentrates, respectively. Concerning investigation of FVIII, 24 different peptides were identified in plasma-derived corresponding to 7, 29, 27, 19 and 67 of percentage coverage for A1, A2, A3, C1 and C2 domains, respectively. About its multimeric carrier von Willebrand factor (VWF), we have sequenced 42% of domain interacting with A3 and C2 domains of FVIII. Finally, it has been observed that normalized parameters, such as total peptide hits obtained by SEQUEST may be used for evaluation of the relative abundance of FVIII in different preparations. Copyright 2010 Elsevier B.V. All rights reserved.

The Cognitive Visualization System with the Dynamic Projection of Multidimensional Data

NASA Astrophysics Data System (ADS)

Gorohov, V.; Vitkovskiy, V.

2008-08-01

The phenomenon of cognitive machine drawing consists in the generation on the screen the special graphic representations, which create in the brain of human operator entertainment means. These means seem man by aesthetically attractive and, thus, they stimulate its descriptive imagination, closely related to the intuitive mechanisms of thinking. The essence of cognitive effect lies in the fact that man receives the moving projection as pseudo-three-dimensional object characterizing multidimensional means in the multidimensional space. After the thorough qualitative study of the visual aspects of multidimensional means with the aid of the enumerated algorithms appears the possibility, using algorithms of standard machine drawing to paint the interesting user separate objects or the groups of objects. Then it is possible to again return to the dynamic behavior of the rotation of means for the purpose of checking the intuitive ideas of user about the clusters and the connections in multidimensional data. Is possible the development of the methods of cognitive machine drawing in combination with other information technologies, first of all with the packets of digital processing of images and multidimensional statistical analysis.

A draft map of the human ovarian proteome for tissue engineering and clinical applications.

PubMed

Ouni, Emna; Vertommen, Didier; Chiti, Maria Costanza; Dolmans, Marie-Madeleine; Amorim, Christiani Andrade

2018-02-23

Fertility preservation research in women today is increasingly taking advantage of bioengineering techniques to develop new biomimetic materials and solutions to safeguard ovarian cell function and microenvironment in vitro and in vivo. However, available data on the human ovary are limited and fundamental differences between animal models and humans are hampering researchers in their quest for more extensive knowledge of human ovarian physiology and key reproductive proteins that need to be preserved. We therefore turned to multi-dimensional label-free mass spectrometry to analyze human ovarian cortex, as it is a high-throughput and conclusive technique providing information on the proteomic composition of complex tissues like the ovary. In-depth proteomic profiling through two-dimensional liquid chromatography-mass spectrometry, western blot, histological and immunohistochemical analyses, and data mining helped us to confidently identify 1,508 proteins. Moreover, our method allowed us to chart the most complete representation so far of the ovarian matrisome, defined as the ensemble of extracellular matrix proteins and associated factors, including more than 80 proteins. In conclusion, this study will provide a better understanding of ovarian proteomics, with a detailed characterization of the ovarian follicle microenvironment, in order to enable bioengineers to create biomimetic scaffolds for transplantation and three-dimensional in vitro culture. By publishing our proteomic data, we also hope to contribute to accelerating biomedical research into ovarian health and disease in general. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

An expert system/ion trap mass spectrometry approach for life support systems monitoring

NASA Technical Reports Server (NTRS)

Palmer, Peter T.; Wong, Carla M.; Yost, Richard A.; Johnson, Jodie V.; Yates, Nathan A.; Story, Michael

1992-01-01

Efforts to develop sensor and control system technology to monitor air quality for life support have resulted in the development and preliminary testing of a concept based on expert systems and ion trap mass spectrometry (ITMS). An ITMS instrument provides the capability to identify and quantitate a large number of suspected contaminants at trace levels through the use of a variety of multidimensional experiments. An expert system provides specialized knowledge for control, analysis, and decision making. The system is intended for real-time, on-line, autonomous monitoring of air quality. The key characteristics of the system, performance data and analytical capabilities of the ITMS instrument, the design and operation of the expert system, and results from preliminary testing of the system for trace contaminant monitoring are described.

An Integrated Hot-Stage Microscope-Direct Analysis in Real Time-Mass Spectrometry System for Studying the Thermal Behavior of Materials.

PubMed

Ashton, Gage P; Harding, Lindsay P; Parkes, Gareth M B

2017-12-19

This paper describes a new analytical instrument that combines a precisely temperature-controlled hot-stage with digital microscopy and Direct Analysis in Real Time-mass spectrometry (DART-MS) detection. The novelty of the instrument lies in its ability to monitor processes as a function of temperature through the simultaneous recording of images, quantitative color changes, and mass spectra. The capability of the instrument was demonstrated through successful application to four very varied systems including profiling an organic reaction, decomposition of silicone polymers, and the desorption of rhodamine B from an alumina surface. The multidimensional, real-time analytical data provided by this instrument allow for a much greater insight into thermal processes than could be achieved previously.

Interactions across Multiple Stimulus Dimensions in Primary Auditory Cortex.

PubMed

Sloas, David C; Zhuo, Ran; Xue, Hongbo; Chambers, Anna R; Kolaczyk, Eric; Polley, Daniel B; Sen, Kamal

2016-01-01

Although sensory cortex is thought to be important for the perception of complex objects, its specific role in representing complex stimuli remains unknown. Complex objects are rich in information along multiple stimulus dimensions. The position of cortex in the sensory hierarchy suggests that cortical neurons may integrate across these dimensions to form a more gestalt representation of auditory objects. Yet, studies of cortical neurons typically explore single or few dimensions due to the difficulty of determining optimal stimuli in a high dimensional stimulus space. Evolutionary algorithms (EAs) provide a potentially powerful approach for exploring multidimensional stimulus spaces based on real-time spike feedback, but two important issues arise in their application. First, it is unclear whether it is necessary to characterize cortical responses to multidimensional stimuli or whether it suffices to characterize cortical responses to a single dimension at a time. Second, quantitative methods for analyzing complex multidimensional data from an EA are lacking. Here, we apply a statistical method for nonlinear regression, the generalized additive model (GAM), to address these issues. The GAM quantitatively describes the dependence between neural response and all stimulus dimensions. We find that auditory cortical neurons in mice are sensitive to interactions across dimensions. These interactions are diverse across the population, indicating significant integration across stimulus dimensions in auditory cortex. This result strongly motivates using multidimensional stimuli in auditory cortex. Together, the EA and the GAM provide a novel quantitative paradigm for investigating neural coding of complex multidimensional stimuli in auditory and other sensory cortices.

[Probabilistic calculations of biomolecule charge states that generate mass spectra of multiply charged ions].

PubMed

Raznikova, M O; Raznikov, V V

2015-01-01

In this work, information relating to charge states of biomolecule ions in solution obtained using the electrospray ionization mass spectrometry of different biopolymers is analyzed. The data analyses have mainly been carried out by solving an inverse problem of calculating the probabilities of retention of protons and other charge carriers by ionogenic groups of biomolecules with known primary structures. The approach is a new one and has no known to us analogues. A program titled "Decomposition" was developed and used to analyze the charge distribution of ions of native and denatured cytochrome c mass spectra. The possibility of splitting of the charge-state distribution of albumin into normal components, which likely corresponds to various conformational states of the biomolecule, has been demonstrated. The applicability criterion for using previously described method of decomposition of multidimensional charge-state distributions with two charge carriers, e.g., a proton and a sodium ion, to characterize the spatial structure of biopolymers in solution has been formulated. In contrast to known mass-spectrometric approaches, this method does not require the use of enzymatic hydrolysis or collision-induced dissociation of the biopolymers.

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

Ibrahim, Yehia M.; Garimella, Sandilya V. B.; Prost, Spencer A.

Complex samples benefit from multidimensional measurements where higher resolution enables more complete characterization of biological and environmental systems. To address this challenge, we developed a drift tube-based ion mobility spectrometry-Orbitrap mass spectrometer (IMS-Orbitrap MS) platform. To circumvent the time scale disparity between the fast IMS separation and the much slower Orbitrap MS acquisition, we utilized a dual gate and pseudorandom sequences to multiplexed injection of ions and allowing operation in signal averaging (SA), single multiplexing (SM) and double multiplexing (DM) IMS modes to optimize the signal-to-noise ratio of the measurements. For the SM measurements, a previously developed algorithm was usedmore » to reconstruct the IMS data. A new algorithm was developed for the DM analyses involving a two-step process that first recovers the SM data and then decodes the SM data. The algorithm also performs multiple refining procedures in order to minimize demultiplexing artifacts. The new IMS-Orbitrap MS platform was demonstrated by the analysis of proteomic and petroleum samples, where the integration of IMS and high mass resolution proved essential for accurate assignment of molecular formulae.« less

Method of multi-dimensional moment analysis for the characterization of signal peaks

DOEpatents

Pfeifer, Kent B; Yelton, William G; Kerr, Dayle R; Bouchier, Francis A

2012-10-23

A method of multi-dimensional moment analysis for the characterization of signal peaks can be used to optimize the operation of an analytical system. With a two-dimensional Peclet analysis, the quality and signal fidelity of peaks in a two-dimensional experimental space can be analyzed and scored. This method is particularly useful in determining optimum operational parameters for an analytical system which requires the automated analysis of large numbers of analyte data peaks. For example, the method can be used to optimize analytical systems including an ion mobility spectrometer that uses a temperature stepped desorption technique for the detection of explosive mixtures.

Multidimensional and comprehensive two-dimensional gas chromatography of dichloromethane soluble products from a high sulfur Jordanian oil shale.

PubMed

Amer, Mohammad W; Mitrevski, Blagoj; Jackson, W Roy; Chaffee, Alan L; Marriott, Philip J

2014-03-01

A high sulfur Jordanian oil shale was converted into liquid hydrocarbons by reaction at 390 °C under N2, and the dichloromethane soluble fraction of the products was isolated then analyzed by using gas chromatography (GC). Comprehensive two-dimensional GC (GC×GC) and multidimensional GC (MDGC) were applied for component separation on a polar - non-polar column set. Flame-ionization detection (FID) was used with GC×GC for general sample profiling, and mass spectrometry (MS) for component identification in MDGC. Multidimensional GC revealed a range of thiophenes (th), benzothiophenes (bth) and small amounts of dibenzothiophenes (dbth) and benzonaphthothiophenes (bnth). In addition, a range of aliphatic alkanes and cycloalkanes, ethers, polar single ring aromatic compounds and small amounts of polycyclic aromatics were also identified. Some of these compound classes were not uniquely observable by conventional 1D GC, and certainly this is true for many of their minor constituent members. The total number of distinct compounds was very large (ca.>1000). GC×GC was shown to be appropriate for general sample profiling, and MDGC-MS proved to be a powerful technique for the separation and identification of sulfur-containing components and other polar compounds. © 2013 Published by Elsevier B.V.

Proteome Analysis of Liver Cells Expressing a Full- Length Hepatitis C Virus (HCV) Replicon and Biopsy Specimens of Posttransplantation Liver from HCV-Infected Patients

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

Jacobs, Jon M.; Diamond, Deborah L.; Chan, Eric Y.

2005-06-01

The development of a reproducible model system for the study of Hepatitis C virus (HCV) infection has the potential to significantly enhance the study of virus-host interactions and provide future direction for modeling the pathogenesis of HCV. While there are studies describing global gene expression changes associated with HCV infection, changes in the proteome have not been characterized. We report the first large scale proteome analysis of the highly permissive Huh-7.5 cell line containing a full length HCV replicon. We detected > 4,400 proteins in this cell line, including HCV replicon proteins, using multidimensional liquid chromatographic (LC) separations coupled tomore » mass spectrometry (MS). The set of Huh-7.5 proteins confidently identified is, to our knowledge, the most comprehensive yet reported for a human cell line. Consistent with the literature, a comparison of Huh-7.5 cells (+) and (-) the HCV replicon identified expression changes of proteins involved in lipid metabolism. We extended these analyses to liver biopsy material from HCV-infected patients where > 1,500 proteins were detected from 2 {micro}g protein lysate using the Huh-7.5 protein database and the accurate mass and time (AMT) tag strategy. These findings demonstrate the utility of multidimensional proteome analysis of the HCV replicon model system for assisting the determination of proteins/pathways affected by HCV infection. Our ability to extend these analyses to the highly complex proteome of small liver biopsies with limiting protein yields offers the unique opportunity to begin evaluating the clinical significance of protein expression changes associated with HCV infection.« less

Accessing Multi-Dimensional Images and Data Cubes in the Virtual Observatory

NASA Astrophysics Data System (ADS)

Tody, Douglas; Plante, R. L.; Berriman, G. B.; Cresitello-Dittmar, M.; Good, J.; Graham, M.; Greene, G.; Hanisch, R. J.; Jenness, T.; Lazio, J.; Norris, P.; Pevunova, O.; Rots, A. H.

2014-01-01

Telescopes across the spectrum are routinely producing multi-dimensional images and datasets, such as Doppler velocity cubes, polarization datasets, and time-resolved “movies.” Examples of current telescopes producing such multi-dimensional images include the JVLA, ALMA, and the IFU instruments on large optical and near-infrared wavelength telescopes. In the near future, both the LSST and JWST will also produce such multi-dimensional images routinely. High-energy instruments such as Chandra produce event datasets that are also a form of multi-dimensional data, in effect being a very sparse multi-dimensional image. Ensuring that the data sets produced by these telescopes can be both discovered and accessed by the community is essential and is part of the mission of the Virtual Observatory (VO). The Virtual Astronomical Observatory (VAO, http://www.usvao.org/), in conjunction with its international partners in the International Virtual Observatory Alliance (IVOA), has developed a protocol and an initial demonstration service designed for the publication, discovery, and access of arbitrarily large multi-dimensional images. The protocol describing multi-dimensional images is the Simple Image Access Protocol, version 2, which provides the minimal set of metadata required to characterize a multi-dimensional image for its discovery and access. A companion Image Data Model formally defines the semantics and structure of multi-dimensional images independently of how they are serialized, while providing capabilities such as support for sparse data that are essential to deal effectively with large cubes. A prototype data access service has been deployed and tested, using a suite of multi-dimensional images from a variety of telescopes. The prototype has demonstrated the capability to discover and remotely access multi-dimensional data via standard VO protocols. The prototype informs the specification of a protocol that will be submitted to the IVOA for approval, with an operational data cube service to be delivered in mid-2014. An associated user-installable VO data service framework will provide the capabilities required to publish VO-compatible multi-dimensional images or data cubes.

Rapid characterization of the chemical constituents of Cortex Fraxini by homogenate extraction followed by UHPLC coupled with Fourier transform ion cyclotron resonance mass spectrometry and GC-MS.

PubMed

Wang, Yinan; Han, Fei; Song, Aihua; Wang, Miao; Zhao, Min; Zhao, Chunjie

2016-11-01

Cortex Fraxini is an important traditional Chinese medicine. In this work, a rapid and reliable homogenate extraction method was applied for the fast extraction for Cortex Fraxini, and the method was optimized by response surface methodology. Ultra high performance liquid chromatography combined with Fourier transform ion cyclotron resonance mass spectrometry and gas chromatography with mass spectrometry were established for the separation and characterization of the constituents of Cortex Fraxini. Liquid chromatography separation was conducted on a C 18 column (150 mm × 2.1 mm, 1.8 μm), and gas chromatography separation was performed on a capillary with a 5% phenyl-methylpolysiloxane stationary phase (30 m × 0.25 mm × 0.25 mm) by injection of silylated samples. According to the results, 33 chemical compounds were characterized by liquid chromatography with mass spectrometry, and 11 chemical compounds were characterized by gas chromatography with mass spectrometry, and coumarins were the major components characterized by both gas chromatography with mass spectrometry and liquid chromatography with mass spectrometry. The proposed homogenate extraction was an efficient and rapid method, and coumarins, phenylethanoid glycosides, iridoid glycosides, phenylpropanoids, and lignans were the main constituents of Cortex Fraxini. This work laid the foundation for further study of Cortex Fraxini and will be helpful for the rapid extraction and characterization of ingredients in other traditional Chinese medicines. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Column-coupling strategies for multidimensional electrophoretic separation techniques.

PubMed

Kler, Pablo A; Sydes, Daniel; Huhn, Carolin

2015-01-01

Multidimensional electrophoretic separations represent one of the most common strategies for dealing with the analysis of complex samples. In recent years we have been witnessing the explosive growth of separation techniques for the analysis of complex samples in applications ranging from life sciences to industry. In this sense, electrophoretic separations offer several strategic advantages such as excellent separation efficiency, different methods with a broad range of separation mechanisms, and low liquid consumption generating less waste effluents and lower costs per analysis, among others. Despite their impressive separation efficiency, multidimensional electrophoretic separations present some drawbacks that have delayed their extensive use: the volumes of the columns, and consequently of the injected sample, are significantly smaller compared to other analytical techniques, thus the coupling interfaces between two separations components must be very efficient in terms of providing geometrical precision with low dead volume. Likewise, very sensitive detection systems are required. Additionally, in electrophoretic separation techniques, the surface properties of the columns play a fundamental role for electroosmosis as well as the unwanted adsorption of proteins or other complex biomolecules. In this sense the requirements for an efficient coupling for electrophoretic separation techniques involve several aspects related to microfluidics and physicochemical interactions of the electrolyte solutions and the solid capillary walls. It is interesting to see how these multidimensional electrophoretic separation techniques have been used jointly with different detection techniques, for intermediate detection as well as for final identification and quantification, particularly important in the case of mass spectrometry. In this work we present a critical review about the different strategies for coupling two or more electrophoretic separation techniques and the different intermediate and final detection methods implemented for such separations.

PedsQL™ Multidimensional Fatigue Scale in sickle cell disease: feasibility, reliability, and validity.

PubMed

Panepinto, Julie A; Torres, Sylvia; Bendo, Cristiane B; McCavit, Timothy L; Dinu, Bogdan; Sherman-Bien, Sandra; Bemrich-Stolz, Christy; Varni, James W

2014-01-01

Sickle cell disease (SCD) is an inherited blood disorder characterized by a chronic hemolytic anemia that can contribute to fatigue and global cognitive impairment in patients. The study objective was to report on the feasibility, reliability, and validity of the PedsQL™ Multidimensional Fatigue Scale in SCD for pediatric patient self-report ages 5-18 years and parent proxy-report for ages 2-18 years. This was a cross-sectional multi-site study whereby 240 pediatric patients with SCD and 303 parents completed the 18-item PedsQL™ Multidimensional Fatigue Scale. Participants also completed the PedsQL™ 4.0 Generic Core Scales. The PedsQL™ Multidimensional Fatigue Scale evidenced excellent feasibility, excellent reliability for the Total Scale Scores (patient self-report α = 0.90; parent proxy-report α = 0.95), and acceptable reliability for the three individual scales (patient self-report α = 0.77-0.84; parent proxy-report α = 0.90-0.97). Intercorrelations of the PedsQL™ Multidimensional Fatigue Scale with the PedsQL™ Generic Core Scales were predominantly in the large (≥0.50) range, supporting construct validity. PedsQL™ Multidimensional Fatigue Scale Scores were significantly worse with large effects sizes (≥0.80) for patients with SCD than for a comparison sample of healthy children, supporting known-groups discriminant validity. Confirmatory factor analysis demonstrated an acceptable to excellent model fit in SCD. The PedsQL™ Multidimensional Fatigue Scale demonstrated acceptable to excellent measurement properties in SCD. The results demonstrate the relative severity of fatigue symptoms in pediatric patients with SCD, indicating the potential clinical utility of multidimensional assessment of fatigue in patients with SCD in clinical research and practice. © 2013 Wiley Periodicals, Inc.

PedsQL™ Multidimensional Fatigue Scale in Sickle Cell Disease: Feasibility, Reliability and Validity

PubMed Central

Panepinto, Julie A.; Torres, Sylvia; Bendo, Cristiane B.; McCavit, Timothy L.; Dinu, Bogdan; Sherman-Bien, Sandra; Bemrich-Stolz, Christy; Varni, James W.

2013-01-01

Background Sickle cell disease (SCD) is an inherited blood disorder characterized by a chronic hemolytic anemia that can contribute to fatigue and global cognitive impairment in patients. The study objective was to report on the feasibility, reliability, and validity of the PedsQL™ Multidimensional Fatigue Scale in SCD for pediatric patient self-report ages 5–18 years and parent proxy-report for ages 2–18 years. Procedure This was a cross-sectional multi-site study whereby 240 pediatric patients with SCD and 303 parents completed the 18-item PedsQL™ Multidimensional Fatigue Scale. Participants also completed the PedsQL™ 4.0 Generic Core Scales. Results The PedsQL™ Multidimensional Fatigue Scale evidenced excellent feasibility, excellent reliability for the Total Scale Scores (patient self-report α = 0.90; parent proxy-report α = 0.95), and acceptable reliability for the three individual scales (patient self-report α = 0.77–0.84; parent proxy-report α = 0.90–0.97). Intercorrelations of the PedsQL™ Multidimensional Fatigue Scale with the PedsQL™ Generic Core Scales were predominantly in the large (≥ 0.50) range, supporting construct validity. PedsQL™ Multidimensional Fatigue Scale Scores were significantly worse with large effects sizes (≥0.80) for patients with SCD than for a comparison sample of healthy children, supporting known-groups discriminant validity. Confirmatory factor analysis demonstrated an acceptable to excellent model fit in SCD. Conclusions The PedsQL™ Multidimensional Fatigue Scale demonstrated acceptable to excellent measurement properties in SCD. The results demonstrate the relative severity of fatigue symptoms in pediatric patients with SCD, indicating the potential clinical utility of multidimensional assessment of fatigue in patients with SCD in clinical research and practice. PMID:24038960

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry combined with multidimensional scaling, binary hierarchical cluster tree and selected diagnostic masses improves species identification of Neolithic keratin sequences from furs of the Tyrolean Iceman Oetzi.

PubMed

Hollemeyer, Klaus; Altmeyer, Wolfgang; Heinzle, Elmar; Pitra, Christian

2012-08-30

The identification of fur origins from the 5300-year-old Tyrolean Iceman's accoutrement is not yet complete, although definite identification is essential for the socio-cultural context of his epoch. Neither have all potential samples been identified so far, nor there has a consensus been reached on the species identified using the classical methods. Archaeological hair often lacks analyzable hair scale patterns in microscopic analyses and polymer chain reaction (PCR)-based techniques are often inapplicable due to the lack of amplifiable ancient DNA. To overcome these drawbacks, a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) method was used exclusively based on hair keratins. Thirteen fur specimens from his accoutrement were analyzed after tryptic digest of native hair. Peptide mass fingerprints (pmfs) from ancient samples and from reference species mostly occurring in the Alpine surroundings at his lifetime were compared to each other using multidimensional scaling and binary hierarchical cluster tree analysis. Both statistical methods highly reflect spectral similarities among pmfs as close zoological relationships. While multidimensional scaling was useful to discriminate specimens on the zoological order level, binary hierarchical cluster tree reached the family or subfamily level. Additionally, the presence and/or absence of order, family and/or species-specific diagnostic masses in their pmfs allowed the identification of mammals mostly down to single species level. Red deer was found in his shoe vamp, goat in the leggings, cattle in his shoe sole and at his quiver's closing flap as well as sheep and chamois in his coat. Canid species, like grey wolf, domestic dog or European red fox, were discovered in his leggings for the first time, but could not be differentiated to species level. This is widening the spectrum of processed fur-bearing species to at least one member of the Canidae family. His fur cap was allocated to a carnivore species, but differentiation between brown bear and a canid species could not be made with certainty. Copyright © 2012 John Wiley & Sons, Ltd.

Tile-Based Fisher-Ratio Software for Improved Feature Selection Analysis of Comprehensive Two-Dimensional Gas Chromatography Time-of-Flight Mass Spectrometry Data

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

Marney, Luke C.; Siegler, William C.; Parsons, Brendon A.

Two-dimensional (2D) gas chromatography coupled with time-of-flight mass spectrometry (GC × GC – TOFMS) is a highly capable instrumental platform that produces complex and information-rich multi-dimensional chemical data. The complex data can be overwhelming, especially when many samples (of various sample classes) are analyzed with multiple injections for each sample. Thus, the data must be analyzed in such a way to extract the most meaningful information. The pixel-based and peak table-based algorithmic use of Fisher ratios has been used successfully in the past to reduce the multi-dimensional data down to those chemical compounds that are changing between classes relative tomore » those that are not (i.e., chemical feature selection). We report on the initial development of a computationally fast novel tile-based Fisher-ratio software that addresses challenges due to 2D retention time misalignment without explicitly aligning the data, which is a problem for both pixel-based and peak table- based methods. Concurrently, the tile-based Fisher-ratio software maximizes the sensitivity contrast of true positives against a background of potential false positives and noise. To study this software, eight compounds, plus one internal standard, were spiked into diesel at various concentrations. The tile-based F-ratio software was able to discover all spiked analytes, within the complex diesel sample matrix with thousands of potential false positives, in each possible concentration comparison, even at the lowest absolute spiked analyte concentration ratio of 1.06.« less

Role of Imaging Specrometer Data for Model-based Cross-calibration of Imaging Sensors

NASA Technical Reports Server (NTRS)

Thome, Kurtis John

2014-01-01

Site characterization benefits from imaging spectrometry to determine spectral bi-directional reflectance of a well-understood surface. Cross calibration approaches, uncertainties, role of imaging spectrometry, model-based site characterization, and application to product validation.

Quantification of polychlorinated dibenzo-p-dioxins and dibenzofurans by direct injection of sample extract into the comprehensive multidimensional gas chromatograph/high-resolution time-of-flight mass spectrometer.

PubMed

Shunji, Hashimoto; Yoshikatsu, Takazawa; Akihiro, Fushimi; Hiroyasu, Ito; Kiyoshi, Tanabe; Yasuyuki, Shibata; Masa-aki, Ubukata; Akihiko, Kusai; Kazuo, Tanaka; Hideyuki, Otsuka; Katsunori, Anezaki

2008-01-18

Polychlorinated dibenzo-p-dioxins and dibenzofurans in crude extracts of fly ash and flue gas from municipal waste incinerators were quantified using a comprehensive multidimensional gas chromatograph (GC x GC) coupled to a high-resolution time-of-flight mass spectrometer (HR-TOFMS). For identification and quantification, we developed our own program to prepare 3D chromatograms of selected mass numbers from the data of the GC x GC/HR-TOFMS. Isolation of all congeners with a TCDD toxic equivalency factor from the other isomers by only one injection was confirmed. The instrumental detection limit of TCDD on the GC x GC/HR-TOFMS was 0.9 pg by the relative calibration method. Quantification of these substances in the crude extracts was achieved by direct injection to the GC x GC/HR-TOFMS. The results agree with the values obtained using a generic gas chromatography/high-resolution mass spectrometry (GC/HRMS) system. It was confirmed that measurement by high-resolution TOFMS and GC x GC effectively reduces interference from other chemicals.

Applications of liquid-based separation in conjunction with mass spectrometry to the analysis of forensic evidence.

PubMed

Moini, Mehdi

2018-05-01

In the past few years, there has been a significant effort by the forensic science community to develop new scientific techniques for the analysis of forensic evidence. Forensic chemists have been spearheaded to develop information-rich confirmatory technologies and techniques and apply them to a broad array of forensic challenges. The purpose of these confirmatory techniques is to provide alternatives to presumptive techniques that rely on data such as color changes, pattern matching, or retention time alone, which are prone to more false positives. To this end, the application of separation techniques in conjunction with mass spectrometry has played an important role in the analysis of forensic evidence. Moreover, in the past few years the role of liquid separation techniques, such as liquid chromatography and capillary electrophoresis in conjunction with mass spectrometry, has gained significant tractions and have been applied to a wide range of chemicals, from small molecules such as drugs and explosives, to large molecules such as proteins. For example, proteomics and peptidomics have been used for identification of humans, organs, and bodily fluids. A wide range of HPLC techniques including reversed phase, hydrophilic interaction, mixed-mode, supercritical fluid, multidimensional chromatography, and nanoLC, as well as several modes of capillary electrophoresis mass spectrometry, including capillary zone electrophoresis, partial filling, full filling, and micellar electrokenetic chromatography have been applied to the analysis drugs, explosives, and questioned documents. In this article, we review recent (2015-2017) applications of liquid separation in conjunction with mass spectrometry to the analysis of forensic evidence. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The identification and characterization of non-coding and coding RNAs and their modified nucleosides by mass spectrometry

PubMed Central

Gaston, Kirk W; Limbach, Patrick A

2014-01-01

The analysis of ribonucleic acids (RNA) by mass spectrometry has been a valuable analytical approach for more than 25 years. In fact, mass spectrometry has become a method of choice for the analysis of modified nucleosides from RNA isolated out of biological samples. This review summarizes recent progress that has been made in both nucleoside and oligonucleotide mass spectral analysis. Applications of mass spectrometry in the identification, characterization and quantification of modified nucleosides are discussed. At the oligonucleotide level, advances in modern mass spectrometry approaches combined with the standard RNA modification mapping protocol enable the characterization of RNAs of varying lengths ranging from low molecular weight short interfering RNAs (siRNAs) to the extremely large 23 S rRNAs. New variations and improvements to this protocol are reviewed, including top-down strategies, as these developments now enable qualitative and quantitative measurements of RNA modification patterns in a variety of biological systems. PMID:25616408

The identification and characterization of non-coding and coding RNAs and their modified nucleosides by mass spectrometry.

PubMed

Gaston, Kirk W; Limbach, Patrick A

2014-01-01

The analysis of ribonucleic acids (RNA) by mass spectrometry has been a valuable analytical approach for more than 25 years. In fact, mass spectrometry has become a method of choice for the analysis of modified nucleosides from RNA isolated out of biological samples. This review summarizes recent progress that has been made in both nucleoside and oligonucleotide mass spectral analysis. Applications of mass spectrometry in the identification, characterization and quantification of modified nucleosides are discussed. At the oligonucleotide level, advances in modern mass spectrometry approaches combined with the standard RNA modification mapping protocol enable the characterization of RNAs of varying lengths ranging from low molecular weight short interfering RNAs (siRNAs) to the extremely large 23 S rRNAs. New variations and improvements to this protocol are reviewed, including top-down strategies, as these developments now enable qualitative and quantitative measurements of RNA modification patterns in a variety of biological systems.

Ultrahigh-resolution FT-ICR mass spectrometry characterization of a-pinene ozonolysis SOA

EPA Science Inventory

Secondary organic aerosol (SOA) of α-pinene ozonolysis with and without hydroxyl radical scavenging hexane was characterized by ultrahigh-resolution. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Molecular formulas for more than 900 negative ions were i...

Identification of aroma-active volatiles in banana Terra spirit using multidimensional gas chromatography with simultaneous mass spectrometry and olfactometry detection.

PubMed

Capobiango, Michely; Mastello, Raíssa Bittar; Chin, Sung-Tong; Oliveira, Evelyn de Souza; Cardeal, Zenilda de Lourdes; Marriott, Philip John

2015-04-03

Fruit spirits have been produced and consumed throughout the world for centuries. However, the aroma composition of banana spirits is still poorly characterised. We have investigated the aroma-impact compounds of the banana Terra spirit for the first time, using multidimensional gas chromatography (MDGC and GC × GC) in a multi-hyphenated system - i.e., coupled to flame ionisation detection (FID), mass spectrometry (MS), and olfactometry (O). Solid-phase microextraction (SPME) was used to isolate the headspace aroma compounds of the banana spirit. The detection frequency (DF) technique was applied and aroma regions, detected in the first column separation at >60% Nasal Impact Frequency (NIF), were screened as target potent odour regions in the sample. Using a polar/non-polar phase column set, the potent odour regions were further subjected to MDGC separation with simultaneous O and MS detection for correlation of the aroma perception with MS data for individual resolved aroma-impact compounds. GC-O analysis enabled 18 aroma-impact regions to be located as providing volatiles of interest for further study; for example, those comprising perceptions of flower, whisky, green, amongst others. Compounds were tentatively identified through MS data matching and retention indices in both first and second dimensions. The principal volatile compounds identified in this work, which are responsible for the characteristic aroma of the banana spirit, are 3-methylbutan-1-ol, 3-methylbutan-1-ol acetate, 2-phenylethyl acetate and phenylethyl alcohol. This is the first such study to reveal the major aroma compounds that contribute to banana spirit aroma. Copyright © 2015 Elsevier B.V. All rights reserved.

Mixed-bed ion exchange chromatography employing a salt-free pH gradient for improved sensitivity and compatibility in MudPIT.

PubMed

Mommen, Geert P M; Meiring, Hugo D; Heck, Albert J R; de Jong, Ad P J M

2013-07-16

In proteomics, comprehensive analysis of peptides mixtures necessitates multiple dimensions of separation prior to mass spectrometry analysis to reduce sample complexity and increase the dynamic range of analysis. The main goal of this work was to improve the performance of (online) multidimensional protein identification technology (MudPIT) in terms of sensitivity, compatibility and recovery. The method employs weak anion and strong cation mixed-bed ion exchange chromatography (ACE) in the first separation dimension and reversed phase chromatography (RP) in the second separation dimension (Motoyama et.al. Anal. Chem 2007, 79, 3623-34.). We demonstrated that the chromatographic behavior of peptides in ACE chromatography depends on both the WAX/SCX mixing ratio as the ionic strength of the mobile phase system. This property allowed us to replace the conventional salt gradient by a (discontinuous) salt-free, pH gradient. First dimensional separation of peptides was accomplished with mixtures of aqueous formic acid and dimethylsulfoxide with increasing concentrations. The overall performance of this mobile phase system was found comparable to ammonium acetate buffers in application to ACE chromatography, but clearly outperformed strong cation exchange for use in first dimensional peptide separation. The dramatically improved compatibility between (salt-free) ion exchange chromatography and reversed phase chromatography-mass spectrometry allowed us to downscale the dimensions of the RP analytical column down to 25 μm i.d. for an additional 2- to 3-fold improvement in performance compared to current technology. The achieved levels of sensitivity, orthogonality, and compatibility demonstrates the potential of salt-free ACE MudPIT for the ultrasensitive, multidimensional analysis of very modest amounts of sample material.

Quantification of free and total bisphenol A and bisphenol B in human urine by dispersive liquid-liquid microextraction (DLLME) and heart-cutting multidimensional gas chromatography-mass spectrometry (MD-GC/MS).

PubMed

Cunha, S C; Fernandes, J O

2010-11-15

A novel method combining dispersive liquid-liquid microextraction (DLLME) and heart-cutting multidimensional gas chromatography coupled to mass spectrometry was developed for the determination of free and total bisphenol A (BPA) and bisphenol B (BPB) in human urine samples. The DLLME procedure combines extraction, derivatization and concentration of the analytes into one step. Several important variables influencing the extraction efficiency and selectivity such as nature and volume of extractive and dispersive solvents as well as the amount of acetylating reagent were investigated. The temperature and time to hydrolyze BPA and BPB conjugates with a β-glucuronidase and sulfatase enzyme preparation were also studied. Under the optimized conditions good efficiency extraction (71-93%) and acceptable total DLLME yields (56-77%) were obtained for both analytes. Matrix-matched calibration curves were linear with correlation coefficients higher than 0.996 in the range level 0.1-5 μg/l, and the relative standard deviations (%RSD) were lower than 20% (n=6). The limits of detection were 0.03 and 0.05 μg/l for BPA and BPB, respectively. The applicability of the proposed method for determining urinary free and total BPA and BPB was assessed by analyzing the human urine of a group of 20 volunteers. Free BPA was detected in 45% of the sample whereas total BPA was detected in 85% of the samples at concentrations ranging between 0.39 and 4.99 μg/l. BPB was detected in conjugated form in two samples. Copyright © 2010 Elsevier B.V. All rights reserved.

Rapid characterization of microorganisms by mass spectrometry--what can be learned and how?

PubMed

Fenselau, Catherine C

2013-08-01

Strategies for the rapid and reliable analysis of microorganisms have been sought to meet national needs in defense, homeland security, space exploration, food and water safety, and clinical diagnosis. Mass spectrometry has long been a candidate technique because it is extremely rapid and can provide highly specific information. It has excellent sensitivity. Molecular and fragment ion masses provide detailed fingerprints, which can also be interpreted. Mass spectrometry is also a broad band method--everything has a mass--and it is automatable. Mass spectrometry is a physiochemical method that is orthogonal and complementary to biochemical and morphological methods used to characterize microorganisms.

Analysis of sulfates on low molecular weight heparin using mass spectrometry: structural characterization of enoxaparin.

PubMed

Gupta, Rohitesh; Ponnusamy, Moorthy P

2018-05-31

Structural characterization of low molecular weight heparin (LMWH) is critical to meet biosimilarity standards. In this context, the review focuses on structural analysis of labile sulfates attached to the side-groups of LMWH using mass spectrometry. A comprehensive review of this topic will help readers to identify key strategies for tackling the problem related to sulfate loss. At the same time, various mass spectrometry techniques are presented to facilitate compositional analysis of LMWH, mainly enoxaparin. Areas covered: This review summarizes findings on mass spectrometry application for LMWH, including modulation of sulfates, using enzymology and sample preparation approaches. Furthermore, popular open-source software packages for automated spectral data interpretation are also discussed. Successful use of LC/MS can decipher structural composition for LMWH and help evaluate their sameness or biosimilarity with the innovator molecule. Overall, the literature has been searched using PubMed by typing various search queries such as 'enoxaparin', 'mass spectrometry', 'low molecular weight heparin', 'structural characterization', etc. Expert commentary: This section highlights clinically relevant areas that need improvement to achieve satisfactory commercialization of LMWHs. It also primarily emphasizes the advancements in instrumentation related to mass spectrometry, and discusses building automated software for data interpretation and analysis.

A new multidimensional stoichiometric classification of compounds: moving beyond the van Krevelen diagram.

NASA Astrophysics Data System (ADS)

Rivas-Ubach, A.; Liu, Y.; Bianchi, T. S.; Tolic, N.; Jansson, C.; Paša-Tolić, L.

2017-12-01

The role of nutrients in organisms, especially primary producers, has been a topic of special interest in ecosystem research for understanding the ecosystem structure and function. The majority of macro-elements in organisms, such as C, H, O, N and P, do not act as single elements but are components of organic compounds (lipids, peptides, carbohydrates, etc), which are more directly related to the physiology of organisms and thus to the ecosystem function. However, accurately deciphering the overall content of the main compound classes (lipids, proteins, carbohydrates,…) in organisms is still a major challenge. van Krevelen (vK) diagrams have been widely used as an estimation of the main compound categories present in environmental samples based on O:C vs H:C molecular ratios, but a stoichiometric classification based exclusively on O:C and H:C ratios is feeble. Different compound classes show large O:C and H:C ratio overlapping and other heteroatoms, such as N and P, should be considered to robustly distinguish the different classes. We propose a new compound classification for biological/environmental samples based on the C:H:O:N:P stoichiometric ratios of thousands of molecular formulas of characterized compounds from 6 different main categories: lipids, peptides, amino-sugars, carbohydrates, nucleotides and phytochemical compounds (oxy-aromatic compounds). This new multidimensional stoichiometric compound constraints classification (MSCC) can be applied to data obtained with high resolution mass spectrometry (HRMS), allowing an accurate overview of the relative abundances of the main compound categories present in organismal samples. The MSCC has been optimized for plants, but it could be also applied to different organisms and serve as a strong starting point to further investigate other environmental complex matrices (soils, aerosols, etc). The proposed MSCC advances environmental research, especially eco-metabolomics, ecophysiology and ecological stoichiometry studies, providing a new tool to understand the ecosystem structure and function at the molecular level.

Systematic review of the multidimensional fatigue symptom inventory-short form.

PubMed

Donovan, Kristine A; Stein, Kevin D; Lee, Morgan; Leach, Corinne R; Ilozumba, Onaedo; Jacobsen, Paul B

2015-01-01

Fatigue is a subjective complaint that is believed to be multifactorial in its etiology and multidimensional in its expression. Fatigue may be experienced by individuals in different dimensions as physical, mental, and emotional tiredness. The purposes of this study were to review and characterize the use of the 30-item Multidimensional Fatigue Symptom Inventory-Short Form (MFSI-SF) in published studies and to evaluate the available evidence for its psychometric properties. A systematic review was conducted to identify published articles reporting results for the MFSI-SF. Data were analyzed to characterize internal consistency reliability of multi-item MFSI-SF scales and test-retest reliability. Correlation coefficients were summarized to characterize concurrent, convergent, and divergent validity. Standardized effect sizes were calculated to characterize the discriminative validity of the MFSI-SF and its sensitivity to change. Seventy articles were identified. Sample sizes reported ranged from 10 to 529 and nearly half consisted exclusively of females. More than half the samples were composed of cancer patients; of those, 59% were breast cancer patients. Mean alpha coefficients for MFSI-SF fatigue subscales ranged from 0.84 for physical fatigue to 0.93 for general fatigue. The MFSI-SF demonstrated moderate test-retest reliability in a small number of studies. Correlations with other fatigue and vitality measures were moderate to large in size and in the expected direction. The MFSI-SF fatigue subscales were positively correlated with measures of distress, depressive, and anxious symptoms. Effect sizes for discriminative validity ranged from medium to large, while effect sizes for sensitivity to change ranged from small to large. Findings demonstrate the positive psychometric properties of the MFSI-SF, provide evidence for its usefulness in medically ill and nonmedically ill individuals, and support its use in future studies.

Chemical fingerprinting of naphthenic acids and oil sands process waters-A review of analytical methods for environmental samples.

PubMed

Headley, J V; Peru, K M; Mohamed, M H; Frank, R A; Martin, J W; Hazewinkel, R R O; Humphries, D; Gurprasad, N P; Hewitt, L M; Muir, D C G; Lindeman, D; Strub, R; Young, R F; Grewer, D M; Whittal, R M; Fedorak, P M; Birkholz, D A; Hindle, R; Reisdorph, R; Wang, X; Kasperski, K L; Hamilton, C; Woudneh, M; Wang, G; Loescher, B; Farwell, A; Dixon, D G; Ross, M; Pereira, A Dos Santos; King, E; Barrow, M P; Fahlman, B; Bailey, J; McMartin, D W; Borchers, C H; Ryan, C H; Toor, N S; Gillis, H M; Zuin, L; Bickerton, G; Mcmaster, M; Sverko, E; Shang, D; Wilson, L D; Wrona, F J

2013-01-01

This article provides a review of the routine methods currently utilized for total naphthenic acid analyses. There is a growing need to develop chemical methods that can selectively distinguish compounds found within industrially derived oil sands process affected waters (OSPW) from those derived from the natural weathering of oil sands deposits. Attention is thus given to the characterization of other OSPW components such as oil sands polar organic compounds, PAHs, and heavy metals along with characterization of chemical additives such as polyacrylamide polymers and trace levels of boron species. Environmental samples discussed cover the following matrices: OSPW containments, on-lease interceptor well systems, on- and off-lease groundwater, and river and lake surface waters. There are diverse ranges of methods available for analyses of total naphthenic acids. However, there is a need for inter-laboratory studies to compare their accuracy and precision for routine analyses. Recent advances in high- and medium-resolution mass spectrometry, concomitant with comprehensive mass spectrometry techniques following multi-dimensional chromatography or ion-mobility separations, have allowed for the speciation of monocarboxylic naphthenic acids along with a wide range of other species including humics. The distributions of oil sands polar organic compounds, particularly the sulphur containing species (i.e., OxS and OxS2) may allow for distinguishing sources of OSPW. The ratios of oxygen- (i.e., Ox) and nitrogen-containing species (i.e., NOx, and N2Ox) are useful for differentiating organic components derived from OSPW from natural components found within receiving waters. Synchronous fluorescence spectroscopy also provides a powerful screening technique capable of quickly detecting the presence of aromatic organic acids contained within oil sands naphthenic acid mixtures. Synchronous fluorescence spectroscopy provides diagnostic profiles for OSPW and potentially impacted groundwater that can be compared against reference groundwater and surface water samples. Novel applications of X-ray absorption near edge spectroscopy (XANES) are emerging for speciation of sulphur-containing species (both organic and inorganic components) as well as industrially derived boron-containing species. There is strong potential for an environmental forensics application of XANES for chemical fingerprinting of weathered sulphur-containing species and industrial additives in OSPW.

Validation of GC-IRMS techniques for δ13C and δ2H CSIA of organophosphorus compounds and their potential for studying the mode of hydrolysis in the environment.

PubMed

Wu, Langping; Kümmel, Steffen; Richnow, Hans H

2017-04-01

Compound-specific stable isotope analysis (CSIA) is among the most promising tools for studying the fate of organic pollutants in the environment. However, the feasibility of multidimensional CSIA was limited by the availability of a robust method for precise isotope analysis of heteroatom-bearing organic compounds. We developed a method for δ 13 C and δ 2 H analysis of eight organophosphorus compounds (OPs) with different chemical properties. In particular, we aimed to compare high-temperature conversion (HTC) and chromium-based HTC (Cr/HTC) units to explore the limitations of hydrogen isotope analysis of heteroatom-bearing compounds. Analysis of the amount dependency of the isotope values (linearity analysis) of OPs indicated that the formation of HCl was a significant isotope fractionation process leading to inaccurate δ 2 H analysis in HTC. In the case of nonchlorinated OPs, by-product formation of HCN, H 2 S, or PH 3 in HTC was observed but did not affect the dynamic range of reproducible isotope values above the limit of detection. No hydrogen-containing by-products were found in the Cr/HTC process by use of ion trap mass spectrometry analysis. The accuracy of gas chromatography - isotope ratio mass spectrometry was validated in comparison with elemental analyzer - isotope ratio mass spectrometry. Dual-isotope fractionation yielded Λ values of 0 ± 0 at pH 7, 7 ± 1 at pH 9, and 30 ± 6 at pH 12, indicating the potential of 2D CSIA to characterize the hydrolysis mechanisms of OPs. This is the first report on the combination of δ 2 H and δ 13 C isotope analysis of OPs, and this is the first study providing a systematic evaluation of HTC and Cr/HTC for hydrogen isotope analysis using OPs as target compounds. Graphical Abstract Comparison of δ 2 H measurement of non-chlorinated and chlorinated OPs via GC-Cr/HTC-IRMS and GC-HTC-IRMS system.

Identification and characterization of new designer drug 4-fluoro-PV9 and α-PHP in the seized materials.

PubMed

Majchrzak, Milena; Rojkiewicz, Marcin; Celiński, Rafał; Kuś, Piotr; Sajewicz, Mieczysław

In this study, we present identification and physicochemical characterization of new cathinone derivatives, 4-fluoro-PV9 and already known α-PHP in seized materials. Although the disclosure of α-PHP from an illegal product had been reported and characterized to some extent, the data on α-PHP are also presented together with those of 4-fluoro-PV9. The data of characterization for the two compounds were obtained by high-performance liquid chromatography (HPLC)-mass spectrometry and HPLC-diode array detection, electrospray ionization/ion trap mass spectrometry in MS 2 and MS 3 modes, gas chromatography-mass spectrometry, thermogravimetric analysis, differential scanning calorimetry, Fourier transform infrared spectroscopy, ultraviolet-visible spectroscopy, and nuclear magnetic resonance spectroscopy. To our knowledge, this is the first report for identification and detailed characterization of 4-fluoro-PV9 circulated on the illegal drug market.

Characterization of extreme ultraviolet laser ablation mass spectrometry for actinide trace analysis and nanoscale isotopic imaging

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

Green, Tyler; Kuznetsov, Ilya; Willingham, David

The purpose of this research was to characterize Extreme Ultraviolet Time-of-Flight (EUV TOF) Laser Ablation Mass Spectrometry for high spatial resolution elemental and isotopic analysis. We compare EUV TOF results with Secondary Ionization Mass Spectrometry (SIMS) to orient the EUV TOF method within the overall field of analytical mass spectrometry. Using the well-characterized NIST 61x glasses, we show that the EUV ionization approach produces relatively few molecular ion interferences in comparison to TOF SIMS. We demonstrate that the ratio of element ion to element oxide ion is adjustable with EUV laser pulse energy and that the EUV TOF instrument hasmore » a sample utilization efficiency of 0.014%. The EUV TOF system also achieves a lateral resolution of 80 nm and we demonstrate this lateral resolution with isotopic imaging of closely spaced particles or uranium isotopic standard materials.« less

Stability behaviour of antiretroviral drugs and their combinations. 5: Characterization of novel degradation products of abacavir sulfate by mass and nuclear magnetic resonance spectrometry.

PubMed

Kurmi, Moolchand; Sahu, Archana; Singh, Saranjit

2017-02-05

In the present study, degradation behaviour of abacavir sulfate was evaluated in solution and solid stress conditions. Solution state studies resulted in formation of eleven degradation products; of which two were also formed on solid stress. The same were separated by high performance liquid chromatography. They were characterized using liquid chromatography-high resolution mass spectrometry, liquid chromatography-multistage mass spectrometry and hydrogen/deuterium exchange mass spectrometry data. Additionally, seven degradation products were isolated and subjected to 1D and 2D nuclear magnetic resonance studies for their structural confirmation. Copyright © 2016 Elsevier B.V. All rights reserved.

THE DYNAMIC REGIME CONCEPT FOR ECOSYSTEM MANAGEMENT AND RESTORATION

EPA Science Inventory

Dynamic regimes of ecosystems are multidimensional basis of attraction, characterized by particular species communities and ecosystems processes. Ecosystem patterns and processes rarely respond linerarly to disturbances, and the nonlinear cynamic regime concept offers a more real...

Systems analysis of singly and multiply O-glycosylated peptides in the human serum glycoproteome via EThcD and HCD mass spectrometry.

PubMed

Zhang, Yong; Xie, Xinfang; Zhao, Xinyuan; Tian, Fang; Lv, Jicheng; Ying, Wantao; Qian, Xiaohong

2018-01-06

Human serum has been intensively studied to identify biomarkers via global proteomic analysis. The altered O-glycoproteome is associated with human pathological state including cancer, inflammatory and degenerative diseases and is an attractive source of disease biomarkers. Because of the microheterogeneity and macroheterogeneity of O-glycosylation, site-specific O-glycosylation analysis in human serum is still challenging. Here, we developed a systematic strategy that combined multiple enzyme digestion, multidimensional separation for sample preparation and high-resolution tandem MS with Byonic software for intact O-glycopeptide characterization. We demonstrated that multiple enzyme digestion or multidimensional separation can make sample preparation more efficient and that EThcD is not only suitable for the identification of singly O-glycosylated peptides (50.3%) but also doubly (21.2%) and triply (28.5%) O-glycosylated peptides. Totally, with the strict scoring criteria, 499 non-redundant intact O-glycopeptides, 173 O-glycosylation sites and 6 types of O-glycans originating from 49 O-glycoprotein groups were identified in human serum, including 121 novel O-glycosylation sites. Currently, this is the largest data set of site-specific native O-glycoproteome from human serum samples. We expect that the strategies developed by this study will facilitate in-depth analyses of native O-glycoproteomes in human serum and provide opportunities to understand the functional roles of protein O-glycosylation in human health and diseases. The altered O-glycoproteome is associated with human pathological state and is an attractive source of disease biomarkers. However, site-specific O-glycosylation analysis is challenging because of the microheterogeneity (different glycoforms attached to one glycosylation site) and macroheterogeneity (site occupancy) of O-glycosylation. In this work, we developed a systematic strategy for intact O-glycopeptide characterization. This study took advantage of the inherent properties of the new fragmentation method called EThcD, which provides more complete fragmentation information about O-glycosylated peptides and a more confident site localization of O-glycans than collision-induced dissociation (HCD). We demonstrated that multiple enzyme digestion or multidimensional separation can make sample preparation more efficient and that EThcD was not only suitable for the identification of singly O-glycosylated peptides (50.3%) but also doubly (21.2%) and triply (28.5%) O-glycosylated peptides. Finally, we got a largest data set of site-specific native O-glycoproteome from human serum samples. Furthermore, quantitative analysis of intact O-glycopeptides from the serum samples of IgA nephropathy (IgAN) patients and healthy donors was performed, and the results showed the potential of the strategy to discover O-glycosylation biomarkers. We expect that the strategies developed by this study will facilitate in-depth analyses of native O-glycoproteomes in human serum and lead to exciting opportunities to understand the functional roles of protein O-glycosylation in human health and diseases. Copyright © 2017. Published by Elsevier B.V.

Characterizing the lipid and metabolite changes associated with placental function and pregnancy complications using ion mobility spectrometry-mass spectrometry and mass spectrometry imaging

DOE PAGES

Burnum-Johnson, Kristin E.; Baker, Erin S.; Metz, Thomas O.

2017-03-29

A successful pregnancy is dependent upon discrete biological events, which include embryo implantation, decidualization, and placentation. Furthermore, problems associated with each of these events can cause infertility or conditions such as preeclampsia. A greater understanding of the molecular changes associated with these complex processes is necessary to aid in identifying treatments for each condition. Previous nuclear magnetic resonance spectroscopy and mass spectrometry studies have been used to identify metabolites and lipids associated with pregnancy-related complications. However, due to limitations associated with conventional implementations of both techniques, novel technology developments are needed to more fully understand the initiation and development ofmore » pregnancy related problems at the molecular level. Here, we describe current analytical techniques for metabolomic and lipidomic characterization of pregnancy complications and discuss the potential for new technologies such as ion mobility spectrometry-mass spectrometry and mass spectrometry imaging to contribute to a better understanding of the molecular changes that affect the placenta and pregnancy outcomes.« less

Characterizing the lipid and metabolite changes associated with placental function and pregnancy complications using ion mobility spectrometry-mass spectrometry and mass spectrometry imaging

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

Burnum-Johnson, Kristin E.; Baker, Erin S.; Metz, Thomas O.

Successful pregnancy is dependent upon discrete biological events, which include embryo implantation, decidualization, and placentation. Problems associated with each of these events can cause infertility or conditions such as preeclampsia. A greater understanding of the molecular changes associated with these complex processes is necessary to aid in identifying treatments for each condition. Previous nuclear magnetic resonance spectroscopy and mass spectrometry studies have been used to identify metabolites and lipids associated with pregnancy-related complications. However, due to limitations associated with conventional implementations of both techniques, novel technology developments are needed to more fully understand the initiation and development of pregnancy relatedmore » problems at the molecular level. In this perspective, we describe current analytical techniques for metabolomic and lipidomic characterization of pregnancy complications and discuss the potential for new technologies such as ion mobility spectrometry-mass spectrometry and mass spectrometry imaging to contribute to a better understanding of the molecular changes that affect the placenta and pregnancy outcomes.« less

Characterizing the lipid and metabolite changes associated with placental function and pregnancy complications using ion mobility spectrometry-mass spectrometry and mass spectrometry imaging

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

Burnum-Johnson, Kristin E.; Baker, Erin S.; Metz, Thomas O.

A successful pregnancy is dependent upon discrete biological events, which include embryo implantation, decidualization, and placentation. Furthermore, problems associated with each of these events can cause infertility or conditions such as preeclampsia. A greater understanding of the molecular changes associated with these complex processes is necessary to aid in identifying treatments for each condition. Previous nuclear magnetic resonance spectroscopy and mass spectrometry studies have been used to identify metabolites and lipids associated with pregnancy-related complications. However, due to limitations associated with conventional implementations of both techniques, novel technology developments are needed to more fully understand the initiation and development ofmore » pregnancy related problems at the molecular level. Here, we describe current analytical techniques for metabolomic and lipidomic characterization of pregnancy complications and discuss the potential for new technologies such as ion mobility spectrometry-mass spectrometry and mass spectrometry imaging to contribute to a better understanding of the molecular changes that affect the placenta and pregnancy outcomes.« less

Characterizing the lipid and metabolite changes associated with placental function and pregnancy complications using ion mobility spectrometry-mass spectrometry and mass spectrometry imaging.

PubMed

Burnum-Johnson, Kristin E; Baker, Erin S; Metz, Thomas O

2017-12-01

Successful pregnancy is dependent upon discrete biological events, which include embryo implantation, decidualization, and placentation. Problems associated with each of these events can cause infertility or conditions such as preeclampsia. A greater understanding of the molecular changes associated with these complex processes is necessary to aid in identifying treatments for each condition. Previous nuclear magnetic resonance spectroscopy and mass spectrometry studies have been used to identify metabolites and lipids associated with pregnancy-related complications. However, due to limitations associated with conventional implementations of both techniques, novel technology developments are needed to more fully understand the initiation and development of pregnancy related problems at the molecular level. In this perspective, we describe current analytical techniques for metabolomic and lipidomic characterization of pregnancy complications and discuss the potential for new technologies such as ion mobility spectrometry-mass spectrometry and mass spectrometry imaging to contribute to a better understanding of the molecular changes that affect the placenta and pregnancy outcomes. Copyright © 2017 IFPA, Elsevier Ltd. Published by Elsevier Ltd.. All rights reserved.

Bayesian Integration and Characterization of Composition C-4 Plastic Explosives Based on Time-of-Flight Secondary Ion Mass Spectrometry and Laser Ablation-Inductively Coupled Plasma Mass Spectrometry

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

Mahoney, Christine M.; Kelly, Ryan T.; Alexander, M. L.

Key elements regarding the use of non-radioactive ionization sources will be presented as related to explosives detection by mass spectrometry and ion mobility spectrometry. Various non-radioactive ionization sources will be discussed along with associated ionization mechanisms pertaining to specific sample types.

Off-Line Multidimensional Liquid Chromatography and Auto Sampling Result in Sample Loss in LC/LC–MS/MS

PubMed Central

2015-01-01

Large-scale proteomics often employs two orthogonal separation methods to fractionate complex peptide mixtures. Fractionation can involve ion exchange separation coupled to reversed-phase separation or, more recently, two reversed-phase separations performed at different pH values. When multidimensional separations are combined with tandem mass spectrometry for protein identification, the strategy is often referred to as multidimensional protein identification technology (MudPIT). MudPIT has been used in either an automated (online) or manual (offline) format. In this study, we evaluated the performance of different MudPIT strategies by both label-free and tandem mass tag (TMT) isobaric tagging. Our findings revealed that online MudPIT provided more peptide/protein identifications and higher sequence coverage than offline platforms. When employing an off-line fractionation method with direct loading of samples onto the column from an eppendorf tube via a high-pressure device, a 5.3% loss in protein identifications is observed. When off-line fractionated samples are loaded via an autosampler, a 44.5% loss in protein identifications is observed compared with direct loading of samples onto a triphasic capillary column. Moreover, peptide recovery was significantly lower after offline fractionation than in online fractionation. Signal-to-noise (S/N) ratio, however, was not significantly altered between experimental groups. It is likely that offline sample collection results in stochastic peptide loss due to noncovalent adsorption to solid surfaces. Therefore, the use of the offline approaches should be considered carefully when processing minute quantities of valuable samples. PMID:25040086

Structural characterization of product ions of regulated veterinary drugs by electrospray ionization and quadrupole time-of-flight mass spectrometry (part 3) Anthelmintics, thyreostats, and flukicides

USDA-ARS?s Scientific Manuscript database

RATIONALE: Previously we have reported a liquid chromatography tandem mass spectrometry method for the identification and quantification of regulated veterinary drugs. The methods used three selected transition ions but most of these ions lacked structural characterization. The work presented here ...

Advances in native high-performance liquid chromatography and intact mass spectrometry for the characterization of biopharmaceutical products.

PubMed

Tassi, Marco; De Vos, Jelle; Chatterjee, Sneha; Sobott, Frank; Bones, Jonathan; Eeltink, Sebastiaan

2018-01-01

The characterization of biotherapeutics represents a major analytical challenge. This review discusses the current state-of-the-art in analytical technologies to profile biopharma products under native conditions, i.e., the protein three dimensional conformation is maintained during liquid chromatographic analysis. Native liquid-chromatographic modes that are discussed include aqueous size-exclusion chromatography, hydrophobic interaction chromatography, and ion-exchange chromatography. Infusion conditions and the possibilities and limitations to hyphenate native liquid chromatography to mass spectrometry are discussed. Furthermore, the applicability of native liquid-chromatography methods and intact mass spectrometry analysis for the characterization of monoclonal antibodies and antibody-drug conjugates is discussed. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multicomponent Transport through Realistic Zeolite Membranes: Characterization & Transport in Nanoporous Networks

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

William C. Conner

These research studies focused on the characterization and transport for porous solids which comprise both microporosity and mesoporosity. Such materials represent membranes made from zeolites as well as for many new nanoporous solids. Several analytical sorption techniques were developed and evaluated by which these multi-dimensional porous solids could be quantitatively characterized. Notably an approach by which intact membranes could be studied was developed and applied to plate-like and tubular supported zeolitic membranes. Transport processes were studied experimentally and theoretically based on the characterization studies.

Chromatographic peak deconvolution of constitutional isomers by multiple-reaction-monitoring mass spectrometry.

PubMed

Trapp, Oliver

2010-02-12

Highly efficient and sophisticated separation techniques are available to analyze complex compound mixtures with superior sensitivities and selectivities often enhanced by a 2nd dimension, e.g. a separation technique or spectroscopic and spectrometric techniques. For enantioselective separations numerous chiral stationary phases (CSPs) exist to cover a broad range of chiral compounds. Despite these advances enantioselective separations can become very challenging for mixtures of stereolabile constitutional isomers, because the on-column interconversion can lead to completely overlapping peak profiles. Typically, multidimensional separation techniques, e.g. multidimensional GC (MDGC), using an achiral 1st separation dimension and transferring selected analytes to a chiral 2nd separation are the method of choice to approach such problems. However, this procedure is very time consuming and only predefined sections of peaks can be transferred by column switching to the second dimension. Here we demonstrate for stereolabile 1,2-dialkylated diaziridines a technique to experimentally deconvolute overlapping gas chromatographic elution profiles of constitutional isomers based on multiple-reaction-monitoring MS (MRM-MS). The here presented technique takes advantage of different fragmentation probabilities and pathways to isolate the elution profile of configurational isomers. Copyright 2009 Elsevier B.V. All rights reserved.

Capillary trap column with strong cation-exchange monolith for automated shotgun proteome analysis.

PubMed

Wang, Fangjun; Dong, Jing; Jiang, Xiaogang; Ye, Mingliang; Zou, Hanfa

2007-09-01

A 150 microm internal diameter capillary monolithic column with a strong cation-exchange stationary phase was prepared by direct in situ polymerization of ethylene glycol methacrylate phosphate and bisacrylamide in a trinary porogenic solvent consisting dimethylsulfoxide, dodecanol, and N,N'-dimethylformamide. This phosphate monolithic column exhibits higher dynamic binding capacity, faster kinetic adsorption of peptides, and more than 10 times higher permeability than the column packed with commercially available strong cation-exchange particles. It was applied as a trap column in a nanoflow liquid chromatography-tandem mass spectrometry system for automated sample injection and online multidimensional separation. It was observed that the sample could be loaded at a flow rate as high as 40 microL/min with a back pressure of approximately 1300 psi and without compromising the separation efficiency. Because of its good orthogonality to the reversed phase separation mechanism, the phosphate monolithic trap column was coupled with a reversed-phase column for online multidimensional separation of 19 microg of the tryptic digest of yeast proteins. A total of 1522 distinct proteins were identified from 5608 unique peptides (total of 54,780 peptides) at the false positive rate only 0.46%.

Mass spectrometry methods for the analysis of biodegradable hybrid materials

NASA Astrophysics Data System (ADS)

Alalwiat, Ahlam

This dissertation focuses on the characterization of hybrid materials and surfactant blends by using mass spectrometry (MS), tandem mass spectrometry (MS/MS), liquid chromatography (LC), and ion mobility (IM) spectrometry combined with measurement and simulation of molecular collision cross sections. Chapter II describes the principles and the history of mass spectrometry (MS) and liquid chromatography (LC). Chapter III introduces the materials and instrumentation used to complete this dissertation. In chapter IV, two hybrid materials containing poly(t-butyl acrylate) (PtBA) or poly(acrylic acid) (PAA) blocks attached to a hydrophobic peptide rich in valine and glycine (VG2), as well as the poly(acrylic acid) (PAA) and VG2 peptide precursor materials, are characterized by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), electrospray ionization mass spectrometry (ESI-MS) and ion mobility mass spectrometry (IM-MS). Collision cross-sections and molecular modeling have been used to determine the final architecture of both hybrid materials. Chapter V investigates a different hybrid material, [BMP-2(HA)2 ], comprised of a dendron with two polyethylene glycol (PEG) branches terminated by a hydroxyapatite binding peptide (HA), and a focal point substituted with a bone morphogenic protein mimicking peptide (BMP-2). MALDI-MS, ESI-MS and IM-MS have been used to characterize the HA and BMP-2 peptides. Collisionally activated dissociation (CAD) and electron transfer dissociation (ETD) have been employed in double stage (i.e. tandem) mass spectrometry (MS/MS) experiments to confirm the sequences of the two peptides HA and BMP-2. The MALDI-MS, ESI-MS and IM-MS methods were also applied to characterize the [BMP-2(HA)2] hybrid material. Collision cross-section measurements and molecular modeling indicated that [BMP-2(HA)2] can attain folded or extended conformation, depending on its degree of protonation (charge state). Chapter VI focuses on the analysis of alkyl polyglycoside (APG) surfactants by MALDI-MS and ESI-MS, MS/MS, and by combining MS and with ion mobility (IM) and/or ultra-performance liquid chromatography (UPLC) separation in LC-IM and LC-IM-MS experiments. Chapter VII summaries this dissertation's findings.

Advanced mass spectrometry-based methods for the analysis of conformational integrity of biopharmaceutical products

PubMed Central

Bobst, Cedric E.; Kaltashov, Igor A.

2012-01-01

Mass spectrometry has already become an indispensable tool in the analytical armamentarium of the biopharmaceutical industry, although its current uses are limited to characterization of covalent structure of recombinant protein drugs. However, the scope of applications of mass spectrometry-based methods is beginning to expand to include characterization of the higher order structure and dynamics of biopharmaceutical products, a development which is catalyzed by the recent progress in mass spectrometry-based methods to study higher order protein structure. The two particularly promising methods that are likely to have the most significant and lasting impact in many areas of biopharmaceutical analysis, direct ESI MS and hydrogen/deuterium exchange, are focus of this article. PMID:21542797

Defining Putative Glycan Cancer Biomarkers by Mass Spectrometry

PubMed Central

Mechref, Yehia; Hu, Yunli; Garcia, Aldo; Hussein, Ahmed

2013-01-01

Summary For decades, the association between aberrant glycosylation and many types of cancers has been shown. However, defining the changes of glycan structures has not been demonstrated until recently. This has been facilitated by the major advances in mass spectrometry and separation science which allowed the detailed characterization of glycan changes associated with cancer. Mass spectrometry glycomics methods have been successfully employed to compare the glycomic profiles of different human specimen collected from disease-free individuals and patients with cancer. Additionally, comparing the glycomic profiles of glycoproteins purified from specimen collected from disease-free individuals and patients with cancer has also been performed. These types of glycan analyses employing mass spectrometry or liquid-chromatography mass spectrometry allowed the characterization of native, labeled, and permethylated glycans. This review discusses the different glycomic and glycoproteomic methods employed for defining glycans as cancer biomarkers of different organs, including breast, colon, esophagus, liver, lung, ovarian, pancreas and prostate. PMID:23157355

On the use of multi-dimensional scaling and electromagnetic tracking in high dose rate brachytherapy

NASA Astrophysics Data System (ADS)

Götz, Th I.; Ermer, M.; Salas-González, D.; Kellermeier, M.; Strnad, V.; Bert, Ch; Hensel, B.; Tomé, A. M.; Lang, E. W.

2017-10-01

High dose rate brachytherapy affords a frequent reassurance of the precise dwell positions of the radiation source. The current investigation proposes a multi-dimensional scaling transformation of both data sets to estimate dwell positions without any external reference. Furthermore, the related distributions of dwell positions are characterized by uni—or bi—modal heavy—tailed distributions. The latter are well represented by α—stable distributions. The newly proposed data analysis provides dwell position deviations with high accuracy, and, furthermore, offers a convenient visualization of the actual shapes of the catheters which guide the radiation source during the treatment.

Identification and characterization of complex bioactive oligosaccharides in white and red wine by a combination of mass spectrometry and gas chromatography.

PubMed

Bordiga, Matteo; Travaglia, Fabiano; Meyrand, Mickael; German, J Bruce; Lebrilla, Carlito B; Coïsson, Jean Daniel; Arlorio, Marco; Barile, Daniela

2012-04-11

Over forty-five complex free oligosaccharides (of which several are novel) have been isolated and chemically characterized by gas chromatography and high resolution and high mass accuracy matrix-assisted laser desorption/ionization mass spectrometry (MALDI-FTICR MS) in red and white wines, Grignolino and Chardonnay, respectively. Oligosaccharides with a degree of polymerization between 3 and 14 were separated from simple monosaccharides and disaccharides by solid-phase extraction. The concentrations of free oligosaccharides were over 100 mg/L in both red and white wines. The free oligosaccharides-characterized for the first time in the present study-include hexose-oligosaccharides, xyloglucans, and arabinogalactans and may be the natural byproduct of the degradation of cell wall polysaccharides. The coupled gas chromatography and accurate mass spectrometry approach revealed an effective method to characterize and quantify complex functional oligosaccharides in both red and white wine.

Identification and Characterization of Complex Bioactive Oligosaccharides in White and Red Wine by a Combination of Mass Spectrometry and Gas Chromatography

PubMed Central

Bordiga, Matteo; Travaglia, Fabiano; Meyrand, Mickael; German, J. Bruce; Lebrilla, Carlito B.; Coïsson, Jean Daniel; Arlorio, Marco; Barile, Daniela

2012-01-01

Over forty-five complex free oligosaccharides (of which several are novel) have been isolated and chemically characterized by gas chromatography and high resolution and high mass accuracy matrix-assisted laser desorption/ionization mass spectrometry (MALDI-FTICR MS) in red and white wines, Grignolino and Chardonnay, respectively. Oligosaccharides with a degree of polymerization between 3 and 14 were separated from simple monosaccharides and disaccharides by solid-phase extraction. The concentrations free oligosaccharides were over 100 mg/L in both red and white wines. The free oligosaccharides—characterized for the first time in the present study include hexose-oligosaccharides, xyloglucans and arabinogalactans, and may be the natural by-products of the degradation of cell wall polysaccharides. The coupled gas chromatography and accurate mass spectrometry approach revealed an effective method to characterize and quantify complex functional oligosaccharides in both red and white wine. PMID:22429017

Categorization and Characterization of American Driving Conditions (Phase I)

DOT National Transportation Integrated Search

1978-11-01

The objectives of the study were: (1) to develop a multidimensional matrix as an analysis framework to classify travel of personal motor vehicles according to fuel consumption, (2) to identify and assess available information on travel and fuel consu...

Evaluation of Ion Mobility-Mass Spectrometry for Comparative Analysis of Monoclonal Antibodies

NASA Astrophysics Data System (ADS)

Ferguson, Carly N.; Gucinski-Ruth, Ashley C.

2016-05-01

Analytical techniques capable of detecting changes in structure are necessary to monitor the quality of monoclonal antibody drug products. Ion mobility mass spectrometry offers an advanced mode of characterization of protein higher order structure. In this work, we evaluated the reproducibility of ion mobility mass spectrometry measurements and mobiligrams, as well as the suitability of this approach to differentiate between and/or characterize different monoclonal antibody drug products. Four mobiligram-derived metrics were identified to be reproducible across a multi-day window of analysis. These metrics were further applied to comparative studies of monoclonal antibody drug products representing different IgG subclasses, manufacturers, and lots. These comparisons resulted in some differences, based on the four metrics derived from ion mobility mass spectrometry mobiligrams. The use of collision-induced unfolding resulted in more observed differences. Use of summed charge state datasets and the analysis of metrics beyond drift time allowed for a more comprehensive comparative study between different monoclonal antibody drug products. Ion mobility mass spectrometry enabled detection of differences between monoclonal antibodies with the same target protein but different production techniques, as well as products with different targets. These differences were not always detectable by traditional collision cross section studies. Ion mobility mass spectrometry, and the added separation capability of collision-induced unfolding, was highly reproducible and remains a promising technique for advanced analytical characterization of protein therapeutics.

Online Ozonolysis Combined with Ion Mobility-Mass Spectrometry Provides a New Platform for Lipid Isomer Analyses

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

Poad, Berwyck L. J.; Zheng, Xueyun; Mitchell, Todd W.

One of the most significant challenges in contemporary lipidomics lies in the separation and identification of lipid isomers that differ only in site(s) of unsaturation or geometric configuration of the carbon-carbon double bonds. While analytical separation techniques including ion mobility spectrometry (IMS) and liquid chromatography (LC) can separate isomeric lipids under appropriate conditions, conventional tandem mass spectrometry cannot provide unequivocal identification. To address this challenge, we have implemented ozone-induced dissociation (OzID) in-line with LC, IMS and high resolution mass spectrometry. Modification of an IMS- capable quadrupole time-of-flight mass spectrometer was undertaken to allow the introduction of ozone into the high-pressuremore » trapping ion funnel region preceding the IMS cell. This enabled the novel LC-OzID-IMS-MS configuration where ozonolysis of ionized lipids occurred rapidly (10 ms) without prior mass-selection. LC-elution time alignment combined with accurate mass and arrival time extraction of ozonolysis products facilitated correlation of precursor and product ions without mass-selection (and associated reductions in duty cycle). Unsaturated lipids across 11 classes were examined using this workflow in both positive and negative ion modalities and in all cases the positions of carbon-carbon double bonds were unequivocally assigned based on predictable OzID transitions. Under these conditions geometric isomers exhibited different IMS arrival time distributions and distinct OzID product ion ratios providing a means for discrimination of cis/trans double bonds in complex lipids. The combination of OzID with multidimensional separations shows significant promise for facile profiling of unsaturation patterns within complex lipidomes.« less

A strategy for identification and structural characterization of compounds from Gardenia jasminoides by integrating macroporous resin column chromatography and liquid chromatography-tandem mass spectrometry combined with ion-mobility spectrometry.

PubMed

Wang, Lu; Liu, Shu; Zhang, Xueju; Xing, Junpeng; Liu, Zhiqiang; Song, Fengrui

2016-06-24

In this paper, an analysis strategy integrating macroporous resin (AB-8) column chromatography and high performance liquid chromatography-electrospray ionization-tandem mass spectrometry (HPLC-ESI-MS/MS) combined with ion mobility spectrometry (IMS) was proposed and applied for identification and structural characterization of compounds from the fruits of Gardenia jasminoides. The extracts of G. jasminoides were separated by AB-8 resin column chromatography combined with reversed phase liquid chromatography (C18 column) and detected by electrospray ionization tandem mass spectrometry. Additionally, ion mobility spectrometry (IMS) was employed as a supplementary separation technique to discover previously undetected isomers from the fruits of G. jasminoides. A total of 71 compounds, including iridoids, flavonoids, triterpenes, monoterpenoids, carotenoids and phenolic acids were identified by the characteristic high resolution mass spectrometry and the ESI-MS/MS fragmentations. In conclusion, the IMS-MS technique achieved the separation of isomers in crocin-3 and crocin-4 according to their acquired mobility drift times differing from classical analysis by mass spectrometry. The proposed strategy can be used as a highly sensitive and efficient procedure for identification and separation isomeric components in extracts of herbal medicines. Copyright © 2016 Elsevier B.V. All rights reserved.

GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems

PubMed Central

Rellán-Álvarez, Rubén; Lobet, Guillaume; Lindner, Heike; Pradier, Pierre-Luc; Sebastian, Jose; Yee, Muh-Ching; Geng, Yu; Trontin, Charlotte; LaRue, Therese; Schrager-Lavelle, Amanda; Haney, Cara H; Nieu, Rita; Maloof, Julin; Vogel, John P; Dinneny, José R

2015-01-01

Root systems develop different root types that individually sense cues from their local environment and integrate this information with systemic signals. This complex multi-dimensional amalgam of inputs enables continuous adjustment of root growth rates, direction, and metabolic activity that define a dynamic physical network. Current methods for analyzing root biology balance physiological relevance with imaging capability. To bridge this divide, we developed an integrated-imaging system called Growth and Luminescence Observatory for Roots (GLO-Roots) that uses luminescence-based reporters to enable studies of root architecture and gene expression patterns in soil-grown, light-shielded roots. We have developed image analysis algorithms that allow the spatial integration of soil properties, gene expression, and root system architecture traits. We propose GLO-Roots as a system that has great utility in presenting environmental stimuli to roots in ways that evoke natural adaptive responses and in providing tools for studying the multi-dimensional nature of such processes. DOI: http://dx.doi.org/10.7554/eLife.07597.001 PMID:26287479

Selective mutism: a review of etiology, comorbidities, and treatment.

PubMed

Wong, Priscilla

2010-03-01

Selective mutism is a rare and multidimensional childhood disorder that typically affects children entering school age. It is characterized by the persistent failure to speak in select social settings despite possessing the ability to speak and speak comfortably in more familiar settings. Many theories attempt to explain the etiology of selective mutism.Comorbidities and treatment. Selective mutism can present a variety of comorbidities including enuresis, encopresis, obsessive-compulsive disorder, depression, premorbid speech and language abnormalities, developmental delay, and Asperger's disorders. The specific manifestations and severity of these comorbidities vary based on the individual. Given the multidimensional manifestations of selective mutism, treatment options are similarly diverse. They include individual behavioral therapy, family therapy, and psychotherapy with antidepressants and anti-anxiety medications.Future directions. While studies have helped to elucidate the phenomenology of selective mutism, limitations and gaps in knowledge still persist. In particular, the literature on selective mutism consists primarily of small sample populations and case reports. Future research aims to develop an increasingly integrated, multidimensional framework for evaluating and treating children with selective mutism.

Selective Mutism

PubMed Central

2010-01-01

Selective mutism is a rare and multidimensional childhood disorder that typically affects children entering school age. It is characterized by the persistent failure to speak in select social settings despite possessing the ability to speak and speak comfortably in more familiar settings. Many theories attempt to explain the etiology of selective mutism. Comorbidities and treatment. Selective mutism can present a variety of comorbidities including enuresis, encopresis, obsessive-compulsive disorder, depression, premorbid speech and language abnormalities, developmental delay, and Asperger's disorders. The specific manifestations and severity of these comorbidities vary based on the individual. Given the multidimensional manifestations of selective mutism, treatment options are similarly diverse. They include individual behavioral therapy, family therapy, and psychotherapy with antidepressants and anti-anxiety medications. Future directions. While studies have helped to elucidate the phenomenology of selective mutism, limitations and gaps in knowledge still persist. In particular, the literature on selective mutism consists primarily of small sample populations and case reports. Future research aims to develop an increasingly integrated, multidimensional framework for evaluating and treating children with selective mutism. PMID:20436772

GLO-Roots: An imaging platform enabling multidimensional characterization of soil-grown root systems

DOE PAGES

Rellan-Alvarez, Ruben; Lobet, Guillaume; Lindner, Heike; ...

2015-08-19

Root systems develop different root types that individually sense cues from their local environment and integrate this information with systemic signals. This complex multi-dimensional amalgam of inputs enables continuous adjustment of root growth rates, direction, and metabolic activity that define a dynamic physical network. Current methods for analyzing root biology balance physiological relevance with imaging capability. To bridge this divide, we developed an integrated-imaging system called Growth and Luminescence Observatory for Roots (GLO-Roots) that uses luminescence-based reporters to enable studies of root architecture and gene expression patterns in soil-grown, light-shielded roots. We have developed image analysis algorithms that allow themore » spatial integration of soil properties, gene expression, and root system architecture traits. We propose GLO-Roots as a system that has great utility in presenting environmental stimuli to roots in ways that evoke natural adaptive responses and in providing tools for studying the multi-dimensional nature of such processes.« less

Multi-dimensional construction of a novel active yolk@conductive shell nanofiber web as a self-standing anode for high-performance lithium-ion batteries

NASA Astrophysics Data System (ADS)

Liu, Hao; Chen, Luyi; Liang, Yeru; Fu, Ruowen; Wu, Dingcai

2015-11-01

A novel active yolk@conductive shell nanofiber web with a unique synergistic advantage of various hierarchical nanodimensional objects including the 0D monodisperse SiO2 yolks, the 1D continuous carbon shell and the 3D interconnected non-woven fabric web has been developed by an innovative multi-dimensional construction method, and thus demonstrates excellent electrochemical properties as a self-standing LIB anode.A novel active yolk@conductive shell nanofiber web with a unique synergistic advantage of various hierarchical nanodimensional objects including the 0D monodisperse SiO2 yolks, the 1D continuous carbon shell and the 3D interconnected non-woven fabric web has been developed by an innovative multi-dimensional construction method, and thus demonstrates excellent electrochemical properties as a self-standing LIB anode. Electronic supplementary information (ESI) available: Experimental details and additional information about material characterization. See DOI: 10.1039/c5nr06531c

Contribution of personal and environmental factors on positive psychological functioning in adolescents.

PubMed

Fadda, Daniela; Scalas, L Francesca; Meleddu, Mauro

2015-08-01

This study examined self-esteem as mediator in the relations of personal (extraversion, neuroticism) and environmental (maternal, paternal, peer-relationships) variables with domains of positive psychological functioning (PPF) in adolescence (Satisfaction with life, Mastery, Vigor, Social Interest, Social Cheerfulness). We compared one-sided and multidimensional models using a sample of 1193 high school students (592 males and 601 females). We examined variations in adolescent PPF as a function of parenting styles via independent examination of maternal and paternal bonding. Results supported the multidimensional models, which indicated direct effects of personality traits, maternal care and peer relationships, as well as indirect effects, mediated by self-esteem, of all predictors on most PPF dimensions. Overall, our study provided a broader picture of personal and environmental predictors on different dimensions of PPF, which supported the mediating role of self-esteem and emphasized the importance of considering multidimensional models to characterize PPF in adolescents. Copyright © 2015 The Foundation for Professionals in Services for Adolescents. Published by Elsevier Ltd. All rights reserved.

Selective extraction of halogenated compounds from data measured by comprehensive multidimensional gas chromatography/high resolution time-of-flight mass spectrometry for non-target analysis of environmental and biological samples.

PubMed

Hashimoto, Shunji; Zushi, Yasuyuki; Fushimi, Akihiro; Takazawa, Yoshikatsu; Tanabe, Kiyoshi; Shibata, Yasuyuki

2013-03-22

We developed a method that selectively extracts a subset from comprehensive 2D gas chromatography (GC×GC) and high-resolution time-of-flight mass spectrometry (HRTOFMS) data to detect and identify trace levels of organohalogens. The data were obtained by measuring several environmental and biological samples, namely fly ash, soil, sediment, the atmosphere, and human urine. For global analysis, some samples were measured without purification. By using our novel software, the mass spectra of organochlorines or organobromines were then extracted into a data subset under high mass accuracy conditions that were approximately equivalent to a mass resolution of 6000 for some samples. Mass defect filtering as pre-screening for the data extraction was very effective in removing the mass spectra of hydrocarbons. Those results showed that data obtained with HRTOFMS are valuable for global analysis of organohalogens, and probably of other compounds if specific data extraction methods can be devised. Copyright © 2013 Elsevier B.V. All rights reserved.

Supervised Semi-Automated Data Analysis Software for Gas Chromatography / Differential Mobility Spectrometry (GC/DMS) Metabolomics Applications.

PubMed

Peirano, Daniel J; Pasamontes, Alberto; Davis, Cristina E

2016-09-01

Modern differential mobility spectrometers (DMS) produce complex and multi-dimensional data streams that allow for near-real-time or post-hoc chemical detection for a variety of applications. An active area of interest for this technology is metabolite monitoring for biological applications, and these data sets regularly have unique technical and data analysis end user requirements. While there are initial publications on how investigators have individually processed and analyzed their DMS metabolomic data, there are no user-ready commercial or open source software packages that are easily used for this purpose. We have created custom software uniquely suited to analyze gas chromatograph / differential mobility spectrometry (GC/DMS) data from biological sources. Here we explain the implementation of the software, describe the user features that are available, and provide an example of how this software functions using a previously-published data set. The software is compatible with many commercial or home-made DMS systems. Because the software is versatile, it can also potentially be used for other similarly structured data sets, such as GC/GC and other IMS modalities.

Knowns and unknowns in metabolomics identified by multidimensional NMR and hybrid MS/NMR methods

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

Bingol, Kerem; Brüschweiler, Rafael

Metabolomics continues to make rapid progress through the development of new and better methods and their applications to gain insight into the metabolism of a wide range of different biological systems from a systems biology perspective. Customization of NMR databases and search tools allows the faster and more accurate identification of known metabolites, whereas the identification of unknowns, without a need for extensive purification, requires new strategies to integrate NMR with mass spectrometry, cheminformatics, and computational methods. For some applications, the use of covalent and non-covalent attachments in the form of labeled tags or nanoparticles can significantly reduce the complexitymore » of these tasks.« less

Glyceraldehyde and glycolaldehyde in interstellar ice analogues and the role of aldehydes in cosmochemical evolution

NASA Astrophysics Data System (ADS)

Meierhenrich, U.; de Marcellus, P.; Meinert, C.; Myrgorodska, I.; Nahon, L.; Buhse, T.; d'Hendecourt, L.

2015-10-01

Our understanding of the molecular origin of life is based on amino acids, ribose, and nucleobases that - after their selection by prebiotic processes - initiated the evolutionary assembly of catalytic and informational polymers, being proteins and ribonucleic acids. Following previous amino acid identifications in the room-temperature residues of simulated circumstellar/interstellar ices [1,2] we have searched for a different family of molecules of potential prebiotic interest. Using multidimensional gas chromatography coupled to time-of-flight mass spectrometry, we have detected ten aldehydes, including the sugar-related glycolaldehyde and glyceraldehyde - two species considered as key prebiotic intermediates in the first steps toward the synthesis of ribonucleotides in a planetary environment.

Med Diet 4.0: the Mediterranean diet with four sustainable benefits.

PubMed

Dernini, S; Berry, E M; Serra-Majem, L; La Vecchia, C; Capone, R; Medina, F X; Aranceta-Bartrina, J; Belahsen, R; Burlingame, B; Calabrese, G; Corella, D; Donini, L M; Lairon, D; Meybeck, A; Pekcan, A G; Piscopo, S; Yngve, A; Trichopoulou, A

2017-05-01

To characterize the multiple dimensions and benefits of the Mediterranean diet as a sustainable diet, in order to revitalize this intangible food heritage at the country level; and to develop a multidimensional framework - the Med Diet 4.0 - in which four sustainability benefits of the Mediterranean diet are presented in parallel: major health and nutrition benefits, low environmental impacts and richness in biodiversity, high sociocultural food values, and positive local economic returns. A narrative review was applied at the country level to highlight the multiple sustainable benefits of the Mediterranean diet into a single multidimensional framework: the Med Diet 4.0. Setting/subjects We included studies published in English in peer-reviewed journals that contained data on the characterization of sustainable diets and of the Mediterranean diet. The methodological framework approach was finalized through a series of meetings, workshops and conferences where the framework was presented, discussed and ultimately refined. The Med Diet 4.0 provides a conceptual multidimensional framework to characterize the Mediterranean diet as a sustainable diet model, by applying principles of sustainability to the Mediterranean diet. By providing a broader understanding of the many sustainable benefits of the Mediterranean diet, the Med Diet 4.0 can contribute to the revitalization of the Mediterranean diet by improving its current perception not only as a healthy diet but also a sustainable lifestyle model, with country-specific and culturally appropriate variations. It also takes into account the identity and diversity of food cultures and systems, expressed within the notion of the Mediterranean diet, across the Mediterranean region and in other parts of the world. Further multidisciplinary studies are needed for the assessment of the sustainability of the Mediterranean diet to include these new dimensions.

Quantifying traditional Chinese medicine patterns using modern test theory: an example of functional constipation.

PubMed

Shen, Minxue; Cui, Yuanwu; Hu, Ming; Xu, Linyong

2017-01-13

The study aimed to validate a scale to assess the severity of "Yin deficiency, intestine heat" pattern of functional constipation based on the modern test theory. Pooled longitudinal data of 237 patients with "Yin deficiency, intestine heat" pattern of constipation from a prospective cohort study were used to validate the scale. Exploratory factor analysis was used to examine the common factors of items. A multidimensional item response model was used to assess the scale with the presence of multidimensionality. The Cronbach's alpha ranged from 0.79 to 0.89, and the split-half reliability ranged from 0.67 to 0.79 at different measurements. Exploratory factor analysis identified two common factors, and all items had cross factor loadings. Bidimensional model had better goodness of fit than the unidimensional model. Multidimensional item response model showed that the all items had moderate to high discrimination parameters. Parameters indicated that the first latent trait signified intestine heat, while the second trait characterized Yin deficiency. Information function showed that items demonstrated highest discrimination power among patients with moderate to high level of disease severity. Multidimensional item response theory provides a useful and rational approach in validating scales for assessing the severity of patterns in traditional Chinese medicine.

Evidence for High Concentrations and Maternal Transfer of Substituted Diphenylamines in European Eels Analyzed by Two-Dimensional Gas Chromatography-Time-of-Flight Mass Spectrometry and Gas Chromatography-Fourier Transform Ion Cyclotron Resonance Mass Spectrometry.

PubMed

Sühring, Roxana; Ortiz, Xavier; Pena-Abaurrea, Miren; Jobst, Karl J; Freese, Marko; Pohlmann, Jan-Dag; Marohn, Lasse; Ebinghaus, Ralf; Backus, Sean; Hanel, Reinhold; Reiner, Eric J

2016-12-06

Chemical pollution is hypothesized to be one of the factors driving the strong decline of the critically endangered European eel population. Specifically, the impact of contaminants on the quality of spawning eels and subsequent embryo survival and development has been discussed as crucial investigation point. However, so far, only very limited information on potential negative effects of contaminants on the reproduction of eels is available. Through the combination of nontargeted ultrahigh-resolution mass spectrometry and multidimensional gas chromatography, combined with more-conventional targeted analytical approaches and multimedia mass-balance modeling, compounds of particular relevance, and their maternal transfer in artificially matured European eels from the German river Ems have been identified. Substituted diphenylamines were, unexpectedly, found to be the primary organic contaminants in the eel samples, with concentrations in the μg g -1 wet weight range. Furthermore, it could be shown that these contaminants, as well as polychlorinated biphenyls (PCBs), organochlorine pesticides, and polyaromatic hydrocarbons (PAHs), are not merely stored in lipid rich tissue of eels but maternally transferred into gonads and eggs. The results of this study provide unique information on both the fate and behavior of substituted diphenylamines in the environment as well as their relevance as contaminants in European eels.

Entropy of Leukemia on Multidimensional Morphological and Molecular Landscapes

NASA Astrophysics Data System (ADS)

Vilar, Jose M. G.

2014-04-01

Leukemia epitomizes the class of highly complex diseases that new technologies aim to tackle by using large sets of single-cell-level information. Achieving such a goal depends critically not only on experimental techniques but also on approaches to interpret the data. A most pressing issue is to identify the salient quantitative features of the disease from the resulting massive amounts of information. Here, I show that the entropies of cell-population distributions on specific multidimensional molecular and morphological landscapes provide a set of measures for the precise characterization of normal and pathological states, such as those corresponding to healthy individuals and acute myeloid leukemia (AML) patients. I provide a systematic procedure to identify the specific landscapes and illustrate how, applied to cell samples from peripheral blood and bone marrow aspirates, this characterization accurately diagnoses AML from just flow cytometry data. The methodology can generally be applied to other types of cell populations and establishes a straightforward link between the traditional statistical thermodynamics methodology and biomedical applications.

Contribution of bulk mass spectrometry isotopic analysis to characterization of materials in the framework of CMX-4

DOE PAGES

Kuchkin, A.; Stebelkov, V.; Zhizhin, K.; ...

2018-01-30

Seven laboratories used the results of bulk uranium isotopic analysis by either inductively coupled plasma mass spectrometry (ICP-MS) or thermal ionization mass spectrometry (TIMS) for characterization of the samples in the Nuclear Forensic International Technical Working Group fourth international collaborative material exercise, CMX-4. Comparison of the measured isotopic compositions of uranium in three exercise samples is implemented for identifying any differences or similarities between the samples. The role of isotopic analyses in the context of a real nuclear forensic investigation is discussed. Several limitations in carrying out ICP-MS or TIMS analysis in CMX-4 are noted.

Rapid Characterization of Microorganisms by Mass Spectrometry—What Can Be Learned and How?

NASA Astrophysics Data System (ADS)

Fenselau, Catherine C.

2013-08-01

Strategies for the rapid and reliable analysis of microorganisms have been sought to meet national needs in defense, homeland security, space exploration, food and water safety, and clinical diagnosis. Mass spectrometry has long been a candidate technique because it is extremely rapid and can provide highly specific information. It has excellent sensitivity. Molecular and fragment ion masses provide detailed fingerprints, which can also be interpreted. Mass spectrometry is also a broad band method—everything has a mass—and it is automatable. Mass spectrometry is a physiochemical method that is orthogonal and complementary to biochemical and morphological methods used to characterize microorganisms.

Contribution of bulk mass spectrometry isotopic analysis to characterization of materials in the framework of CMX-4

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

Kuchkin, A.; Stebelkov, V.; Zhizhin, K.

Seven laboratories used the results of bulk uranium isotopic analysis by either inductively coupled plasma mass spectrometry (ICP-MS) or thermal ionization mass spectrometry (TIMS) for characterization of the samples in the Nuclear Forensic International Technical Working Group fourth international collaborative material exercise, CMX-4. Comparison of the measured isotopic compositions of uranium in three exercise samples is implemented for identifying any differences or similarities between the samples. The role of isotopic analyses in the context of a real nuclear forensic investigation is discussed. Several limitations in carrying out ICP-MS or TIMS analysis in CMX-4 are noted.

Division of Labor in Colonies of the Eusocial Wasp, Mischocyttarus consimilis

PubMed Central

Torres, Viviana O.; Montagna, Thiago S.; Raizer, Josué; Antonialli-Junior, William F.

2012-01-01

The division of labor between castes and the division of labor in workers according to age (temporal polyethism) in social wasps are crucial for maintaining social organization. This study evaluated the division of labor between castes, and the temporal polyethism in workers of Mischocyttarus consimilis Zikán (Hymenoptera: Vespidae). To describe the behavioral repertory of this species, observations were made of 21 colonies, with 100 hours of observations. In order to observe temporal polyethism, each newly emerged wasp was marked with colored dots on the upper area of the thorax. This allowed the observation of behavioral acts performed by each worker from the time of emergence to its death. Through hybrid multidimensional scaling, a clear division between queens and workers could be identified, in which the behaviors of physical dominance and food solicitation characterized the queen caste; while behaviors such as adult—adult trophallaxis, destruction of cells, alarm, foraging for prey, foraging for nectar, and unsuccessful foraging characterized the worker caste. Hybrid multidimensional scaling characterized two groups, with intra—nest activities preferentially accomplished by younger workers, while extra—nest activities such as foraging were executed more frequently by older workers. PMID:22954231

Why do Ladybugs Smell Bad? In-vivo Quantification of Odorous Insect Kairomones with SPME and Multidimensional GC-MS-Olfactometry

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

Cai Lingshuang; Koziel, Jacek A.; O'Neal, Matthew E.

2009-05-23

Winemakers, small fruit growers, and homeowners are concerned with noxious compounds released by multicolored Asian ladybird beetles (Harmonia axyridis, Coleoptera: Coccinellidae). New method based on headspace solid phase microextraction (HS-SPME) coupled with multidimensional gas chromatography mass spectrometry--olfactometry (MDGC-MS-O) system was developed for extraction, isolation and simultaneous identification of compounds responsible for the characteristic odor of live H. axyridis. Four methoxypyrazines (MPs) were identified in headspace volatiles of live H. axyridis as those responsible for the characteristic odor: 2, 5-dimethy1-3-methoxypyrazine (DMMP), 2-isopropy1-3-methoxypyrazine (IPMP), 2-sec-buty1-3-methoxypyrazine (SBMP), and 2-isobuty1-3-methoxypyrazine (IBMP). To the best of our knowledge this is the first report of H.more » axyridis releasing DMMP and the first report of this compound being a component of the H. axyridis characteristic odor. Quantification of three MPs (IPMP, SBMP and IBMP) emitted from live H. axyridis were performed using external calibration with HS-SPME and direct injections. A linear relationship (R{sup 2}>0.9958 for all 3 MPs) between MS response and concentration of standard was observed over a concentration range from 0.1 ng L{sup -1} to 0.05 {mu}g L{sup -1} for HS-SPME-GC-MS. The method detection limits (MDL) based on multidimensional GC-MS approach for three MPs were estimated to be between 0.020 ng L{sup -1}. to 0.022 ng L{sup -1}. This methodology is applicable for in vivo determination of odor-causing chemicals associated with emissions of volatiles from insects.« less

A structural examination and collision cross section database for over 500 metabolites and xenobiotics using drift tube ion mobility spectrometry† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc03464d

PubMed Central

Zheng, Xueyun; Aly, Noor A.; Zhou, Yuxuan; Dupuis, Kevin T.; Bilbao, Aivett; Paurus, Vanessa L.; Orton, Daniel J.; Wilson, Ryan; Payne, Samuel H.; Smith, Richard D.

2017-01-01

The confident identification of metabolites and xenobiotics in biological and environmental studies is an analytical challenge due to their immense dynamic range, vast chemical space and structural diversity. Ion mobility spectrometry (IMS) is widely used for small molecule analyses since it can separate isomeric species and be easily coupled with front end separations and mass spectrometry for multidimensional characterizations. However, to date IMS metabolomic and exposomic studies have been limited by an inadequate number of accurate collision cross section (CCS) values for small molecules, causing features to be detected but not confidently identified. In this work, we utilized drift tube IMS (DTIMS) to directly measure CCS values for over 500 small molecules including primary metabolites, secondary metabolites and xenobiotics. Since DTIMS measurements do not need calibrant ions or calibration like some other IMS techniques, they avoid calibration errors which can cause problems in distinguishing structurally similar molecules. All measurements were performed in triplicate in both positive and negative polarities with nitrogen gas and seven different electric fields, so that relative standard deviations (RSD) could be assessed for each molecule and structural differences studied. The primary metabolites analyzed to date have come from key metabolism pathways such as glycolysis, the pentose phosphate pathway and the tricarboxylic acid cycle, while the secondary metabolites consisted of classes such as terpenes and flavonoids, and the xenobiotics represented a range of molecules from antibiotics to polycyclic aromatic hydrocarbons. Different CCS trends were observed for several of the diverse small molecule classes and when urine features were matched to the database, the addition of the IMS dimension greatly reduced the possible number of candidate molecules. This CCS database and structural information are freely available for download at http://panomics.pnnl.gov/metabolites/ with new molecules being added frequently. PMID:29568436

Multidimensional daily diary of fatigue-fibromyalgia-17 items (MDF-fibro-17). part 1: development and content validity.

PubMed

Morris, S; Li, Y; Smith, J A M; Dube', S; Burbridge, C; Symonds, T

2017-05-16

Fibromyalgia (FM), a disorder characterized by chronic widespread pain and tenderness, affects greater than five million individuals in the United States alone. Patients experience multiple symptoms in addition to pain, and among them, fatigue is one of the most bothersome and disabling. There is a growing body of literature suggesting that fatigue is a multidimensional concept. Currently, to our knowledge, no multidimensional Patient Reported Outcome (PRO) measure of FM-related fatigue meets Food and Drug Administration (FDA) requirements to support a product label claim. Therefore, the objective of this research was to evaluate qualitative and quantitative data previously gathered to inform the development of a comprehensive, multidimensional, PRO measure to assess FM-related fatigue in FM clinical trials. Existing qualitative and quantitative data from three previously conducted studies in patients with FM were reviewed to inform the initial development of a multidimensional PRO measure of FM-related fatigue: 1) a concept elicitation study involving in-depth, open-ended interviews with patients with FM in the United States (US) (N = 20), Germany (N = 10), and France (N = 10); 2) a cognitive debriefing and pilot study of a preliminary pool of 23 items (N = 20 US patients with FM); and 3) a methodology study that explored initial psychometrics of the item pool (N = 145 US patients with FM). Five domains were identified that intend to capture the broad experience of FM-related fatigue reported in the qualitative research: the Global Fatigue Experience, Cognitive Fatigue, Physical Fatigue, Motivation, and Impact on Function. Seventeen of the original pool of 23 items were selected to best capture these five dimensions. These 17 items formed the basis of a newly developed multidimensional PRO measure to assess FM-related fatigue in clinical trials: the Multidimensional Daily Diary of Fatigue-Fibromyalgia-17 (MDF-Fibro-17). Qualitative analysis, and preliminary quantitative item level data, confirmed that FM-related fatigue is multidimensional and provided strong support for the content validity of the MDF-Fibro-17. The next stage was to quantitatively evaluate the measure to confirm the factor structure, psychometric properties, sensitivity to change, and meaningful change. This has been conducted and is being reported separately.

Qualitative Characterization of the Aqueous Fraction from Hydrothermal Liquefaction of Algae Using 2D Gas Chromatography with Time-of-flight Mass Spectrometry

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

Maddi, Balakrishna; Panisko, Ellen; Albrecht, Karl

Two-dimensional gas chromatography coupled with time of flight mass spectrometry is a powerful tool for identifying and quantifying components in complex mixtures. It has been used to analyze gasoline, jet fuel, diesel, bio-diesel and organic fraction of bio-crude/bio-oil. In these experiments, the first dimension of separation was non-polar, followed by a polar separation. Aqueous fractions of bio-crude and other aqueous samples have been examined with similar column combinations. However, sample preparation techniques such as derivatization, solvent extraction, and solid-phase extraction were necessary prior to analysis. In this study, aqueous fraction obtained from hydrothermal liquefaction of algae was characterized by two-dimensionalmore » gas chromatography coupled with time of flight mass spectrometry without prior sample preparation techniques using a polar separation in the first dimension followed by a non-polar separation. Two-dimensional plots from this analysis were compared with those obtained from the more traditional column combination. Results from qualitative characterization aqueous fractions of algal bio-crude are discussed in detail. The advantages of using a polar separation followed by a non-polar separation for characterization of organics in aqueous samples by two-dimensional gas chromatography coupled with time of flight mass spectrometry are highlighted.« less

Changes in Illness-Related Behavior and Dysphoria Accompanying Behavioral Treatment of Recurrent Headache.

ERIC Educational Resources Information Center

Rains, Jeanetta C.; Lohr, Jeffrey M.

Psychophysiologic research indicates that muscle-contraction headache often is not characterized by excessive or unusual muscular activity, and muscular changes seldom accompany headache improvement resulting from treatment. Multidimensional models have been proposed, which emphasize the interdependence of physiological and psychological systems…

Development of stereotactic mass spectrometry for brain tumor surgery.

PubMed

Agar, Nathalie Y R; Golby, Alexandra J; Ligon, Keith L; Norton, Isaiah; Mohan, Vandana; Wiseman, Justin M; Tannenbaum, Allen; Jolesz, Ferenc A

2011-02-01

Surgery remains the first and most important treatment modality for the majority of solid tumors. Across a range of brain tumor types and grades, postoperative residual tumor has a great impact on prognosis. The principal challenge and objective of neurosurgical intervention is therefore to maximize tumor resection while minimizing the potential for neurological deficit by preserving critical tissue. To introduce the integration of desorption electrospray ionization mass spectrometry into surgery for in vivo molecular tissue characterization and intraoperative definition of tumor boundaries without systemic injection of contrast agents. Using a frameless stereotactic sampling approach and by integrating a 3-dimensional navigation system with an ultrasonic surgical probe, we obtained image-registered surgical specimens. The samples were analyzed with ambient desorption/ionization mass spectrometry and validated against standard histopathology. This new approach will enable neurosurgeons to detect tumor infiltration of the normal brain intraoperatively with mass spectrometry and to obtain spatially resolved molecular tissue characterization without any exogenous agent and with high sensitivity and specificity. Proof of concept is presented in using mass spectrometry intraoperatively for real-time measurement of molecular structure and using that tissue characterization method to detect tumor boundaries. Multiple sampling sites within the tumor mass were defined for a patient with a recurrent left frontal oligodendroglioma, World Health Organization grade II with chromosome 1p/19q codeletion, and mass spectrometry data indicated a correlation between lipid constitution and tumor cell prevalence. The mass spectrometry measurements reflect a complex molecular structure and are integrated with frameless stereotaxy and imaging, providing 3-dimensional molecular imaging without systemic injection of any agents, which can be implemented for surgical margins delineation of any organ and with a rapidity that allows real-time analysis.

Two multidimensional chromatographic methods for enantiomeric analysis of o,p'-DDT and o,p'-DDD in contaminated soil and air in a malaria area of South Africa.

PubMed

Naudé, Yvette; Rohwer, Egmont R

2012-06-12

In rural parts of South Africa the organochlorine insecticide DDT (1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane) is still used for malaria vector control where traditional dwellings are sprayed on the inside with small quantities of technical DDT. Since o,p'-DDT may show enantioselective oestrogenicity and biodegradability, it is important to analyse enantiomers of o,p'-DDT and its chiral degradation product, o,p'-DDD, for both health and environmental-forensic considerations. Generally, chiral analysis is performed using heart-cut multidimensional gas chromatography (MDGC) and, more recently, comprehensive two-dimensional gas chromatography (GC×GC). We developed an off-line gas chromatographic fraction collection (heart-cut) procedure for the selective capturing of the appropriate isomers from a first apolar column, followed by reinjection and separation on a second chiral column. Only the o,p'-isomers of DDT and DDD fractions from the first dimension complex chromatogram (achiral apolar GC column separation) were selectively collected onto a polydimethylsiloxane (PDMS) multichannel open tubular silicone rubber trap by simply placing the latter device on the flame tip of an inactivated flame ionisation detector (FID). The multichannel trap containing the o,p'-heart-cuts was then thermally desorbed into a GC with time-of-flight mass spectrometry detection (GC-TOFMS) for second dimension enantioselective separation on a chiral column (β-cyclodextrin-based). By selectively capturing only the o,p'-isomers from the complex sample chromatogram, (1)D separation of ultra-trace level enantiomers could be achieved on the second chiral column without matrix interference. Here, we present solventless concentration techniques for extraction of DDT from contaminated soil and air, and report enantiomeric fraction (EF) values of o,p'-DDT and o,p'-DDD obtained by a new multidimensional approach for heart-cut gas chromatographic fraction collection for off-line second dimension enantiomeric separation by (1)D GC-TOFMS of selected isomers. This multidimensional method is compared to the complementary technique of comprehensive GC×GC-TOFMS using the same enantioselective column, this time as the first dimension of separation. Copyright © 2012 Elsevier B.V. All rights reserved.

Combining micro-RNA and protein sequencing to detect robust biomarkers for Graves' disease and orbitopathy.

PubMed

Zhang, Lei; Masetti, Giulia; Colucci, Giuseppe; Salvi, Mario; Covelli, Danila; Eckstein, Anja; Kaiser, Ulrike; Draman, Mohd Shazli; Muller, Ilaria; Ludgate, Marian; Lucini, Luigi; Biscarini, Filippo

2018-05-30

Graves' Disease (GD) is an autoimmune condition in which thyroid-stimulating antibodies (TRAB) mimic thyroid-stimulating hormone function causing hyperthyroidism. 5% of GD patients develop inflammatory Graves' orbitopathy (GO) characterized by proptosis and attendant sight problems. A major challenge is to identify which GD patients are most likely to develop GO and has relied on TRAB measurement. We screened sera/plasma from 14 GD, 19 GO and 13 healthy controls using high-throughput proteomics and miRNA sequencing (Illumina's HiSeq2000 and Agilent-6550 Funnel quadrupole-time-of-flight mass spectrometry) to identify potential biomarkers for diagnosis or prognosis evaluation. Euclidean distances and differential expression (DE) based on miRNA and protein quantification were analysed by multidimensional scaling (MDS) and multinomial regression respectively. We detected 3025 miRNAs and 1886 proteins and MDS revealed good separation of the 3 groups. Biomarkers were identified by combined DE and Lasso-penalized predictive models; accuracy of predictions was 0.86 (±0:18), and 5 miRNA and 20 proteins were found including Zonulin, Alpha-2 macroglobulin, Beta-2 glycoprotein 1 and Fibronectin. Functional analysis identified relevant metabolic pathways, including hippo signaling, bacterial invasion of epithelial cells and mRNA surveillance. Proteomic and miRNA analyses, combined with robust bioinformatics, identified circulating biomarkers applicable to diagnose GD, predict GO disease status and optimize patient management.

High-time resolved measurements of biogenic and anthropogenic secondary organic aerosol precursors and products in urban air

NASA Astrophysics Data System (ADS)

Flores, Rosa M.; Doskey, Paul V.

2016-04-01

Volatile organic compounds (VOCs), which are present in the atmosphere entirely in the gas phase are directly emitted by biogenic (~1089 Tg yr-1) and anthropogenic sources (~185 Tg yr-1). However, the sources and molecular speciation of intermediate VOCs (IVOCs), which are for the most part also present almost entirely in the gas phase, are not well characterized. The VOCs and IVOCs participate in reactions that form ozone and semivolatile OC (SVOC) that partition into the aerosol phase. Formation and evolution of secondary organic aerosol (SOA) are part of a complex dynamic process that depends on the molecular speciation and concentration of VOCs, IVOCs, primary organic aerosol (POA), and the level of oxidants (NO3, OH, O3). The current lack of understanding of OA properties and their impact on radiative forcing, ecosystems, and human health is partly due to limitations of models to predict SOA production on local, regional, and global scales. More accurate forecasting of SOA production requires high-temporal resolution measurement and molecular characterization of SOA precursors and products. For the subject study, the IVOCs and aerosol-phase organic matter were collected using the high-volume sampling technique and were analyzed by multidimensional gas chromatography with time-of-flight mass spectrometry (GCxGC-ToFMS). The IVOCs included terpenes, terpenoids, n-alkanes, branched alkanes, isoprenoids, alkylbenzenes, cycloalkylbenzenes, PAH, alkyl PAH, and an unresolved complex mixture (UCM). Diurnal variations of OA species containing multiple oxygenated functionalities and selected SOA tracers of isorprene, α-pinene, toluene, cyclohexene, and n-dodecane oxidation were also quantified. The data for SOA precursor and oxidation products presented here will be useful for evaluating the ability of molecular-specific SOA models to forecast SOA production in and downwind of urban areas.

An accurate proteomic quantification method: fluorescence labeling absolute quantification (FLAQ) using multidimensional liquid chromatography and tandem mass spectrometry.

PubMed

Liu, Junyan; Liu, Yang; Gao, Mingxia; Zhang, Xiangmin

2012-08-01

A facile proteomic quantification method, fluorescent labeling absolute quantification (FLAQ), was developed. Instead of using MS for quantification, the FLAQ method is a chromatography-based quantification in combination with MS for identification. Multidimensional liquid chromatography (MDLC) with laser-induced fluorescence (LIF) detection with high accuracy and tandem MS system were employed for FLAQ. Several requirements should be met for fluorescent labeling in MS identification: Labeling completeness, minimum side-reactions, simple MS spectra, and no extra tandem MS fragmentations for structure elucidations. A fluorescence dye, 5-iodoacetamidofluorescein, was finally chosen to label proteins on all cysteine residues. The fluorescent dye was compatible with the process of the trypsin digestion and MALDI MS identification. Quantitative labeling was achieved with optimization of reacting conditions. A synthesized peptide and model proteins, BSA (35 cysteines), OVA (five cysteines), were used for verifying the completeness of labeling. Proteins were separated through MDLC and quantified based on fluorescent intensities, followed by MS identification. High accuracy (RSD% < 1.58) and wide linearity of quantification (1-10(5) ) were achieved by LIF detection. The limit of quantitation for the model protein was as low as 0.34 amol. Parts of proteins in human liver proteome were quantified and demonstrated using FLAQ. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Visualization and dissemination of multidimensional proteomics data comparing protein abundance during Caenorhabditis elegans development.

PubMed

Riffle, Michael; Merrihew, Gennifer E; Jaschob, Daniel; Sharma, Vagisha; Davis, Trisha N; Noble, William S; MacCoss, Michael J

2015-11-01

Regulation of protein abundance is a critical aspect of cellular function, organism development, and aging. Alternative splicing may give rise to multiple possible proteoforms of gene products where the abundance of each proteoform is independently regulated. Understanding how the abundances of these distinct gene products change is essential to understanding the underlying mechanisms of many biological processes. Bottom-up proteomics mass spectrometry techniques may be used to estimate protein abundance indirectly by sequencing and quantifying peptides that are later mapped to proteins based on sequence. However, quantifying the abundance of distinct gene products is routinely confounded by peptides that map to multiple possible proteoforms. In this work, we describe a technique that may be used to help mitigate the effects of confounding ambiguous peptides and multiple proteoforms when quantifying proteins. We have applied this technique to visualize the distribution of distinct gene products for the whole proteome across 11 developmental stages of the model organism Caenorhabditis elegans. The result is a large multidimensional dataset for which web-based tools were developed for visualizing how translated gene products change during development and identifying possible proteoforms. The underlying instrument raw files and tandem mass spectra may also be downloaded. The data resource is freely available on the web at http://www.yeastrc.org/wormpes/ . Graphical Abstract ᅟ.

Visualization and Dissemination of Multidimensional Proteomics Data Comparing Protein Abundance During Caenorhabditis elegans Development

NASA Astrophysics Data System (ADS)

Riffle, Michael; Merrihew, Gennifer E.; Jaschob, Daniel; Sharma, Vagisha; Davis, Trisha N.; Noble, William S.; MacCoss, Michael J.

2015-11-01

Regulation of protein abundance is a critical aspect of cellular function, organism development, and aging. Alternative splicing may give rise to multiple possible proteoforms of gene products where the abundance of each proteoform is independently regulated. Understanding how the abundances of these distinct gene products change is essential to understanding the underlying mechanisms of many biological processes. Bottom-up proteomics mass spectrometry techniques may be used to estimate protein abundance indirectly by sequencing and quantifying peptides that are later mapped to proteins based on sequence. However, quantifying the abundance of distinct gene products is routinely confounded by peptides that map to multiple possible proteoforms. In this work, we describe a technique that may be used to help mitigate the effects of confounding ambiguous peptides and multiple proteoforms when quantifying proteins. We have applied this technique to visualize the distribution of distinct gene products for the whole proteome across 11 developmental stages of the model organism Caenorhabditis elegans. The result is a large multidimensional dataset for which web-based tools were developed for visualizing how translated gene products change during development and identifying possible proteoforms. The underlying instrument raw files and tandem mass spectra may also be downloaded. The data resource is freely available on the web at http://www.yeastrc.org/wormpes/.

Determination of cocaine and metabolites in hair by column-switching LC-MS-MS analysis.

PubMed

Alves, Marcela Nogueira Rabelo; Zanchetti, Gabriele; Piccinotti, Alberto; Tameni, Silvia; De Martinis, Bruno Spinosa; Polettini, Aldo

2013-07-01

A method for rapid, selective, and robust determination of cocaine (CO) and metabolites in 5-mg hair samples was developed and fully validated using a column-switching liquid chromatography-tandem mass spectrometry system (LC-MS-MS). Hair samples were decontaminated, segmented, incubated overnight in diluted HCl, and centrifuged, and the diluted (1:10 with distilled water) extracts were analyzed in positive ionization mode monitoring two reactions per analyte. Quantifier transitions were: m/z 304.2→182.2 for CO, m/z 290.1→168.1 for benzoylecgonine (BE), and m/z 318.2→196.2 for cocaethylene (CE). The lower limit of quantification (LLOQ) was set at 0.05 ng/mg for CO and CE, and 0.012 ng/mg for BE. Imprecision and inaccuracy at LLOQ were lower than 20 % for all analytes. Linearity ranged between 0.05 and 50.0 ng/mg for CO and CE and 0.012 and 12.50 ng/mg for BE. Selectivity, matrix effect, process efficiency, recovery, carryover, cross talk, and autosampler stability were also evaluated during validation. Eighteen real hair samples and five samples from a commercial proficiency testing program were comparatively examined with the proposed multidimensional chromatography coupled with tandem mass spectrometry procedure and our reference gas chromatography coupled to mass spectrometry (GC-MS) method. Compared with our reference GC-MS method, column-switching technique and the high sensitivity of the tandem mass spectrometry detection system allowed to significantly reduce sample amount (×10) with increased sensitivity (×2) and sample throughput (×4), to simplify sample preparation, and to avoid that interfering compounds and ions impaired the ionization and detection of the analytes and deteriorate the performance of the ion source.

An Operational Definition of Learning

ERIC Educational Resources Information Center

Harel, Guershon; Koichu, Boris

2010-01-01

An operational definition offered in this paper posits learning as a multi-dimensional and multi-phase phenomenon occurring when individuals attempt to solve what they view as a problem. To model someone's learning accordingly to the definition, it suffices to characterize a particular sequence of that person's disequilibrium-equilibrium phases in…

Evidence for a Multi-Dimensional Latent Structural Model of Externalizing Disorders

ERIC Educational Resources Information Center

Witkiewitz, Katie; King, Kevin; McMahon, Robert J.; Wu, Johnny; Luk, Jeremy; Bierman, Karen L.; Coie, John D.; Dodge, Kenneth A.; Greenberg, Mark T.; Lochman, John E.; Pinderhughes, Ellen E.

2013-01-01

Strong associations between conduct disorder (CD), antisocial personality disorder (ASPD) and substance use disorders (SUD) seem to reflect a general vulnerability to externalizing behaviors. Recent studies have characterized this vulnerability on a continuous scale, rather than as distinct categories, suggesting that the revision of the…

Visualization of metallodrugs in single cells by secondary ion mass spectrometry imaging.

PubMed

Wu, Kui; Jia, Feifei; Zheng, Wei; Luo, Qun; Zhao, Yao; Wang, Fuyi

2017-07-01

Secondary ion mass spectrometry, including nanoscale secondary ion mass spectrometry (NanoSIMS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS), has emerged as a powerful tool for biological imaging, especially for single cell imaging. SIMS imaging can provide information on subcellular distribution of endogenous and exogenous chemicals, including metallodrugs, from membrane through to cytoplasm and nucleus without labeling, and with high spatial resolution and chemical specificity. In this mini-review, we summarize recent progress in the field of SIMS imaging, particularly in the characterization of the subcellular distribution of metallodrugs. We anticipate that the SIMS imaging method will be widely applied to visualize subcellular distributions of drugs and drug candidates in single cells, exerting significant influence on early drug evaluation and metabolism in medicinal and pharmaceutical chemistry. Recent progress of SIMS applications in characterizing the subcellular distributions of metallodrugs was summarized.

Characterization of anti-theft devices directly from the surface of banknotes via easy ambient sonic spray ionization mass spectrometry.

PubMed

Schmidt, Eduardo Morgado; Franco, Marcos Fernando; Cuelbas, Claudio José; Zacca, Jorge Jardim; de Carvalho Rocha, Werickson Fortunato; Borges, Rodrigo; de Souza, Wanderley; Sawaya, Alexandra Christine Helena Frankland; Eberlin, Marcos Nogueira; Correa, Deleon Nascimento

2015-09-01

Using Brazilian banknotes as a test case, forensic examination and identification of Rhodamine B dye anti-theft device (ATD) staining on banknotes were performed. Easy ambient sonic spray ionization mass spectrometry (EASI-MS) was used since it allows fast and simple analysis with no sample preparation providing molecular screening of the surface with direct desorption and ionization of the security dye. For a more accurate molecular characterization of the ATD dye, Q Exactive Orbitrap™ Fourier transform (tandem) mass spectrometry using eletrospray ionization (ESI-HRMS/MS) was also applied. Copyright © 2015 The Chartered Society of Forensic Sciences. Published by Elsevier Ireland Ltd. All rights reserved.

Self-Learning Adaptive Umbrella Sampling Method for the Determination of Free Energy Landscapes in Multiple Dimensions

PubMed Central

Wojtas-Niziurski, Wojciech; Meng, Yilin; Roux, Benoit; Bernèche, Simon

2013-01-01

The potential of mean force describing conformational changes of biomolecules is a central quantity that determines the function of biomolecular systems. Calculating an energy landscape of a process that depends on three or more reaction coordinates might require a lot of computational power, making some of multidimensional calculations practically impossible. Here, we present an efficient automatized umbrella sampling strategy for calculating multidimensional potential of mean force. The method progressively learns by itself, through a feedback mechanism, which regions of a multidimensional space are worth exploring and automatically generates a set of umbrella sampling windows that is adapted to the system. The self-learning adaptive umbrella sampling method is first explained with illustrative examples based on simplified reduced model systems, and then applied to two non-trivial situations: the conformational equilibrium of the pentapeptide Met-enkephalin in solution and ion permeation in the KcsA potassium channel. With this method, it is demonstrated that a significant smaller number of umbrella windows needs to be employed to characterize the free energy landscape over the most relevant regions without any loss in accuracy. PMID:23814508

Multidimensional custom-made non-linear microscope: from ex-vivo to in-vivo imaging

NASA Astrophysics Data System (ADS)

Cicchi, R.; Sacconi, L.; Jasaitis, A.; O'Connor, R. P.; Massi, D.; Sestini, S.; de Giorgi, V.; Lotti, T.; Pavone, F. S.

2008-09-01

We have built a custom-made multidimensional non-linear microscope equipped with a combination of several non-linear laser imaging techniques involving fluorescence lifetime, multispectral two-photon and second-harmonic generation imaging. The optical system was mounted on a vertical honeycomb breadboard in an upright configuration, using two galvo-mirrors relayed by two spherical mirrors as scanners. A double detection system working in non-descanning mode has allowed both photon counting and a proportional regime. This experimental setup offering high spatial (micrometric) and temporal (sub-nanosecond) resolution has been used to image both ex-vivo and in-vivo biological samples, including cells, tissues, and living animals. Multidimensional imaging was used to spectroscopically characterize human skin lesions, as malignant melanoma and naevi. Moreover, two-color detection of two photon excited fluorescence was applied to in-vivo imaging of living mice intact neocortex, as well as to induce neuronal microlesions by femtosecond laser burning. The presented applications demonstrate the capability of the instrument to be used in a wide range of biological and biomedical studies.

Minimal disease detection of B-cell lymphoproliferative disorders by flow cytometry: multidimensional cluster analysis.

PubMed

Duque, Ricardo E

2012-04-01

Flow cytometric analysis of cell suspensions involves the sequential 'registration' of intrinsic and extrinsic parameters of thousands of cells in list mode files. Thus, it is almost irresistible to describe phenomena in numerical terms or by 'ratios' that have the appearance of 'accuracy' due to the presence of numbers obtained from thousands of cells. The concepts involved in the detection and characterization of B cell lymphoproliferative processes are revisited in this paper by identifying parameters that, when analyzed appropriately, are both necessary and sufficient. The neoplastic process (cluster) can be visualized easily because the parameters that distinguish it form a cluster in multidimensional space that is unique and distinguishable from neighboring clusters that are not of diagnostic interest but serve to provide a background. For B cell neoplasia it is operationally necessary to identify the multidimensional space occupied by a cluster whose kappa:lambda ratio is 100:0 or 0:100. Thus, the concept of kappa:lambda ratio is without meaning and would not detect B cell neoplasia in an unacceptably high number of cases.

ARO - Terrestrial Research Program, Methodologies and Protocols for Characterization of Geomaterials

DTIC Science & Technology

2015-05-14

of ice involves melting, digestion, and analysis using inductively coupled plasma – mass spectrometry (ICPMS). ICP-MS analysis established elemental...4] have distinct chemical compositions. Knowledge of the chemical composition of the mineral assemblage present in a rock is critical to...activation analysis (INAA), to inductively-coupled plasma analysis and mass spectrometry (ICP & ICP-MS), mass spectrometry (MS), and laser-ablation

Integrating qualitative and quantitative characterization of traditional Chinese medicine injection by high-performance liquid chromatography with diode array detection and tandem mass spectrometry.

PubMed

Xie, Yuan-yuan; Xiao, Xue; Luo, Juan-min; Fu, Chan; Wang, Qiao-wei; Wang, Yi-ming; Liang, Qiong-lin; Luo, Guo-an

2014-06-01

The present study aims to describe and exemplify an integrated strategy of the combination of qualitative and quantitative characterization of a multicomponent mixture for the quality control of traditional Chinese medicine injections with the example of Danhong injection (DHI). The standardized chemical profile of DHI has been established based on liquid chromatography with diode array detection. High-performance liquid chromatography coupled with time-of-flight mass spectrometry and high-performance liquid chromatography with electrospray multistage tandem ion-trap mass spectrometry have been developed to identify the major constituents in DHI. The structures of 26 compounds including nucleotides, phenolic acids, and flavonoid glycosides were identified or tentatively characterized. Meanwhile, the simultaneous determination of seven marker constituents, including uridine, adenosine, danshensu, protocatechuic aldehyde, p-coumaric acid, rosmarinic acid, and salvianolic acid B, in DHI was performed by multiwavelength detection based on high-performance liquid chromatography with diode array detection. The integrated qualitative and quantitative characterization strategy provided an effective and reliable pattern for the comprehensive and systematic characterization of the complex traditional Chinese medicine system. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Atmospheric Solid Analysis Probe Coupled to Ion Mobility Spectrometry-Mass Spectrometry, a Fast and Simple Method for Polyalphaolefin Characterization

NASA Astrophysics Data System (ADS)

Mendes Siqueira, Anna Luiza; Beaumesnil, Mathieu; Hubert-Roux, Marie; Loutelier-Bourhis, Corinne; Afonso, Carlos; Bai, Yang; Courtiade, Marion; Racaud, Amandine

2018-05-01

Polyalphaolefins (PAOs) are polymers produced from linear alpha olefins through catalytic oligomerization processes. The PAOs are known as synthetic high-performance base stock fluids used to improve the efficiency of many other synthetic products. In this study, we report the direct characterization of PAOs using atmospheric solid analysis probe (ASAP) coupled with ion mobility spectrometry-mass spectrometry (IMS-MS). We studied different PAOs grades exhibiting low- and high-viscosity index. Specific adjustments of the ASAP source parameters permitted the monitoring of ionization processes as three mechanisms could occur for these compounds: hydride abstraction, nitrogen addition, and/or the formation of [M-2H]+• ions. Several series of fragment ions were obtained, which allowed the identification of the alpha olefin used to synthesize the PAO. The use of the ion mobility separation dimension provides information on isomeric species. In addition, the drift time versus m/z plots permitted rapid comparison between PAO samples and to evidence their complexity. These 2D plots appear as fingerprints of PAO samples. To conclude, the resort to ASAP-IMS-MS provides a rapid characterization of the PAO samples in a direct analysis approach, without any sample preparation.

Hydrogen-Exchange Mass Spectrometry for the Study of Intrinsic Disorder in Proteins

PubMed Central

Balasubramaniam, Deepa; Komives, Elizabeth A.

2012-01-01

Amide hydrogen/deuterium exchange detected by mass spectrometry (HXMS) is seeing wider use for the identification of intrinsically disordered parts of proteins. In this review, we discuss examples of how discovery of intrinsically disordered regions and their removal can aid in structure determination, biopharmaceutical quality control, the characterization of how posttranslational modifications affect weak structuring of disordered regions, the study of coupled folding and binding, and the characterization of amyloid formation. PMID:23099262

Qualitative Characterization of the Aqueous Fraction from Hydrothermal Liquefaction of Algae Using 2D Gas Chromatography with Time-of-flight Mass Spectrometry

PubMed Central

Maddi, Balakrishna; Panisko, Ellen; Albrecht, Karl; Howe, Daniel

2016-01-01

Two-dimensional gas chromatography coupled with time-of-flight mass spectrometry is a powerful tool for identifying and quantifying chemical components in complex mixtures. It is often used to analyze gasoline, jet fuel, diesel, bio-diesel and the organic fraction of bio-crude/bio-oil. In most of those analyses, the first dimension of separation is non-polar, followed by a polar separation. The aqueous fractions of bio-crude and other aqueous samples from biofuels production have been examined with similar column combinations. However, sample preparation techniques such as derivatization, solvent extraction, and solid-phase extraction were necessaryprior to analysis. In this study, aqueous fractions obtained from the hydrothermal liquefaction of algae were characterized by two-dimensional gas chromatography coupled with time-of-flight mass spectrometry without prior sample preparation techniques using a polar separation in the first dimension followed by a non-polar separation in the second. Two-dimensional plots from this analysis were compared with those obtained from the more traditional column configuration. Results from qualitative characterization of the aqueous fractions of algal bio-crude are discussed in detail. The advantages of using a polar separation followed by a non-polar separation for characterization of organics in aqueous samples by two-dimensional gas chromatography coupled with time-of-flight mass spectrometry are highlighted. PMID:27022829

Qualitative Characterization of the Aqueous Fraction from Hydrothermal Liquefaction of Algae Using 2D Gas Chromatography with Time-of-flight Mass Spectrometry.

PubMed

Maddi, Balakrishna; Panisko, Ellen; Albrecht, Karl; Howe, Daniel

2016-03-06

Two-dimensional gas chromatography coupled with time-of-flight mass spectrometry is a powerful tool for identifying and quantifying chemical components in complex mixtures. It is often used to analyze gasoline, jet fuel, diesel, bio-diesel and the organic fraction of bio-crude/bio-oil. In most of those analyses, the first dimension of separation is non-polar, followed by a polar separation. The aqueous fractions of bio-crude and other aqueous samples from biofuels production have been examined with similar column combinations. However, sample preparation techniques such as derivatization, solvent extraction, and solid-phase extraction were necessary prior to analysis. In this study, aqueous fractions obtained from the hydrothermal liquefaction of algae were characterized by two-dimensional gas chromatography coupled with time-of-flight mass spectrometry without prior sample preparation techniques using a polar separation in the first dimension followed by a non-polar separation in the second. Two-dimensional plots from this analysis were compared with those obtained from the more traditional column configuration. Results from qualitative characterization of the aqueous fractions of algal bio-crude are discussed in detail. The advantages of using a polar separation followed by a non-polar separation for characterization of organics in aqueous samples by two-dimensional gas chromatography coupled with time-of-flight mass spectrometry are highlighted.

Direct Determination of Nonmetals in Solution with Atomic Spectrometry.

ERIC Educational Resources Information Center

McGregor, David A.; And Others

1988-01-01

Addresses solution nonmetal determinations on a fundamental level. Characterizes research in this area of chemical instrumentation. Discusses the fundamental limitations of nonmetal atomic spectrometry, the status of nonmetals and atomic spectroscopic techniques, and current directions in solution nonmetal determinations. (CW)

MASS SPECTROMETRY OF INDIVIDUAL AEROSOL PARTICLES. (R823980)

EPA Science Inventory

Typically, in real-time aerosol mass spectrometry (RTAMS), individual airborne particles
are ablated and ionized with a single focused laser pulse. This technique yields information that
permits bulk characterization of the particle, but information about the particle's sur...

Identification of marker proteins for the adulteration of meat products with soybean proteins by multidimensional liquid chromatography-tandem mass spectrometry.

PubMed

Leitner, Alexander; Castro-Rubio, Florentina; Marina, Maria Luisa; Lindner, Wolfgang

2006-09-01

Soybean proteins are frequently added to processed meat products for economic reasons and to improve their functional properties. Monitoring of the addition of soybean protein to meat products is of high interest due to the existence of regulations forbidding or limiting the amount of soybean proteins that can be added during the processing of meat products. We have used chromatographic prefractionation on the protein level by perfusion liquid chromatography to isolate peaks of interest from extracts of soybean protein isolate (SPI) and of meat products containing SPI. After enzymatic digestion using trypsin, the collected fractions were analyzed by nanoflow liquid chromatography-tandem mass spectrometry. Several variants and subunits of the major seed proteins, glycinin and beta-conglycinin, were identified in SPI, along with two other proteins. In soybean-protein-containing meat samples, different glycinin A subunits could be identified from the peak discriminating between samples with and without soybean proteins added. Among those, glycinin G4 subunit A4 was consistently found in all samples. Consequently, this protein (subunit) can be used as a target for new analytical techniques in the course of identifying the addition of soybean protein to meat products.

Preliminary investigation of human exhaled breath for tuberculosis diagnosis by multidimensional gas chromatography - Time of flight mass spectrometry and machine learning.

PubMed

Beccaria, Marco; Mellors, Theodore R; Petion, Jacky S; Rees, Christiaan A; Nasir, Mavra; Systrom, Hannah K; Sairistil, Jean W; Jean-Juste, Marc-Antoine; Rivera, Vanessa; Lavoile, Kerline; Severe, Patrice; Pape, Jean W; Wright, Peter F; Hill, Jane E

2018-02-01

Tuberculosis (TB) remains a global public health malady that claims almost 1.8 million lives annually. Diagnosis of TB represents perhaps one of the most challenging aspects of tuberculosis control. Gold standards for diagnosis of active TB (culture and nucleic acid amplification) are sputum-dependent, however, in up to a third of TB cases, an adequate biological sputum sample is not readily available. The analysis of exhaled breath, as an alternative to sputum-dependent tests, has the potential to provide a simple, fast, and non-invasive, and ready-available diagnostic service that could positively change TB detection. Human breath has been evaluated in the setting of active tuberculosis using thermal desorption-comprehensive two-dimensional gas chromatography-time of flight mass spectrometry methodology. From the entire spectrum of volatile metabolites in breath, three random forest machine learning models were applied leading to the generation of a panel of 46 breath features. The twenty-two common features within each random forest model used were selected as a set that could distinguish subjects with confirmed pulmonary M. tuberculosis infection and people with other pathologies than TB. Copyright © 2018 Elsevier B.V. All rights reserved.

Computer language for identifying chemicals with comprehensive two-dimensional gas chromatography and mass spectrometry.

PubMed

Reichenbach, Stephen E; Kottapalli, Visweswara; Ni, Mingtian; Visvanathan, Arvind

2005-04-15

This paper describes a language for expressing criteria for chemical identification with comprehensive two-dimensional gas chromatography paired with mass spectrometry (GC x GC-MS) and presents computer-based tools implementing the language. The Computer Language for Indentifying Chemicals (CLIC) allows expressions that describe rules (or constraints) for selecting chemical peaks or data points based on multi-dimensional chromatographic properties and mass spectral characteristics. CLIC offers chromatographic functions of retention times, functions of mass spectra, numbers for quantitative and relational evaluation, and logical and arithmetic operators. The language is demonstrated with the compound-class selection rules described by Welthagen et al. [W. Welthagen, J. Schnelle-Kreis, R. Zimmermann, J. Chromatogr. A 1019 (2003) 233-249]. A software implementation of CLIC provides a calculator-like graphical user-interface (GUI) for building and applying selection expressions. From the selection calculator, expressions can be used to select chromatographic peaks that meet the criteria or create selection chromatograms that mask data points inconsistent with the criteria. Selection expressions can be combined with graphical, geometric constraints in the retention-time plane as a powerful component for chemical identification with template matching or used to speed and improve mass spectrum library searches.

Discovery and characterization of antibody variants using mass spectrometry-based comparative analysis for biosimilar candidates of monoclonal antibody drugs.

PubMed

Li, Wenhua; Yang, Bin; Zhou, Dongmei; Xu, Jun; Ke, Zhi; Suen, Wen-Chen

2016-07-01

Liquid chromatography mass spectrometry (LC-MS) is the most commonly used technique for the characterization of antibody variants. MAb-X and mAb-Y are two approved IgG1 subtype monoclonal antibody drugs recombinantly produced in Chinese hamster ovary (CHO) cells. We report here that two unexpected and rare antibody variants have been discovered during cell culture process development of biosimilars for these two approved drugs through intact mass analysis. We then used comprehensive mass spectrometry-based comparative analysis including reduced light, heavy chains, and domain-specific mass as well as peptide mapping analysis to fully characterize the observed antibody variants. The "middle-up" mass comparative analysis demonstrated that the antibody variant from mAb-X biosimilar candidate was caused by mass variation of antibody crystalline fragment (Fc), whereas a different variant with mass variation in antibody antigen-binding fragment (Fab) from mAb-Y biosimilar candidate was identified. Endoproteinase Lys-C digested peptide mapping and tandem mass spectrometry analysis further revealed that a leucine to glutamine change in N-terminal 402 site of heavy chain was responsible for the generation of mAb-X antibody variant. Lys-C and trypsin coupled non-reduced and reduced peptide mapping comparative analysis showed that the formation of the light-heavy interchain trisulfide bond resulted in the mAb-Y antibody variant. These two cases confirmed that mass spectrometry-based comparative analysis plays a critical role for the characterization of monoclonal antibody variants, and biosimilar developers should start with a comprehensive structural assessment and comparative analysis to decrease the risk of the process development for biosimilars. Copyright © 2016 Elsevier B.V. All rights reserved.

Application of mass spectrometry in the characterization of chemicals in coal-derived liquids.

PubMed

Liu, Fang-Jing; Fan, Maohong; Wei, Xian-Yong; Zong, Zhi-Min

2017-07-01

Coal-derived liquids (CDLs) are primarily generated from pyrolysis, carbonization, gasification, direct liquefaction, low-temperature extraction, thermal dissolution, and mild oxidation. CDLs are important feedstocks for producing value-added chemicals and clean liquid fuels as well as high performance carbon materials. Accordingly, the compositional characterization of chemicals in CDLs at the molecular level with advanced analytical techniques is significant for the efficient utilization of CDLs. Although reviews on advancements have been rarely reported, great progress has been achieved in this area by using gas chromatography/mass spectrometry (GC/MS), two-dimensional GC-time of flight mass spectrometry (GC × GC-TOFMS), and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). This review focuses on characterizing hydrocarbon, oxygen-containing, nitrogen-containing, sulfur-containing, and halogen-containing chemicals in various CDLs with these three mass spectrometry techniques. Small molecular (< 500 u), volatile and semi-volatile, and less polar chemicals in CDLs have been identified with GC/MS and GC × GC-TOFMS. By equipped with two-dimensional GC, GC × GC-TOFMS can achieve a clearly chromatographic separation of complex chemicals in CDLs without prior fractionation, and thus can overcome the disadvantages of co-elution and serious peak overlap in GC/MS analysis, providing much more compositional information. With ultrahigh resolving power and mass accuracy, FT-ICR MS reveals a huge number of compositionally distinct compounds assigned to various chemical classes in CDLs. It shows excellent performance in resolving and characterizing higher-molecular, less volatile, and polar chemicals that cannot be detected by GC/MS and GC × GC-TOFMS. The application of GC × GC-TOFMS and FT-ICR MS to chemical characterization of CDLs is not as prevalent as that of petroleum and largely remains to be developed in many respects. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:543-579, 2017. © 2016 Wiley Periodicals, Inc.

Polymeric spatial resolution test patterns for mass spectrometry imaging using nano-thermal analysis with atomic force microscopy

DOE PAGES

Tai, Tamin; Kertesz, Vilmos; Lin, Ming -Wei; ...

2017-05-11

As the spatial resolution of mass spectrometry imaging technologies has begun to reach into the nanometer regime, finding readily available or easily made resolution reference materials has become particularly challenging for molecular imaging purposes. This study describes the fabrication, characterization and use of vertical line array polymeric spatial resolution test patterns for nano-thermal analysis/atomic force microscopy/mass spectrometry chemical imaging.

Polymeric spatial resolution test patterns for mass spectrometry imaging using nano-thermal analysis with atomic force microscopy

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

Tai, Tamin; Kertesz, Vilmos; Lin, Ming -Wei

As the spatial resolution of mass spectrometry imaging technologies has begun to reach into the nanometer regime, finding readily available or easily made resolution reference materials has become particularly challenging for molecular imaging purposes. This study describes the fabrication, characterization and use of vertical line array polymeric spatial resolution test patterns for nano-thermal analysis/atomic force microscopy/mass spectrometry chemical imaging.

Designing the Holographic Whole Language Program. Opinion Paper.

ERIC Educational Resources Information Center

Fluellen, Jerry

A paper describes how David Bohm's holographic world view can be used to design a whole language program. Characterized by interconnectedness and multidimensionality, Bohm's holographic paradigm joins Eastern and Western belief systems in an old fashion pursuit of wisdom, on the one hand, and a new fashion pursuit of solutions to nonlinear…

Regional variation in epiphytic macrolichen communities in northern and central California forests

Treesearch

Sarah Jovan; Bruce McCune

2004-01-01

We studied epiphytic macrolichen communities in northern and central California to 1) describe how gradients in community composition relate to climate, topography, and stand structure and 2) define subregions of relatively homogeneous lichen communities and environmental conditions. Non-metric multidimensional scaling was used to characterize landscape-level trends in...

Towards the robotic characterization of the constitutive response of composite materials

Treesearch

John G. Michopoulos; John C. Hermanson; Tomonari Furukawa

2008-01-01

A historical and technical overview of a paradigm for automating research procedures on the area of constitutive identification of composite materials is presented. Computationally controlled robotic, multiple degree-of-freedom mechatronic systems are used to accelerate the rate of performing data-collecting experiments along loading paths defined in multidimensional...

Characterization of Households and its Implications for the Vegetation of Urban Ecosystems

Treesearch

J.M. Grove; A.R. Troy; J.P.M. O' Neil-Dunne; W.R., Jr. Burch; M.L. Cadenasso; S.T.A. Pickett; S.T.A. Pickett

2006-01-01

Our understanding of the dynamics of urban ecosystems can be enhanced by examining the multidimensional social characteristics of households. To this end, we investigated the relative significance of three social theories of household structure-population, lifestyle behavior, and social stratification-to the distribution of vegetation cover in Baltimore, Maryland, USA...

CHARACTERIZATION OF CRYPTOSPORIDIUM PARVUM BY MATRIX-ASSISTED LASER DESORPTION -- IONIZATION TIME OF FLIGHT MASS SPECTROMETRY

EPA Science Inventory

Matrix assisted laser desorption/ionization (MALDI) mass spectrometry was used to investigate whole and freeze thawed Cryptosporidium parvum oocysts. Whole oocysts revealed some mass spectral features. Reproducible patterns of spectral markers and increased sensitivity were obtai...

Pyrolysis Mass Spectrometry of Complex Organic Materials.

ERIC Educational Resources Information Center

Meuzelaar, Henk L. C.; And Others

1984-01-01

Illustrates the state of the art in pyrolysis mass spectrometry techniques through applications in: (1) structural determination and quality control of synthetic polymers; (2) quantitative analysis of polymer mixtures; (3) classification and structural characterization of fossil organic matter; and (4) nonsupervised numerical extraction of…

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

NASA Astrophysics Data System (ADS)

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

2010-04-01

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

Mass Spectrometry and Ion Mobility Characterization of Bioactive Peptide-Synthetic Polymer Conjugates.

PubMed

Alalwiat, Ahlam; Tang, Wen; Gerişlioğlu, Selim; Becker, Matthew L; Wesdemiotis, Chrys

2017-01-17

The bioconjugate BMP2-(PEO-HA) 2 , composed of a dendron with two monodisperse poly(ethylene oxide) (PEO) branches terminated by a hydroxyapatite binding peptide (HA), and a focal point substituted with a bone growth stimulating peptide (BMP2), has been comprehensively characterized by mass spectrometry (MS) methods, encompassing matrix-assisted laser desorption ionization (MALDI), electrospray ionization (ESI), tandem mass spectrometry (MS 2 ), and ion mobility mass spectrometry (IM-MS). MS 2 experiments using different ion activation techniques validated the sequences of the synthetic, bioactive peptides HA and BMP2, which contained highly basic amino acid residues either at the N-terminus (BMP2) or C-terminus (HA). Application of MALDI-MS, ESI-MS, and IM-MS to the polymer-peptide biomaterial confirmed its composition. Collision cross-section measurements and molecular modeling indicated that BMP2-(PEO-HA) 2 exists in several folded and extended conformations, depending on the degree of protonation. Protonation of all basic sites of the hybrid material nearly doubles its conformational space and accessible surface area.

Discrimination of epimeric glycans and glycopeptides using IM-MS and its potential for carbohydrate sequencing

NASA Astrophysics Data System (ADS)

Both, P.; Green, A. P.; Gray, C. J.; Šardzík, R.; Voglmeir, J.; Fontana, C.; Austeri, M.; Rejzek, M.; Richardson, D.; Field, R. A.; Widmalm, G.; Flitsch, S. L.; Eyers, C. E.

2014-01-01

Mass spectrometry is the primary analytical technique used to characterize the complex oligosaccharides that decorate cell surfaces. Monosaccharide building blocks are often simple epimers, which when combined produce diastereomeric glycoconjugates indistinguishable by mass spectrometry. Structure elucidation frequently relies on assumptions that biosynthetic pathways are highly conserved. Here, we show that biosynthetic enzymes can display unexpected promiscuity, with human glycosyltransferase pp-α-GanT2 able to utilize both uridine diphosphate N-acetylglucosamine and uridine diphosphate N-acetylgalactosamine, leading to the synthesis of epimeric glycopeptides in vitro. Ion-mobility mass spectrometry (IM-MS) was used to separate these structures and, significantly, enabled characterization of the attached glycan based on the drift times of the monosaccharide product ions generated following collision-induced dissociation. Finally, ion-mobility mass spectrometry following fragmentation was used to determine the nature of both the reducing and non-reducing glycans of a series of epimeric disaccharides and the branched pentasaccharide Man3 glycan, demonstrating that this technique may prove useful for the sequencing of complex oligosaccharides.

Preparation, Separation, and Conformational Analysis of Differentially Sulfated Heparin Octasaccharide Isomers using Ion Mobility Mass Spectrometry

PubMed Central

Seo, Youjin; Andaya, Armann; Leary, Julie A.

2012-01-01

Heparin is a linear sulfated polysaccharide widely used in medicine because of its anticoagulant properties. The various sulfation and/or acetylation patterns on heparin impart different degrees of conformational change around the glycosidic bonds and subsequently alter its function as an anticoagulant, anticancer, or antiviral drug. Characterization of these structures is important for eventual elucidation of its function but presents itself as an analytical challenge due to the inherent heterogeneity of the carbohydrates. Heparin octasaccharide structural isomers of various sulfation patterns were investigated using ion mobility mass spectrometry (IMMS). In addition to distinguishing the isomers, we report the preparation and tandem mass spectrometry analysis for multiple sulfated or acetylated oligosaccharides. Herein, our data indicate that heparin octasaccharide isomers were separated based on their structural conformations in the ion mobility cell. Subsequent to this separation, isomers were further distinguished using product ions resulting from tandem mass spectrometry. Overall, IMMS analysis was used to successfully characterize and separate individual isomers and subsequently measure their conformations. PMID:22283665

GCMS/MS Analyses of Biological Samples in Support of Evaluation of Toxicity Associated with Intravenous Exposure to VX Stereoisomers in Guinea Pigs

DTIC Science & Technology

2017-07-01

14. ABSTRACT: This report documents the results of the gas chromatography–tandem mass spectrometry analyses of blood, tissues, and organs (heart...quantified using chemical ionization mass spectrometry with isotope dilution. 15. SUBJECT TERMS Gas chromatography–tandem mass spectrometry (GC–MS...characterize the pharmacokinetics of the individual stereoisomers and their racemic mixtures. This report details the results of gas chromatography–tandem

Tandem Mass Spectrometry for Structural Identification of Sesquiterpene Alkaloids from the Stems of Dendrobium nobile Using LC-QToF.

PubMed

Wang, Yan-Hong; Avula, Bharathi; Abe, Naohito; Wei, Feng; Wang, Mei; Ma, Shuang-Cheng; Ali, Zulfiqar; Elsohly, Mahmoud A; Khan, Ikhlas A

2016-05-01

Dendrobium nobile is one of the fundamental herbs in traditional Chinese medicine. Sesquiterpene alkaloids are the main active components in this plant. Due to weak ultraviolet absorption and low content in D. nobile, these sesquiterpene alkaloids have not been extensively studied using chromatographic methods. Herein, tandem mass spectrometry combined with liquid chromatography separation provides a tool for the identification and characterization of the alkaloids from D. nobile. A total of nine sesquiterpene alkaloids were characterized by ultrahigh-performance liquid chromatography tandem mass spectrometry. These alkaloids can be classified into two subgroups that are represented by dendrobine and nobilonine. Tandem mass spectrometric studies revealed the fragmentation pathways of these two subgroup alkaloids that were used for the identification and characterization of other alkaloids in D. nobile. Characterization of these alkaloids using accurate mass and diagnostic fragments provided a reliable methodology for the analysis of D. nobile by ultrahigh-performance liquid chromatography tandem mass spectrometry. The limit of detection was defined as the signal-to-noise ratio equal to 3 : 1. Limits of detection of dendrobine and nobilonine were less than 30 ng/mL. The developed method was applied for the analysis of various Dendrobium species and related dietary supplements. Alkaloids were identified from D. nobile, but not detected from commercial samples including 13 other Dendrobium species and the 7 dietary supplements. Georg Thieme Verlag KG Stuttgart · New York.

Human Proteinpedia enables sharing of human protein data

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

Mathivanan, Suresh; Ahmed, Mukhtar; Ahn, Natalie G.

2008-02-01

Proteomic technologies, such as yeast twohybrid, mass spectrometry (MS), protein/ peptide arrays and fluorescence microscopy, yield multi-dimensional data sets, which are often quite large and either not published or published as supplementary information that is not easily searchable. Without a system in place for standardizing and sharing data, it is not fruitful for the biomedical community to contribute these types of data to centralized repositories. Even more difficult is the annotation and display of pertinent information in the context of the corresponding proteins. Wikipedia, an online encyclopedia that anyone can edit, has already proven quite successful1 and can be usedmore » as a model for sharing biological data. However, the need for experimental evidence, data standardization and ownership of data creates scientific obstacles.« less

Rapid analysis of drug dissolution by paper spray ionization mass spectrometry.

PubMed

Liu, Yang; Liu, Ning; Zhou, Ya-Nan; Lin, Lan; He, Lan

2017-03-20

With a great quantity of solid dosage tested by dissolution technology, developing a rapid and sensitive method to access the content of drug within dissolution media is highly desired by analysts and scientists. Traditionally, dissolution media is not compatible with mass spectrometry since the inorganic salts in the media might damage the mass spectrometer. Here, paper spray ionization mass spectrometry (PSI-MS), one of the ambient mass spectrometry technologies, is developed to characterize the content of drugs in dissolution media. The porous structure of paper can effectively retain salts from entering mass spectrometer. This makes the measurement of drug content within dissolution media by mass spectrometer possible. After the experimental parameters were optimized, calibration curves of model drugs - enalapril, quinapril and benazepril were established by using corresponding deuterated internal standards. PSI-MS was then deployed to characterize the content of enalapril from the dissolution testing of enalapril tablets. The results from PSI-MS are comparable to those from HPLC characterization. More importantly, the analysis time of 6 samples is shortened from 90min to 6min. Detection limit of enalapril maleate tablets by PSI-MS is 1/300 of LC. PSI-MS is rapid, sensitive and accurate in analyzing drug content from dissolution tests. Copyright © 2016 Elsevier B.V. All rights reserved.

Vegetation succession among and within structural layers following wildfire in managed forests

Treesearch

Lori J. Kayes; Paul D. Anderson; Klaus J. Puettmann

2010-01-01

In severely burned plantations, dynamics of (1) shrub, herbaceous, and cryptogam richness; (2) cover; (3) topographic, overstory, and site influences were characterized on two contrasting aspects 2 to 4 years following fire. Analysis of variance was used to examine change in structural layer richness and cover over time. Non-metric multidimensional scaling, multi-...

The Renewed Primary School in Belgium: Analysis of the Local Innovation Policy.

ERIC Educational Resources Information Center

Vandenberghe, Roland

The Renewed Primary School project in Belgium is analyzed in this paper in terms of organizational response to a large-scale innovation, which is characterized by its multidimensionality, by the large number of participating schools, and by a complex support structure. Section 2 of the report presents an elaborated description of these…

Probing Lexical Representations: Simultaneous Modeling of Word and Reader Contributions to Multidimensional Lexical Representations

ERIC Educational Resources Information Center

Goodwin, Amanda P.; Gilbert, Jennifer K.; Cho, Sun-Joo; Kearns, Devin M.

2014-01-01

The current study models reader, item, and word contributions to the lexical representations of 39 morphologically complex words for 172 middle school students using a crossed random-effects item response model with multiple outcomes. We report 3 findings. First, results suggest that lexical representations can be characterized by separate but…

Application of comprehensive multidimensional gas chromatography combined with time-of-flight mass spectrometry (GC x GC-TOFMS) for high resolution analysis of hop essential oil.

PubMed

Roberts, Mark T; Dufour, Jean-Pierre; Lewis, Alastair C

2004-04-01

The selection and quality of hops is a major determinant in beer flavour. Brewers acknowledge that distinctive characteristics of different hop varieties can be traced to the composition of their essential oils. The difficulty in characterising complex mixtures such as hop oil using 1-D chromatography is that many compounds co-elute. With the introduction of comprehensive multidimensional capillary gas chromatography (GC x GC), there is a tremendous improvement in the separation power or peak capacity. Recent work using GC x GC with flame ionisation detection has suggested that there may be over 1,000 compounds in hop oil. This work describes the use of GC x GC combined with TOFMS detection (Leco Pegasus 4D instrument) to analyse Target hop oil. The TOFMS spectral acquisition rate of 60 Hz provided sufficient spectra per peak (2-D peak base width of 0.1-0.2 s) for identification (119 components were identified with 45 previously unreported compounds). When analysing results, an advantage of GC x GC coupled to TOFMS is that 2-D chromatograms can be viewed for individual masses that are characteristic of particular functional groups. This allows the analyst to view the various homologous series of compounds although in certain cases coelution may still be present as shown by the esters with mass 75.

The human embryonic stem cell proteome revealed by multidimensional fractionation followed by tandem mass spectrometry

PubMed Central

Zhao, Peng; Schulz, Thomas C.; Sherrer, Eric S.; Weatherly, D. Brent; Robins, Allan J.; Wells, Lance

2015-01-01

Human embryonic stem cells (hESCs) have received considerable attention due to their therapeutic potential and usefulness in understanding early development and cell fate commitment. In order to appreciate the unique properties of these pluripotent, self-renewing cells, we have performed an in-depth multidimensional fractionation followed by LC-MS/MS analysis of the hESCs harvested from defined media to elucidate expressed, phosphorylated, O-linked β-N-acetylglucosamine (O-GlcNAc) modified, and secreted proteins. From the triplicate analysis, we were able to assign more than 3000 proteins with less than 1% false-discovery rate. This analysis also allowed us to identify nearly 500 phosphorylation sites and 68 sites of O-GlcNAc modification with the same high confidence. Investigation of the phosphorylation sites allowed us to deduce the set of kinases that are likely active in these cells. We also identified more than 100 secreted proteins of hESCs that likely play a role in extracellular matrix formation and remodeling, as well as autocrine signaling for self-renewal and maintenance of the undifferentiated state. Finally, by performing in-depth analysis in triplicate, spectral counts were obtained for these proteins and posttranslationally modified peptides, which will allow us to perform relative quantitative analysis between these cells and any derived cell type in the future. PMID:25367160

Rapid identification of fatty acid methyl esters using a multidimensional gas chromatography-mass spectrometry database.

PubMed

Härtig, Claus

2008-01-04

A multidimensional approach for the identification of fatty acid methyl esters (FAME) based on GC/MS analysis is described. Mass spectra and retention data of more than 130 FAME from various sources (chain lengths in the range from 4 to 24 carbon atoms) were collected in a database. Hints for the interpretation of FAME mass spectra are given and relevant diagnostic marker ions are deduced indicating specific groups of fatty acids. To verify the identity of single species and to ensure an optimized chromatographic resolution, the database was compiled with retention data libraries acquired on columns of different polarity (HP-5, DB-23, and HP-88). For a combined use of mass spectra and retention data standardized methods of measurement for each of these columns are required. Such master methods were developed and always applied under the conditions of retention time locking (RTL) which allowed an excellent reproducibility and comparability of absolute retention times. Moreover, as a relative retention index system, equivalent chain lengths (ECL) of FAME were determined by linear interpolation. To compare and to predict ECL values by means of structural features, fractional chain lengths (FCL) were calculated and fitted as well. As shown in an example, the use of retention data and mass spectral information together in a database search leads to an improved and reliable identification of FAME (including positional and geometrical isomers) without further derivatizations.

Multi-dimensional TOF-SIMS analysis for effective profiling of disease-related ions from the tissue surface.

PubMed

Park, Ji-Won; Jeong, Hyobin; Kang, Byeongsoo; Kim, Su Jin; Park, Sang Yoon; Kang, Sokbom; Kim, Hark Kyun; Choi, Joon Sig; Hwang, Daehee; Lee, Tae Geol

2015-06-05

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) emerges as a promising tool to identify the ions (small molecules) indicative of disease states from the surface of patient tissues. In TOF-SIMS analysis, an enhanced ionization of surface molecules is critical to increase the number of detected ions. Several methods have been developed to enhance ionization capability. However, how these methods improve identification of disease-related ions has not been systematically explored. Here, we present a multi-dimensional SIMS (MD-SIMS) that combines conventional TOF-SIMS and metal-assisted SIMS (MetA-SIMS). Using this approach, we analyzed cancer and adjacent normal tissues first by TOF-SIMS and subsequently by MetA-SIMS. In total, TOF- and MetA-SIMS detected 632 and 959 ions, respectively. Among them, 426 were commonly detected by both methods, while 206 and 533 were detected uniquely by TOF- and MetA-SIMS, respectively. Of the 426 commonly detected ions, 250 increased in their intensities by MetA-SIMS, whereas 176 decreased. The integrated analysis of the ions detected by the two methods resulted in an increased number of discriminatory ions leading to an enhanced separation between cancer and normal tissues. Therefore, the results show that MD-SIMS can be a useful approach to provide a comprehensive list of discriminatory ions indicative of disease states.

Multi-dimensional TOF-SIMS analysis for effective profiling of disease-related ions from the tissue surface

PubMed Central

Park, Ji-Won; Jeong, Hyobin; Kang, Byeongsoo; Kim, Su Jin; Park, Sang Yoon; Kang, Sokbom; Kim, Hark Kyun; Choi, Joon Sig; Hwang, Daehee; Lee, Tae Geol

2015-01-01

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) emerges as a promising tool to identify the ions (small molecules) indicative of disease states from the surface of patient tissues. In TOF-SIMS analysis, an enhanced ionization of surface molecules is critical to increase the number of detected ions. Several methods have been developed to enhance ionization capability. However, how these methods improve identification of disease-related ions has not been systematically explored. Here, we present a multi-dimensional SIMS (MD-SIMS) that combines conventional TOF-SIMS and metal-assisted SIMS (MetA-SIMS). Using this approach, we analyzed cancer and adjacent normal tissues first by TOF-SIMS and subsequently by MetA-SIMS. In total, TOF- and MetA-SIMS detected 632 and 959 ions, respectively. Among them, 426 were commonly detected by both methods, while 206 and 533 were detected uniquely by TOF- and MetA-SIMS, respectively. Of the 426 commonly detected ions, 250 increased in their intensities by MetA-SIMS, whereas 176 decreased. The integrated analysis of the ions detected by the two methods resulted in an increased number of discriminatory ions leading to an enhanced separation between cancer and normal tissues. Therefore, the results show that MD-SIMS can be a useful approach to provide a comprehensive list of discriminatory ions indicative of disease states. PMID:26046669

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.

Characterization of Atypical Off-Flavor Compounds in Natural Cork Stoppers by Multidimensional Gas Chromatographic Techniques.

PubMed

Slabizki, Petra; Fischer, Claus; Legrum, Charlotte; Schmarr, Hans-Georg

2015-09-09

Natural cork stoppers with sensory deviations other than the typical cork taint were subgrouped according to their sensory descriptions and compared with unaffected control cork stoppers. The assessment of purge and trap extracts obtained from corresponding cork soaks was performed by heart-cut multidimensional gas chromatography-olfactometry (MDGC-O). The identification of compounds responsible for atypical cork taint detected in MDGC-O was further supported with additional multidimensional GC analysis in combination with mass spectrometric detection. Geosmin and 2-methylisoborneol were mainly found in cork stoppers described as moldy and cellarlike; 3-isopropyl-2-methoxypyrazine and 3-isobutyl-2-methoxypyrazine were found in cork stoppers described with green attributes. Across all cork subgroups, the impact compound for typical cork taint, 2,4,6-trichloroanisole (TCA), was present and is therefore a good marker for cork taint in general. Another potent aroma compound, 3,5-dimethyl-2-methoxypyrazine (MDMP), was also detected in each subgroup, obviously playing an important role with regard to the atypical cork taint. Sensory deviations possibly affecting the wine could be generated by MDMP and its presence should thus be monitored in routine quality control.

Multidimensional infrared spectroscopy reveals the vibrational and solvation dynamics of isoniazid

NASA Astrophysics Data System (ADS)

Shaw, Daniel J.; Adamczyk, Katrin; Frederix, Pim W. J. M.; Simpson, Niall; Robb, Kirsty; Greetham, Gregory M.; Towrie, Michael; Parker, Anthony W.; Hoskisson, Paul A.; Hunt, Neil T.

2015-06-01

The results of infrared spectroscopic investigations into the band assignments, vibrational relaxation, and solvation dynamics of the common anti-tuberculosis treatment Isoniazid (INH) are reported. INH is known to inhibit InhA, a 2-trans-enoyl-acyl carrier protein reductase enzyme responsible for the maintenance of cell walls in Mycobacterium tuberculosis but as new drug-resistant strains of the bacterium appear, next-generation therapeutics will be essential to combat the rise of the disease. Small molecules such as INH offer the potential for use as a biomolecular marker through which ultrafast multidimensional spectroscopies can probe drug binding and so inform design strategies but a complete characterization of the spectroscopy and dynamics of INH in solution is required to inform such activity. Infrared absorption spectroscopy, in combination with density functional theory calculations, is used to assign the vibrational modes of INH in the 1400-1700 cm-1 region of the infrared spectrum while ultrafast multidimensional spectroscopy measurements determine the vibrational relaxation dynamics and the effects of solvation via spectral diffusion of the carbonyl stretching vibrational mode. These results are discussed in the context of previous linear spectroscopy studies on solid-phase INH and its usefulness as a biomolecular probe.

Rapid characterization of the chemical constituents of Sijunzi decoction by UHPLC coupled with Fourier transform ion cyclotron resonance mass spectrometry.

PubMed

Guan, Zhibo; Wang, Miao; Cai, Yi; Yang, Hongmei; Zhao, Min; Zhao, Chunjie

2018-06-01

Sijunzi decoction, a renowned Chinese prescription has long been utilized to treat gastrointestinal problems. In the context of this research work, the use of Ultra high performance liquid chromatography combined with Fourier transform ion cyclotron resonance mass spectrometry was made to separate and characterize the components of Sijunzi decoction. The performance of Liquid chromatography was carried out on a C8 column (150 mm × 2.1 mm, 1.8 μm); moreover, the mobile phase were consisted of 0.2% formic acid (A) and acetonitrile (B). In accordance with the findings, characterization of 120 chemical compounds was performed by liquid chromatography with mass spectrometry. The key constituents among them included ginsenosides (in Radix Ginseng), 16 triterpene carboxylic acids (in Poria), sesquiterpenes (in Rhizoma Atractylodis Macrocephalae), triterpenesaponins (in Glycyrrhizae Radix et Rhizoma Praeparata Cum Melle) as well as flavonoids (in Glycyrrhizae Radix et Rhizoma Praeparata Cum Melle) in Sijunzi decoction. This research developed the bases for prospective research associated with Sijunzi decoction, together with being expected to be useful to rapidly extract and characterize the constituents in other Traditional Chinese herbal formulations. Copyright © 2018 Elsevier B.V. All rights reserved.

Rapid Characterization of Microalgae and Microalgae Mixtures Using Matrix-Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS)

PubMed Central

Barbano, Duane; Diaz, Regina; Zhang, Lin; Sandrin, Todd; Gerken, Henri; Dempster, Thomas

2015-01-01

Current molecular methods to characterize microalgae are time-intensive and expensive. Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) may represent a rapid and economical alternative approach. The objectives of this study were to determine whether MALDI-TOF MS can be used to: 1) differentiate microalgae at the species and strain levels and 2) characterize simple microalgal mixtures. A common protein extraction sample preparation method was used to facilitate rapid mass spectrometry-based analysis of 31 microalgae. Each yielded spectra containing between 6 and 56 peaks in the m/z 2,000 to 20,000 range. The taxonomic resolution of this approach appeared higher than that of 18S rDNA sequence analysis. For example, two strains of Scenedesmus acutus differed only by two 18S rDNA nucleotides, but yielded distinct MALDI-TOF mass spectra. Mixtures of two and three microalgae yielded relatively complex spectra that contained peaks associated with members of each mixture. Interestingly, though, mixture-specific peaks were observed at m/z 11,048 and 11,230. Our results suggest that MALDI-TOF MS affords rapid characterization of individual microalgae and simple microalgal mixtures. PMID:26271045

An improved methodology of asymmetric flow field flow fractionation hyphenated with inductively coupled mass spectrometry for the determination of size distribution of gold nanoparticles in dietary supplements.

PubMed

Mudalige, Thilak K; Qu, Haiou; Linder, Sean W

2015-11-13

Engineered nanoparticles are available in large numbers of commercial products claiming various health benefits. Nanoparticle absorption, distribution, metabolism, excretion, and toxicity in a biological system are dependent on particle size, thus the determination of size and size distribution is essential for full characterization. Number based average size and size distribution is a major parameter for full characterization of the nanoparticle. In the case of polydispersed samples, large numbers of particles are needed to obtain accurate size distribution data. Herein, we report a rapid methodology, demonstrating improved nanoparticle recovery and excellent size resolution, for the characterization of gold nanoparticles in dietary supplements using asymmetric flow field flow fractionation coupled with visible absorption spectrometry and inductively coupled plasma mass spectrometry. A linear relationship between gold nanoparticle size and retention times was observed, and used for characterization of unknown samples. The particle size results from unknown samples were compared to results from traditional size analysis by transmission electron microscopy, and found to have less than a 5% deviation in size for unknown product over the size range from 7 to 30 nm. Published by Elsevier B.V.

A Retrospective Evaluation of the Use of Mass Spectrometry in FDA Biologics License Applications

NASA Astrophysics Data System (ADS)

Rogstad, Sarah; Faustino, Anneliese; Ruth, Ashley; Keire, David; Boyne, Michael; Park, Jun

2017-05-01

The characterization sections of biologics license applications (BLAs) approved by the United States Food and Drug Administration (FDA) between 2000 and 2015 were investigated to examine the extent of the use of mass spectrometry. Mass spectrometry was found to be integral to the characterization of these biotherapeutics. Of the 80 electronically submitted monoclonal antibody and protein biotherapeutic BLAs included in this study, 79 were found to use mass spectrometric workflows for protein or impurity characterization. To further examine how MS is being used in successful BLAs, the applications were filtered based on the type and number of quality attributes characterized, the mass spectrometric workflows used (peptide mapping, intact mass analysis, and cleaved glycan analysis), the methods used to introduce the proteins into the gas phase (ESI, MALDI, or LC-ESI), and the specific types of instrumentation used. Analyses were conducted over a time course based on the FDA BLA approval to determine if any trends in utilization could be observed over time. Additionally, the different classes of protein-based biotherapeutics among the approved BLAs were clustered to determine if any trends could be attributed to the specific type of biotherapeutic.

Study of gamma spectrometry laboratory measurement in various sediment and vulcanic rocks

NASA Astrophysics Data System (ADS)

Nurhandoko, Bagus Endar B.; Kurniadi, Rizal; Rizka Asmara Hadi, Muhammad; Rizal Komara, Insan

2017-01-01

Gamma-ray spectroscopy is the quantitative study of the energy spectra of gamma-ray sources. This method is powerful to characterize some minerals, especially to differentiate rocks which contains among Potassium, Uranium, dan Thorium. Rock contains radioactive material which produce gamma rays in various energies and intensities. When these emissions are detected and analyzed with a spectroscopy system, a gamma-ray energy spectrum can be used as indicator for mineral content of rock. Some sediment and vulcanic rock have been collected from East Java Basin. Samples are ranging from Andesite vulcanics, Tuff, Shale, various vulcanic clay and Alluvial clay. We present some unique characteristics of gamma spectrometry in various sedimentar and vulcanic rocks of East Java Basins. Details contents of gamma ray spectra give enrichments to characterize sample of sediment and vulcanic in East Java. Weathered vulcanic clay has lower counting rate of gamma ray than alluvial deltaic clay counting rate. Therefore, gamma spectrometrometry can be used as tool for characterizing the enviroment of clay whether vulcanic or alluvial-deltaic. This phenomena indicates that gamma ray spectrometry can be as tool for characterizing the clay whether it tends to Smectite or Illite

Characterization of Aggregation Propensity of a Human Fc-Fusion Protein Therapeutic by Hydrogen/Deuterium Exchange Mass Spectrometry

NASA Astrophysics Data System (ADS)

Huang, Richard Y.-C.; Iacob, Roxana E.; Krystek, Stanley R.; Jin, Mi; Wei, Hui; Tao, Li; Das, Tapan K.; Tymiak, Adrienne A.; Engen, John R.; Chen, Guodong

2017-05-01

Aggregation of protein therapeutics has long been a concern across different stages of manufacturing processes in the biopharmaceutical industry. It is often indicative of aberrant protein therapeutic higher-order structure. In this study, the aggregation propensity of a human Fc-fusion protein therapeutic was characterized. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) was applied to examine the conformational dynamics of dimers collected from a bioreactor. HDX-MS data combined with spatial aggregation propensity calculations revealed a potential aggregation interface in the Fc domain. This study provides a general strategy for the characterization of the aggregation propensity of Fc-fusion proteins at the molecular level.

Establishment of a protein frequency library and its application in the reliable identification of specific protein interaction partners.

PubMed

Boulon, Séverine; Ahmad, Yasmeen; Trinkle-Mulcahy, Laura; Verheggen, Céline; Cobley, Andy; Gregor, Peter; Bertrand, Edouard; Whitehorn, Mark; Lamond, Angus I

2010-05-01

The reliable identification of protein interaction partners and how such interactions change in response to physiological or pathological perturbations is a key goal in most areas of cell biology. Stable isotope labeling with amino acids in cell culture (SILAC)-based mass spectrometry has been shown to provide a powerful strategy for characterizing protein complexes and identifying specific interactions. Here, we show how SILAC can be combined with computational methods drawn from the business intelligence field for multidimensional data analysis to improve the discrimination between specific and nonspecific protein associations and to analyze dynamic protein complexes. A strategy is shown for developing a protein frequency library (PFL) that improves on previous use of static "bead proteomes." The PFL annotates the frequency of detection in co-immunoprecipitation and pulldown experiments for all proteins in the human proteome. It can provide a flexible and objective filter for discriminating between contaminants and specifically bound proteins and can be used to normalize data values and facilitate comparisons between data obtained in separate experiments. The PFL is a dynamic tool that can be filtered for specific experimental parameters to generate a customized library. It will be continuously updated as data from each new experiment are added to the library, thereby progressively enhancing its utility. The application of the PFL to pulldown experiments is especially helpful in identifying either lower abundance or less tightly bound specific components of protein complexes that are otherwise lost among the large, nonspecific background.

Moving beyond the van Krevelen Diagram: A New Stoichiometric Approach for Compound Classification in Organisms

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

Rivas-Ubach, Albert; Liu, Yina; Bianchi, Thomas S.

van Krevelen diagrams (O:C vs H:C ratios of elemental formulas) have been widely used in studies to obtain an estimation of the main compound categories present in environmental samples. However, the limits defining a specific compound category based solely on O:C and H:C ratios of elemental formulas have never been accurately listed or proposed to classify metabolites in biological samples. Furthermore, while O:C vs. H:C ratios of elemental formulas can provide an overview of the compound categories, such classification is inefficient because of the large overlap among different compound categories along both axes. We propose a more accurate compound classificationmore » for biological samples analyzed by high-resolution mass spectrometry-based on an assessment of the C:H:O:N:P stoichiometric ratios of over 130,000 elemental formulas of compounds classified in 6 main categories: lipids, peptides, amino-sugars, carbohydrates, nucleotides and phytochemical compounds (oxy-aromatic compounds). Our multidimensional stoichiometric compound classification (MSCC) constraints showed a highly accurate categorization of elemental formulas to the main compound categories in biological samples with over 98% of accuracy representing a substantial improvement over any classification based on the classic van Krevelen diagram. This method represents a significant step forward in environmental research, especially ecological stoichiometry and eco-metabolomics studies, by providing a novel and robust tool to further our understanding the ecosystem structure and function through the chemical characterization of different biological samples.« less

CHARACTERIZATION OF DANSYLATED CYSTEINE, CYSTINE, GLUTATHIONE, AND GLUTATHIONE DISULFIDE BY NARROW BORE LIQUID CHROMATOGRAPHY - ELECTROSPRAY IONIZATION MASS SPECTROMETRY

EPA Science Inventory

A method using reversed phase high performance liquid chromtography/electrospray ionization-mass spectrometry (RP-LC/ESI-MS) has been developed to confirm the dientity of dansylated derivatives of cysteine (C) and glutathione (GSH), and their respective dimers, cystine (CSSC) and...

Characterization of phenolic amides from cortex lycii by ultra high-performance liquid chromatography coupled with LTQ-Orbitrap mass spectrometry

USDA-ARS?s Scientific Manuscript database

High performance liquid chromatography (UPLC) and flow injection electrospray ionization with ion trap mass spectrometry (FIMS) fingerprints combined with the principal component analysis (PCA) were examined for their potential in differentiating commercial organic and conventional sage samples. The...

Isolation and Puification of Uranium Isotopes for Measurement by Mass-Spectrometry (233, 234, 235, 236, 238U) and Alpha Spectrometry (232U)

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

Marinelli, R; Hamilton, T; Brown, T

2006-05-30

This report describes a standardized methodology used by researchers from the Center for Accelerator Mass Spectrometry (CAMS) (Energy and Environment Directorate) and the Environmental Radiochemistry Group (Chemistry and Materials Science Directorate) at the Lawrence Livermore National Laboratory (LLNL) for the full isotopic analysis of uranium from solution. The methodology has largely been developed for use in characterizing the uranium composition of selected nuclear materials but may also be applicable to environmental studies and assessments of public, military or occupational exposures to uranium using in-vitro bioassay monitoring techniques. Uranium isotope concentrations and isotopic ratios are measured using a combination of Multimore » Collector Inductively Coupled Plasma Mass Spectrometry (MC ICP-MS), Accelerator Mass Spectrometry (AMS) and Alpha Spectrometry.« less

Characterization of exopolymers of aquatic bacteria by pyrolysis-mass spectrometry

NASA Technical Reports Server (NTRS)

Ford, T.; Sacco, E.; Black, J.; Kelley, T.; Goodacre, R.; Berkeley, R. C.; Mitchell, R.

1991-01-01

Exopolymers from a diverse collection of marine and freshwater bacteria were characterized by pyrolysis-mass spectrometry (Py-MS). Py-MS provides spectra of pyrolysis fragments that are characteristic of the original material. Analysis of the spectra by multivariate statistical techniques (principal component and canonical variate analysis) separated these exopolymers into distinct groups. Py-MS clearly distinguished characteristic fragments, which may be derived from components responsible for functional differences between polymers. The importance of these distinctions and the relevance of pyrolysis information to exopolysaccharide function in aquatic bacteria is discussed.

EuroFlow antibody panels for standardized n-dimensional flow cytometric immunophenotyping of normal, reactive and malignant leukocytes

PubMed Central

van Dongen, J J M; Lhermitte, L; Böttcher, S; Almeida, J; van der Velden, V H J; Flores-Montero, J; Rawstron, A; Asnafi, V; Lécrevisse, Q; Lucio, P; Mejstrikova, E; Szczepański, T; Kalina, T; de Tute, R; Brüggemann, M; Sedek, L; Cullen, M; Langerak, A W; Mendonça, A; Macintyre, E; Martin-Ayuso, M; Hrusak, O; Vidriales, M B; Orfao, A

2012-01-01

Most consensus leukemia & lymphoma antibody panels consist of lists of markers based on expert opinions, but they have not been validated. Here we present the validated EuroFlow 8-color antibody panels for immunophenotyping of hematological malignancies. The single-tube screening panels and multi-tube classification panels fit into the EuroFlow diagnostic algorithm with entries defined by clinical and laboratory parameters. The panels were constructed in 2–7 sequential design–evaluation–redesign rounds, using novel Infinicyt software tools for multivariate data analysis. Two groups of markers are combined in each 8-color tube: (i) backbone markers to identify distinct cell populations in a sample, and (ii) markers for characterization of specific cell populations. In multi-tube panels, the backbone markers were optimally placed at the same fluorochrome position in every tube, to provide identical multidimensional localization of the target cell population(s). The characterization markers were positioned according to the diagnostic utility of the combined markers. Each proposed antibody combination was tested against reference databases of normal and malignant cells from healthy subjects and WHO-based disease entities, respectively. The EuroFlow studies resulted in validated and flexible 8-color antibody panels for multidimensional identification and characterization of normal and aberrant cells, optimally suited for immunophenotypic screening and classification of hematological malignancies. PMID:22552007

Detection of Cocaine and Metabolites in Bone Following Decomposition Using 2D LC-MS-MS.

PubMed

Mella, Malorie; Schweitzer, Brendan; Mallet, Claude R; Moore, Tara; Botch-Jones, Sabra

2017-12-28

In forensic toxicology, challenges exist with quantification analysis of cocaine and metabolites in postmortem samples following extensive decomposition. Alternative matrices, such as bone could prove useful when other specimens are not available. Detection and quantification of drugs in complex matrices require time-consuming extraction processes. The objective of this study was to develop a robust extraction and clean-up methodology to efficiently extract cocaine, and its metabolites, in bone and reach target limits of detection using multidimensional chromatography. Under an Institutional Animal Care and Use Committee protocol, rat specimens underwent a 10-12 weeks chronic intravenous self-administration of cocaine with average daily dosages ranging 13-19 mg/kg. This was followed by a 6-week period of abstinence, followed again by a 3-week period of cocaine self-administration before being euthanized. Fourteen cocaine positive rats were placed at the Boston University Forensic Anthropology Outdoor Research Facility (Holliston, MA, USA) for a period of 12 months. Skeletal remains were collected for testing as well as drug-free control rats. After homogenization of whole bones, the extraction process was performed using a mixed mode reversed-phase/ion exchange sorbent with an extraction time of 1 h followed by analysis using a 2D liquid chromatography-mass spectrometry-mass spectrometry which allowed for direct injection of the eluent without evaporation or reconstitution. The analysis was performed using 100 μL of the final methanol extracts. The limit of quantitation for cocaine and benzoylecgonine was measured at 0.05ng/g and for ecgonine methyl ester it was 0.1ng/g. The analytical method for cocaine gave a linear dynamic range of 0.05-10ng/g with an R2 = 0.998. The microextraction protocol combined with a multidimensional chromatography used in this study decreased sample preparation time without sacrificing the quality seen with current single dimension chromatography techniques. © The Author(s) 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Mass spectrometry in systems biology an introduction.

PubMed

Dunn, Warwick B

2011-01-01

The qualitative detection, quantification, and structural characterization of analytes in biological systems are important requirements for objectives to be fulfilled in systems biology research. One analytical tool applied to a multitude of systems biology studies is mass spectrometry, particularly for the study of proteins and metabolites. Here, the role of mass spectrometry in systems biology will be assessed, the advantages and disadvantages discussed, and the instrument configurations available described. Finally, general applications will be briefly reviewed. Copyright © 2011 Elsevier Inc. All rights reserved.

Collision induced unfolding of isolated proteins in the gas phase: past, present, and future.

PubMed

Dixit, Sugyan M; Polasky, Daniel A; Ruotolo, Brandon T

2018-02-01

Rapidly characterizing the three-dimensional structures of proteins and the multimeric machines they form remains one of the great challenges facing modern biological and medical sciences. Ion mobility-mass spectrometry based techniques are playing an expanding role in characterizing these functional complexes, especially in drug discovery and development workflows. Despite this expansion, ion mobility-mass spectrometry faces many challenges, especially in the context of detecting small differences in protein tertiary structure that bear functional consequences. Collision induced unfolding is an ion mobility-mass spectrometry method that enables the rapid differentiation of subtly-different protein isoforms based on their unfolding patterns and stabilities. In this review, we summarize the modern implementation of such gas-phase unfolding experiments and provide an overview of recent developments in both methods and applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

Fluorescence Intrinsic Characterization of Excitation-Emission Matrix Using Multi-Dimensional Ensemble Empirical Mode Decomposition

PubMed Central

Chang, Chi-Ying; Chang, Chia-Chi; Hsiao, Tzu-Chien

2013-01-01

Excitation-emission matrix (EEM) fluorescence spectroscopy is a noninvasive method for tissue diagnosis and has become important in clinical use. However, the intrinsic characterization of EEM fluorescence remains unclear. Photobleaching and the complexity of the chemical compounds make it difficult to distinguish individual compounds due to overlapping features. Conventional studies use principal component analysis (PCA) for EEM fluorescence analysis, and the relationship between the EEM features extracted by PCA and diseases has been examined. The spectral features of different tissue constituents are not fully separable or clearly defined. Recently, a non-stationary method called multi-dimensional ensemble empirical mode decomposition (MEEMD) was introduced; this method can extract the intrinsic oscillations on multiple spatial scales without loss of information. The aim of this study was to propose a fluorescence spectroscopy system for EEM measurements and to describe a method for extracting the intrinsic characteristics of EEM by MEEMD. The results indicate that, although PCA provides the principal factor for the spectral features associated with chemical compounds, MEEMD can provide additional intrinsic features with more reliable mapping of the chemical compounds. MEEMD has the potential to extract intrinsic fluorescence features and improve the detection of biochemical changes. PMID:24240806

Automated On-tip Affinity Capture Coupled with Mass Spectrometry to Characterize Intact Antibody-Drug Conjugates from Blood

NASA Astrophysics Data System (ADS)

Li, Ke Sherry; Chu, Phillip Y.; Fourie-O'Donohue, Aimee; Srikumar, Neha; Kozak, Katherine R.; Liu, Yichin; Tran, John C.

2018-05-01

Antibody-drug conjugates (ADCs) present unique challenges for ligand-binding assays primarily due to the dynamic changes of the drug-to-antibody ratio (DAR) distribution in vivo and in vitro. Here, an automated on-tip affinity capture platform with subsequent mass spectrometry analysis was developed to accurately characterize the DAR distribution of ADCs from biological matrices. A variety of elution buffers were tested to offer optimal recovery, with trastuzumab serving as a surrogate to the ADCs. High assay repeatability (CV 3%) was achieved for trastuzumab antibody when captured below the maximal binding capacity of 7.5 μg. Efficient on-tip deglycosylation was also demonstrated in 1 h followed by affinity capture. Moreover, this tip-based platform affords higher throughput for DAR characterization when compared with a well-characterized bead-based method.

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

PubMed

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

2014-02-01

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

CHARACTERIZATION OF GROUNDWATER SAMPLES FROM SUPERFUND SITES BY AS CHROMATOGRAPHY/MASS SPECTROMETRY AND LIQUID CHROMATOGRAPHY/MASS SPECTROMETRY.

EPA Science Inventory

Groundwater at or near Superfund sites often contains much organic matter,as indicated by total organic carbon (TOC) measurements. Analyses by standard GC and GC/MS methodology often miss the more polar or nonvolatile of these organic compounds. The identification of the highly p...

A versatile mass spectrometry-based method to both identify kinase client-relationships and characterize signaling network topology

USDA-ARS?s Scientific Manuscript database

While more than a thousand protein kinases (PK) have been identified in the Arabidopsis thaliana genome, relatively little progress has been made towards identifying their individual client proteins. Herein we describe use of a mass spectrometry-based in vitro phosphorylation strategy, termed Kinase...

THE USE OF MATRIX-ASSISTED LASER DESORPTION/IONIZATION-MASS SPECTROMETRY FOR THE IDENTIFICATION OF AEROMONAS ISOLATES OBTAINED FROM WATER DISTRIBUTION SYSTEMS

EPA Science Inventory

Matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) has long been established as a tool by which microorganisms can be characterized and identified. EPA is investigating the potential of using this technology as a way to rapidly identify Aeromonas species fo...

Online Coupling of Flow-Field Flow Fractionation and Single Particle Inductively Coupled Plasma-Mass Spectrometry: Characterization of Nanoparticle Surface Coating Thickness and Aggregation State

EPA Science Inventory

Surface coating thickness and aggregation state have strong influence on the environmental fate, transport, and toxicity of engineered nanomaterials. In this study, flow-field flow fractionation coupled on-line with single particle inductively coupled plasma-mass spectrometry i...

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

On-line characterization of monoclonal antibody variants by liquid chromatography-mass spectrometry operating in a two-dimensional format.

PubMed

Alvarez, Melissa; Tremintin, Guillaume; Wang, Jennifer; Eng, Marian; Kao, Yung-Hsiang; Jeong, Justin; Ling, Victor T; Borisov, Oleg V

2011-12-01

Recombinant monoclonal antibodies (MAbs) have become one of the most rapidly growing classes of biotherapeutics in the treatment of human disease. MAbs are highly heterogeneous proteins, thereby requiring a battery of analytical technologies for their characterization. However, incompatibility between separation and subsequent detection is often encountered. Here we demonstrate the utility of a generic on-line liquid chromatography-mass spectrometry (LC-MS) method operated in a two-dimensional format toward the rapid characterization of MAb charge and size variants. Using a single chromatographic system capable of running two independent gradients, up to six fractions of interest from an ion exchange (IEC) or size exclusion (SEC) separation can be identified by trapping and desalting the fractions onto a series of reversed phase trap cartridges with subsequent on-line analysis by mass spectrometry. Analysis of poorly resolved and low-level peaks in the IEC or SEC profile was facilitated by preconcentrating fractions on the traps using multiple injections. An on-line disulfide reduction step was successfully incorporated into the workflow, allowing more detailed characterization of modified MAbs by providing chain-specific information. The system is fully automated, thereby enabling high-throughput analysis with minimal sample handling. This technology provides rapid data turnaround time, a much needed feature during product characterization and development of multiple biotherapeutic proteins. Copyright © 2011 Elsevier Inc. All rights reserved.

Site-specific detection of radicals on α-lactalbumin after a riboflavin-sensitized reaction, detected by immuno-spin trapping, ESR, and MS.

PubMed

Dalsgaard, Trine K; Triquigneaux, Mathilde; Deterding, Leesa; Summers, Fiona; Ranguelova, Kalina; Mortensen, Grith; Mason, Ronald P

2013-01-16

Free radicals and other oxidation products were characterized on α-lactalbumin with electron spin resonance (ESR), immuno-spin trapping, and mass spectrometry (MS) after riboflavin-mediated oxidation. Radicals were detected using the spin trap 5,5-dimethyl-1-pyrroline N-oxide (DMPO) in immuno-spin trapping with both enzyme-linked immunosorbent assay (ELISA) and Western blotting and further characterized with mass spectrometry. A DMPO-trapped radical was identified at His68 and another at one of the tyrosine residues, Tyr50 or Tyr36, respectively, generated by a type II or I mechanism. Not all tyrosyl radicals were trapped, as the secondary oxidation product, 3,4-dihydroxyphenylalanine (DOPA), was detected by mass spectrometry at Tyr18 and Tyr50. A further oxidation of DOPA resulted in the DOPA o-semiquinone radical, which was characterized by ESR. Both surface exposure and the neighboring residues in the local environment of the tertiary structure of α-lactalbumin seem to play a role in the generation of DMPO trapped radicals and secondary oxidation products.

Characterization of polyoxyethylene tallow amine surfactants in technical mixtures and glyphosate formulations using ultra-high performance liquid chromatography and triple quadrupole mass spectrometry

USGS Publications Warehouse

Tush, Daniel; Loftin, Keith A.; Meyer, Michael T.

2013-01-01

Little is known about the occurrence, fate, and effects of the ancillary additives in pesticide formulations. Polyoxyethylene tallow amine (POEA) is a non-ionic surfactant used in many glyphosate formulations, a widely applied herbicide both in agricultural and urban environments. POEA has not been previously well characterized, but has been shown to be toxic to various aquatic organisms. Characterization of technical mixtures using ultra-high performance liquid chromatography (UHPLC) and mass spectrometry shows POEA is a complex combination of homologs of different aliphatic moieties and ranges of ethoxylate units. Tandem mass spectrometry experiments indicate that POEA homologs generate no product ions readily suitable for quantitative analysis due to poor sensitivity. A comparison of multiple high performance liquid chromatography (HPLC) and UHPLC analytical columns indicates that the stationary phase is more important in column selection than other parameters for the separation of POEA. Analysis of several agricultural and household glyphosate formulations confirms that POEA is a common ingredient but ethoxylate distributions among formulations vary.

Cryogenic Vibrational Spectroscopy Provides Unique Fingerprints for Glycan Identification.

PubMed

Masellis, Chiara; Khanal, Neelam; Kamrath, Michael Z; Clemmer, David E; Rizzo, Thomas R

2017-10-01

The structural characterization of glycans by mass spectrometry is particularly challenging. This is because of the high degree of isomerism in which glycans of the same mass can differ in their stereochemistry, attachment points, and degree of branching. Here we show that the addition of cryogenic vibrational spectroscopy to mass and mobility measurements allows one to uniquely identify and characterize these complex biopolymers. We investigate six disaccharide isomers that differ in their stereochemistry, attachment point of the glycosidic bond, and monosaccharide content, and demonstrate that we can identify each one unambiguously. Even disaccharides that differ by a single stereogenic center or in the monosaccharide sequence order show distinct vibrational fingerprints that would clearly allow their identification in a mixture, which is not possible by ion mobility spectrometry/mass spectrometry alone. Moreover, this technique can be applied to larger glycans, which we demonstrate by distinguishing isomeric branched and linear pentasaccharides. The creation of a database containing mass, collision cross section, and vibrational fingerprint measurements for glycan standards should allow unambiguous identification and characterization of these biopolymers in mixtures, providing an enabling technology for all fields of glycoscience. Graphical Abstract ᅟ.

Measuring masses of large biomolecules and bioparticles using mass spectrometric techniques.

PubMed

Peng, Wen-Ping; Chou, Szu-Wei; Patil, Avinash A

2014-07-21

Large biomolecules and bioparticles play a vital role in biology, chemistry, biomedical science and physics. Mass is a critical parameter for the characterization of large biomolecules and bioparticles. To achieve mass analysis, choosing a suitable ion source is the first step and the instruments for detecting ions, mass analyzers and detectors should also be considered. Abundant mass spectrometric techniques have been proposed to determine the masses of large biomolecules and bioparticles and these techniques can be divided into two categories. The first category measures the mass (or size) of intact particles, including single particle quadrupole ion trap mass spectrometry, cell mass spectrometry, charge detection mass spectrometry and differential mobility mass analysis; the second category aims to measure the mass and tandem mass of biomolecular ions, including quadrupole ion trap mass spectrometry, time-of-flight mass spectrometry, quadrupole orthogonal time-of-flight mass spectrometry and orbitrap mass spectrometry. Moreover, algorithms for the mass and stoichiometry assignment of electrospray mass spectra are developed to obtain accurate structure information and subunit combinations.

Ultra-fast liquid chromatography coupled with electrospray ionization time-of-flight mass spectrometry for the rapid phenolic profiling of red maple (Acer rubrum) leaves.

PubMed

Li, Chunting; Seeram, Navindra P

2018-03-07

The red maple (Acer rubrum) species is economically important to North America because of its sap, which is used to produce maple syrup. In addition, various other red maple plant parts, including leaves, were used as a traditional medicine by the Native Americans. Currently, red maple leaves are being used for nutraceutical and cosmetic applications but there are no published analytical methods for comprehensive phytochemical characterization of this material. Herein, a rapid and sensitive method using liquid chromatography with electrospray ionization time-of-flight tandem mass spectrometry was developed to characterize the phenolics in a methanol extract of red maple leaves and a proprietary phenolic-enriched red maple leaves extract (Maplifa™). Time-of-flight mass spectrometry and tandem mass spectrometry experiments led to the identification of 106 phenolic compounds in red maples leaves with the vast majority of these compounds also detected in Maplifa™. The compounds included 68 gallotannins, 25 flavonoids, gallic acid, quinic acid, catechin, epicatechin, and nine other gallic acid derivatives among which 11 are potentially new and 75 are being reported from red maple for the first time. The developed method to characterize red maple leaves phenolics is rapid and highly sensitive and could aid in future standardization and quality control of this botanical ingredient. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multidimensional profiling of components in complex mixtures of natural products for metabolic analysis, proof of concept: application to Quillaja saponins.

PubMed

Bankefors, Johan; Nord, Lars I; Kenne, Lennart

2010-02-01

A method for separation and detection of major and minor components in complex mixtures has been developed, utilising two-dimensional high-performance liquid chromatography (2D-HPLC) combined with electrospray ionisation ion-trap multiple-stage mass spectrometry (ESI-ITMS(n)). Chromatographic conditions were matched with mass spectrometric detection to maximise the number of components that could be separated. The described procedure has proven useful to discern several hundreds of saponin components when applied to Quillaja saponaria Molina bark extracts. The discrimination of each saponin component relies on the fact that three coordinates (x, y, z) for each component can be derived from the retention time of the two chromatographic steps (x, y) and the m/z-values from the multiple-stage mass spectrometry (z(n), n=1, 2, ...). Thus an improved graphical representation was obtained by combining retention times from the two-stage separation with +MS(1) (z(1)) and the additional structural information from the second mass stage +MS(2) (z(2), z(3)) corresponding to the main fragment ions. By this approach three-dimensional plots can be made that reveal both the chromatographic and structural properties of a specific mixture which can be useful in fingerprinting of complex mixtures. 2009 Elsevier B.V. All rights reserved.

Inorganic trace analysis by mass spectrometry

NASA Astrophysics Data System (ADS)

Becker, Johanna Sabine; Dietze, Hans-Joachim

1998-10-01

Mass spectrometric methods for the trace analysis of inorganic materials with their ability to provide a very sensitive multielemental analysis have been established for the determination of trace and ultratrace elements in high-purity materials (metals, semiconductors and insulators), in different technical samples (e.g. alloys, pure chemicals, ceramics, thin films, ion-implanted semiconductors), in environmental samples (waters, soils, biological and medical materials) and geological samples. Whereas such techniques as spark source mass spectrometry (SSMS), laser ionization mass spectrometry (LIMS), laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), glow discharge mass spectrometry (GDMS), secondary ion mass spectrometry (SIMS) and inductively coupled plasma mass spectrometry (ICP-MS) have multielemental capability, other methods such as thermal ionization mass spectrometry (TIMS), accelerator mass spectrometry (AMS) and resonance ionization mass spectrometry (RIMS) have been used for sensitive mono- or oligoelemental ultratrace analysis (and precise determination of isotopic ratios) in solid samples. The limits of detection for chemical elements using these mass spectrometric techniques are in the low ng g -1 concentration range. The quantification of the analytical results of mass spectrometric methods is sometimes difficult due to a lack of matrix-fitted multielement standard reference materials (SRMs) for many solid samples. Therefore, owing to the simple quantification procedure of the aqueous solution, inductively coupled plasma mass spectrometry (ICP-MS) is being increasingly used for the characterization of solid samples after sample dissolution. ICP-MS is often combined with special sample introduction equipment (e.g. flow injection, hydride generation, high performance liquid chromatography (HPLC) or electrothermal vaporization) or an off-line matrix separation and enrichment of trace impurities (especially for characterization of high-purity materials and environmental samples) is used in order to improve the detection limits of trace elements. Furthermore, the determination of chemical elements in the trace and ultratrace concentration range is often difficult and can be disturbed through mass interferences of analyte ions by molecular ions at the same nominal mass. By applying double-focusing sector field mass spectrometry at the required mass resolution—by the mass spectrometric separation of molecular ions from the analyte ions—it is often possible to overcome these interference problems. Commercial instrumental equipment, the capability (detection limits, accuracy, precision) and the analytical application fields of mass spectrometric methods for the determination of trace and ultratrace elements and for surface analysis are discussed.

Characterization of Hydrophobic Peptides in the Presence of Detergent by Photoionization Mass Spectrometry

PubMed Central

Bagag, Aïcha; Jault, Jean-Michel; Sidahmed-Adrar, Nazha; Réfrégiers, Matthieu; Giuliani, Alexandre; Le Naour, François

2013-01-01

The characterization of membrane proteins is still challenging. The major issue is the high hydrophobicity of membrane proteins that necessitates the use of detergents for their extraction and solubilization. The very poor compatibility of mass spectrometry with detergents remains a tremendous obstacle in studies of membrane proteins. Here, we investigated the potential of atmospheric pressure photoionization (APPI) for mass spectrometry study of membrane proteins. This work was focused on the tetraspanin CD9 and the multidrug transporter BmrA. A set of peptides from CD9, exhibiting a broad range of hydropathicity, was investigated using APPI as compared to electrospray ionization (ESI). Mass spectrometry experiments revealed that the most hydrophobic peptides were hardly ionized by ESI whereas all peptides, including the highly hydrophobic one that corresponds to the full sequence of the first transmembrane domain of CD9, were easily ionized by APPI. The native protein BmrA purified in the presence of the non-ionic detergent beta-D-dodecyl maltoside (DDM) was digested in-solution using trypsin. The resulting peptides were investigated by flow injection analysis of the mixture followed by mass spectrometry. Upon ESI, only detergent ions were detected and the ionic signals from the peptides were totally suppressed. In contrast, APPI allowed many peptides distributed along the sequence of the protein to be detected. Furthermore, the parent ion corresponding to the first transmembrane domain of the protein BmrA was detected under APPI conditions. Careful examination of the APPI mass spectrum revealed a-, b-, c- and y- fragment ions generated by in-source fragmentation. Those fragment ions allowed unambiguous structural characterization of the transmembrane domain. In conclusion, APPI–MS appears as a versatile method allowing the ionization and fragmentation of hydrophobic peptides in the presence of detergent. PMID:24236085

Glow discharge spectrometry for the characterization of nuclear and radioactively contaminated environmental samples

NASA Astrophysics Data System (ADS)

Betti, Maria; Aldave de las Heras, Laura

2004-09-01

Glow discharge (GD) spectrometry as applied to characterize nuclear samples as well as for the determination of radionuclides in environmental samples is reviewed. The use of instrumentation for direct current (d.c.) glow discharge mass spectrometry (GDMS) and radio frequency glow discharge optical emission spectrometry (rf GDOES), installed inside a glove-box for the handling of radioactive samples as well as the two installations and their analytical possibilities, is described in detail. The applications of GD techniques for the characterization of samples of nuclear concern both with respect to their major and trace elements, as well as to the matrix isotopic composition are presented. Procedures for quantitative determination of major, minor, and trace elements in conductive samples are reported. As for non-conductive samples three different approaches for their measurement can be followed. Namely, the use of rf sources, the mixing of the sample with a binder conducting host matrix, and the use of a secondary cathode. In the case of oxide-based samples, the employment of a tantalum secondary cathode, acting as an oxygen getter, reduces the availability of oxygen to form polyatomic species and to produce quenching. Considerations on the use of the relative sensitivity factors (RSFs) in different matrices are reported. The analytical capabilities of GDMS are compared with ICP-MS in terms of accuracy, precision, and detection limit for the determination of trace elements in uranium oxide specimens. As for the determination of isotopic composition, GDMS was found to be competitive with thermal ionisation mass spectrometry (TIMS) as well as for bulk determinations of major elements with titration methods. Applications of GDMS to the determination of radioisotopes in environmental samples, as well for depth profiling of trace elements in oxide layers, are discussed.

Rapid identification of triterpenoid sulfates and hydroxy fatty acids including two new constituents from Tydemania expeditionis by liquid chromatography-mass spectrometry.

PubMed

Zhang, Jian-Long; Kubanek, Julia; Hay, Mark E; Aalbersberg, William; Ye, Wen-Cai; Jiang, Ren-Wang

2011-09-01

Tydemania expeditionis Weber-van Bosse (Udoteaceae) is a weakly calcified green alga. In the present paper, liquid chromatography coupled with photodiode array detection and electrospray mass spectrometry was developed to identify the fingerprint components. A total of four triterpenoid sulfates and three hydroxy fatty acids in the ethyl acetate fraction of the crude extract were structurally characterized on the basis of retention time, online UV spectrum, and mass fragmentation pattern. Furthermore, a detailed liquid chromatography-mass spectrometry analysis revealed two new hydroxy fatty acids, which were then prepared and characterized by extensive nuclear magnetic resonance (NMR) analyses. The proposed method provides a scientific and technical platform for the rapid identification of triterpenoid sulfates and hydroxy fatty acids in similar marine algae and terrestrial plants. Copyright © 2011 John Wiley & Sons, Ltd.

The Search Engine for Multi-Proteoform Complexes: An Online Tool for the Identification and Stoichiometry Determination of Protein Complexes.

PubMed

Skinner, Owen S; Schachner, Luis F; Kelleher, Neil L

2016-12-08

Recent advances in top-down mass spectrometry using native electrospray now enable the analysis of intact protein complexes with relatively small sample amounts in an untargeted mode. Here, we describe how to characterize both homo- and heteropolymeric complexes with high molecular specificity using input data produced by tandem mass spectrometry of whole protein assemblies. The tool described is a "search engine for multi-proteoform complexes," (SEMPC) and is available for free online. The output is a list of candidate multi-proteoform complexes and scoring metrics, which are used to define a distinct set of one or more unique protein subunits, their overall stoichiometry in the intact complex, and their pre- and post-translational modifications. Thus, we present an approach for the identification and characterization of intact protein complexes from native mass spectrometry data. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

Characterization of a Protein Interactome by Co-Immunoprecipitation and Shotgun Mass Spectrometry.

PubMed

Maccarrone, Giuseppina; Bonfiglio, Juan Jose; Silberstein, Susana; Turck, Christoph W; Martins-de-Souza, Daniel

2017-01-01

Identifying the partners of a given protein (the interactome) may provide leads about the protein's function and the molecular mechanisms in which it is involved. One of the alternative strategies used to characterize protein interactomes consists of co-immunoprecipitation (co-IP) followed by shotgun mass spectrometry. This enables the isolation and identification of a protein target in its native state and its interactome from cells or tissue lysates under physiological conditions. In this chapter, we describe a co-IP protocol for interactome studies that uses an antibody against a protein of interest bound to protein A/G plus agarose beads to isolate a protein complex. The interacting proteins may be further fractionated by SDS-PAGE, followed by in-gel tryptic digestion and nano liquid chromatography high-resolution tandem mass spectrometry (nLC ESI-MS/MS) for identification purposes. The computational tools, strategy for protein identification, and use of interactome databases also will be described.

Biomass Characterization | Bioenergy | NREL

Science.gov Websites

analytical methods for biomass characterization available for downloading. View the Biomass Compositional Methods Molecular Beam Mass Spectrometry Photo of a man in front of multiple computer screens that present Characterization of Biomass We develop new methods and tools to understand the chemical composition of raw biomass

A Developmental History of Polymer Mass Spectrometry

ERIC Educational Resources Information Center

Vergne, Matthew J.; Hercules, David M.; Lattimer, Robert P.

2007-01-01

The history of the development of mass spectroscopic methods used to characterize polymers is discussed. The continued improvements in methods and instrumentation will offer new and better ways for the mass spectral characterization of polymers and mass spectroscopy (MS) should be recognized as a complementary polymer characterization method along…

REAL TIME, ON-LINE CHARACTERIZATION OF DIESEL GENERATOR AIR TOXIC EMISSIONS BY RESONANCE ENHANCED MULTI-PHOTON IONIZATION TIME OF FLIGHT MASS SPECTROMETRY

EPA Science Inventory

The laser based resonance, enhanced multi-photon ionization time-of-flight mass spectrometry (REMPI-TOFMS) technique has been applied to the exhaust gas stream of a diesel generator to measure, in real time, concentration levels of aromatic air toxics. Volatile organic compounds ...

Affinity purification combined with mass spectrometry to identify herpes simplex virus protein-protein interactions.

PubMed

Meckes, David G

2014-01-01

The identification and characterization of herpes simplex virus protein interaction complexes are fundamental to understanding the molecular mechanisms governing the replication and pathogenesis of the virus. Recent advances in affinity-based methods, mass spectrometry configurations, and bioinformatics tools have greatly increased the quantity and quality of protein-protein interaction datasets. In this chapter, detailed and reliable methods that can easily be implemented are presented for the identification of protein-protein interactions using cryogenic cell lysis, affinity purification, trypsin digestion, and mass spectrometry.

Mass spectrometry for the biophysical characterization of therapeutic monoclonal antibodies.

PubMed

Zhang, Hao; Cui, Weidong; Gross, Michael L

2014-01-21

Monoclonal antibodies (mAbs) are powerful therapeutics, and their characterization has drawn considerable attention and urgency. Unlike small-molecule drugs (150-600 Da) that have rigid structures, mAbs (∼150 kDa) are engineered proteins that undergo complicated folding and can exist in a number of low-energy structures, posing a challenge for traditional methods in structural biology. Mass spectrometry (MS)-based biophysical characterization approaches can provide structural information, bringing high sensitivity, fast turnaround, and small sample consumption. This review outlines various MS-based strategies for protein biophysical characterization and then reviews how these strategies provide structural information of mAbs at the protein level (intact or top-down approaches), peptide, and residue level (bottom-up approaches), affording information on higher order structure, aggregation, and the nature of antibody complexes. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Two chemically distinct light-absorbing pools of urban organic aerosols: A comprehensive multidimensional analysis of trends.

PubMed

Paula, Andreia S; Matos, João T V; Duarte, Regina M B O; Duarte, Armando C

2016-02-01

The chemical and light-absorption dynamics of organic aerosols (OAs), a master variable in the atmosphere, have yet to be resolved. This study uses a comprehensive multidimensional analysis approach for exploiting simultaneously the compositional changes over a molecular size continuum and associated light-absorption (ultraviolet absorbance and fluorescence) properties of two chemically distinct pools of urban OAs chromophores. Up to 45% of aerosol organic carbon (OC) is soluble in water and consists of a complex mixture of fluorescent and UV-absorbing constituents, with diverse relative abundances, hydrophobic, and molecular weight (Mw) characteristics between warm and cold periods. In contrast, the refractory alkaline-soluble OC pool (up to 18%) is represented along a similar Mw and light-absorption continuum throughout the different seasons. Results suggest that these alkaline-soluble chromophores may actually originate from primary OAs sources in the urban site. This work shows that the comprehensive multidimensional analysis method is a powerful and complementary tool for the characterization of OAs fractions. The great diversity in the chemical composition and optical properties of OAs chromophores, including both water-soluble and alkaline-soluble OC, may be an important contribution to explain the contrasting photo-reactivity and atmospheric behavior of OAs. Copyright © 2015 Elsevier Ltd. All rights reserved.

Application of information-retrieval methods to the classification of physical data

NASA Technical Reports Server (NTRS)

Mamotko, Z. N.; Khorolskaya, S. K.; Shatrovskiy, L. I.

1975-01-01

Scientific data received from satellites are characterized as a multi-dimensional time series, whose terms are vector functions of a vector of measurement conditions. Information retrieval methods are used to construct lower dimensional samples on the basis of the condition vector, in order to obtain these data and to construct partial relations. The methods are applied to the joint Soviet-French Arkad project.

WFIRST: Exoplanet Data Challenge. Atmospheric retrieval results

NASA Astrophysics Data System (ADS)

Hildebrandt, Sergi; Turnbull, Margaret; Exoplanet Data Challenge Team

2018-01-01

We present the results of the Exoplanet Data Challenge for its first 2016/17 cycle and the current cycle 2. Some input spectra for extra-solar systems are processed through the WFIRST IFS instrument model, producing simulated data representative of the flight data. Atmospheric properties are then recovered using complex atmospheric models and multidimensional optimization. The results inform about WFIRST CGI ability to characterize exo-planetray atmospheres.

Highly Transparent Water-Repelling Surfaces based on Biomimetic Hierarchical Structure

NASA Astrophysics Data System (ADS)

Wooh, Sanghyuk; Koh, Jai; Yoon, Hyunsik; Char, Kookheon

2013-03-01

Nature is a great source of inspiration for creating unique structures with special functions. The representative examples of water-repelling surfaces in nature, such as lotus leaves, rose petals, and insect wings, consist of an array of bumps (or long hairs) and nanoscale surface features with different dimension scales. Herein, we introduced a method of realizing multi-dimensional hierarchical structures and water-repellancy of the surfaces with different drop impact scenarios. The multi-dimensional hierarchical structures were fabricated by soft imprinting method with TiO2 nanoparticle pastes. In order to achieve the enhanced hydrophobicity, fluorinated moieties were attached to the etched surfaces to lower the surface energy. As a result, super-hydrophobic surfaces with high transparency were realized (over 176° water contact angle), and for further investigation, these hierarchical surfaces with different drop impact scenarios were characterized by varying the impact speed, drop size, and the geometry of the surfaces.

Evaluating lipid mediator structural complexity using ion mobility spectrometry combined with mass spectrometry

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

Kyle, Jennifer E.; Aly, Noor; Zheng, Xueyun

Lipid mediators (LMs) are broadly defined as a class of bioactive lipophilic molecules that regulate cell-to-cell communication events with many having a strong correlation with various human diseases and conditions. LMs are usually analyzed with liquid chromatography and mass spectrometry (LC-MS), but their numerous isomers greatly complicate the measurements with essentially identical fragmentation spectra and LC separations not always sufficient for distinguishing the features. In this work, we characterized LMs having specific categories using ion mobility spectrometry coupled with mass spectrometry (IMS-MS). The IMS collision cross sections and MS m/z values displayed distinct trends for each LM category studied. LC-IMS-MSmore » analyses on flu infected mouse tissue samples also illustrated the presence of additional LM species not in our databases.« less

Pathology and diagnosis of renal non-AL amyloidosis.

PubMed

Sethi, Sanjeev; Theis, Jason D

2018-06-01

Renal amyloidosis is characterized by acellular Congo red positive deposits in the glomeruli, interstitium and/or arteries. Light chain restriction on immunofluorescence studies is present in AL-amyloidosis, the most common type of amyloidosis involving the kidney. The detection of Congo red positive deposits coupled with negative immunofluorescence studies is highly suggestive of non-AL amyloidosis. Some of the non-AL amyloidosis are common while others are relatively rare. The clinical features, laboratory and renal pathology findings are helpful in the diagnosis and typing of non-AL amyloidosis. Thus, ALECT2 amyloidosis is characterized by diffuse cortical interstitial amyloid deposits, AA amyloidosis shows vascular deposits in addition to the glomerular deposits, AFib amyloidosis is characterized by massive amyloid accumulation limited to the glomeruli resulting in the obliteration of glomerular architecture, AApoA1 and AApoAIV are characterized by large amyloid deposits restricted to the medulla, and AGel shows swirling patterns of amyloid fibrils on electron microscopy. While light microscopy is very helpful, accurate typing of non-AL amyloidosis then requires immunohistochemical or laser microdissection/mass spectrometry studies of the Congo red positive deposits. Immunohistochemical studies are available for some of the non-AL amyloidosis. On the other hand, mass spectrometry analysis is a one stop methodology for confirmation and typing of amyloidosis. The diagnosis and typing of amyloidosis by mass spectrometry is based on finding the signature amyloid peptides, apolipoprotein E and serum amyloid-P component, followed by detection of precursor amyloidogenic protein such as LECT2, fibrinogen-α, gelsolin, etc. To, summarize, non-AL amyloidosis is a group of amyloidosis with distinctive clinical, laboratory and renal pathology findings. Typing of the amyloidosis is best performed using mass spectrometry methodology. Accurate typing of non-AL amyloidosis is imperative for correct management, prognosis, and genetic counseling.

Online Nanoflow Multidimensional Fractionation for High Efficiency Phosphopeptide Analysis*

PubMed Central

Ficarro, Scott B.; Zhang, Yi; Carrasco-Alfonso, Marlene J.; Garg, Brijesh; Adelmant, Guillaume; Webber, James T.; Luckey, C. John; Marto, Jarrod A.

2011-01-01

Despite intense, continued interest in global analyses of signaling cascades through mass spectrometry-based studies, the large-scale, systematic production of phosphoproteomics data has been hampered in-part by inefficient fractionation strategies subsequent to phosphopeptide enrichment. Here we explore two novel multidimensional fractionation strategies for analysis of phosphopeptides. In the first technique we utilize aliphatic ion pairing agents to improve retention of phosphopeptides at high pH in the first dimension of a two-dimensional RP-RP. The second approach is based on the addition of strong anion exchange as the second dimension in a three-dimensional reversed phase (RP)-strong anion exchange (SAX)-RP configuration. Both techniques provide for automated, online data acquisition, with the 3-D platform providing the highest performance both in terms of separation peak capacity and the number of unique phosphopeptide sequences identified per μg of cell lysate consumed. Our integrated RP-SAX-RP platform provides several analytical figures of merit, including: (1) orthogonal separation mechanisms in each dimension; (2) high separation peak capacity (3) efficient retention of singly- and multiply-phosphorylated peptides; (4) compatibility with automated, online LC-MS analysis. We demonstrate the reproducibility of RP-SAX-RP and apply it to the analysis of phosphopeptides derived from multiple biological contexts, including an in vitro model of acute myeloid leukemia in addition to primary polyclonal CD8+ T-cells activated in vivo through bacterial infection and then purified from a single mouse. PMID:21788404

A multi-method approach toward de novo glycan characterization: a Man-5 case study.

PubMed

Prien, Justin M; Prater, Bradley D; Cockrill, Steven L

2010-05-01

Regulatory agencies' expectations for biotherapeutic approval are becoming more stringent with regard to product characterization, where minor species as low as 0.1% of a given profile are typically identified. The mission of this manuscript is to demonstrate a multi-method approach toward de novo glycan characterization and quantitation, including minor species at or approaching the 0.1% benchmark. Recently, unexpected isomers of the Man(5)GlcNAc(2) (M(5)) were reported (Prien JM, Ashline DJ, Lapadula AJ, Zhang H, Reinhold VN. 2009. The high mannose glycans from bovine ribonuclease B isomer characterization by ion trap mass spectrometry (MS). J Am Soc Mass Spectrom. 20:539-556). In the current study, quantitative analysis of these isomers found in commercial M(5) standard demonstrated that they are in low abundance (<1% of the total) and therefore an exemplary "litmus test" for minor species characterization. A simple workflow devised around three core well-established analytical procedures: (1) fluorescence derivatization; (2) online rapid resolution reversed-phase separation coupled with negative-mode sequential mass spectrometry (RRRP-(-)-MS(n)); and (3) permethylation derivatization with nanospray sequential mass spectrometry (NSI-MS(n)) provides comprehensive glycan structural determination. All methods have limitations; however, a multi-method workflow is an at-line stopgap/solution which mitigates each method's individual shortcoming(s) providing greater opportunity for more comprehensive characterization. This manuscript is the first to demonstrate quantitative chromatographic separation of the M(5) isomers and the use of a commercially available stable isotope variant of 2-aminobenzoic acid to detect and chromatographically resolve multiple M(5) isomers in bovine ribonuclease B. With this multi-method approach, we have the capabilities to comprehensively characterize a biotherapeutic's glycan array in a de novo manner, including structural isomers at >/=0.1% of the total chromatographic peak area.

Epiandrosterone sulfate prolongs the detectability of testosterone, 4-androstenedione, and dihydrotestosterone misuse by means of carbon isotope ratio mass spectrometry.

PubMed

Piper, Thomas; Putz, Marlen; Schänzer, Wilhelm; Pop, Valentin; McLeod, Malcolm D; Uduwela, Dimanthi R; Stevenson, Bradley J; Thevis, Mario

2017-11-01

In the course of investigations into the metabolism of testosterone (T) by means of deuterated T and hydrogen isotope ratio mass spectrometry, a pronounced influence of the oral administration of T on sulfoconjugated steroid metabolites was observed. Especially in case of epiandrosterone sulfate (EPIA_S), the contribution of exogenous T to the urinary metabolite was traceable up to 8 days after a single oral dose of 40 mg of T. These findings initiated follow-up studies on the capability of EPIA_S to extend the detection of T and T analogue misuse by carbon isotope ratio (CIR) mass spectrometry in sports drug testing. Excretion study urine samples obtained after transdermal application of T and after oral administration of 4-androstenedione, dihydrotestosterone, and EPIA were investigated regarding urinary concentrations and CIR. With each administered steroid, EPIA_S was significantly depleted and prolonged the detectability when compared to routinely used steroidal target compounds by a factor of 2 to 5. In order to simplify the sample preparation procedure for sulfoconjugated compounds, enzymatic cleavage by Pseudomonas aeruginosa arylsulfatase was tested and implemented into CIR measurements for the first time. Further simplification was achieved by employing multidimensional gas chromatography to ensure the required peak purity for CIR determinations, instead of sample purification strategies using liquid chromatographic fractionation. Taking into account these results that demonstrate the unique and broad applicability of EPIA_S for the detection of illicit administrations of T or T-related steroids, careful consideration of how this steroid can be implemented into routine doping control analysis appears warranted. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Differential Mobility Spectrometry for Improved Selectivity in Hydrophilic Interaction Liquid Chromatography-Tandem Mass Spectrometry Analysis of Paralytic Shellfish Toxins

NASA Astrophysics Data System (ADS)

Beach, Daniel G.

2017-08-01

Paralytic shellfish toxins (PSTs) are neurotoxins produced by dinoflagellates and cyanobacteria that cause paralytic shellfish poisoning in humans. PST quantitation by LC-MS is challenging because of their high polarity, lability as gas-phase ions, and large number of potentially interfering analogues. Differential mobility spectrometry (DMS) has the potential to improve the performance of LC-MS methods for PSTs in terms of selectivity and limits of detection. This work describes a comprehensive investigation of the separation of 16 regulated PSTs by DMS and the development of highly selective LC-DMS-MS methods for PST quantitation. The effects of all DMS parameters on the separation of PSTs from one another were first investigated in detail. The labile nature of 11α-gonyautoxin epimers gave unique insight into fragmentation of labile analytes before, during, and after the DMS analyzer. Two sets of DMS parameters were identified that either optimized the resolution of PSTs from one another or transmitted them at a limited number of compensation voltage (CV) values corresponding to structural subclasses. These were used to develop multidimensional LC-DMS-MS/MS methods using existing HILIC-MS/MS parameters. In both cases, improved selectivity was observed when using DMS, and the quantitative capabilities of a rapid UPLC-DMS-MS/MS method were evaluated. Limits of detection of the developed method were similar to those without DMS, and differences were highly analyte-dependant. Analysis of shellfish matrix reference materials showed good agreement with established methods. The developed methods will be useful in cases where specific matrix interferences are encountered in the LC-MS/MS analysis of PSTs in complex biological samples.

Characterization of goat colostrum oligosaccharides by nano-liquid chromatography on chip quadrupole time-of-flight mass spectrometry and hydrophilic interaction liquid chromatography-quadrupole mass spectrometry

PubMed Central

Martín-Ortiz, A.; Salcedo, J.; Barile, D.; Bunyatratchata, A.; Moreno, F.J.; Martin-García, I.; Clemente, A.; Sanz, M.L.; Ruiz-Matute, A.I.

2016-01-01

A detailed qualitative and quantitative characterization of goat colostrum oligosaccharides (GCO) has been carried out for the first time. Defatted and deproteinized colostrum samples, previously treated by size exclusion chromatography (SEC) to remove lactose, were analyzed by nanoflow liquid chromatography-quadrupole-time of flight mass spectrometry (Nano-LC-Chip-Q-TOF MS). Up to 78 oligosaccharides containing hexose, hexosamine, fucose, N-acetylneuraminic acid or N-glycolylneuraminic acid monomeric units were identified in the samples, some of them detected for the first time in goat colostra. As a second step, a hydrophilic interaction liquid chromatography coupled to mass spectrometry (HILIC-MS) methodology was developed for the separation and quantitation of the main GCO, both acidic and neutral carbohydrates. Among other experimental chromatographic conditions, mobile phase additives and column temperature were evaluated in terms of retention time, resolution, peak width and symmetry of target carbohydrates. Narrow peaks (wh: 0.2–0.6 min) and good symmetry (As: 0.8–1.4) were obtained for GCO using an acetonitrile:water gradient with 0.1% ammonium hydroxide at 40 °C. These conditions were selected to quantify the main oligosaccharides in goat colostrum samples. Values ranging from 140 to 315 mg L−1 for neutral oligosaccharides and from 83 to 251 mg L−1 for acidic oligosaccharides were found. The combination of both techniques resulted to be useful to achieve a comprehensive characterization of GCO. PMID:26427327

Actinide Corroles: Synthesis and Characterization of Thorium(IV) and Uranium(IV) bis(-chloride) Dimers

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

Ward, Ashleigh L.; Buckley, Heather L.; Gryko, Daniel T.

2013-12-01

The first synthesis and structural characterization of actinide corroles is presented. Thorium(IV) and uranium(IV) macrocycles of Mes2(p-OMePh)corrole were synthesised and characterized by single-crystal X-ray diffraction, UV-Visible spectroscopy, variable-temperature 1H NMR, ESI mass spectrometry and cyclic voltammetry.

Qualitative characterization of Desmodium adscendens constituents by high-performance liquid chromatography-diode array ultraviolet-electrospray ionization multistage mass spectrometry.

PubMed

Baiocchi, Claudio; Medana, Claudio; Giancotti, Valeria; Aigotti, Riccardo; Dal Bello, Frederica; Massolino, Cristina; Gastaldi, Daniela; Grandi, Maurizio

2013-01-01

The many effects of the African medicinal herb Desmodium adscendens were studied in the 1980s and 1990s. In spite of this, a comprehensive analytical protocol for the quality control of its constituents (soyasaponins, alkaloids and flavonoids) has not yet been formulated and reported. This study deals with the optimization of extraction conditions from the plant and qualitative identification of the constituents by HPLC-diode array UV and multistage mass spectrometry. Plant constituents were extracted from leaves by liquid-liquid and solid matrix dispersion extraction. Separation was achieved via RP-C18 liquid chromatographywith UV and MS(n) detection and mass spectrometry analysis was conducted by electrospray ionization ion trap or orbitrap mass spectrometry. High resolution mass spectrometry (HRMS) was used for structural identification of active molecules relating to soyasaponins and alkaloids. The flavonoid fragmentations were preliminarily studied by HRMS in order to accurately characterize the more common neutral losses. However, the high number of isomeric species induced us to make recourse to a more extended chromatographic separation in order to enable useful tandem mass spectrometry and ultraviolet spectral interpretation to propose a reasonable chemical classification of these polyphenols. 35 compounds of this class were identified herein with respect to the five reported in literature in this way we made up a comprehensive protocol for the qualitative analysis of the high complexity content of this plant. This result paves the way for both reliable quality control of potential phytochemical medicaments and possible future systematic clinical studies.

Structural characterization of product ions by electrospray ionization and quadrupole time-of-flight mass spectrometry to support regulatory analysis of veterinary drug residues in foods Part 2: Benzimidazoles nitromidaz.....

USDA-ARS?s Scientific Manuscript database

RATIONALE: Analysis for identification and quantification of regulated veterinary drug residues in foods are usually achieved by liquid chromatography coupled to tandem mass spectrometry. The instrument method requires the selection of characteristic ions, but structure elucidation is seldom perform...

Toxin Detection in Patients' Sera by Mass Spectrometry during Two Outbreaks of Type A Botulism in France

PubMed Central

Mazuet, Christelle; Ezan, Eric; Volland, Hervé; Becher, François

2012-01-01

In two outbreaks of food-borne botulism in France, Clostridium botulinum type A was isolated and characterized from incriminated foods. Botulinum neurotoxin type A was detected in the patients' sera by mouse bioassay and in vitro endopeptidase assay with an immunocapture step and identification of the cleavage products by mass spectrometry. PMID:22993181

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).

Development of a certified reference material (NMIJ CRM 7531-a) for the determination of trace cadmium and other elements in brown rice flour.

PubMed

Miyashita, Shin-ichi; Inagaki, Kazumi; Narukawa, Tomohiro; Zhu, Yanbei; Kuroiwa, Takayoshi; Hioki, Akiharu; Chiba, Koichi

2012-01-01

A certified reference material (CRM) for trace cadmium and other elements in brown rice flour was developed at the National Metrology Institute of Japan (NMIJ). The CRM was provided as a dry powder after drying and frozen pulverization of fresh brown rice obtained from a Japanese domestic market. Characterization of the property value for each element was carried out exclusively by NMIJ with at least two independent analytical methods, including inductively coupled plasma mass spectrometry (ICP-MS), ICP high-resolution mass spectrometry, isotope-dilution ICP-MS, ICP optical emission spectrometry, and graphite-furnace atomic-absorption spectrometry. Property values were provided for six elements (Mn, Fe, Cu, Zn, As, and Cd). The concentration range of the property values was from 0.280 mg kg(-1) of As to 31.8 mg kg(-1) of Zn. The combined relative standard uncertainties of the property values were estimated by considering the uncertainties of the homogeneity, characterization, difference among analytical methods, dry-mass correction factor, and calibration standard. The range of the relative combined standard uncertainties was from 1.1% of Zn to 1.6% of As.

Multidimensional poverty, household environment and short-term morbidity in India.

PubMed

Dehury, Bidyadhar; Mohanty, Sanjay K

2017-01-01

Using the unit data from the second round of the Indian Human Development Survey (IHDS-II), 2011-2012, which covered 42,152 households, this paper examines the association between multidimensional poverty, household environmental deprivation and short-term morbidities (fever, cough and diarrhoea) in India. Poverty is measured in a multidimensional framework that includes the dimensions of education, health and income, while household environmental deprivation is defined as lack of access to improved sanitation, drinking water and cooking fuel. A composite index combining multidimensional poverty and household environmental deprivation has been computed, and households are classified as follows: multidimensional poor and living in a poor household environment, multidimensional non-poor and living in a poor household environment, multidimensional poor and living in a good household environment and multidimensional non-poor and living in a good household environment. Results suggest that about 23% of the population belonging to multidimensional poor households and living in a poor household environment had experienced short-term morbidities in a reference period of 30 days compared to 20% of the population belonging to multidimensional non-poor households and living in a poor household environment, 19% of the population belonging to multidimensional poor households and living in a good household environment and 15% of the population belonging to multidimensional non-poor households and living in a good household environment. Controlling for socioeconomic covariates, the odds of short-term morbidity was 1.47 [CI 1.40-1.53] among the multidimensional poor and living in a poor household environment, 1.28 [CI 1.21-1.37] among the multidimensional non-poor and living in a poor household environment and 1.21 [CI 1.64-1.28] among the multidimensional poor and living in a good household environment compared to the multidimensional non-poor and living in a good household environment. Results are robust across states and hold good for each of the three morbidities: fever, cough and diarrhoea. This establishes that along with poverty, household environmental conditions have a significant bearing on short-term morbidities in India. Public investment in sanitation, drinking water and cooking fuel can reduce the morbidity and improve the health of the population.

The Characterization of Laser Ablation Patterns and a New Definition of Resolution in Matrix Assisted Laser Desorption Ionization Imaging Mass Spectrometry (MALDI-IMS).

PubMed

O'Rourke, Matthew B; Raymond, Benjamin B A; Padula, Matthew P

2017-05-01

Matrix assisted laser desorption ionization imaging mass spectrometry (MALDI-IMS) is a technique that has seen a sharp rise in both use and development. Despite this rapid adoption, there have been few thorough investigations into the actual physical mechanisms that underlie the acquisition of IMS images. We therefore set out to characterize the effect of IMS laser ablation patterns on the surface of a sample. We also concluded that the governing factors that control spatial resolution have not been correctly defined and therefore propose a new definition of resolution. Graphical Abstract ᅟ.

Alkyd paints in art: characterization using integrated mass spectrometry.

PubMed

La Nasa, Jacopo; Degano, Ilaria; Modugno, Francesca; Colombini, Maria Perla

2013-10-03

Alkyd resins have been commonly used as binders in artist paints since the 1940s. The characterization of alkyds in samples from artworks can help to solve attribution and dating issues, investigate decay processes, and contribute to the planning of conservation strategies. Being able to assess the components of industrially formulated paint materials and to differentiate between different trademarks and producers is extremely interesting and requires multi-analytical approaches. In this paper we describe the characterization of commercial alkyd paint materials using a multi-analytical approach based on the integration of three different mass spectrometric techniques: gas chromatography-mass spectrometry (GC/MS), high performance liquid chromatography coupled with electrospray ionization mass spectrometry with a tandem quadrupole-time of flight mass spectrometer (HPLC-ESI-Q-ToF), and flow injection analysis (FIA) in the ESI-Q-ToF mass spectrometer. GC/MS was successful in determining the fatty acid and aromatic fractions of the resins after hydrolysis; HPLC-ESI-Q-ToF analysis enabled us to identify the triglycerides (TAGs) and diglycerides (DAGs) profile of each resin, and FIA analysis was used as a rapid method to evaluate the presence of possible additives such as synthetic polymers. Copyright © 2013 Elsevier B.V. All rights reserved.

Morphological and compositional study of 238U thin film targets for nuclear experiments

NASA Astrophysics Data System (ADS)

Sibbens, Goedele; Ernstberger, Markus; Gouder, Thomas; Marouli, Maria; Moens, André; Seibert, Alice; Vanleeuw, David; Zúñiga, Martin Vargas; Wiss, Thierry; Zampella, Mariavittoria; Zuleger, Evelyn

2018-05-01

The uncertainty in neutron cross section values strongly depends on the quality and characteristics of the deposited actinide films which are used as "targets" in the nuclear experiments. Until recently, at the Joint Research Centre in Geel (JRC-Geel), mass and areal densities of actinide layers were determined by measuring activity (using alpha-particle counting), isotopic composition (using thermal ionisation mass spectrometry) and diameter. In this study a series of 238U deposits, prepared by molecular plating and vacuum deposition on different substrates, were characterized with additional non-destructive and destructive analysis techniques. The quality of the deposits was investigated by autoradiography, high-resolution alpha-particle spectrometry, and scanning electron microscopy. The elemental composition was determined by x-ray photoelectron spectroscopy and inductively coupled plasma mass spectrometry. The latter technique was also applied on the U3O8 starting material and the converted UF4 powder. This paper compares the quality and morphology of deposited 238U films prepared by molecular plating and vacuum deposition on various backings, including their elemental composition determined by different characterization techniques. Also discussed are problems in target preparation and characterization.

xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry.

PubMed

Walzthoeni, Thomas; Joachimiak, Lukasz A; Rosenberger, George; Röst, Hannes L; Malmström, Lars; Leitner, Alexander; Frydman, Judith; Aebersold, Ruedi

2015-12-01

Chemical cross-linking in combination with mass spectrometry generates distance restraints of amino acid pairs in close proximity on the surface of native proteins and protein complexes. In this study we used quantitative mass spectrometry and chemical cross-linking to quantify differences in cross-linked peptides obtained from complexes in spatially discrete states. We describe a generic computational pipeline for quantitative cross-linking mass spectrometry consisting of modules for quantitative data extraction and statistical assessment of the obtained results. We used the method to detect conformational changes in two model systems: firefly luciferase and the bovine TRiC complex. Our method discovers and explains the structural heterogeneity of protein complexes using only sparse structural information.

Cobalt coated substrate for matrix-free analysis of small molecules by laser desorption/ionization mass spectrometry

NASA Astrophysics Data System (ADS)

Yalcin, Talat; Li, Liang

2009-12-01

Small molecule analysis is one of the most challenging issues in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. We have developed a cobalt coated substrate as a target for matrix-free analysis of small molecules in laser desorption/ionization mass spectrometry. Cobalt coating of 60-70 nm thickness has been characterized by scanning electron microscopy, energy dispersive X-ray analysis, X-ray diffraction, and laser induced breakdown spectroscopy. This target facilitates hundreds of samples to be spotted and analyzed without mixing any matrices, in a very short time. This can save a lot of time and money and can be a very practical approach for the analysis of small molecules by laser desorption/ionization mass spectrometry.

Self-assembly of triangular metallomacrocycles using unsymmetrical bisterpyridine ligands: isomer differentiation via TWIM mass spectrometry.

PubMed

Liang, Yen-Peng; He, Yun-Jui; Lee, Yin-Hsuan; Chan, Yi-Tsu

2015-03-21

Three unsymmetrical, 60°-bended bisterpyridine ligands with varying phenylene spacer lengths have been synthesized via the Suzuki-Miyaura coupling reactions. Their self-assembly processes were found to be strongly dependent on the ligand geometry. Upon complexation with Zn(II) ions, only 2,4''-di(4'-terpyridinyl)-1,1':4',1''-terphenyl underwent self-selection to give a trinuclear metallomacrocycle with perfect heteroleptic connectivity and the other two afforded a mixture of constitutional isomers. The metallosupramolecular assemblies were characterized by NMR spectroscopy, electrospray mass spectrometry (ESI MS), and single-crystal X-ray diffraction. In particular, the identification of isomeric architecture was accomplished using tandem mass spectrometry (MS(2)) coupled with traveling wave ion mobility mass spectrometry (TWIM MS).

Extraction and characterization of montmorency (Prunus cerasus L.) sour cherry pit oil

USDA-ARS?s Scientific Manuscript database

Montmorency sour cherry (Prunus cerasus L.) pit oil was extracted and characterized by various methods including: gas chromatography (GC), liquid chromatography coupled with mass spectrometry (LC-MS), nuclear magnetic resonance (NMR), thermogravimetric analysis (TGA), differential scanning calorime...

Proteomic analysis of corneal endothelial cell-descemet membrane tissues reveals influence of insulin dependence and disease severity in type 2 diabetes mellitus.

PubMed

Skeie, Jessica M; Aldrich, Benjamin T; Goldstein, Andrew S; Schmidt, Gregory A; Reed, Cynthia R; Greiner, Mark A

2018-01-01

The objective of this study was to characterize the proteome of the corneal endothelial cell layer and its basement membrane (Descemet membrane) in humans with various severities of type II diabetes mellitus compared to controls, and identify differentially expressed proteins across a range of diabetic disease severities that may influence corneal endothelial cell health. Endothelium-Descemet membrane complex tissues were peeled from transplant suitable donor corneas. Protein fractions were isolated from each sample and subjected to multidimensional liquid chromatography and tandem mass spectrometry. Peptide spectra were matched to the human proteome, assigned gene ontology, and grouped into protein signaling pathways unique to each of the disease states. We identified an average of 12,472 unique proteins in each of the endothelium-Descemet membrane complex tissue samples. There were 2,409 differentially expressed protein isoforms that included previously known risk factors for type II diabetes mellitus related to metabolic processes, oxidative stress, and inflammation. Gene ontology analysis demonstrated that diabetes progression has many protein footprints related to metabolic processes, binding, and catalysis. The most represented pathways involved in diabetes progression included mitochondrial dysfunction, cell-cell junction structure, and protein synthesis regulation. This proteomic dataset identifies novel corneal endothelial cell and Descemet membrane protein expression in various stages of diabetic disease. These findings give insight into the mechanisms involved in diabetes progression relevant to the corneal endothelium and its basement membrane, prioritize new pathways for therapeutic targeting, and provide insight into potential biomarkers for determining the health of this tissue.

Multidimensional chromatography in food analysis.

PubMed

Herrero, Miguel; Ibáñez, Elena; Cifuentes, Alejandro; Bernal, Jose

2009-10-23

In this work, the main developments and applications of multidimensional chromatographic techniques in food analysis are reviewed. Different aspects related to the existing couplings involving chromatographic techniques are examined. These couplings include multidimensional GC, multidimensional LC, multidimensional SFC as well as all their possible combinations. Main advantages and drawbacks of each coupling are critically discussed and their key applications in food analysis described.

Broad Separation of Isomeric Lipids by High-Resolution Differential Ion Mobility Spectrometry with Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Bowman, Andrew P.; Abzalimov, Rinat R.; Shvartsburg, Alexandre A.

2017-08-01

Maturation of metabolomics has brought a deeper appreciation for the importance of isomeric identity of lipids to their biological role, mirroring that for proteoforms in proteomics. However, full characterization of the lipid isomerism has been thwarted by paucity of rapid and effective analytical tools. A novel approach is ion mobility spectrometry (IMS) and particularly differential or field asymmetric waveform IMS (FAIMS) at high electric fields, which is more orthogonal to mass spectrometry. Here we broadly explore the power of FAIMS to separate lipid isomers, and find a 75% success rate across the four major types of glycero- and phospho- lipids ( sn, chain length, double bond position, and cis/ trans). The resolved isomers were identified using standards, and (for the first two types) tandem mass spectrometry. These results demonstrate the general merit of incorporating high-resolution FAIMS into lipidomic analyses.

Detection of poly(ethylene glycol) residues from nonionic surfactants in surface water by1h and13c nuclear magnetic resonance spectrometry

USGS Publications Warehouse

Leenheer, J.A.; Wershaw, R. L.; Brown, P.A.; Noyes, T.I.

1991-01-01

??? Poly(ethylene glycol) (PEG) residues were detected in organic solute isolates from surface water by 1H nuclear magnetic resonance spectrometry (NMR), 13C NMR spectrometry, and colorimetric assay. PEG residues were separated from natural organic solutes in Clear Creek, CO, by a combination of methylation and chromatographic procedures. The isolated PEG residues, characterized by NMR spectrometry, were found to consist of neutral and acidic residues that also contained poly(propylene glycol) moieties. The 1H NMR and the colorimetric assays for poly(ethylene glycol) residues were done on samples collected in the lower Mississippi River and tributaries between St. Louis, MO, and New Orleans, LA, in July-August and November-December 1987. Aqueous concentrations for poly(ethylene glycol) residues based on colorimetric assay ranged from undetectable to ???28 ??g/L. Concentrations based on 1H NMR spectrometry ranged from undetectable to 145 ??g/L.

Multidimensional Riemann problem with self-similar internal structure - part III - a multidimensional analogue of the HLLI Riemann solver for conservative hyperbolic systems

NASA Astrophysics Data System (ADS)

Balsara, Dinshaw S.; Nkonga, Boniface

2017-10-01

Just as the quality of a one-dimensional approximate Riemann solver is improved by the inclusion of internal sub-structure, the quality of a multidimensional Riemann solver is also similarly improved. Such multidimensional Riemann problems arise when multiple states come together at the vertex of a mesh. The interaction of the resulting one-dimensional Riemann problems gives rise to a strongly-interacting state. We wish to endow this strongly-interacting state with physically-motivated sub-structure. The fastest way of endowing such sub-structure consists of making a multidimensional extension of the HLLI Riemann solver for hyperbolic conservation laws. Presenting such a multidimensional analogue of the HLLI Riemann solver with linear sub-structure for use on structured meshes is the goal of this work. The multidimensional MuSIC Riemann solver documented here is universal in the sense that it can be applied to any hyperbolic conservation law. The multidimensional Riemann solver is made to be consistent with constraints that emerge naturally from the Galerkin projection of the self-similar states within the wave model. When the full eigenstructure in both directions is used in the present Riemann solver, it becomes a complete Riemann solver in a multidimensional sense. I.e., all the intermediate waves are represented in the multidimensional wave model. The work also presents, for the very first time, an important analysis of the dissipation characteristics of multidimensional Riemann solvers. The present Riemann solver results in the most efficient implementation of a multidimensional Riemann solver with sub-structure. Because it preserves stationary linearly degenerate waves, it might also help with well-balancing. Implementation-related details are presented in pointwise fashion for the one-dimensional HLLI Riemann solver as well as the multidimensional MuSIC Riemann solver.

Combined Multidimensional Microscopy as a Histopathology Imaging Tool.

PubMed

Shami, Gerald J; Cheng, Delfine; Braet, Filip

2017-02-01

Herein, we present a highly versatile bioimaging workflow for the multidimensional imaging of biological structures across vastly different length scales. Such an approach allows for the optimised preparation of samples in one go for consecutive X-ray micro-computed tomography, bright-field light microscopy and backscattered scanning electron microscopy, thus, facilitating the disclosure of combined structural information ranging from the gross tissue or cellular level, down to the nanometre scale. In this current study, we characterize various aspects of the hepatic vasculature, ranging from such large vessels as branches of the hepatic portal vein and hepatic artery, down to the smallest sinusoidal capillaries. By employing high-resolution backscattered scanning electron microscopy, we were able to further characterize the subcellular features of a range of hepatic sinusoidal cells including, liver sinusoidal endothelial cells, pit cells and Kupffer cells. Above all, we demonstrate the capabilities of a specimen manipulation workflow that can be applied and adapted to a plethora of functional and structural investigations and experimental models. Such an approach harnesses the fundamental advantages inherent to the various imaging modalities presented herein, and when combined, offers information not currently available by any single imaging platform. J. Cell. Physiol. 232: 249-256, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Ultrafast quantum control of ionization dynamics in krypton.

PubMed

Hütten, Konrad; Mittermair, Michael; Stock, Sebastian O; Beerwerth, Randolf; Shirvanyan, Vahe; Riemensberger, Johann; Duensing, Andreas; Heider, Rupert; Wagner, Martin S; Guggenmos, Alexander; Fritzsche, Stephan; Kabachnik, Nikolay M; Kienberger, Reinhard; Bernhardt, Birgitta

2018-02-19

Ultrafast spectroscopy with attosecond resolution has enabled the real time observation of ultrafast electron dynamics in atoms, molecules and solids. These experiments employ attosecond pulses or pulse trains and explore dynamical processes in a pump-probe scheme that is selectively sensitive to electronic state of matter via photoelectron or XUV absorption spectroscopy or that includes changes of the ionic state detected via photo-ion mass spectrometry. Here, we demonstrate how the implementation of combined photo-ion and absorption spectroscopy with attosecond resolution enables tracking the complex multidimensional excitation and decay cascade of an Auger auto-ionization process of a few femtoseconds in highly excited krypton. In tandem with theory, our study reveals the role of intermediate electronic states in the formation of multiply charged ions. Amplitude tuning of a dressing laser field addresses different groups of decay channels and allows exerting temporal and quantitative control over the ionization dynamics in rare gas atoms.

A simple, multidimensional approach to high-throughput discovery of catalytic reactions.

PubMed

Robbins, Daniel W; Hartwig, John F

2011-09-09

Transition metal complexes catalyze many important reactions that are employed in medicine, materials science, and energy production. Although high-throughput methods for the discovery of catalysts that would mirror related approaches for the discovery of medicinally active compounds have been the focus of much attention, these methods have not been sufficiently general or accessible to typical synthetic laboratories to be adopted widely. We report a method to evaluate a broad range of catalysts for potential coupling reactions with the use of simple laboratory equipment. Specifically, we screen an array of catalysts and ligands with a diverse mixture of substrates and then use mass spectrometry to identify reaction products that, by design, exceed the mass of any single substrate. With this method, we discovered a copper-catalyzed alkyne hydroamination and two nickel-catalyzed hydroarylation reactions, each of which displays excellent functional-group tolerance.

Coupled LC-GC techniques for the characterisation of polycyclic aromatic compounds in fuel materials

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

Askey, S.A.; Holden, K.M.L.; Bartle, K.D.

1995-12-31

Exposure to polycyclic aromatic compounds (PAC) has long been identified as of considerable environmental concern. Originating from both natural and anthropogenic sources, many PAC exhibit significant carcinogenic and mutagenic properties. Multi-dimensional chromatographic techniques which provide separation by virtue of chemical class (group-type) or by molecular mass greatly simplifies the analysis of inherently complex fuel materials. In this study, on-line LC-GC techniques in which high resolution gas chromatography (HPLC) have been investigated. Comprehensive characterisation of fuel feedstocks and post-pyrolysis and combustion products was achieved by coupling LC-GC to low resolution ion trap mass spectrometry (ITD-MS) and atomic emission detection (AED). Themore » identification of PAC in diesel and coal materials, as well as urban air and diesel exhaust particulate extracts has provided valuable insight into the source, formation and distribution of such compounds pre- and post processing.« less

Characterization and use of new monoclonal antibodies to CD11c,CD14, and CD163 to analyze the phenotypic complexity of ruminantmonocyte subsets

USDA-ARS?s Scientific Manuscript database

The sequencing of the bovine genome and development of mass spectrometry, in conjunction with flow cytometry (FC), have afforded an opportunity to complete the characterization of the specificity of monoclonal antibodies (mAbs), only partially characterized during previous international workshops fo...

Multidimensional spectrometer

DOEpatents

Zanni, Martin Thomas; Damrauer, Niels H.

2010-07-20

A multidimensional spectrometer for the infrared, visible, and ultraviolet regions of the electromagnetic spectrum, and a method for making multidimensional spectroscopic measurements in the infrared, visible, and ultraviolet regions of the electromagnetic spectrum. The multidimensional spectrometer facilitates measurements of inter- and intra-molecular interactions.

Introducing Students to Gas Chromatography-Mass Spectrometry Analysis and Determination of Kerosene Components in a Complex Mixture

ERIC Educational Resources Information Center

Pacot, Giselle Mae M.; Lee, Lyn May; Chin, Sung-Tong; Marriott, Philip J.

2016-01-01

Gas chromatography-mass spectrometry (GC-MS) and GC-tandem MS (GC-MS/MS) are useful in many separation and characterization procedures. GC-MS is now a common tool in industry and research, and increasingly, GC-MS/MS is applied to the measurement of trace components in complex mixtures. This report describes an upper-level undergraduate experiment…

Reusable rocket engine optical condition monitoring

NASA Technical Reports Server (NTRS)

Wyett, L.; Maram, J.; Barkhoudarian, S.; Reinert, J.

1987-01-01

Plume emission spectrometry and optical leak detection are described as two new applications of optical techniques to reusable rocket engine condition monitoring. Plume spectrometry has been used with laboratory flames and reusable rocket engines to characterize both the nominal combustion spectra and anomalous spectra of contaminants burning in these plumes. Holographic interferometry has been used to identify leaks and quantify leak rates from reusable rocket engine joints and welds.

Qualification and initial characterization of a high-purity 233U spike for use in uranium analyses

DOE PAGES

Mathew, K. J.; Canaan, R. D.; Hexel, C.; ...

2015-08-20

Several high-purity 233U items potentially useful as isotope dilution mass spectrometry standards for safeguards, non-proliferation, and nuclear forensics measurements are identified and rescued from downblending. By preserving the supply of 233U materials of different pedigree for use as source materials for certified reference materials (CRMs), it is ensured that the safeguards community has high quality uranium isotopic standards required for calibration of the analytical instruments. One of the items identified as a source material for a high-purity CRM is characterized for the uranium isotope-amount ratios using thermal ionization mass spectrometry (TIMS). Additional verification measurements on this material using quadrupole inductivelymore » coupled plasma mass spectrometry (ICPMS) are also performed. As a result, the comparison of the ICPMS uranium isotope-amount ratios with the TIMS data, with much smaller uncertainties, validated the ICPMS measurement practices. ICPMS is proposed for the initial screening of the purity of items in the rescue campaign.« less

Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation

NASA Astrophysics Data System (ADS)

Sheynkman, Gloria M.; Shortreed, Michael R.; Cesnik, Anthony J.; Smith, Lloyd M.

2016-06-01

Mass spectrometry-based proteomics has emerged as the leading method for detection, quantification, and characterization of proteins. Nearly all proteomic workflows rely on proteomic databases to identify peptides and proteins, but these databases typically contain a generic set of proteins that lack variations unique to a given sample, precluding their detection. Fortunately, proteogenomics enables the detection of such proteomic variations and can be defined, broadly, as the use of nucleotide sequences to generate candidate protein sequences for mass spectrometry database searching. Proteogenomics is experiencing heightened significance due to two developments: (a) advances in DNA sequencing technologies that have made complete sequencing of human genomes and transcriptomes routine, and (b) the unveiling of the tremendous complexity of the human proteome as expressed at the levels of genes, cells, tissues, individuals, and populations. We review here the field of human proteogenomics, with an emphasis on its history, current implementations, the types of proteomic variations it reveals, and several important applications.

Analysis of hydraulic fracturing additives by LC/Q-TOF-MS.

PubMed

Ferrer, Imma; Thurman, E Michael

2015-08-01

The chemical additives used in fracturing fluids can be used as tracers of water contamination caused by hydraulic fracturing operations. For this purpose, a complete chemical characterization is necessary using advanced analytical techniques. Liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (LC/Q-TOF-MS) was used to identify chemical additives present in flowback and produced waters. Accurate mass measurements of main ions and fragments were used to characterize the major components of fracking fluids. Sodium adducts turned out to be the main molecular adduct ions detected for some additives due to oxygen-rich structures. Among the classes of chemical components analyzed by mass spectrometry include gels (guar gum), biocides (glutaraldehyde and alkyl dimethyl benzyl ammonium chloride), and surfactants (cocamidopropyl dimethylamines, cocamidopropyl hydroxysultaines, and cocamidopropyl derivatives). The capabilities of accurate mass and MS-MS fragmentation are explored for the unequivocal identification of these compounds. A special emphasis is given to the mass spectrometry elucidation approaches used to identify a major class of hydraulic fracturing compounds, surfactants.

Characterization of high explosive particles using cluster secondary ion mass spectrometry.

PubMed

Gillen, Greg; Mahoney, Christine; Wight, Scott; Lareau, Richard

2006-01-01

The use of secondary ion mass spectrometry (SIMS) for the detection and spatially resolved analysis of individual high explosive particles is described. A C(8) (-) carbon cluster primary ion beam was used in a commercial SIMS instrument to analyze samples of high explosives dispersed as particles on silicon substrates. In comparison with monatomic primary ion bombardment, the carbon cluster primary ion beam was found to greatly enhance characteristic secondary ion signals from the explosive compounds while causing minimal beam-induced degradation. The resistance of these compounds to degradation under ion bombardment allows explosive particles to be analyzed under high primary ion dose bombardment (dynamic SIMS) conditions, facilitating the rapid acquisition of spatially resolved molecular information. The use of cluster SIMS combined with computer control of the sample stage position allows for the automated identification and counting of explosive particle distributions on silicon surfaces. This will be useful for characterizing the efficiency of transfer of particulates in trace explosive detection portal collectors and/or swipes utilized for ion mobility spectrometry applications.

Profiling the indole alkaloids in yohimbe bark with ultra-performance liquid chromatography coupled with ion mobility quadrupole time-of-flight mass spectrometry.

PubMed

Sun, Jianghao; Baker, Andrew; Chen, Pei

2011-09-30

An ultra-performance liquid chromatography/ion mobility quadrupole time-of-flight mass spectrometry (UPLC/IM-QTOF-MS) method was developed for profiling the indole alkaloids in yohimbe bark. Many indole alkaloids with the yohimbine or ajmalicine core structure, plus methylated, oxidized and reduced species, were characterized. Common fragments and mass differences are described. It was shown that the use of IMS could provide another molecular descriptor, i.e. molecular shape by rotationally averaged collision cross-section; this is of great value for identification of constituents when reference materials are usually not available. Using the combination of high resolution (~40000) accurate mass measurement with time-aligned parallel (TAP) fragmentation, MS(E) (where E represents collision energy), ion mobility mass spectrometry (IMS) and UPLC chromatography, a total 55 indole alkaloids were characterized and a few new indole alkaloids are reported for the first time. Published in 2011 by John Wiley & Sons, Ltd.

Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring.

PubMed

Lange, Vinzenz; Malmström, Johan A; Didion, John; King, Nichole L; Johansson, Björn P; Schäfer, Juliane; Rameseder, Jonathan; Wong, Chee-Hong; Deutsch, Eric W; Brusniak, Mi-Youn; Bühlmann, Peter; Björck, Lars; Domon, Bruno; Aebersold, Ruedi

2008-08-01

In many studies, particularly in the field of systems biology, it is essential that identical protein sets are precisely quantified in multiple samples such as those representing differentially perturbed cell states. The high degree of reproducibility required for such experiments has not been achieved by classical mass spectrometry-based proteomics methods. In this study we describe the implementation of a targeted quantitative approach by which predetermined protein sets are first identified and subsequently quantified at high sensitivity reliably in multiple samples. This approach consists of three steps. First, the proteome is extensively mapped out by multidimensional fractionation and tandem mass spectrometry, and the data generated are assembled in the PeptideAtlas database. Second, based on this proteome map, peptides uniquely identifying the proteins of interest, proteotypic peptides, are selected, and multiple reaction monitoring (MRM) transitions are established and validated by MS2 spectrum acquisition. This process of peptide selection, transition selection, and validation is supported by a suite of software tools, TIQAM (Targeted Identification for Quantitative Analysis by MRM), described in this study. Third, the selected target protein set is quantified in multiple samples by MRM. Applying this approach we were able to reliably quantify low abundance virulence factors from cultures of the human pathogen Streptococcus pyogenes exposed to increasing amounts of plasma. The resulting quantitative protein patterns enabled us to clearly define the subset of virulence proteins that is regulated upon plasma exposure.

Multidimensional fractionation is a requirement for quantitation of Golgi-resident glycosylation enzymes from cultured human cells.

PubMed

Lin, Chi-Hung; Chik, Jenny H L; Packer, Nicolle H; Molloy, Mark P

2015-02-06

Glycosylation results from the concerted action of glycosylation enzymes in the secretory pathway. In general, gene expression serves as the primary control mechanism, but post-translational fine-tuning of glycosylation enzyme functions is often necessary for efficient synthesis of specific glycan epitopes. While the field of glycomics has rapidly advanced, there lacks routine proteomic methods to measure expression of specific glycosylation enzymes needed to fill the gap between mRNA expression and the glycomic profile in a "reverse genomics" workflow. Toward developing this workflow we enriched Golgi membranes from two human colon cancer cell lines by sucrose density centrifugation and further mass-based fractionation by SDS-PAGE. We then applied mass spectrometry to demonstrate a doubling in the number of Golgi resident proteins identified, compared to the unenriched, low speed centrifuged supernatant of lysed cells. A total of 35 Golgi-resident glycosylation enzymes, of which 23 were glycosyltransferases, were identified making this the largest protein database so far of Golgi resident glycosylation enzymes experimentally identified in cultured human cells. We developed targeted mass spectrometry assays for specific quantitation of many of these glycosylation enzymes. Our results show that alterations in abundance of glycosylation enzymes at the protein level were generally consistent with the resultant glycomic profiles, but not necessarily with the corresponding glycosyltransferase mRNA expression as exemplified by the case of O-glycan core 1 T synthase.

Profiling oil sands mixtures from industrial developments and natural groundwaters for source identification.

PubMed

Frank, Richard A; Roy, James W; Bickerton, Greg; Rowland, Steve J; Headley, John V; Scarlett, Alan G; West, Charles E; Peru, Kerry M; Parrott, Joanne L; Conly, F Malcolm; Hewitt, L Mark

2014-01-01

The objective of this study was to identify chemical components that could distinguish chemical mixtures in oil sands process-affected water (OSPW) that had potentially migrated to groundwater in the oil sands development area of northern Alberta, Canada. In the first part of the study, OSPW samples from two different tailings ponds and a broad range of natural groundwater samples were assessed with historically employed techniques as Level-1 analyses, including geochemistry, total concentrations of naphthenic acids (NAs) and synchronous fluorescence spectroscopy (SFS). While these analyses did not allow for reliable source differentiation, they did identify samples containing significant concentrations of oil sands acid-extractable organics (AEOs). In applying Level-2 profiling analyses using electrospray ionization high resolution mass spectrometry (ESI-HRMS) and comprehensive multidimensional gas chromatography time-of-flight mass spectrometry (GC × GC-TOF/MS) to samples containing appreciable AEO concentrations, differentiation of natural from OSPW sources was apparent through measurements of O2:O4 ion class ratios (ESI-HRMS) and diagnostic ions for two families of suspected monoaromatic acids (GC × GC-TOF/MS). The resemblance between the AEO profiles from OSPW and from 6 groundwater samples adjacent to two tailings ponds implies a common source, supporting the use of these complimentary analyses for source identification. These samples included two of upward flowing groundwater collected <1 m beneath the Athabasca River, suggesting OSPW-affected groundwater is reaching the river system.

Enantioselective column coupled electrophoresis employing large bore capillaries hyphenated with tandem mass spectrometry for ultra-trace determination of chiral compounds in complex real samples.

PubMed

Piešťanský, Juraj; Maráková, Katarína; Kovaľ, Marián; Havránek, Emil; Mikuš, Peter

2015-12-01

A new multidimensional analytical approach for the ultra-trace determination of target chiral compounds in unpretreated complex real samples was developed in this work. The proposed analytical system provided high orthogonality due to on-line combination of three different methods (separation mechanisms), i.e. (1) isotachophoresis (ITP), (2) chiral capillary zone electrophoresis (chiral CZE), and (3) triple quadrupole mass spectrometry (QqQ MS). The ITP step, performed in a large bore capillary (800 μm), was utilized for the effective sample pretreatment (preconcentration and matrix clean-up) in a large injection volume (1-10 μL) enabling to obtain as low as ca. 80 pg/mL limits of detection for the target enantiomers in urine matrices. In the chiral CZE step, the different chiral selectors (neutral, ionizable, and permanently charged cyclodextrins) and buffer systems were tested in terms of enantioselectivity and influence on the MS detection response. The performance parameters of the optimized ITP - chiral CZE-QqQ MS method were evaluated according to the FDA guidance for bioanalytical method validation. Successful validation and application (enantioselective monitoring of renally eliminated pheniramine and its metabolite in human urine) highlighted great potential of this chiral approach in advanced enantioselective biomedical applications. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Reforming the taxonomy in disorders of consciousness.

PubMed

Bayne, Tim; Hohwy, Jakob; Owen, Adrian M

2017-12-01

This article examines the serious shortcomings that characterize the current taxonomy of postcomatose disorders of consciousness (DoC), and it provides guidelines for how an improved DoC taxonomy might be developed. In particular, it is argued that behavioral criteria for the application of DoC categories should be supplemented with brain-based criteria (eg, information derived from electroencephalography and functional magnetic resonance imaging), and that the categorical framework that currently characterizes DoC should be replaced by a multidimensional framework that better captures the performance of patients across a range of cognitive and behavioural tasks. Ann Neurol 2017;82:866-872. © 2017 American Neurological Association.

Tackling saponin diversity in marine animals by mass spectrometry: data acquisition and integration.

PubMed

Decroo, Corentin; Colson, Emmanuel; Demeyer, Marie; Lemaur, Vincent; Caulier, Guillaume; Eeckhaut, Igor; Cornil, Jérôme; Flammang, Patrick; Gerbaux, Pascal

2017-05-01

Saponin analysis by mass spectrometry methods is nowadays progressively supplementing other analytical methods such as nuclear magnetic resonance (NMR). Indeed, saponin extracts from plant or marine animals are often constituted by a complex mixture of (slightly) different saponin molecules that requires extensive purification and separation steps to meet the requirement for NMR spectroscopy measurements. Based on its intrinsic features, mass spectrometry represents an inescapable tool to access the structures of saponins within extracts by using LC-MS, MALDI-MS, and tandem mass spectrometry experiments. The combination of different MS methods nowadays allows for a nice description of saponin structures, without extensive purification. However, the structural characterization process is based on low kinetic energy CID which cannot afford a total structure elucidation as far as stereochemistry is concerned. Moreover, the structural difference between saponins in a same extract is often so small that coelution upon LC-MS analysis is unavoidable, rendering the isomeric distinction and characterization by CID challenging or impossible. In the present paper, we introduce ion mobility in combination with liquid chromatography to better tackle the structural complexity of saponin congeners. When analyzing saponin extracts with MS-based methods, handling the data remains problematic for the comprehensive report of the results, but also for their efficient comparison. We here introduce an original schematic representation using sector diagrams that are constructed from mass spectrometry data. We strongly believe that the proposed data integration could be useful for data interpretation since it allows for a direct and fast comparison, both in terms of composition and relative proportion of the saponin contents in different extracts. Graphical Abstract A combination of state-of-the-art mass spectrometry methods, including ion mobility spectroscopy, is developed to afford a complete description of the saponin molecules in natural extracts.

Characterization of solution-phase and gas-phase reactions in on-line electrochemistry-thermospray tandem mass spectrometry.

PubMed

Volk, K J; Yost, R A; Brajter-Toth, A

1989-07-14

Electrochemistry was used on-line with high-performance liquid chromatography-thermospray tandem mass spectrometry to provide insight into the solution-phase decomposition reactions of electrochemically generated oxidation products. Products formed during electrooxidation were monitored as the electrode potential was varied. The solution reactions which follow the initial electron transfer at the electrode are affected by the vaporizer tip temperature of the thermospray probe and the composition of the thermospray buffer. Either hydrolysis or ammonolysis reactions of the initial electrochemical oxidation products can occur with pH 7 ammonium acetate buffer. Both the electrochemically generated and the synthesized disulfide of 6-thiopurine decompose under thermospray conditions to produce 6-thiopurine and purine-6-sulfinate. Solution-phase studies indicate that nucleophilic and electrophilic substitution reactions with purine-6-sulfinate result in the formation of purine, adenine, and hypoxanthine. Products were identified and characterized by tandem mass spectrometry. This work shows the first example of high-performance liquid chromatography used on-line with electrochemistry to separate stable oxidation products prior to analysis by thermospray tandem mass spectrometry. In addition, solution-phase and gas-phase studies with methylamine show that the site of the nucleophilic and electrophilic reactions is probably inside the thermospray probe. Most importantly, these results also show that the on-line combination of electrochemistry with thermospray tandem mass spectrometry provides valuable information about redox and associated chemical reactions of biological molecules such as the structures of intermediates or products as well as providing insight into reaction pathways.

Nucleic Acid analysis by fourier transform ion cyclotron resonance mass spectrometry at the beginning of the twenty-first century.

PubMed

Frahm, J L; Muddiman, D C

2005-01-01

Mass spectrometers measure an intrinsic property (i.e., mass) of a molecule, which makes it an ideal platform for nucleic acid analysis. Importantly, the unparalleled capabilities of Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry further extend its usefulness for nucleic acid analysis. The beginning of the twenty-first century has been marked with notable advances in the field of FT-ICR mass spectrometry analysis of nucleic acids. Some of these accomplishments include fundamental studies of nucleic acid properties, improvements in sample clean up and preparation, better methods to obtain higher mass measurement accuracy, analysis of noncovalent complexes, tandem mass spectrometry, and characterization of peptide nucleic acids. This diverse range of studies will be presented herein.

Analysis of the Proteome of Hair-Cell Stereocilia by Mass Spectrometry

PubMed Central

Krey, Jocelyn F.; Wilmarth, Philip A.; David, Larry L.; Barr-Gillespie, Peter G.

2017-01-01

Characterization of proteins that mediate mechanotransduction by hair cells, the sensory cells of the inner ear, is hampered by the scarcity of these cells and their sensory organelle, the hair bundle. Mass spectrometry, with its high sensitivity and identification precision, is the ideal method for determining which proteins are present in bundles and what proteins they interact with. We describe here the isolation of mouse hair bundles, as well as preparation of bundle-protein samples for mass spectrometry. We also describe protocols for data-dependent (shotgun) and parallel-reaction-monitoring (targeted) mass spectrometry that allow us to identify and quantify proteins of the hair bundle. These sensitive methods are particularly useful for comparing proteomes of wild-type and mice with deafness mutations affecting hair-bundle proteins. (120 words; maximum 250) PMID:28109437

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

PubMed

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

2016-12-15

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

Secondary Ion Mass Spectrometry SIMS XI

NASA Astrophysics Data System (ADS)

Gillen, G.; Lareau, R.; Bennett, J.; Stevie, F.

2003-05-01

This volume contains 252 contributions presented as plenary, invited and contributed poster and oral presentations at the 11th International Conference on Secondary Ion Mass Spectrometry (SIMS XI) held at the Hilton Hotel, Walt Disney World Village, Orlando, Florida, 7 12 September, 1997. The book covers a diverse range of research, reflecting the rapid growth in advanced semiconductor characterization, ultra shallow depth profiling, TOF-SIMS and the new areas in which SIMS techniques are being used, for example in biological sciences and organic surface characterization. Papers are presented under the following categories: Isotopic SIMS Biological SIMS Semiconductor Characterization Techniques and Applications Ultra Shallow Depth Profiling Depth Profiling Fundamental/Modelling and Diffusion Sputter-Induced Topography Fundamentals of Molecular Desorption Organic Materials Practical TOF-SIMS Polyatomic Primary Ions Materials/Surface Analysis Postionization Instrumentation Geological SIMS Imaging Fundamentals of Sputtering Ion Formation and Cluster Formation Quantitative Analysis Environmental/Particle Characterization Related Techniques These proceedings provide an invaluable source of reference for both newcomers to the field and experienced SIMS users.

Characterization of the components of meleumycin by liquid chromatography with photo-diode array detection and electrospray ionization tandem mass spectrometry.

PubMed

Wang, Ming-Juan; Li, Ya-Ping; Wang, Yan; Li, Jin; Hu, Chang-Qin; Hoogmartens, Jos; Van Schepdael, Ann; Adams, Erwin

2013-10-01

Reversed-phase liquid chromatography coupled with photo-diode array (PDA) detection and electrospray ionization tandem mass spectrometry (ESI-MS/MS) was used to characterize the components of meleumycin, a 16-membered macrolide antibiotic produced by fermentation. In total 31 components were characterized in commercial samples, including 12 impurities that had never been reported before and 12 others that were partially characterized. The structures of these unknown compounds were deduced by comparison of their fragmentation patterns with those of known components. Their ultraviolet spectra and chromatographic behavior were used to confirm the proposed structures: e.g. λmax shift from 232 nm to 282 nm would indicate the presence of an α-, β-, γ-, δ-unsaturated ketone instead of a normal α-, β-, γ-, δ-unsaturated alcohol in the 16-membered ring of the examined components. Compared to other methods, this LC/MS(n) method is particularly advantageous to characterize minor components at trace levels in multi-components antibiotics, in terms of sensitivity and efficiency. Copyright © 2013 Elsevier B.V. All rights reserved.

Characterization of goat colostrum oligosaccharides by nano-liquid chromatography on chip quadrupole time-of-flight mass spectrometry and hydrophilic interaction liquid chromatography-quadrupole mass spectrometry.

PubMed

Martín-Ortiz, A; Salcedo, J; Barile, D; Bunyatratchata, A; Moreno, F J; Martin-García, I; Clemente, A; Sanz, M L; Ruiz-Matute, A I

2016-01-08

A detailed qualitative and quantitative characterization of goat colostrum oligosaccharides (GCO) has been carried out for the first time. Defatted and deproteinized colostrum samples, previously treated by size exclusion chromatography (SEC) to remove lactose, were analyzed by nanoflow liquid chromatography-quadrupole-time of flight mass spectrometry (Nano-LC-Chip-Q-TOF MS). Up to 78 oligosaccharides containing hexose, hexosamine, fucose, N-acetylneuraminic acid or N-glycolylneuraminic acid monomeric units were identified in the samples, some of them detected for the first time in goat colostra. As a second step, a hydrophilic interaction liquid chromatography coupled to mass spectrometry (HILIC-MS) methodology was developed for the separation and quantitation of the main GCO, both acidic and neutral carbohydrates. Among other experimental chromatographic conditions, mobile phase additives and column temperature were evaluated in terms of retention time, resolution, peak width and symmetry of target carbohydrates. Narrow peaks (wh: 0.2-0.6min) and good symmetry (As: 0.8-1.4) were obtained for GCO using an acetonitrile:water gradient with 0.1% ammonium hydroxide at 40°C. These conditions were selected to quantify the main oligosaccharides in goat colostrum samples. Values ranging from 140 to 315mgL(-1) for neutral oligosaccharides and from 83 to 251mgL(-1) for acidic oligosaccharides were found. The combination of both techniques resulted to be useful to achieve a comprehensive characterization of GCO. Copyright © 2015 Elsevier B.V. All rights reserved.

The contribution of multidimensional spatial analysis to a waste management policy: implementation of the ELECTRE method for characterizing transfer centers in the region of Oran

NASA Astrophysics Data System (ADS)

Saidi, A.; Trache, M. A.; Khelfi, M. F.

2016-08-01

The social and economic activity steadily growing in our cities creates a significant waste production in constantly evolving. The management of this waste is problematic because it is the center of many issues and interests. Indeed, any action or decision to the collection, transportation, treatment and disposal of waste should be considered in the economic, social, political and especially environmental aspect. A global Geomatic solution requires implementing a GIS with powerful multidimensional spatial analysis tools that support really waste management problem. Algeria has adopted a solution of waste landfill for all urban cities. In the Oran region, it exists three Centers Controlled landfill (CET) which the most important is that of Hassi-Bounif. This center currently meeting the needs of the region is unsustainable solution at the long-term because of its rapid saturation and its geographic location, which is still far from city centers (20-30 km) implying a negative impact on the vehicle park collecting such frequent breakdowns, the rapid degradation, slow delivery time and especially the high cost of the maintenance operation. This phenomenon is aggravated by the absence of real and actual initiatives targeting the recycling and recovery of waste, which makes the CET an endpoint for all types of waste. We present in this study, the use of the ELECTRE method (Multicriteria Analysis) integrated into a GIS to characterize the impact of the implementation of transfers centers at Oran region. The results of this study will accentuate the advantages of the activation of waste warehouse closer to the city, and relieving considerably the volume of transfer towards CET. The objective of our presentation is to show the leading role of the new Geomatics tools and the multidimensional spatial analysis in the apprehension of an environmental problem such the waste management and more generally in the urban management.

Gamma-ray spectrometry method used for radioactive waste drums characterization for final disposal at National Repository for Low and Intermediate Radioactive Waste--Baita, Romania.

PubMed

Done, L; Tugulan, L C; Dragolici, F; Alexandru, C

2014-05-01

The Radioactive Waste Management Department from IFIN-HH, Bucharest, performs the conditioning of the institutional radioactive waste in concrete matrix, in 200 l drums with concrete shield, for final disposal at DNDR - Baita, Bihor county, in an old exhausted uranium mine. This paper presents a gamma-ray spectrometry method for the characterization of the radioactive waste drums' radionuclides content, for final disposal. In order to study the accuracy of the method, a similar concrete matrix with Portland cement in a 200 l drum was used. © 2013 The Authors. Published by Elsevier Ltd All rights reserved.

Pyrolysis-mass spectrometry/pattern recognition on a well-characterized suite of humic samples

USGS Publications Warehouse

MacCarthy, P.; DeLuca, S.J.; Voorhees, K.J.; Malcolm, R.L.; Thurman, E.M.

1985-01-01

A suite of well-characterized humic and fulvic acids of freshwater, soil and plant origin was subjected to pyrolysis-mass spectrometry and the resulting data were analyzed by pattern recognition and factor analysis. A factor analysis plot of the data shows that the humic acids and fulvic acids can be segregated into two distinct classes. Carbohydrate and phenolic components are more pronounced in the pyrolysis products of the fulvic acids, and saturated and unsaturated hydrocarbons contribute more to the humic acid pyrolysis products. A second factor analysis plot shows a separation which appears to be based primarily on whether the samples are of aquatic or soil origin. ?? 1985.

Optical characterization of extremely small volumes of liquid in sub-micro-holes by simultaneous reflectivity, ellipsometry and spectrometry.

PubMed

Holgado, M; Casquel, R; Sánchez, B; Molpeceres, C; Morales, M; Ocaña, J L

2007-10-01

We have fabricated and characterized a lattice of submicron cone-shaped holes on a SiO(2)/Si wafer. Reflectivity profiles as a function of angle of incidence and polarization, phase shift and spectrometry are obtained for several fluids with different refractive indexes filling the holes. The optical setup allows measuring in the center of a single hole and collecting all data simultaneously, which can be applied for measuring extremely low volumes of fluid (in the order of 0.1 femtolitres) and label-free immunoassays, as it works as a refractive index sensor. A three layer film stack model is defined to perform theoretical calculations.

Native MS and ECD Characterization of a Fab-Antigen Complex May Facilitate Crystallization for X-ray Diffraction

NASA Astrophysics Data System (ADS)

Zhang, Ying; Cui, Weidong; Wecksler, Aaron T.; Zhang, Hao; Molina, Patricia; Deperalta, Galahad; Gross, Michael L.

2016-07-01

Native mass spectrometry (MS) and top-down electron-capture dissociation (ECD) combine as a powerful approach for characterizing large proteins and protein assemblies. Here, we report their use to study an antibody Fab (Fab-1)-VEGF complex in its near-native state. Native ESI with analysis by FTICR mass spectrometry confirms that VEGF is a dimer in solution and that its complex with Fab-1 has a binding stoichiometry of 2:2. Applying combinations of collisionally activated dissociation (CAD), ECD, and infrared multiphoton dissociation (IRMPD) allows identification of flexible regions of the complex, potentially serving as a guide for crystallization and X-ray diffraction analysis.

[New iron-porphyrin/vanadium-substituted polyoxometalate catalyst: synthesis, characterization and catalytic activity].

PubMed

Dong, Xiao-li; Zhang, Zhen-cheng; An, Qing-da; Zhang, Shao-yin; Wang, Shao-jun

2007-12-01

A new kind of iron-porphyrin/vanadium-substituted polyoxometalate coordination compound was synthesized by the ion exchange reaction of FeTTMAPPI and H5PMo10V2o40 in solution. The new catalyst was characterized by IR spectrometry and UV-Vis spectrometry. As an excellent catalyst, its effects on benzene hydroxylation and catalytic capabilities were studied with H2O2 solution as the oxidant. The results indicated that the products contained the conjugated structure of porphyrin and the cage structure of polyoxometalate, the V atom in polyoxometalate is the main centre of catalytic activity, meanwhile the presence of iron-porphyrin could increase its catalytic activity greatly.

Numeric invariants from multidimensional persistence

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

Skryzalin, Jacek; Carlsson, Gunnar

2017-05-19

In this paper, we analyze the space of multidimensional persistence modules from the perspectives of algebraic geometry. We first build a moduli space of a certain subclass of easily analyzed multidimensional persistence modules, which we construct specifically to capture much of the information which can be gained by using multidimensional persistence over one-dimensional persistence. We argue that the global sections of this space provide interesting numeric invariants when evaluated against our subclass of multidimensional persistence modules. Lastly, we extend these global sections to the space of all multidimensional persistence modules and discuss how the resulting numeric invariants might be usedmore » to study data.« less

Frontiers in imaging magnetism with polarized x-rays

DOE PAGES

Fischer, Peter

2015-01-08

Although magnetic imaging with polarized x-rays is a rather young scientific discipline, the various types of established x-ray microscopes have already taken an important role in state-of-the-art characterization of the properties and behavior of spin textures in advanced materials. Furthermore, the opportunities ahead will be to obtain in a unique way indispensable multidimensional information of the structure, dynamics and composition of scientifically interesting and technologically relevant magnetic materials.

Isolation and characterization of yuremamine, a new phytoindole.

PubMed

Vepsäläinen, Jouko J; Auriola, Seppo; Tukiainen, Mikko; Ropponen, Nina; Callaway, J C

2005-11-01

Yuremamine was isolated and characterized from the stem bark of Mimosa tenuiflora. This plant is still used by indigenous peoples in North-eastern Brazil to make yurema, a psychoactive beverage that is used for medico-religious purpose ( jurema preta or vinho da jurema, in Portuguese). The characterization of this novel compound by NMR and mass spectrometry introduces a new class of phytoindoles.

Characterization of non-polar aromatic hydrocarbons in crude oil using atmospheric pressure laser ionization and Fourier transform ion cyclotron resonance mass spectrometry (APLI FT-ICR MS).

PubMed

Schrader, Wolfgang; Panda, Saroj K; Brockmann, Klaus J; Benter, Thorsten

2008-07-01

We report on the successful application of the recently introduced atmospheric pressure laser ionization (APLI) method as a novel tool for the analysis of crude oil and its components. Using Fourier transform ion cyclotron resonance mass spectrometry, unambiguous determination of key compounds in this complex matrix with unprecedented sensitivity is presented.

Characterization of Nitrated Sugar Alcohols by Atmospheric-Pressure Chemical-Ionization Mass Spectrometry

DTIC Science & Technology

2016-07-27

disclosed here will benefit the area of explosives trace detection for counterterrorism and forensics . INTRODUCTION The military-grade...plasticizer formulation.[4] As a result, methods to detect MHN, SHN, and XPN should be pursued for the same security and forensics applications as...with ion mobility mass spectrometry (IMS) provide direct detection of molecular ions,[8] and thus are preferred for most security and forensic

Characterization of the General Electric CID-17 as a Detector for Plasma Emission Spectrometry.

DTIC Science & Technology

1985-11-25

multiwavelength disreteetectors. All tnToes oF detectors ’or plasma emission snectroscopv must mntil there o eapresetutisemhas. been, byes ereounu ai!- numer...photomultiplier tubes. With almost 100,000 channels, true multiwavelength detection is obtained making a new wealth of information available to the analytical...of complex mixtures by optical emission spectrometry requires sensitive simultaneous multiwavelength detection. Until the present, this has been

Rapid Analysis of Microalgal Triacylglycerols with Direct-Infusion Mass Spectrometry

DOE PAGES

Christensen, Earl; Sudasinghe, Nilusha; Dandamudi, Kodanda Phani Raj; ...

2015-09-01

Cultivation of microalgae has the potential to provide lipid-derived feedstocks for conversion to liquid transportation fuels. Lipid extracts from microalgae are significantly more complex than those of traditional seed oils, and their composition changes significantly throughout the microalgal growth period. With three acyl side chains per molecule, triglycerides (TAGs) are an important fuel precursor, and the distribution of acyl chain composition for TAGs has a significant impact on fuel properties and processing. Therefore, determination of the distribution of microalgal TAG production is needed to assess the value of algal extracts designed for fuel production and to optimize strain, cultivation, andmore » harvesting practices. Methods utilized for TAG speciation commonly involve complicated and time-consuming chromatographic techniques. Here we present a method for TAG speciation and quantification based on direct-infusion mass spectrometry, which provides rapid characterization of TAG profiles without chromatographic separation. Specifically, we utilize Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to provide a reference library of TAGs for the microalgae Nannochloropsis sp. that provides the basis for high-throughput TAG quantitation by time-of-flight mass spectrometry (TOF MS). In conclusion, we demonstrate the application of this novel approach for lipid characterization with respect to TAG compound distribution, which informs both immediate and future strain and process optimization strategies.« less

Identifying the site of spin trapping in proteins by a combination of liquid chromatography, ELISA, and off-line tandem mass spectrometry.

PubMed

Lardinois, Olivier M; Detweiler, Charles D; Tomer, Kenneth B; Mason, Ronald P; Deterding, Leesa J

2008-03-01

An off-line mass spectrometry method that combines immuno-spin trapping and chromatographic procedures has been developed for selective detection of the nitrone spin trap 5,5-dimethyl-1-pyrroline-N-oxide (DMPO) covalently attached to proteins, an attachment which occurs only subsequent to DMPO trapping of free radicals. In this technique, the protein-DMPO nitrone adducts are digested to peptides with proteolytic agents, peptides from the enzymatic digest are separated by HPLC, and enzyme-linked immunosorbent assays (ELISA) using polyclonal anti-DMPO nitrone antiserum are used to detect the eluted HPLC fractions that contain DMPO nitrone adducts. The fractions showing positive ELISA signals are then concentrated and characterized by tandem mass spectrometry (MS/MS). This method, which constitutes the first liquid chromatography-ELISA-mass spectrometry (LC-ELISA-MS)-based strategy for selective identification of DMPO-trapped protein residues in complex peptide mixtures, facilitates location and preparative fractionation of DMPO nitrone adducts for further structural characterization. The strategy is demonstrated for human hemoglobin, horse heart myoglobin, and sperm whale myoglobin, three globin proteins known to form DMPO-trappable protein radicals on treatment with H(2)O(2). The results demonstrate the power of the new experimental strategy to select DMPO-labeled peptides and identify sites of DMPO covalent attachments.

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.

Rapid profiling of polymeric phenolic acids in Salvia miltiorrhiza by hybrid data-dependent/targeted multistage mass spectrometry acquisition based on expected compounds prediction and fragment ion searching.

PubMed

Shen, Yao; Feng, Zijin; Yang, Min; Zhou, Zhe; Han, Sumei; Hou, Jinjun; Li, Zhenwei; Wu, Wanying; Guo, De-An

2018-04-01

Phenolic acids are the major water-soluble components in Salvia miltiorrhiza (>5%). According to previous studies, many of them contribute to the cardiovascular effects and antioxidant effects of S. miltiorrhiza. Polymeric phenolic acids can be considered as the tanshinol derived metabolites, e.g., dimmers, trimers, and tetramers. A strategy combined with tanshinol-based expected compounds prediction, total ion chromatogram filtering, fragment ion searching, and parent list-based multistage mass spectrometry acquisition by linear trap quadropole-orbitrap Velos mass spectrometry was proposed to rapid profile polymeric phenolic acids in S. miltiorrhiza. More than 480 potential polymeric phenolic acids could be screened out by this strategy. Based on the fragment information obtained by parent list-activated data dependent multistage mass spectrometry acquisition, 190 polymeric phenolic acids were characterized by comparing their mass information with literature data, and 18 of them were firstly detected from S. miltiorrhiza. Seven potential compounds were tentatively characterized as new polymeric phenolic acids from S. miltiorrhiza. This strategy facilitates identification of polymeric phenolic acids in complex matrix with both selectivity and sensitivity, which could be expanded for rapid discovery and identification of compounds from complex matrix. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Comparative Study of Online Item Calibration Methods in Multidimensional Computerized Adaptive Testing

ERIC Educational Resources Information Center

Chen, Ping

2017-01-01

Calibration of new items online has been an important topic in item replenishment for multidimensional computerized adaptive testing (MCAT). Several online calibration methods have been proposed for MCAT, such as multidimensional "one expectation-maximization (EM) cycle" (M-OEM) and multidimensional "multiple EM cycles"…

Best Design for Multidimensional Computerized Adaptive Testing with the Bifactor Model

ERIC Educational Resources Information Center

Seo, Dong Gi; Weiss, David J.

2015-01-01

Most computerized adaptive tests (CATs) have been studied using the framework of unidimensional item response theory. However, many psychological variables are multidimensional and might benefit from using a multidimensional approach to CATs. This study investigated the accuracy, fidelity, and efficiency of a fully multidimensional CAT algorithm…

Multidimensional Measurement of Poverty among Women in Sub-Saharan Africa

ERIC Educational Resources Information Center

Batana, Yele Maweki

2013-01-01

Since the seminal work of Sen, poverty has been recognized as a multidimensional phenomenon. The recent availability of relevant databases renewed the interest in this approach. This paper estimates multidimensional poverty among women in fourteen Sub-Saharan African countries using the Alkire and Foster multidimensional poverty measures, whose…

The Efficacy of Multidimensional Constraint Keys in Database Query Performance

ERIC Educational Resources Information Center

Cardwell, Leslie K.

2012-01-01

This work is intended to introduce a database design method to resolve the two-dimensional complexities inherent in the relational data model and its resulting performance challenges through abstract multidimensional constructs. A multidimensional constraint is derived and utilized to implement an indexed Multidimensional Key (MK) to abstract a…

Rapid kinetic characterization of glycosyl hydrolases based on oxime derivatization and nanostructure-initiator mass spectrometry (NIMS).

PubMed

Deng, Kai; Takasuka, Taichi E; Heins, Richard; Cheng, Xiaoliang; Bergeman, Lai F; Shi, Jian; Aschenbrener, Ryan; Deutsch, Sam; Singh, Seema; Sale, Kenneth L; Simmons, Blake A; Adams, Paul D; Singh, Anup K; Fox, Brian G; Northen, Trent R

2014-07-18

Glycoside hydrolases (GHs) are critical to cycling of plant biomass in the environment, digestion of complex polysaccharides by the human gut microbiome, and industrial activities such as deployment of cellulosic biofuels. High-throughput sequencing methods show tremendous sequence diversity among GHs, yet relatively few examples from the over 150,000 unique domain arrangements containing GHs have been functionally characterized. Here, we show how cell-free expression, bioconjugate chemistry, and surface-based mass spectrometry can be used to study glycoside hydrolase reactions with plant biomass. Detection of soluble products is achieved by coupling a unique chemical probe to the reducing end of oligosaccharides in a stable oxime linkage, while the use of (13)C-labeled monosaccharide standards (xylose and glucose) allows quantitation of the derivatized glycans. We apply this oxime-based nanostructure-initiator mass spectrometry (NIMS) method to characterize the functional diversity of GHs secreted by Clostridium thermocellum, a model cellulolytic organism. New reaction specificities are identified, and differences in rates and yields of individual enzymes are demonstrated in reactions with biomass substrates. Numerical analyses of time series data suggests that synergistic combinations of mono- and multifunctional GHs can decrease the complexity of enzymes needed for the hydrolysis of plant biomass during the production of biofuels.

Natural proteins: Sources, isolation, characterization and applications

PubMed Central

Nehete, Jitendra Y.; Bhambar, Rajendra S.; Narkhede, Minal R.; Gawali, Sonali R.

2013-01-01

Worldwide, plant protein contributes substantially as a food resource because it contains essential amino acids for meeting human physiological requirements. However, many versatile plant proteins are used as medicinal agents as they are produced by using molecular tools of biotechnology. Proteins can be obtained from plants, animals and microorganism cells. The abundant economical proteins can be obtained from plant seeds. These natural proteins are obtained by isolation procedures depending on the physicochemical properties of proteins. Isolation and purification of single protein from cells containing mixtures of unrelated proteins is achievable due to the physical and chemical attributes of proteins. The following characteristics are unique to each protein: Amino acid composition, sequence, subunit structures, size, shape, net charge, isoelectric point, solubility, heat stability and hydrophobicity. Based on these properties, various methods of isolation exist, like salting out and isoionic precipitation. Purification of proteins is quiet challenging and, therefore, several approaches like sodium dodecyl sulfate gel electrophoresis and chromatography are available. Characterization of proteins can be performed by mass spectrometry/liquid chromatography-mass spectrometry (LC-MS). The amino acid sequence of a protein can be detected by using tandem mass spectrometry. In this article, a review has been made on the sources, isolation, purification and characterization of natural proteins. PMID:24347918

Fourier Transform Mass Spectrometry and Nuclear Magnetic Resonance Analysis for the Rapid and Accurate Characterization of Hexacosanoylceramide.

PubMed

Ross, Charles W; Simonsick, William J; Bogusky, Michael J; Celikay, Recep W; Guare, James P; Newton, Randall C

2016-06-28

Ceramides are a central unit of all sphingolipids which have been identified as sites of biological recognition on cellular membranes mediating cell growth and differentiation. Several glycosphingolipids have been isolated, displaying immunomodulatory and anti-tumor activities. These molecules have generated considerable interest as potential vaccine adjuvants in humans. Accurate analyses of these and related sphingosine analogues are important for the characterization of structure, biological function, and metabolism. We report the complementary use of direct laser desorption ionization (DLDI), sheath flow electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) and high-field nuclear magnetic resonance (NMR) analysis for the rapid, accurate identification of hexacosanoylceramide and starting materials. DLDI does not require stringent sample preparation and yields representative ions. Sheath-flow ESI yields ions of the product and byproducts and was significantly better than monospray ESI due to improved compound solubility. Negative ion sheath flow ESI provided data of starting materials and products all in one acquisition as hexacosanoic acid does not ionize efficiently when ceramides are present. NMR provided characterization of these lipid molecules complementing the results obtained from MS analyses. NMR data was able to differentiate straight chain versus branched chain alkyl groups not easily obtained from mass spectrometry.

Detailed characterization of bio-oil from pyrolysis of non-edible seed-cakes by Fourier Transform Infrared Spectroscopy (FTIR) and gas chromatography mass spectrometry (GC-MS) techniques.

PubMed

Sugumaran, Vatsala; Prakash, Shanti; Ramu, Emmandi; Arora, Ajay Kumar; Bansal, Veena; Kagdiyal, Vivekanand; Saxena, Deepak

2017-07-15

Bio-oil obtained from pyrolysis is highly complicated mixture with valued chemicals. In order to reduce the complexity for unambiguous characterization of components present in bio-oil, solvent extractions using different solvents with increasing polarity have been adopted. The fractions have been analyzed by Fourier transform infrared (FTIR) spectroscopy for identifying the functional groups and Gas chromatography-mass spectrometry (GC-MS), for detailed characterization of components present in various fractions, thereby providing in-depth information at molecular level of various components in bio-oil. This paper reveals the potential of the analytical techniques in identification and brings out the similarities as well as differences in the components present in the bio-oil obtained from two non-edible oil seed-cakes, viz., Jatropha and Karanjia. Copyright © 2017 Elsevier B.V. All rights reserved.

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

PubMed Central

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

2008-01-01

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

Rapid Characterization and Identification of Flavonoids in Radix Astragali by Ultra-High-Pressure Liquid Chromatography Coupled with Linear Ion Trap-Orbitrap Mass Spectrometry.

PubMed

Zhang, Jing; Xu, Xiao-Jie; Xu, Wen; Huang, Juan; Zhu, Da-yuan; Qiu, Xiao-Hui

2015-07-01

A simple and effective method was established for separation and characterization of flavonoid constituents in Radix Astragali (RA) by combination of ultra-high-pressure liquid chromatography with LTQ-Orbitrap tandem mass spectrometry (u-HPLC-LTQ-Orbitrap-MS(n)). For three major structural types of flavonoids, the proposed fragmentation pathways and major diagnostic fragment ions of isoflavones, pterocarpans and isoflavans were investigated to trace isoflavonoid derivatives in crude plant extracts. Based on the systematic identification strategy, 48 constituents were rapidly detected and characterized or tentatively identified, many of which were first reported in RA. The u-PHLC-LTQ-Orbitrap MS(n) platform was proved as an effective tool for rapid qualitative analysis of secondary metabolite productions from natural resources. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Pedologic Factors Affecting Virgin Olive Oil Quality of "Chemlali" Olive Trees (Olea europaea L.).

PubMed

Rached, Mouna Ben; Galaverna, Gianni; Cirlini, Martina; Boujneh, Dalenda; Zarrouk, Mokhtar; Guerfel, Mokhtar

2017-08-01

The aim of this study examined the characterization of extra virgin olive oil samples from the main cultivar Chemlali, grown in five olive orchards with different soil type (Sandy, Clay, Stony, Brown, Limestone and Gypsum). Volatile compounds were studied using headspace-solid phase micro-extraction (HS-SPME) and gas chromatography-mass spectrometry (GC-MS) technics. Moreover, the sterol profile was established using gas chromatography-mass spectrometry. 35 different volatile compounds were identified: alcohols, esters, aldehydes, ketones and hydrocarbons. The chemical composition of the volatile fraction was characterized by the preeminence of 2-hexenal (32.75%) and 1-hexanol (31.88%). Three sterols were identified and characterized. For all olive oil samples, ß-sitosterol (302.25 mg/kg) was the most abundant sterol. Interestingly, our results showed significant qualitative and quantitative differences in the levels of the volatile compounds and sterols from oils obtained from olive trees grown in different soil type.

Characterization of polymethoxylated flavones in Fructus aurantii by liquid chromatography with atmospheric pressure chemical ionization combined with tandem mass spectrometry.

PubMed

Zhou, Da-Yong; Chen, De-Liang; Xu, Qing; Xue, Xing-Ya; Zhang, Fei-Fang; Liang, Xin-Miao

2007-04-11

Atmospheric pressure chemical ionization mass spectrometry (APCI-MS) was operated in positive mode (PI) to characterize polymethoxylated flavonoids (PMFs) through its specific radical cations by collision-induced dissociation (CID). The fragments of [M + H - n x 15]+ produced by loss of one or more methyl group from the protonated molecule, as well as [M + H - 29]+, [M + H - 31]+, [M + H - 33]+, [M + H - 43]+, [M + H - 46]+, and [M + H - 61]+ fragment ions were detected, which were diagnostic for the polymethoxylated species, and could be adopted to form the multiple MS (MS(n)) "fingerprint" of PMFs. Based on this "fingerprint", 29 PMFs were screened out from extracts of Fructus aurantii, among which two of them were identified as sinensetin and tangeretin. It was proved that the PI was suitable for structural characterization of PMFs by APCI-MS(n).

Characterization of ANFO explosive by high accuracy ESI(±)-FTMS with forensic identification on real samples by EASI(-)-MS.

PubMed

Hernandes, Vinicius Veri; Franco, Marcos Fernado; Santos, Jandyson Machado; Melendez-Perez, Jose J; de Morais, Damila Rodrigues; Rocha, Werickson Fortunato de Carvalho; Borges, Rodrigo; de Souza, Wanderley; Zacca, Jorge Jardim; Logrado, Lucio Paulo Lima; Eberlin, Marcos Nogueira; Correa, Deleon Nascimento

2015-04-01

Ammonium nitrate fuel oil (ANFO) is an explosive used in many civil applications. In Brazil, ANFO has unfortunately also been used in criminal attacks, mainly in automated teller machine (ATM) explosions. In this paper, we describe a detailed characterization of the ANFO composition and its two main constituents (diesel and a nitrate explosive) using high resolution and accuracy mass spectrometry performed on an FT-ICR-mass spectrometer with electrospray ionization (ESI(±)-FTMS) in both the positive and negative ion modes. Via ESI(-)-MS, an ion marker for ANFO was characterized. Using a direct and simple ambient desorption/ionization technique, i.e., easy ambient sonic-spray ionization mass spectrometry (EASI-MS), in a simpler, lower accuracy but robust single quadrupole mass spectrometer, the ANFO ion marker was directly detected from the surface of banknotes collected from ATM explosion theft. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Qualitative and quantitative characterization of secondary metabolites and carbohydrates in Bai-Hu-Tang using ultraperformance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry and ultraperformance liquid chromatography coupled with photodiode array detector.

PubMed

Zhong, Wei-Fang; Tong, Wing-Sum; Zhou, Shan-Shan; Yip, Ka-Man; Li, Song-Lin; Zhao, Zhong-Zhen; Xu, Jun; Chen, Hu-Biao

2017-10-01

Bai-Hu-Tang (BHT), a classic traditional Chinese medicine (TCM) formula used for clearing heat and promoting body fluid, consists of four traditional Chinese medicines, i.e., Gypsum Fibrosum (Shigao), Anemarrhenae Rhizoma (Zhimu), Glycyrrhizae Radix et Rhizoma Praeparata cum Melle (Zhigancao), and nonglutinous rice (Jingmi). The chemical composition of BHT still remains largely elusive thus far. To qualitatively and quantitatively characterize secondary metabolites and carbohydrates in BHT, here a combination of analytical approaches using ultraperformance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry and ultraperformance liquid chromatography coupled with photodiode array detector was developed and validated. A total of 42 secondary metabolites in BHT were tentatively or definitely identified, of which 10 major chemicals were quantified by the extracting ion mode of quadrupole time-of-flight mass spectrometry. Meanwhile, polysaccharides, oligosaccharides, and monosaccharides in BHT were also characterized via sample pretreatment followed by sugar composition analysis. The quantitative results indicated that the determined chemicals accounted for 35.76% of the total extract of BHT, which demonstrated that the study could be instrumental in chemical dissection and quality control of BHT. The research deliverables not only laid the root for further chemical and biological evaluation of BHT, but also provided a comprehensive analytical strategy for chemical characterization of secondary metabolites and carbohydrates in traditional Chinese medicine formulas. Copyright © 2017. Published by Elsevier B.V.

Psychometric properties of the multidimensional perfectionism scale of Hewitt in a dutch-speaking sample: associations with the big five personality traits.

PubMed

De Cuyper, Kathleen; Claes, Laurence; Hermans, Dirk; Pieters, Guido; Smits, Dirk

2015-01-01

We administered the Dutch Multidimensional Perfectionism Scale of Hewitt and Flett (1991, 2004) in a large student sample (N = 959) and performed a confirmatory factor analysis to test the factorial structure proposed by the original authors. The existence of a method factor referring to the negatively keyed items in the questionnaire was investigated by including it in the tested models. Next, we investigated how the 3 perfectionism dimensions are associated with the Five-factor model (FFM) of personality. The 3-factor structure originally observed by the authors was confirmed, at least when a method factor that refers to the negatively keyed items was included in the model. Self-oriented and socially prescribed perfectionism were both distinguished by low extraversion and low emotional stability. Self-oriented perfectionism's positive relationship with both conscientiousness and openness to experience differentiated the 2 perfectionism dimensions from each other. Other-oriented perfectionism was not well-characterized by the Big Five personality traits.

Bridging the gap between supernovae and their remnants through multi-dimensional hydrodynamic modeling

NASA Astrophysics Data System (ADS)

Orlando, S.; Miceli, M.; Petruk, O.

2017-02-01

Supernova remnants (SNRs) are diffuse extended sources characterized by a complex morphology and a non-uniform distribution of ejecta. Such a morphology reflects pristine structures and features of the progenitor supernova (SN) and the early interaction of the SN blast wave with the inhomogeneous circumstellar medium (CSM). Deciphering the observations of SNRs might open the possibility to investigate the physical properties of both the interacting ejecta and the shocked CSM. This requires accurate numerical models which describe the evolution from the SN explosion to the remnant development and which connect the emission properties of the remnants to the progenitor SNe. Here we show how multi-dimensional SN-SNR hydrodynamic models have been very effective in deciphering observations of SNR Cassiopeia A and SN 1987A, thus unveiling the structure of ejecta in the immediate aftermath of the SN explosion and constraining the 3D pre-supernova structure and geometry of the environment surrounding the progenitor SN.

Continuum and discrete approach in modeling biofilm development and structure: a review.

PubMed

Mattei, M R; Frunzo, L; D'Acunto, B; Pechaud, Y; Pirozzi, F; Esposito, G

2018-03-01

The scientific community has recognized that almost 99% of the microbial life on earth is represented by biofilms. Considering the impacts of their sessile lifestyle on both natural and human activities, extensive experimental activity has been carried out to understand how biofilms grow and interact with the environment. Many mathematical models have also been developed to simulate and elucidate the main processes characterizing the biofilm growth. Two main mathematical approaches for biomass representation can be distinguished: continuum and discrete. This review is aimed at exploring the main characteristics of each approach. Continuum models can simulate the biofilm processes in a quantitative and deterministic way. However, they require a multidimensional formulation to take into account the biofilm spatial heterogeneity, which makes the models quite complicated, requiring significant computational effort. Discrete models are more recent and can represent the typical multidimensional structural heterogeneity of biofilm reflecting the experimental expectations, but they generate computational results including elements of randomness and introduce stochastic effects into the solutions.

Measurement of ²²⁶Ra in soil from oil field: advantages of γ-ray spectrometry and application to the IAEA-448 CRM.

PubMed

Ceccatelli, A; Katona, R; Kis-Benedek, G; Pitois, A

2014-05-01

The analytical performance of gamma-ray spectrometry for the measurement of (226)Ra in TENORM (Technically Enhanced Naturally Occurring Radioactive Material) soil was investigated by the IAEA. Fast results were obtained for characterization and certification of a new TENORM Certified Reference Material (CRM), identified as IAEA-448 (soil from oil field). The combined standard uncertainty of the gamma-ray spectrometry results is of the order of 2-3% for massic activity measurement values ranging from 16500 Bq kg(-1) to 21500 Bq kg(-1). Methodologies used for the production and certification of the IAEA-448 CRM are presented. Analytical results were confirmed by alpha spectrometry. The "t" test showed agreement between alpha and gamma results at 95% confidence level. © 2013 Published by Elsevier Ltd.

Ion mobility-mass spectrometry as a tool to investigate protein-ligand interactions.

PubMed

Göth, Melanie; Pagel, Kevin

2017-07-01

Ion mobility-mass spectrometry (IM-MS) is a powerful tool for the simultaneous analysis of mass, charge, size, and shape of ionic species. It allows the characterization of even low-abundant species in complex samples and is therefore particularly suitable for the analysis of proteins and their assemblies. In the last few years even complex and intractable species have been investigated successfully with IM-MS and the number of publications in this field is steadily growing. This trend article highlights recent advances in which IM-MS was used to study protein-ligand complexes and in particular focuses on the catch and release (CaR) strategy and collision-induced unfolding (CIU). Graphical Abstract Native mass spectrometry and ion mobility-mass spectrometry are versatile tools to follow the stoichiometry, energetics, and structural impact of protein-ligand binding.

Characterization Of Commonly Encountered Explosives Using Highfield Asymmetric Waveform Ion Mobility Spectrometry Coupled With Mass Spectrometry

DTIC Science & Technology

2007-05-01

symptoms depending on the relative concentration, even leading to death.32 2.4. Instrument Settings Both positive and negative ions can be formed...Detection Technology, pp. 619-633, 1992. 7. Osorio, Celia ; Gomez, Lewis M.; Hernandez, Samuel P.; Castro, Miguel E., Time-of- flight Mass Spectroscopy...vol. 15, pp. 1950-1952. 34. Federal Facilities Assessment Branch, Public Health Assessment, US Army Umatilla Depot Activity, Centers for Disease

Identification of Non-Pertechnetate Species In Hanford Tank Waste, Their Synthesis, Characterization, And Fundamental Chemistry

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

Kenneth R. Ashely; Norman Schroeder; Jose A. Olivares

2004-12-10

This proposal had three major goals: (1) develop capillary electrophoresis mass spectrometry as a characterization technique, (2) separate a non-pertechnetate fraction from a waste sample and identify the non-pertechnetate species in it by CEMS, and (3) synthesize and characterize bulk quantities of the identified non-pertechnetate species and study their ligand substitution and redox chemistry.

Multidimensional Unfolding by Nonmetric Multidimensional Scaling of Spearman Distances in the Extended Permutation Polytope

ERIC Educational Resources Information Center

Van Deun, Katrijn; Heiser, Willem J.; Delbeke, Luc

2007-01-01

A multidimensional unfolding technique that is not prone to degenerate solutions and is based on multidimensional scaling of a complete data matrix is proposed: distance information about the unfolding data and about the distances both among judges and among objects is included in the complete matrix. The latter information is derived from the…

Ultra-high performance supercritical fluid chromatography hyphenated to atmospheric pressure chemical ionization high resolution mass spectrometry for the characterization of fast pyrolysis bio-oils.

PubMed

Crepier, Julien; Le Masle, Agnès; Charon, Nadège; Albrieux, Florian; Duchene, Pascal; Heinisch, Sabine

2018-06-01

Extensive characterization of complex mixtures requires the combination of powerful analytical techniques. A Supercritical Fluid Chromatography (SFC) method was previously developed, for the specific case of fast pyrolysis bio oils, as an alternative to gas chromatography (GC and GC × GC) or liquid chromatography (LC and LC × LC), both separation methods being generally used prior to mass spectrometry (MS) for the characterization of such complex matrices. In this study we investigated the potential of SFC hyphenated to high resolution mass spectrometry (SFC-HRMS) for this characterization using Negative ion Atmospheric Pressure Chemical ionization ((-)APCI) for the ionization source. The interface between SFC and (-)APCI/HRMS was optimized from a mix of model compounds with the objective of maximizing the signal to noise ratio. The main studied parameters included both make-up flow-rate and make-up composition. A methodology for the treatment of APCI/HRMS data is proposed. This latter allowed for the identification of molecular formulae. Both SFC-APCI/HRMS method and data processing method were applied to a mixture of 36 model compounds, first analyzed alone and then spiked in a bio-oil. In both cases, 19 compounds could be detected. Among them 9 could be detected in a fast pyrolysis bio-oil by targeted analysis. The whole procedure was applied to the characterization of a bio-oil using helpful representations such as mass-plots, van Krevelen diagrams and heteroatom class distributions. Finally the results were compared with those obtained with a Fourier Transform ion-cyclotron resonance mass spectrometer (FT-ICR/MS). Copyright © 2018 Elsevier B.V. All rights reserved.

Recent mass spectrometry-based techniques and considerations for disulfide bond characterization in proteins.

PubMed

Lakbub, Jude C; Shipman, Joshua T; Desaire, Heather

2018-04-01

Disulfide bonds are important structural moieties of proteins: they ensure proper folding, provide stability, and ensure proper function. With the increasing use of proteins for biotherapeutics, particularly monoclonal antibodies, which are highly disulfide bonded, it is now important to confirm the correct disulfide bond connectivity and to verify the presence, or absence, of disulfide bond variants in the protein therapeutics. These studies help to ensure safety and efficacy. Hence, disulfide bonds are among the critical quality attributes of proteins that have to be monitored closely during the development of biotherapeutics. However, disulfide bond analysis is challenging because of the complexity of the biomolecules. Mass spectrometry (MS) has been the go-to analytical tool for the characterization of such complex biomolecules, and several methods have been reported to meet the challenging task of mapping disulfide bonds in proteins. In this review, we describe the relevant, recent MS-based techniques and provide important considerations needed for efficient disulfide bond analysis in proteins. The review focuses on methods for proper sample preparation, fragmentation techniques for disulfide bond analysis, recent disulfide bond mapping methods based on the fragmentation techniques, and automated algorithms designed for rapid analysis of disulfide bonds from liquid chromatography-MS/MS data. Researchers involved in method development for protein characterization can use the information herein to facilitate development of new MS-based methods for protein disulfide bond analysis. In addition, individuals characterizing biotherapeutics, especially by disulfide bond mapping in antibodies, can use this review to choose the best strategies for disulfide bond assignment of their biologic products. Graphical Abstract This review, describing characterization methods for disulfide bonds in proteins, focuses on three critical components: sample preparation, mass spectrometry data, and software tools.

Portfolio 2000: managing clinical systems.

PubMed

Hunter, L L

1998-01-01

Powerful forces are changing the provision of health care. Management is transitioning into new responsibility for a leaner, more flexible, customer-focused operation to support the goals of integrated systems of the 21st century--to minimize disease and to promote health. In response to this evolution, the clinical systems management concept describes multidimensional competencies, which are transportable throughout the continuum of care (1). These new knowledge competencies and core competencies applied in a different context are characterized in this paper.

Application of a trap-free two-dimensional liquid chromatography combined with ion trap/time-of-flight mass spectrometry for separation and characterization of impurities and isomers in cefpiramide.

PubMed

Wang, Jian; Xu, Yu; Wen, Chunmei; Wang, Zhijian

2017-11-01

High-resolution mass spectrometry had been routinely used for structure identification of impurity. However, all LC-MS methods were based on a volatile mobile phase, and a non-volatile system is used in the official analytical method of United States Pharmacopoeia for cefpiramide which limited the use of mass spectrometry for structure characterization of the impurities. Here we presented the utilization of a trap-free two-dimensional liquid chromatography coupled to high resolution ion trap/time-of-flight mass spectrometry (2D LC-IT-TOF MS) with positive and negative modes of electrospray ionization for characterization of eight impurities in cefpiramide. Trap-free two-dimensional liquid chromatography and online desalting technique made it possible to characterize the impurity in cefpiramide in the condition of official standard, and the TIC chromatogram of LC-MS was in conformity with the LC chromatogram of the official analytical method in the peak sequence of impurities, which could further improve the method of official monographs in pharmacopoeias. Each peak separated by the non-volatile mobile phase was trapped by a 20 μL quantitative loop then transferred into a system with a volatile mobile phase connected to a MS detector. In the first dimension, the column was Kromasil C 8 analytical column (250 mm × 4.6 mm, 5 μm) with a non-volatile salt mobile phase at the flow rate of 0.8 mL min -1 . In the second dimension, the column was Shimadzu Shim-pack GISS C 18 (50 mm × 2.1 mm, 1.9 μm) with a volatile salt mobile phase at the flow rate of 0.3 mL min -1 . Through the multiple heart-cutting 2D-LC approach and online desalting technique, the problem of incompatibility between non-volatile salt mobile phase and mass spectrometry was solved completely. The fragmentation behavior of cefpiramide and its eight impurities were studied. The structures of eight impurities in cefpiramide drug substance were deduced based on the HPLC-MS n data, in which seven impurities were novel impurities. The forming mechanisms of degradation products in cefpiramide were also studied. Copyright © 2017 Elsevier B.V. All rights reserved.

Pyrolysis-high resolution gas chromatography and pyrolysis gas chromatography-mass spectrometry of kerogens and kerogen precursors

NASA Technical Reports Server (NTRS)

Van De Meent, D.; Brown, S. C.; Philp, R. P.; Simoneit, B. R. T.

1980-01-01

A series of kerogens and kerogen precursors isolated from DSDP samples, oil shales and recent algal mats have been examined by Curie point pyrolysis-high resolution gas chromatography and gas chromatography-mass spectrometry. This study has shown that the three main types of kerogens (marine, terrestrial and mixtures of both) can be characterized using these techniques. The marine (algal) kerogens yield principally aliphatic products and the terrestrial kerogens yield more aromatic and phenolic products with some n-alkanes and n-alkenes. The yields of n-alkanes and n-alkenes increase and phenols decrease with increasing geologic age, however, pyrolysis-GC cannot be used to characterize the influence of short term diagenesis on the kerogen structure.

Identification and characterization of monomeric, volatile SiCl3NH2 as product of the reaction between SiCl4 and NH3: an important intermediate on the way to silicon nitride?

PubMed

Himmel, Hans-Jörg; Schiefenhövel, Nils; Binnewies, Michael

2003-03-17

We studied the reaction of SiCl(4) with NH(3) by mass spectrometry and IR spectroscopy. By means of mass spectrometry, SiCl(3)NH(2) was for the first time identified as an intermediate generated in significant amounts in the course of the reaction. In additional experiments, SiCl(3)NH(2) was formed as a stable gaseous product of the ammonolysis of SiCl(4), and the product was identified and characterized in detail by IR spectroscopic methods (gas phase and matrix isolation) in combination with quantum-chemical calculations. The calculations also gave access to important thermodynamical data.

Synthesis, characterization, and anticancer activity of a series of ketone-N(4)-substituted thiosemicarbazones and their ruthenium(II) arene complexes.

PubMed

Su, Wei; Qian, Quanquan; Li, Peiyuan; Lei, Xiaolin; Xiao, Qi; Huang, Shan; Huang, Chusheng; Cui, Jianguo

2013-11-04

A series of ketone-N(4)-substituted thiosemicarbazone (TSC) compounds (L1-L9) and their corresponding [(η(6)-p-cymene)Ru(II)(TSC)Cl](+/0) complexes (1-9) were synthesized and characterized by NMR, IR, elemental analysis, and HR-ESI-mass spectrometry. The molecular structures of L4, L9, 1-6, and 9 were determined by single-crystal X-ray diffraction analysis. The compounds were further evaluated for their in vitro antiproliferative activities against the SGC-7901 human gastric cancer, BEL-7404 human liver cancer, and HEK-293T noncancerous cell lines. Furthermore, the interactions of the compounds with DNA were followed by electrophoretic mobility spectrometry studies.

Device for two-dimensional gas-phase separation and characterization of ion mixtures

DOEpatents

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

2006-12-12

The present invention relates to a device for separation and characterization of gas-phase ions. The device incorporates an ion source, a field asymmetric waveform ion mobility spectrometry (FAIMS) analyzer, an ion mobility spectrometry (IMS) drift tube, and an ion detector. In one aspect of the invention, FAIMS operating voltages are electrically floated on top of the IMS drift voltage. In the other aspect, the FAIMS/IMS interface is implemented employing an electrodynamic ion funnel, including in particular an hourglass ion funnel. The present invention improves the efficiency (peak capacity) and sensitivity of gas-phase separations; the online FAIMS/IMS coupling creates a fundamentally novel two-dimensional gas-phase separation technology with high peak capacity, specificity, and exceptional throughput.

Fast characterization of cheeses by dynamic headspace-mass spectrometry.

PubMed

Pérès, Christophe; Denoyer, Christian; Tournayre, Pascal; Berdagué, Jean-Louis

2002-03-15

This study describes a rapid method to characterize cheeses by analysis of their volatile fraction using dynamic headspace-mass spectrometry. Major factors governing the extraction and concentration of the volatile components were first studied. These components were extracted from the headspace of the cheeses in a stream of helium and concentrated on a Tenax TA trap. They were then desorbed by heating and injected directly into the source of a mass spectrometer via a short deactivated silica transfer line. The mass spectra of the mixture of volatile components were considered as fingerprints of the analyzed substances. Forward stepwise factorial discriminant analysis afforded a limited number of characteristic mass fragments that allowed a good classification of the batches of cheeses studied.

Interlaboratory Study on Differential Analysis of Protein Glycosylation by Mass Spectrometry: The ABRF Glycoprotein Research Multi-Institutional Study 2012*

PubMed Central

Leymarie, Nancy; Griffin, Paula J.; Jonscher, Karen; Kolarich, Daniel; Orlando, Ron; McComb, Mark; Zaia, Joseph; Aguilan, Jennifer; Alley, William R.; Altmann, Friederich; Ball, Lauren E.; Basumallick, Lipika; Bazemore-Walker, Carthene R.; Behnken, Henning; Blank, Michael A.; Brown, Kristy J.; Bunz, Svenja-Catharina; Cairo, Christopher W.; Cipollo, John F.; Daneshfar, Rambod; Desaire, Heather; Drake, Richard R.; Go, Eden P.; Goldman, Radoslav; Gruber, Clemens; Halim, Adnan; Hathout, Yetrib; Hensbergen, Paul J.; Horn, David M.; Hurum, Deanna; Jabs, Wolfgang; Larson, Göran; Ly, Mellisa; Mann, Benjamin F.; Marx, Kristina; Mechref, Yehia; Meyer, Bernd; Möginger, Uwe; Neusüβ, Christian; Nilsson, Jonas; Novotny, Milos V.; Nyalwidhe, Julius O.; Packer, Nicolle H.; Pompach, Petr; Reiz, Bela; Resemann, Anja; Rohrer, Jeffrey S.; Ruthenbeck, Alexandra; Sanda, Miloslav; Schulz, Jan Mirco; Schweiger-Hufnagel, Ulrike; Sihlbom, Carina; Song, Ehwang; Staples, Gregory O.; Suckau, Detlev; Tang, Haixu; Thaysen-Andersen, Morten; Viner, Rosa I.; An, Yanming; Valmu, Leena; Wada, Yoshinao; Watson, Megan; Windwarder, Markus; Whittal, Randy; Wuhrer, Manfred; Zhu, Yiying; Zou, Chunxia

2013-01-01

One of the principal goals of glycoprotein research is to correlate glycan structure and function. Such correlation is necessary in order for one to understand the mechanisms whereby glycoprotein structure elaborates the functions of myriad proteins. The accurate comparison of glycoforms and quantification of glycosites are essential steps in this direction. Mass spectrometry has emerged as a powerful analytical technique in the field of glycoprotein characterization. Its sensitivity, high dynamic range, and mass accuracy provide both quantitative and sequence/structural information. As part of the 2012 ABRF Glycoprotein Research Group study, we explored the use of mass spectrometry and ancillary methodologies to characterize the glycoforms of two sources of human prostate specific antigen (PSA). PSA is used as a tumor marker for prostate cancer, with increasing blood levels used to distinguish between normal and cancer states. The glycans on PSA are believed to be biantennary N-linked, and it has been observed that prostate cancer tissues and cell lines contain more antennae than their benign counterparts. Thus, the ability to quantify differences in glycosylation associated with cancer has the potential to positively impact the use of PSA as a biomarker. We studied standard peptide-based proteomics/glycomics methodologies, including LC-MS/MS for peptide/glycopeptide sequencing and label-free approaches for differential quantification. We performed an interlaboratory study to determine the ability of different laboratories to correctly characterize the differences between glycoforms from two different sources using mass spectrometry methods. We used clustering analysis and ancillary statistical data treatment on the data sets submitted by participating laboratories to obtain a consensus of the glycoforms and abundances. The results demonstrate the relative strengths and weaknesses of top-down glycoproteomics, bottom-up glycoproteomics, and glycomics methods. PMID:23764502

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

PubMed

Bonaduce, I; Colombini, M P; Degano, I; Di Girolamo, F; La Nasa, J; Modugno, F; Orsini, S

2013-01-01

The molecular structure of three low-molecular-weight resins used as paint varnishes has been characterized by use of an approach based on three different mass spectrometric techniques. We investigated the ketone resin MS2A, the aldehyde resin Laropal A81, and the hydrocarbon resin Regalrez 1094, now commonly used in restoration. To date, the molecular structures of these resins have not been completely elucidated. To improve current knowledge of the chemical composition of these materials, information obtained by gas chromatography-mass spectrometry (GC/MS), pyrolysis-gas chromatography-mass spectrometry (Py/GC/MS), and electrospray ionization mass spectrometry (ESI-Q-ToF) was combined. Analysis, in solution, of the whole polymeric fraction of the resins by flow-injection ESI-Q-ToF, and of the non-polymeric fraction by GC-MS, enabled us to identify previously unreported features of the polymer structures. In addition, the Py-GC/MS profiles that we obtained will help to enhance the databases currently available in the literature. The proposed approach can be extended to other low-molecular-weight resins used as varnishes in conservation.

UV laser-induced cross-linking in peptides

PubMed Central

Leo, Gabriella; Altucci, Carlo; Bourgoin-Voillard, Sandrine; Gravagnuolo, Alfredo M.; Esposito, Rosario; Marino, Gennaro; Costello, Catherine E.; Velotta, Raffaele; Birolo, Leila

2013-01-01

RATIONALE The aim of this study was to demonstrate, and to characterize by high resolution mass spectrometry, that it is possible to preferentially induce covalent cross-links in peptides by using high energy femtosecond UV laser pulses. The cross-link is readily formed only when aromatic amino acids are present in the peptide sequence. METHODS Three peptides, xenopsin, angiotensin I, interleukin, individually or in combination, were exposed to high energy femtosecond UV laser pulses, either alone or in the presence of spin trapping molecules, the reaction products being characterized by high resolution mass spectrometry. RESULTS High resolution mass spectrometry and spin trapping strategies showed that cross-linking occurs readily, proceeds via a radical mechanism, and is the highly dominant reaction, proceeding without causing significant photo-damage in the investigated range of experimental parameters. CONCLUSIONS High energy femtosecond UV laser pulses can be used to induce covalent cross-links between aromatic amino acids in peptides, overcoming photo-oxidation processes, that predominate as the mean laser pulse intensity approaches illumination conditions achievable with conventional UV light sources. PMID:23754800

Categorizing Cells on the Basis of their Chemical Profiles: Progress in Single-Cell Mass Spectrometry.

PubMed

Comi, Troy J; Do, Thanh D; Rubakhin, Stanislav S; Sweedler, Jonathan V

2017-03-22

The chemical differences between individual cells within large cellular populations provide unique information on organisms' homeostasis and the development of diseased states. Even genetically identical cell lineages diverge due to local microenvironments and stochastic processes. The minute sample volumes and low abundance of some constituents in cells hinder our understanding of cellular heterogeneity. Although amplification methods facilitate single-cell genomics and transcriptomics, the characterization of metabolites and proteins remains challenging both because of the lack of effective amplification approaches and the wide diversity in cellular constituents. Mass spectrometry has become an enabling technology for the investigation of individual cellular metabolite profiles with its exquisite sensitivity, large dynamic range, and ability to characterize hundreds to thousands of compounds. While advances in instrumentation have improved figures of merit, acquiring measurements at high throughput and sampling from large populations of cells are still not routine. In this Perspective, we highlight the current trends and progress in mass-spectrometry-based analysis of single cells, with a focus on the technologies that will enable the next generation of single-cell measurements.

The treatment action campaign and the three dimensions of lawyering: Reflections from the rainbow nation

PubMed Central

Ahmad, Hassan

2013-01-01

The spread and perpetuation of the HIV/AIDS epidemic in South Africa has hindered the country's social and economic growth after apartheid. This paper documents my experiences while working with the Projects Abroad Human Rights Office and specifically my interactions with the Treatment Action Campaign (TAC), an organization which has taken a multi-dimensional approach in order to educate people about HIV/AIDS and attempt to provide access to medicines for millions of South Africans afflicted with the disease. I discuss how TAC has used both traditional and non-traditional methods of advocacy to combat the epidemic and equate access to health care to a social justice issue by empowering marginalized communities. The paper's dual purpose is to applaud TAC's continuous success in combating HIV/AIDS with such a multi-dimensional approach and illustrate how other organizations can utilize such an approach in order to affect social change. To illustrate TAC's approach, I utilize Lucie White's three dimensions of lawyering and equate TAC to a single cause lawyer, signifying that White's characterization of multi-dimensional activism is not limited to individuals, but can rather be applied at the firm level. White's three dimensions include: (a) advocacy through litigation, (b) advocacy in stimulating progressive change, and (c) advocacy as a pedagogic process. From this analysis, I conclude that TAC's multi-dimensional approach and specifically its inherent practice of White's three dimensions has been the root of its success in educating millions about the virus and advocating for access to medicines for those who have contracted HIV. TAC's innovative advocacy has also mobilized a new generation of South African activists who have helped TAC grow into a vibrant and integral organization within the country's post-apartheid culture. Such an example can serve as a framework for future organizations who wish to tackle other challenges that face the country. PMID:23819672

The Treatment Action Campaign and the three dimensions of lawyering: reflections from the rainbow nation.

PubMed

Ahmad, Hassan

2013-03-01

The spread and perpetuation of the HIV/AIDS epidemic in South Africa has hindered the country's social and economic growth after apartheid. This paper documents my experiences while working with the Projects Abroad Human Rights Office and specifically my interactions with the Treatment Action Campaign (TAC), an organization which has taken a multi-dimensional approach in order to educate people about HIV/AIDS and attempt to provide access to medicines for millions of South Africans afflicted with the disease. I discuss how TAC has used both traditional and non-traditional methods of advocacy to combat the epidemic and equate access to health care to a social justice issue by empowering marginalized communities. The paper's dual purpose is to applaud TAC's continuous success in combating HIV/AIDS with such a multi-dimensional approach and illustrate how other organizations can utilize such an approach in order to affect social change. To illustrate TAC's approach, I utilize Lucie White's three dimensions of lawyering and equate TAC to a single cause lawyer, signifying that White's characterization of multi-dimensional activism is not limited to individuals, but can rather be applied at the firm level. White's three dimensions include: (a) advocacy through litigation, (b) advocacy in stimulating progressive change, and (c) advocacy as a pedagogic process. From this analysis, I conclude that TAC's multi-dimensional approach and specifically its inherent practice of White's three dimensions has been the root of its success in educating millions about the virus and advocating for access to medicines for those who have contracted HIV. TAC's innovative advocacy has also mobilized a new generation of South African activists who have helped TAC grow into a vibrant and integral organization within the country's post-apartheid culture. Such an example can serve as a framework for future organizations who wish to tackle other challenges that face the country.

Quantitative Proteomic Profiling of Prostate Cancer Reveals a Role for miR-128 in Prostate Cancer*

PubMed Central

Khan, Amjad P.; Poisson, Laila M.; Bhat, Vadiraja B.; Fermin, Damian; Zhao, Rong; Kalyana-Sundaram, Shanker; Michailidis, George; Nesvizhskii, Alexey I.; Omenn, Gilbert S.; Chinnaiyan, Arul M.; Sreekumar, Arun

2010-01-01

Multiple, complex molecular events characterize cancer development and progression. Deciphering the molecular networks that distinguish organ-confined disease from metastatic disease may lead to the identification of biomarkers of cancer invasion and disease aggressiveness. Although alterations in gene expression have been extensively quantified during neoplastic progression, complementary analyses of proteomic changes have been limited. Here we interrogate the proteomic alterations in a cohort of 15 prostate-derived tissues that included five each from adjacent benign prostate, clinically localized prostate cancer, and metastatic disease from distant sites. The experimental strategy couples isobaric tags for relative and absolute quantitation with multidimensional liquid phase peptide fractionation followed by tandem mass spectrometry. Over 1000 proteins were quantified across the specimens and delineated into clinically localized and metastatic prostate cancer-specific signatures. Included in these class-specific profiles were both proteins that were known to be dysregulated during prostate cancer progression and new ones defined by this study. Enrichment analysis of the prostate cancer-specific proteomic signature, to gain insight into the functional consequences of these alterations, revealed involvement of miR-128-a/b regulation during prostate cancer progression. This finding was validated using real time PCR analysis for microRNA transcript levels in an independent set of 15 clinical specimens. miR-128 levels were elevated in benign prostate epithelial cell lines compared with invasive prostate cancer cells. Knockdown of miR-128 induced invasion in benign prostate epithelial cells, whereas its overexpression attenuated invasion in prostate cancer cells. Taken together, our profiles of the proteomic alterations of prostate cancer progression revealed miR-128 as a potentially important negative regulator of prostate cancer cell invasion. PMID:19955085

Proteomic profiling of the planarian Schmidtea mediterranea and its mucous reveals similarities with human secretions and those predicted for parasitic flatworms.

PubMed

Bocchinfuso, Donald G; Taylor, Paul; Ross, Eric; Ignatchenko, Alex; Ignatchenko, Vladimir; Kislinger, Thomas; Pearson, Bret J; Moran, Michael F

2012-09-01

The freshwater planarian Schmidtea mediterranea has been used in research for over 100 years, and is an emerging stem cell model because of its capability of regenerating large portions of missing body parts. Exteriorly, planarians are covered in mucous secretions of unknown composition, implicated in locomotion, predation, innate immunity, and substrate adhesion. Although the planarian genome has been sequenced, it remains mostly unannotated, challenging both genomic and proteomic analyses. The goal of the current study was to annotate the proteome of the whole planarian and its mucous fraction. The S. mediterranea proteome was analyzed via mass spectrometry by using multidimensional protein identification technology with whole-worm tryptic digests. By using a proteogenomics approach, MS data were searched against an in silico translated planarian transcript database, and by using the Swiss-Prot BLAST algorithm to identify proteins similar to planarian queries. A total of 1604 proteins were identified. The mucous subproteome was defined through analysis of a mucous trail fraction and an extract obtained by treating whole worms with the mucolytic agent N-acetylcysteine. Gene Ontology analysis confirmed that the mucous fractions were enriched with secreted proteins. The S. mediterranea proteome is highly similar to that predicted for the trematode Schistosoma mansoni associated with intestinal schistosomiasis, with the mucous subproteome particularly highly conserved. Remarkably, orthologs of 119 planarian mucous proteins are present in human mucosal secretions and tear fluid. We suggest planarians have potential to be a model system for the characterization of mucous protein function and relevant to parasitic flatworm infections and diseases underlined by mucous aberrancies, such as cystic fibrosis, asthma, and other lung diseases.

Characterization of Fish Sauce Aroma Impact Compounds Using GC-MS, SPME-Osme-GCO, and Stevens' Power Law Exponents

USDA-ARS?s Scientific Manuscript database

The objectives of this study were to characterize volatile compounds and to determine the characteristic aromas associated with impact compounds in 4 fish sauces using solid-phase micro-extraction, gas chromatography-mass spectrometry, Osme, and gas chromatography olfactometry (SPME-Osme-GCO) couple...

Exposomics research using suspect screening and non-targeted analysis methods and tools at the U.S. Environmental Protection Agency (ASMS Presentation)

EPA Science Inventory

High-resolution mass spectrometry (HRMS) is used for suspect screening (SSA) and non-targeted analysis (NTA) in an attempt to characterize xenobiotic chemicals in various samples broadly and efficiently. These important techniques aid characterization of the exposome, the totalit...

Analysis of biodiesel and biodiesel-petrodiesel blends by high performance thin layer chromatography combined with easy ambient sonic-spray ionization mass spectrometry.

PubMed

Eberlin, Livia S; Abdelnur, Patricia V; Passero, Alan; de Sa, Gilberto F; Daroda, Romeu J; de Souza, Vanderlea; Eberlin, Marcos N

2009-08-01

High performance thin layer chromatography (HPTLC) combined with on-spot detection and characterization via easy ambient sonic-spray ionization mass spectrometry (EASI-MS) is applied to the analysis of biodiesel (B100) and biodiesel-petrodiesel blends (BX). HPTLC provides chromatographic resolution of major components whereas EASI-MS allows on-spot characterization performed directly on the HPTLC surface at ambient conditions. Constituents (M) are detected by EASI-MS in a one component-one ion fashion as either [M + Na](+) or [M + H](+). For both B100 and BX samples, typical profiles of fatty acid methyl esters (FAME) detected as [FAME + Na](+) ions allow biodiesel typification. The spectrum of the petrodiesel spot displays a homologous series of protonated alkyl pyridines which are characteristic for petrofuels (natural markers). The spectrum for residual or admixture oil spots is characterized by sodiated triglycerides [TAG + Na](+). The application of HPTLC to analyze B100 and BX samples and its combination with EASI-MS for on-spot characterization and quality control is demonstrated.

Mapping of low molecular weight heparins using reversed phase ion pair liquid chromatography-mass spectrometry.

PubMed

Li, Daoyuan; Chi, Lequan; Jin, Lan; Xu, Xiaohui; Du, Xuzhao; Ji, Shengli; Chi, Lianli

2014-01-01

Low molecular weight heparins (LMWHs) are structurally complex, highly sulfated and negatively charged, linear carbohydrate polymers prepared by chemical or enzymatic depolymerization of heparin. They are widely used as anticoagulant drugs possessing better bioavailability, longer half-life, and lower side effects than heparin. Comprehensive structure characterization of LMWHs is important for drug quality assurance, generic drug application, and new drug research and development. However, fully characterization of all oligosaccharide chains in LMWHs is not feasible for current available analytical technologies due to their structure complexity and heterogeneity. Fingerprinting profiling is an efficient way for LMWHs' characterization and comparison. In this work, we present a simple, sensitive, and powerful analytical approach for structural characterization of LMWHs. Two different LMWHs, enoxaparin and nadroparin, were analyzed using reversed phase ion pair electrospray ionization mass spectrometry (RPIP-ESI-MS). More than 200 components were identified, including major structures, minor structures, and process related impurities. This approach is robust for high resolution and complementary fingerprinting analysis of LMWHs. Copyright © 2013 Elsevier Ltd. All rights reserved.

A review of direct numerical simulations of astrophysical detonations and their implications

DOE PAGES

Parete-Koon, Suzanne T.; Smith, Christopher R.; Papatheodore, Thomas L.; ...

2013-04-11

Multi-dimensional direct numerical simulations (DNS) of astrophysical detonations in degenerate matter have revealed that the nuclear burning is typically characterized by cellular structure caused by transverse instabilities in the detonation front. Type Ia supernova modelers often use one- dimensional DNS of detonations as inputs or constraints for their whole star simulations. While these one-dimensional studies are useful tools, the true nature of the detonation is multi-dimensional. The multi-dimensional structure of the burning influences the speed, stability, and the composition of the detonation and its burning products, and therefore, could have an impact on the spectra of Type Ia supernovae. Considerablemore » effort has been expended modeling Type Ia supernovae at densities above 1x10 7 g∙cm -3 where the complexities of turbulent burning dominate the flame propagation. However, most full star models turn the nuclear burning schemes off when the density falls below 1x10 7 g∙cm -3 and distributed burning begins. The deflagration to detonation transition (DDT) is believed to occur at just these densities and consequently they are the densities important for studying the properties of the subsequent detonation. In conclusion, this work reviews the status of DNS studies of detonations and their possible implications for Type Ia supernova models. It will cover the development of Detonation theory from the first simple Chapman-Jouguet (CJ) detonation models to the current models based on the time-dependent, compressible, reactive flow Euler equations of fluid dynamics.« less

Comprehensive drought characteristics analysis based on a nonlinear multivariate drought index

NASA Astrophysics Data System (ADS)

Yang, Jie; Chang, Jianxia; Wang, Yimin; Li, Yunyun; Hu, Hui; Chen, Yutong; Huang, Qiang; Yao, Jun

2018-02-01

It is vital to identify drought events and to evaluate multivariate drought characteristics based on a composite drought index for better drought risk assessment and sustainable development of water resources. However, most composite drought indices are constructed by the linear combination, principal component analysis and entropy weight method assuming a linear relationship among different drought indices. In this study, the multidimensional copulas function was applied to construct a nonlinear multivariate drought index (NMDI) to solve the complicated and nonlinear relationship due to its dependence structure and flexibility. The NMDI was constructed by combining meteorological, hydrological, and agricultural variables (precipitation, runoff, and soil moisture) to better reflect the multivariate variables simultaneously. Based on the constructed NMDI and runs theory, drought events for a particular area regarding three drought characteristics: duration, peak, and severity were identified. Finally, multivariate drought risk was analyzed as a tool for providing reliable support in drought decision-making. The results indicate that: (1) multidimensional copulas can effectively solve the complicated and nonlinear relationship among multivariate variables; (2) compared with single and other composite drought indices, the NMDI is slightly more sensitive in capturing recorded drought events; and (3) drought risk shows a spatial variation; out of the five partitions studied, the Jing River Basin as well as the upstream and midstream of the Wei River Basin are characterized by a higher multivariate drought risk. In general, multidimensional copulas provides a reliable way to solve the nonlinear relationship when constructing a comprehensive drought index and evaluating multivariate drought characteristics.

Soil carbon content and character in an old-growth forest in northwestern Pennsylvania: a case study introducing pyrolysis molecular beam mass spectrometry (py-MBMS)

Treesearch

C.M. Hoover; K.A. Magrini; R.J. Evans

2002-01-01

This study was conducted to: (1) test the utility of a new and rapid analytical method, pyrolysis molecular beam mass spectrometry (py-MBMS), for the measurement and characterization of carbon in forest soils, and (2) examine the effects of natural disturbance on soil carbon dynamics. An additional objective was to test the ability of py-MBMS to distinguish recent from...

Comprehensive characterization of ethoxyquin transformation products in fish feed by traveling-wave ion mobility spectrometry coupled to quadrupole time-of-flight mass spectrometry.

PubMed

Negreira, Noelia; Regueiro, Jorge; Valdersnes, Stig; Berntssen, Marc H G; Ørnsrud, Robin

2017-05-01

Feed additives are typically used in intensive farming production over long periods, and hence, they can accumulate in farmed animal tissues. Concerns regarding the use of ethoxyquin as an antioxidant feed additive, have recently arisen due to its potential conversion into a series of transformation products (TPs). The aim of this work was to characterize the TPs of ethoxyquin in fish feed by a novel approach based on the use of traveling-wave ion mobility spectrometry (TWIMS) coupled to high-resolution quadrupole time-of-flight mass spectrometry (QTOFMS). First, ethoxyquin was oxidized under controlled conditions and the generated TPs were added to a comprehensive database. Atlantic salmon feeds were then screened for ethoxyquin TPs using both targeted and untargeted approaches. Twenty-seven TPs were tentatively identified during the oxidation experiments, fifteen of them also being present in the feed samples. In addition, ten other potential TPs were detected in fish feed following the untargeted approach. Thirty-one of these TPs have been reported for the first time in this work through the oxidation experiments and the feed samples. Therefore, this study provides valuable information on the oxidative fate of ethoxyquin in feed, which can be used for future evaluations of potential risk related to this additive. Copyright © 2017 Elsevier B.V. All rights reserved.

Determining Double Bond Position in Lipids Using Online Ozonolysis Coupled to Liquid Chromatography and Ion Mobility-Mass Spectrometry.

PubMed

Harris, Rachel A; May, Jody C; Stinson, Craig A; Xia, Yu; McLean, John A

2018-02-06

The increasing focus on lipid metabolism has revealed a need for analytical techniques capable of structurally characterizing lipids with a high degree of specificity. Lipids can exist as any one of a large number of double bond positional isomers, which are indistinguishable by single-stage mass spectrometry alone. Ozonolysis reactions coupled to mass spectrometry have previously been demonstrated as a means for localizing double bonds in unsaturated lipids. Here we describe an online, solution-phase reactor using ozone produced via a low-pressure mercury lamp, which generates aldehyde products diagnostic of cleavage at a particular double bond position. This flow-cell device is utilized in conjunction with structurally selective ion mobility-mass spectrometry. The lamp-mediated reaction was found to be effective for multiple lipid species in both positive and negative ionization modes, and the conversion efficiency from precursor to product ions was tunable across a wide range (20-95%) by varying the flow rate through the ozonolysis device. Ion mobility separation of the ozonolysis products generated additional structural information and revealed the presence of saturated species in a complex mixture. The method presented here is simple, robust, and readily coupled to existing instrument platforms with minimal modifications necessary. For these reasons, application to standard lipidomic workflows is possible and aids in more comprehensive structural characterization of a myriad of lipid species.

Characterization of a novel miniaturized burst-mode infrared laser system for IR-MALDESI mass spectrometry imaging.

PubMed

Ekelöf, Måns; Manni, Jeffrey; Nazari, Milad; Bokhart, Mark; Muddiman, David C

2018-03-01

Laser systems are widely used in mass spectrometry as sample probes and ionization sources. Mid-infrared lasers are particularly suitable for analysis of high water content samples such as animal and plant tissues, using water as a resonantly excited sacrificial matrix. Commercially available mid-IR lasers have historically been bulky and expensive due to cooling requirements. This work presents a novel air-cooled miniature mid-IR laser with adjustable burst-mode output and details an evaluation of its performance for mass spectrometry imaging. The miniature laser was found capable of generating sufficient energy for complete ablation of animal tissue in the context of an IR-MALDESI experiment with exogenously added ice matrix, yielding several hundred confident metabolite identifications. Graphical abstract The use of a novel miniature 2.94 μm burst-mode laser in IR-MALDESI allows for rapid and sensitive mass spectrometry imaging of a whole mouse.

Rapid screening and structural elucidation of a novel sibutramine analogue in a weight loss supplement: 11-desisobutyl-11-benzylsibutramine.

PubMed

Mans, Daniel J; Gucinski, Ashley C; Dunn, Jamie D; Gryniewicz-Ruzicka, Connie M; Mecker-Pogue, Laura C; Kao, Jeff L-F; Ge, Xia

2013-09-01

A novel analogue of sibutramine, 11-desisobutyl-11-benzylsibutramine, has been discovered. During routine ion mobility spectrometry (IMS) screening of a weight loss supplement collected at an US FDA import operation facility an unknown peak was observed. Further analysis of the supplement by liquid chromatography-mass spectrometry (LC-MS) and high resolution mass spectrometry revealed an unknown peak with a relative retention time of 1.04 with respect to sibutramine and a predicted formula of C20H24NCl. In order to elucidate the analogue's structure, it was isolated from the supplement and characterized by tandem mass spectrometry and nuclear magnetic resonance (NMR), which revealed the analogue possessed a benzyl moiety at the 11 position in place of the isobutyl group associated with sibutramine. Copyright © 2013. Published by Elsevier B.V.

Trace and surface analysis of ceramic layers of solid oxide fuel cells by mass spectrometry.

PubMed

Becker, J S; Breuer, U; Westheide, J; Saprykin, A I; Holzbrecher, H; Nickel, H; Dietze, H J

1996-06-01

For the trace analysis of impurities in thick ceramic layers of a solid oxide fuel cell (SOFC) sensitive solid-state mass spectrometric methods, such as laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) and radiofrequency glow discharge mass spectrometry (rf-GDMS) have been developed and used. In order to quantify the analytical results of LA-ICP-MS, the relative sensitivity coefficients of elements in a La(0.6)Sr(0.35)MnO(3) matrix have been determined using synthetic standards. Secondary ion mass spectrometry (SIMS) - as a surface analytical method - has been used to characterize the element distribution and diffusion profiles of matrix elements on the interface of a perovskite/Y-stabilized ZrO(2) layer. The application of different mass spectrometric methods for process control in the preparation of ceramic layers for the SOFC is described.

Characterization of dicarboxylic naphthenic acid fraction compounds utilizing amide derivatization: Proof of concept.

PubMed

Kovalchik, Kevin A; MacLennan, Matthew S; Peru, Kerry M; Ajaero, Chukwuemeka; McMartin, Dena W; Headley, John V; Chen, David D Y

2017-12-30

The characterization of naphthenic acid fraction compounds (NAFCs) in oil sands process affected water (OSPW) is of interest for both toxicology studies and regulatory reasons. Previous studies utilizing authentic standards have identified dicarboxylic naphthenic acids using two-dimensional gas chromatography hyphenated to time-of-flight mass spectrometry (GC × GC/TOFMS). The selective derivatization of hydroxyl groups has also recently aided in the characterization of oxy-NAFCs, and indirectly the characterization of dicarboxylic NAFCs. However, there has been no previous report of derivatization being used to directly aid in the standard-free characterization of NAFCs with multiple carboxylic acid functional groups. Herein we present proof-of-concept for the characterization of dicarboxylic NAFCs utilizing amide derivatization. Carboxylic acid groups in OSPW extract and in a dicarboxylic acidstandard were derivatized to amides using a previously described method. The derivatized extract and derivatized standard were analyzed by direct-injection positive-mode electrospray ionization ((+)ESI) high-resolution mass spectrometry (HRMS), and the underivatized extract was analyzed by (-)ESI MS. Tandem mass spectrometry (MS/MS) was carried out on selected ions of the derivatized standard and derivatized OSPW. Data analysis was carried out using the Python programming language. The distribution of monocarboxylic NAFCs observed in the amide-derivatized OSPW sample by (+)ESI-MS was generally similar to that seen in underivatized OSPW by (-)ESI-MS. The dicarboxylic acid standard shows evidence of being doubly derivatized, although the second derivatization appears to be inefficient. Furthermore, a spectrum of potential diacid NAFCs is presented, identified by both charge state and derivatization mass. Interference due to the presence of multiple derivatization products is noted, but can be eliminated using on-line separation or an isotopically labelled derivatization reagent. Proof of concept for the characterization of dicarboxylic NAFCs utilizing amide derivatization is demonstrated. Furthermore, (+)ESI-HRMS of the derivatized monocarboxylic NAFCS yields similar information to (-)ESI-MS analysis of underivatized NAFCs, with the benefit of added selectivity for carboxylic acid species and the characterization of diacids. Copyright © 2017 John Wiley & Sons, Ltd.

Neuropeptide Signaling in Crustaceans Probed by Mass Spectrometry

NASA Astrophysics Data System (ADS)

Liang, Zhidan

Neuropeptides are one of the most diverse classes of signaling molecules whose identities and functions are not yet fully understood. They have been implicated in the regulation of a wide range of physiological processes, including feeding-related and motivated behaviors, and also environmental adaptations. In this work, improved mass spectrometry-based analytical platforms were developed and applied to the crustacean systems to characterize signaling molecules. This dissertation begins with a review of mass spectrometry-based neuropeptide studies from both temporal- and spatial-domains. This review is then followed by several chapters detailing a few research projects related to the crustacean neuropeptidomic characterization and comparative analysis. The neuropeptidome of crayfish, Orconectes rusticus is characterized for the first time using mass spectrometry-based tools. In vivo microdialysis sampling technique offers the capability of direct sampling from extracellular space in a time-resolved manner. It is used to investigate the secreted neuropeptide and neurotransmitter content in Jonah crab, Cancer borealis, in this work. A new quantitation strategy using alternative mass spectrometry data acquisition approach is developed and applied for the first time to quantify neuropeptides. Coupling of this method with microdialysis enables the study of neuropeptide dynamics concurrent with different behaviors. Proof-of-principle experiments validating this approach have been carried out in Jonah crab, Cancer borealis to study feeding- and circadian rhythm-related neuropeptide changes using micoridialysis in a time-resolved manner. This permits a close correlation between behavioral and neurochemical changes, providing potential candidates for future validation of regulatory roles. In addition to providing spatial information, mass spectrometry imaging (MSI) technique enables the characterization of signaling molecules while preserving the temporal resolution. A novel MSI-based platform is developed by interfacing with microdialysis sample collection and is applied to the study of in vivo neuropeptide degradation profiles in an off-line 'real-time' fashion. This unique platform provides novel insights into neuropeptide inactivation/elimination process, which is an essential step to understand peptidergic signaling pathway. In addition to neuropeptides, this platform has been further modified to study secreted neurotransmitters, and small molecule metabolites that might interact with neuropeptides in crustacean for the first time. This work not only reports improvements upon neuropeptides identification and quantitation by developing improved analytical strategies, but also provides important evidence for the potential roles of several neuropeptides in regulating food intake and circadian rhythm behaviors. Novel platform that integrates MALDI-MSI with microdialysis in exploring neurochemical changes in dynamic biological events is also presented, which could be potentially applied to many other systems in future research. Collectively this dissertation research develops new analytical methods and improves our fundamental understanding of neuropeptide signaling.

Multidimensional effects in nonadiabatic statistical theories of spin- forbidden kinetics. A case study of 3O + CO → CO 2

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

Jasper, Ahren

2015-04-14

The appropriateness of treating crossing seams of electronic states of different spins as nonadiabatic transition states in statistical calculations of spin-forbidden reaction rates is considered. We show that the spin-forbidden reaction coordinate, the nuclear coordinate perpendicular to the crossing seam, is coupled to the remaining nuclear degrees of freedom. We found that this coupling gives rise to multidimensional effects that are not typically included in statistical treatments of spin-forbidden kinetics. Three qualitative categories of multidimensional effects may be identified: static multidimensional effects due to the geometry-dependence of the local shape of the crossing seam and of the spin–orbit coupling, dynamicalmore » multidimensional effects due to energy exchange with the reaction coordinate during the seam crossing, and nonlocal(history-dependent) multidimensional effects due to interference of the electronic variables at second, third, and later seam crossings. Nonlocal multidimensional effects are intimately related to electronic decoherence, where electronic dephasing acts to erase the history of the system. A semiclassical model based on short-time full-dimensional trajectories that includes all three multidimensional effects as well as a model for electronic decoherence is presented. The results of this multidimensional nonadiabatic statistical theory (MNST) for the 3O + CO → CO 2 reaction are compared with the results of statistical theories employing one-dimensional (Landau–Zener and weak coupling) models for the transition probability and with those calculated previously using multistate trajectories. The MNST method is shown to accurately reproduce the multistate decay-of-mixing trajectory results, so long as consistent thresholds are used. Furthermore, the MNST approach has several advantages over multistate trajectory approaches and is more suitable in chemical kinetics calculations at low temperatures and for complex systems. The error in statistical calculations that neglect multidimensional effects is shown to be as large as a factor of 2 for this system, with static multidimensional effects identified as the largest source of error.« less

A Versatile Strategy for Characterization and Imaging of Drip Flow Microbial Biofilms.

PubMed

Li, Bin; Dunham, Sage J B; Ellis, Joseph F; Lange, Justin D; Smith, Justin R; Yang, Ning; King, Travis L; Amaya, Kensey R; Arnett, Clint M; Sweedler, Jonathan V

2018-06-05

The inherent architectural and chemical complexities of microbial biofilms mask our understanding of how these communities form, survive, propagate, and influence their surrounding environment. Here we describe a simple and versatile workflow for the cultivation and characterization of model flow-cell-based microbial ecosystems. A customized low-shear drip flow reactor was designed and employed to cultivate single and coculture flow-cell biofilms at the air-liquid interface of several metal surfaces. Pseudomonas putida F1 and Shewanella oneidensis MR-1 were selected as model organisms for this study. The utility and versatility of this platform was demonstrated via the application of several chemical and morphological imaging techniques-including matrix-assisted laser desorption/ionization mass spectrometry imaging, secondary ion mass spectrometry imaging, and scanning electron microscopy-and through the examination of model systems grown on iron substrates of varying compositions. Implementation of these techniques in combination with tandem mass spectrometry and a two-step imaging principal component analysis strategy resulted in the identification and characterization of 23 lipids and 3 oligosaccharides in P. putida F1 biofilms, the discovery of interaction-specific analytes, and the observation of several variations in cell and substrate morphology present during microbially influenced corrosion. The presented workflow is well-suited for examination of both single and multispecies drip flow biofilms and offers a platform for fundamental inquiries into biofilm formation, microbe-microbe interactions, and microbially influenced corrosion.

Screening and identification of steroidal saponins from Anemarrhena asphodeloides employing UPLC tandem triple quadrupole linear ion trap mass spectrometry.

PubMed

Xia, Yong-Gang; Guo, Xin-Dong; Liang, Jun; Yang, Bing-You; Kuang, Hai-Xue

2017-09-01

This study presents a practical and valid strategy for the screening and structural characterization of Anemarrhena asphodeloides Bge steroidal saponins (SSs) using ultra-high performance liquid chromatography coupled with triple quadrupole linear ion trap mass spectrometry. The whole analytical protocols integrate four-step procedures in the positive mode: (1) rational deduction of mass fragmentation pathways of A. asphodeloides SSs; (2) untargeted screening of potential A. asphodeloides SSs by multiple-ion monitoring-information-dependent-acquiring-enhanced product ion (MIM-IDA-EPI) scan through reverse phase liquid chromatography; (3) comprehensive construction of an ammoniated precursor ion database by combining untargeted MIM-IDA-EPI scans and data literature; and (4) structural interpretation of targeted A. asphodeloides SSs using MIM-IDA-EPI and multiple reaction monitoring (MRM)-IDA-EPI with an energy-resolved technique. The protocols were used to analyze SSs in A. asphodeloides; of the 87 detected SSs that were unambiguously characterized or tentatively identified, 19 compounds were the first to be reported from A. asphodeloides and 13 ones were characterized as potential new compounds. Accuracy of the analytical procedure was demonstrated by structural identification of three SSs by NMR spectroscopy. The proposed schemes hold an excellent promise in the structural prediction and interpretation of complex SSs from plant medicines by mass spectrometry. Copyright © 2017 Elsevier Inc. All rights reserved.

Separations and characterizations of fractions from Mayan, Heavy Arabian, and Hondo crude oils

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

Kircher, C.C.

1989-04-01

The results from hydrotreating the atmospheric residua of Hondo, Heavy Arabian, and Mayan crude oils have been reported recently. Over the same fixed-bed catalyst, the hydrosulfurization activities varied by a factor of two and the hydrodemetallation activities varied almost four-fold. Correlations among the relative activities and the elemental compositions of the feed oils showed a direct relationship between the hydrodemetallation activity and the metals content of the petroleum resins fractions, hereafter called polars. Thus, to discover chemical differences in feed oils and polars that may affect a catalysts activity, they have developed separation schemes to separate the oils into theirmore » component fractions and used various analytical techniques to characterize the fractions. The separation scheme developed is a modification and extension of the ASTM D2007 procedure. The sample is separated into saturates, aromatics, polars, and asphaltenes by precipitation/filtration and chromatography with Attapulgus cla and silica gel; then the polars are separated into various acids, bases, and neutral polars with macroporous ion exchange resins. This separation scheme has been applied to 650{degree}F + cut from Hondo (offshore California) crude. The fractions were characterized with carbon and hydrogen elemental analysis, XRF spectrometry for nickel, vanadium, and sulfur, chemiluminescence spectrometry for nitrogen. GC simulated distillations (saturates only), vapor pressure osmetry (number-average molecular weight) in toluene, flame emission spectrometry, and {sup 13}C-NMR spectroscopy.« less

In-depth analyses of native N-linked glycans facilitated by high-performance anion exchange chromatography-pulsed amperometric detection coupled to mass spectrometry.

PubMed

Szabo, Zoltan; Thayer, James R; Agroskin, Yury; Lin, Shanhua; Liu, Yan; Srinivasan, Kannan; Saba, Julian; Viner, Rosa; Huhmer, Andreas; Rohrer, Jeff; Reusch, Dietmar; Harfouche, Rania; Khan, Shaheer H; Pohl, Christopher

2017-05-01

Characterization of glycans present on glycoproteins has become of increasing importance due to their biological implications, such as protein folding, immunogenicity, cell-cell adhesion, clearance, receptor interactions, etc. In this study, the resolving power of high-performance anion exchange chromatography with pulsed amperometric detection (HPAE-PAD) was applied to glycan separations and coupled to mass spectrometry to characterize native glycans released from different glycoproteins. A new, rapid workflow generates glycans from 200 μg of glycoprotein supporting reliable and reproducible annotation by mass spectrometry (MS). With the relatively high flow rate of HPAE-PAD, post-column splitting diverted 60% of the flow to a novel desalter, then to the mass spectrometer. The delay between PAD and MS detectors is consistent, and salt removal after the column supports MS. HPAE resolves sialylated (charged) glycans and their linkage and positional isomers very well; separations of neutral glycans are sufficient for highly reproducible glycoprofiling. Data-dependent MS 2 in negative mode provides highly informative, mostly C- and Z-type glycosidic and cross-ring fragments, making software-assisted and manual annotation reliable. Fractionation of glycans followed by exoglycosidase digestion confirms MS-based annotations. Combining the isomer resolution of HPAE with MS 2 permitted thorough N-glycan annotation and led to characterization of 17 new structures from glycoproteins with challenging glycan profiles.

Metabolic profile of glyburide in human liver microsomes using LC-DAD-Q-TRAP-MS/MS.

PubMed

Ravindran, Selvan; Basu, Sudipta; Gorti, Santosh Kapil Kumar; Surve, Prashant; Sloka, Navya

2013-05-01

The sulfonylurea urea drug glyburide (glibenclamide) is widely used for the treatment of diabetes milletus and gestational diabetes. In previous studies monohydroxylated metabolites were identified and characterized for glyburide in different species, but the metabolite owing to the loss of cyclohexyl ring was identified only in mouse. Glyburide upon incubation with hepatic microsomes resulted in 10 metabolites for human. The current study identifies new metabolites of glyburide along with the hydroxylated metabolites that were reported earlier. The newly identified drug metabolites are dihydroxylated metabolites, a metabolite owing to the loss of cyclohexyl ring and one owing to hydroxylation with dehydrogenation. Among the 10 identified metabolites, there were six monohydroxylated metabolites, one dihydroxylated metabolite, two metabolites owing to hydroxylation and dehydrogenation, and one metabolite owing to the loss of cyclohexyl ring. New metabolites of glyburide were identified and characterized using liquid chromatography-diode array detector-quadruple-ion trap-mass spectrometry/mass spectrometry (LC-DAD-Q-TRAP-MS/MS). An enhanced mass scan-enhanced product ion scan with information-dependent acquisition mode in a Q-TRAP-MS/MS system was used to characterize the metabolites. Liquid chromatography with diode array detection was used as a complimentary technique to confirm and identify the metabolites. Metabolites formed in higher amounts were detected in both diode array detection and mass spectrometry detection. Copyright © 2012 John Wiley & Sons, Ltd.

A Multidimensional Analytical Comparison of Remicade and the Biosimilar Remsima.

PubMed

Pisupati, Karthik; Tian, Yuwei; Okbazghi, Solomon; Benet, Alexander; Ackermann, Rose; Ford, Michael; Saveliev, Sergei; Hosfield, Christopher M; Urh, Marjeta; Carlson, Eric; Becker, Christopher; Tolbert, Thomas J; Schwendeman, Steven P; Ruotolo, Brandon T; Schwendeman, Anna

2017-05-02

In April 2016, the Food and Drug Administration approved the first biosimilar monoclonal antibody (mAb), Inflectra/Remsima (Celltrion), based off the original product Remicade (infliximab, Janssen). Biosimilars promise significant cost savings for patients, but the unavoidable differences between innovator and copycat biologics raise questions regarding product interchangeability. In this study, Remicade and Remsima were examined by native mass spectrometry, ion mobility, and quantitative peptide mapping. The levels of oxidation, deamidation, and mutation of individual amino acids were remarkably similar. We found different levels of C-terminal truncation, soluble protein aggregates, and glycation that all likely have a limited clinical impact. Importantly, we identified more than 25 glycoforms for each product and observed glycoform population differences, with afucosylated glycans accounting for 19.7% of Remicade and 13.2% of Remsima glycoforms, which translated into a 2-fold reduction in the level of FcγIIIa receptor binding for Remsima. While this difference was acknowledged in Remsima regulatory filings, our glycoform analysis and receptor binding results appear to be somewhat different from the published values, likely because of methodological differences between laboratories and improved glycoform identification by our laboratory using a peptide map-based method. Our mass spectrometry-based analysis provides rapid and robust analytical information vital for biosimilar development. We have demonstrated the utility of our multiple-attribute monitoring workflow using the model mAbs Remicade and Remsima and have provided a template for analysis of future mAb biosimilars.

Prototype of an Interface for Hyphenating Distillation with Gas Chromatography and Mass Spectrometry

PubMed Central

Tang, Ya-Ru; Yang, Hui-Hsien; Urban, Pawel L.

2017-01-01

Chemical analysis of complex matrices—containing hundreds of compounds—is challenging. Two-dimensional separation techniques provide an efficient way to reduce complexity of mixtures analyzed by mass spectrometry (MS). For example, gasoline is a mixture of numerous compounds, which can be fractionated by distillation techniques. However, coupling conventional distillation with other separations as well as MS is not straightforward. We have established an automatic system for online coupling of simple microscale distillation with gas chromatography (GC) and electron ionization MS. The developed system incorporates an interface between the distillation condenser and the injector of a fused silica capillary GC column. Development of this multidimensional separation (distillation-GC-MS) was preceded by a series of preliminary off-line experiments. In the developed technique, the components with different boiling points are fractionated and instantly analyzed by GC-MS. The obtained data sets illustrate dynamics of the distillation process. An important advantage of the distillation-GC-MS technique is that raw samples can directly be analyzed without removal of the non-volatile matrix residues that could contaminate the GC injection port and the column. Distilling the samples immediately before the injection to the GC column may reduce possible matrix effects—especially in the early phase of separation, when molecules with different volatilities co-migrate. It can also reduce losses of highly volatile components (during fraction collection and transfer). The two separation steps are partly orthogonal, what can slightly increase selectivity of the entire analysis. PMID:28337400

Novel proline-hydroxyproline glycopeptides from the dandelion (Taraxacum officinale Wigg.) flowers: de novo sequencing and biological activity.

PubMed

Astafieva, Alexandra A; Enyenihi, Atim A; Rogozhin, Eugene A; Kozlov, Sergey A; Grishin, Eugene V; Odintsova, Tatyana I; Zubarev, Roman A; Egorov, Tsezi A

2015-09-01

Two novel homologous peptides named ToHyp1 and ToHyp2 that show no similarity to any known proteins were isolated from Taraxacum officinale Wigg. flowers by multidimensional liquid chromatography. Amino acid and mass spectrometry analyses demonstrated that the peptides have unusual structure: they are cysteine-free, proline-hydroxyproline-rich and post-translationally glycosylated by pentoses, with 5 carbohydrates in ToHyp2 and 10 in ToHyp1. The ToHyp2 peptide with a monoisotopic molecular mass of 4350.3Da was completely sequenced by a combination of Edman degradation and de novo sequencing via top down multistage collision induced dissociation (CID) and higher energy dissociation (HCD) tandem mass spectrometry (MS(n)). ToHyp2 consists of 35 amino acids, contains eighteen proline residues, of which 8 prolines are hydroxylated. The peptide displays antifungal activity and inhibits growth of Gram-positive and Gram-negative bacteria. We further showed that carbohydrate moieties have no significant impact on the peptide structure, but are important for antifungal activity although not absolutely necessary. The deglycosylated ToHyp2 peptide was less active against the susceptible fungus Bipolaris sorokiniana than the native peptide. Unique structural features of the ToHyp2 peptide place it into a new family of plant defense peptides. The discovery of ToHyp peptides in T. officinale flowers expands the repertoire of molecules of plant origin with practical applications. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Tile-Based Fisher Ratio Analysis of Comprehensive Two-Dimensional Gas Chromatography Time-of-Flight Mass Spectrometry (GC × GC – TOFMS) Data using a Null Distribution Approach

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

Parsons, Brendon A.; Marney, Luke C.; Siegler, William C.

Multi-dimensional chromatographic instrumentation produces information-rich, and chemically complex data containing meaningful chemical signals and/or chemical patterns. Two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC × GC – TOFMS) is a prominent instrumental platform that has been applied extensively for discovery-based experimentation, where samples are sufficiently volatile or amenable to derivatization. Use of GC × GC – TOFMS and associated data analysis strategies aim to uncover meaningful chemical signals or chemical patterns. However, for complex samples, meaningful chemical information is often buried in a background of less meaningful chemical signal and noise. In this report, we utilize the tile-based F-ratiomore » software in concert with the standard addition method by spiking non-native chemicals into a diesel fuel matrix at low concentrations. While the previous work studied the concentration range of 100-1000 ppm, the current study focuses on the 0 ppm to 100 ppm analyte spike range. This study demonstrates the sensitivity and selectivity of the tile-based F-ratio software for discovery of true positives in the non-targeted analysis of a chemically complex and analytically challenging sample matrix. By exploring the low concentration spike levels, we gain a better understanding of the limit of detection (LOD) of the tile-based F-ratio software with GC × GC – TOFMS data.« less

On the Need for Multidimensional Stirling Simulations

NASA Technical Reports Server (NTRS)

Dyson, Rodger W.; Wilson, Scott D.; Tew, Roy C.; Demko, Rikako

2005-01-01

Given the cost and complication of simulating Stirling convertors, do we really need multidimensional modeling when one-dimensional capabilities exist? This paper provides a comprehensive description of when and why multidimensional simulation is needed.

Multidimensional Scaling in the Poincare Disk

DTIC Science & Technology

2011-05-01

REPORT Multidimensional Scaling in the Poincare Dis 14. ABSTRACT 16. SECURITY CLASSIFICATION OF: Multidimensional scaling (MDS) is a class of projective...DATES COVERED (From - To) Standard Form 298 (Rev 8/98) Prescribed by ANSI Std. Z39.18 - Multidimensional Scaling in the Poincare Dis Report Title... plane . Our construction is based on an approximate hyperbolic line search and exempli?es some of the particulars that need to be addressed when

Scaling Laws for the Multidimensional Burgers Equation with Quadratic External Potential

NASA Astrophysics Data System (ADS)

Leonenko, N. N.; Ruiz-Medina, M. D.

2006-07-01

The reordering of the multidimensional exponential quadratic operator in coordinate-momentum space (see X. Wang, C.H. Oh and L.C. Kwek (1998). J. Phys. A.: Math. Gen. 31:4329-4336) is applied to derive an explicit formulation of the solution to the multidimensional heat equation with quadratic external potential and random initial conditions. The solution to the multidimensional Burgers equation with quadratic external potential under Gaussian strongly dependent scenarios is also obtained via the Hopf-Cole transformation. The limiting distributions of scaling solutions to the multidimensional heat and Burgers equations with quadratic external potential are then obtained under such scenarios.

Models of multidimensional discrete distribution of probabilities of random variables in information systems

NASA Astrophysics Data System (ADS)

Gromov, Yu Yu; Minin, Yu V.; Ivanova, O. G.; Morozova, O. N.

2018-03-01

Multidimensional discrete distributions of probabilities of independent random values were received. Their one-dimensional distribution is widely used in probability theory. Producing functions of those multidimensional distributions were also received.

Structural characterization of phenolics and betacyanins in Gomphrena globosa by high-performance liquid chromatography-diode array detection/electrospray ionization multi-stage mass spectrometry.

PubMed

Ferreres, Federico; Gil-Izquierdo, Angel; Valentão, Patrícia; Andrade, Paula B

2011-11-30

The metabolite profiling of Gomphrena globosa inflorescences was performed by high-performance liquid chromatography-diode array detection/electrospray ionization multi-stage mass spectrometry (HPLC-DAD/ESI-MS(n)). Based on the fragmentation patterns, 24 phenolic compounds were characterized. The identified phenolics include p-coumaric and ferulic acids, quercetin, kaempferol, isorhamnetin, and hydroxylated 6,7-methylenedioxyflavone derivatives, as well as their aglycones, none of them reported before in the species. This is also the first time that tetrahydroxy-methylenedioxyflavone derivatives and acetylglycosides are described in nature. Betacyanins were also found. This study significantly extends the knowledge of the G. globosa metabolome, by providing further insights into its phenolic composition. Copyright © 2011 John Wiley & Sons, Ltd.

The leaf volatile constituents of Isatis tinctoria by Solid-Phase Microextraction and Gas chromatography/Mass Spectrometry.

PubMed

Condurso, Cettina; Verzera, Antonella; Romeo, Vincenza; Ziino, Marisa; Trozzi, Alessandra; Ragusa, Salvatore

2006-08-01

The leaf volatile constituents of Isatis tinctoria L. (Brassicaceae) have been studied by Solid-Phase Microextraction and Gas chromatography/Mass Spectrometry (SPME/GC-MS). Seventy components were fully characterized by mass spectra, linear retention indices, and injection of standards; the average composition (ppm) as single components and classes of substances is reported. Aliphatic hydrocarbons, acids, alcohols, aldehydes and esters, aromatic aldehydes, esters and ethers, furans, isothiocyanates and thiocyanates, sulfurated compounds, nitriles, terpenes and sesquiterpenes were identified. Leaf volatiles in Isatis tinctoria L. were characterized by a high amount of isothiocyanates which accounted for about 40 % of the total volatile fraction. Isothiocyanates are important and characteristic flavour compounds in Brassica vegetables and the cancer chemo-protective attributes are recently responsible for their growing interest.

Molecular characterization and comparison of shale oils generated by different pyrolysis methods using FT-ICR mass spectrometry

USGS Publications Warehouse

Jin, J.M.; Kim, S.; Birdwell, J.E.

2011-01-01

Fourier transform ion cyclotron resonance mass spectrometry (FT ICR-MS) was applied in the analysis of shale oils generated using two different pyrolysis systems under laboratory conditions meant to simulate surface and in situ oil shale retorting. Significant variations were observed in the shale oils, particularly the degree of conjugation of the constituent molecules. Comparison of FT ICR-MS results to standard oil characterization methods (API gravity, SARA fractionation, gas chromatography-flame ionization detection) indicated correspondence between the average Double Bond Equivalence (DBE) and asphaltene content. The results show that, based on the average DBE values and DBE distributions of the shale oils examined, highly conjugated species are enriched in samples produced under low pressure, high temperature conditions and in the presence of water.

Time-of-flight scattering and recoiling spectrometry (TOF-SARS) analysis of Pt{110}. II. The (1 × 2)-to-(1 × 3) interconversion and characterization of the (1 × 3) phase

NASA Astrophysics Data System (ADS)

Masson, F.; Rabalais, J. W.

1991-08-01

The (1 × 3) phase of Pt{110} is shown to be stabilized by Ca and K impurities in the outermost layers of the surface. This structural phase is characterized by time-of-flight scattering and recoiling spectrometry (TOF-SARS). The results reveal that the surface is reconstructed into (1 × 3) troughs in which part of the central second-layer rows remain. Å 0.24 ± 0.08 Å inward relaxation of the first layer atoms is observed. The proposed structure of (1 × 3)-Pt{110} is contrasted with previous work on the (1 × 3)-{110} surfaces of Pt, Au, and Ir.

A perspective on extracellular vesicles proteomics

NASA Astrophysics Data System (ADS)

Rosa-Fernandes, Livia; Rocha, Victória Bombarda; Carregari, Victor Corasolla; Urbani, Andrea; Palmisano, Giuseppe

2017-11-01

Increasing attention has been given to secreted extracellular vesicles (EVs) in the past decades, especially in the portrayal of their molecular cargo and role as messengers in both homeostasis and pathophysiological conditions. This review presents the state-of-the-art proteomic technologies to identify and quantify EVs proteins along with their PTMs, interacting partners and structural details. The rapid growth of mass spectrometry-based analytical strategies for protein sequencing, PTMs and structural characterization has improved the level of molecular details that can be achieve from limited amount of EVs isolated from different biological sources. Here we will provide a perspective view on the achievements and challenges on EVs proteome characterization using mass spectrometry. A detailed bioinformatics approach will help us to picture the molecular fingerprint of EVs and understand better their pathophysiological function.

Conformational Assessment of Adnectin and Adnectin-Drug Conjugate by Hydrogen/Deuterium Exchange Mass Spectrometry

NASA Astrophysics Data System (ADS)

Huang, Richard Y.-C.; O'Neil, Steven R.; Lipovšek, Daša; Chen, Guodong

2018-05-01

Higher-order structure (HOS) characterization of therapeutic protein-drug conjugates for comprehensive assessment of conjugation-induced protein conformational changes is an important consideration in the biopharmaceutical industry to ensure proper behavior of protein therapeutics. In this study, conformational dynamics of a small therapeutic protein, adnectin 1, together with its drug conjugate were characterized by hydrogen/deuterium exchange mass spectrometry (HDX-MS) with different spatial resolutions. Top-down HDX allows detailed assessment of the residue-level deuterium content in the payload conjugation region. HDX-MS dataset revealed the ability of peptide-based payload/linker to retain deuterium in HDX experiments. Combined results from intact, top-down, and bottom-up HDX indicated no significant conformational changes of adnectin 1 upon payload conjugation. [Figure not available: see fulltext.

Synthesis and physico-chemical characterization of a polysialate-hydroxyapatite composite for potential biomedical application

NASA Astrophysics Data System (ADS)

Zoulgami, M.; Lucas-Girot, A.; Michaud, V.; Briard, P.; Gaudé, J.; Oudadesse, H.

2002-09-01

New composite materials based on aluminosilicate materials were developed to be used in orthopaedic or maxillo-facial surgery. They are called geopolymers or polysialate-siloxo (PSS) and were studied alone or mixed with hydroxyapatite (HAP). The properties of these materials were investigated for potential use in biological or surgery applications. In this work, the chemistry involved in materials preparation was described. Samples were characterized by some physico-chemical methods like X-ray diffraction (XRD), infrared spectrometry (IR) and electron dispersion X-ray spectrometry (EDX). Results indicate that the mixing hydroxyapatite-geopolymer (PSS) leads to a neutral porous composite material with interesting physico-chemical properties. A preliminary evaluation of its cytotoxicity reveals an harmlessness towards fibroblasts. These properties allow to envisage this association as a potential biomaterial.

A New Time-varying Concept of Risk in a Changing Climate.

PubMed

Sarhadi, Ali; Ausín, María Concepción; Wiper, Michael P

2016-10-20

In a changing climate arising from anthropogenic global warming, the nature of extreme climatic events is changing over time. Existing analytical stationary-based risk methods, however, assume multi-dimensional extreme climate phenomena will not significantly vary over time. To strengthen the reliability of infrastructure designs and the management of water systems in the changing environment, multidimensional stationary risk studies should be replaced with a new adaptive perspective. The results of a comparison indicate that current multi-dimensional stationary risk frameworks are no longer applicable to projecting the changing behaviour of multi-dimensional extreme climate processes. Using static stationary-based multivariate risk methods may lead to undesirable consequences in designing water system infrastructures. The static stationary concept should be replaced with a flexible multi-dimensional time-varying risk framework. The present study introduces a new multi-dimensional time-varying risk concept to be incorporated in updating infrastructure design strategies under changing environments arising from human-induced climate change. The proposed generalized time-varying risk concept can be applied for all stochastic multi-dimensional systems that are under the influence of changing environments.

May the Best Molecule Win: Competition ESI Mass Spectrometry

PubMed Central

Laughlin, Sarah; Wilson, W. David

2015-01-01

Electrospray ionization mass spectrometry has become invaluable in the characterization of macromolecular biological systems such as nucleic acids and proteins. Recent advances in the field of mass spectrometry and the soft conditions characteristic of electrospray ionization allow for the investigation of non-covalent interactions among large biomolecules and ligands. Modulation of genetic processes through the use of small molecule inhibitors with the DNA minor groove is gaining attention as a potential therapeutic approach. In this review, we discuss the development of a competition method using electrospray ionization mass spectrometry to probe the interactions of multiple DNA sequences with libraries of minor groove binding molecules. Such an approach acts as a high-throughput screening method to determine important information including the stoichiometry, binding mode, cooperativity, and relative binding affinity. In addition to small molecule-DNA complexes, we highlight other applications in which competition mass spectrometry has been used. A competitive approach to simultaneously investigate complex interactions promises to be a powerful tool in the discovery of small molecule inhibitors with high specificity and for specific, important DNA sequences. PMID:26501262

Structural elucidation of fucosylated chondroitin sulfates from sea cucumber using FTICR-MS/MS.

PubMed

Agyekum, Isaac; Pepi, Lauren; Yu, Yanlei; Li, Junhui; Yan, Lufeng; Linhardt, Robert J; Chen, Shiguo; Amster, I Jonathan

2018-02-01

Fucosylated chondroitin sulfates are complex polysaccharides extracted from sea cucumber. They have been extensively studied for their anticoagulant properties and have been implicated in other biological activities. While nuclear magnetic resonance spectroscopy has been used to extensively characterize fucosylated chondroitin sulfate oligomers, we herein report the first detailed mass characterization of fucosylated chondroitin sulfate using high-resolution Fourier transform ion cyclotron resonance mass spectrometry. The two species of fucosylated chondroitin sulfates considered for this work include Pearsonothuria graeffei (FCS-Pg) and Isostichopus badionotus (FCS-Ib). Fucosylated chondroitin sulfate oligosaccharides were prepared by N-deacetylation-deaminative cleavage of the two fucosylated chondroitin sulfates and purified by repeated gel filtration. Accurate mass measurements obtained from electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry measurements confirmed the oligomeric nature of these two fucosylated chondroitin sulfate oligosaccharides with each trisaccharide repeating unit averaging four sulfates per trisaccharide. Collision-induced dissociation of efficiently deprotonated molecular ions through Na/H + exchange proved useful in providing structurally relevant glycosidic and cross-ring product ions, capable of assigning the sulfate modifications on the fucosylated chondroitin sulfate oligomers. Careful examination of the tandem mass spectrometry of both species deferring in the positions of sulfate groups on the fucose residue (FCS-Pg-3,4- OS) and (FCS-Ib-2,4- OS) revealed cross-ring products 0,2 A αf and 2,4 X 2αf which were diagnostic for (FCS-Pg-3,4- OS) and 0,2 X 2αf diagnostic for (FCS-Ib-2,4- OS). Mass spectrometry and tandem mass spectrometry data acquired for both species varying in oligomer length (dp3-dp15) are presented.

Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition.

PubMed

Lambert, Jean-Philippe; Ivosev, Gordana; Couzens, Amber L; Larsen, Brett; Taipale, Mikko; Lin, Zhen-Yuan; Zhong, Quan; Lindquist, Susan; Vidal, Marc; Aebersold, Ruedi; Pawson, Tony; Bonner, Ron; Tate, Stephen; Gingras, Anne-Claude

2013-12-01

Characterizing changes in protein-protein interactions associated with sequence variants (e.g., disease-associated mutations or splice forms) or following exposure to drugs, growth factors or hormones is critical to understanding how protein complexes are built, localized and regulated. Affinity purification (AP) coupled with mass spectrometry permits the analysis of protein interactions under near-physiological conditions, yet monitoring interaction changes requires the development of a robust and sensitive quantitative approach, especially for large-scale studies in which cost and time are major considerations. We have coupled AP to data-independent mass spectrometric acquisition (sequential window acquisition of all theoretical spectra, SWATH) and implemented an automated data extraction and statistical analysis pipeline to score modulated interactions. We used AP-SWATH to characterize changes in protein-protein interactions imparted by the HSP90 inhibitor NVP-AUY922 or melanoma-associated mutations in the human kinase CDK4. We show that AP-SWATH is a robust label-free approach to characterize such changes and propose a scalable pipeline for systems biology studies.

Development of extraction method for characterization of free and bonded polyphenols in barley (Hordeum vulgare L.) grown in Czech Republic using liquid chromatography-tandem mass spectrometry.

PubMed

Arigò, Adriana; Česla, Petr; Šilarová, Petra; Calabrò, Maria Luisa; Česlová, Lenka

2018-04-15

Complete characterizations of free and bonded phenolic compounds, presented in four cultivars of barley from two regions of Czech Republic, were achieved, using optimized solvent extraction and liquid chromatography coupled with tandem mass spectrometry. The optimization of extraction of free polyphenols was performed using Box-Behnken design and response surface methodology. The intra-day and extra-day precision of developed method were below 6% and 12%, respectively. The isolation of polyphenols bonded to the cell wall structure was carried out by a hydrolysis process. In all cultivars, p-hydroxybenzoic, p-coumaric and ferulic acids were the most abundant compounds. Their average amounts in barley samples were 17.6, 15.2 and 54.4% (m/m), respectively. The highest amount of these compounds was found in the bonded form, proving the importance of this procedure for the correct characterization of total polyphenols in food matrices. Copyright © 2017 Elsevier Ltd. All rights reserved.

Gold and gold-iron oxide magnetic glyconanoparticles: synthesis, characterization and magnetic properties.

PubMed

de la Fuente, Jesús M; Alcántara, David; Eaton, Peter; Crespo, Patricia; Rojas, Teresa C; Fernandez, Asunción; Hernando, Antonio; Penadés, Soledad

2006-07-06

The preparation, characterization and the magnetic properties of gold and gold-iron oxide glyconanoparticles (GNPs) are described. Glyconanoparticles were prepared in a single step procedure in the presence of aqueous solution of thiol functionalized neoglycoconjugates and either gold salts or both gold and iron salts. Neoglycoconjugates of lactose and maltose disaccharides with different linkers were used. Iron-free gold or gold-iron oxide GNPs with controlled gold-iron ratios were obtained. The average core-size diameters are in the range of 1.5-2.5 nm. The GNPs are fully characterized by (1)H NMR spectrometry, transmission electron microscopy (TEM), and UV-vis and X-ray absorption (XAS) spectroscopies. Inductive plasma-atomic emission spectrometry (ICP) and elemental analysis gave the average number of neoglycoconjugates per cluster. The magnetic properties were measured in a SQUID magnetometer. The most remarkable results was the observation of a permanent magnetism up to room temperature in the iron-free gold GNPs, that was not present in the corresponding gold-iron oxide GNPs.

Separation and characterization of silybin, isosilybin, silydianin and silychristin in milk thistle extract by liquid chromatography-electrospray tandem mass spectrometry.

PubMed

Lee, James I; Hsu, Bih H; Wu, Di; Barrett, Jeffrey S

2006-05-26

A selective and sensitive liquid chromatography/tandem mass spectrometry (LC/MS/MS) method has been developed for the characterization of silymarin in commercially available milk thistle extract. In this study, six main active constituents, including silydianin, silychristin, diastereomers of silybin (silybin A and B) and diastereomers of isosilybin (isosilybin A and B) in silymarin, were completely separated on a YMC ODS-AQ HPLC column using a gradient mobile phase system comprised of ammonium acetate and methanol/water/formic acid. Identification and characterization of the major constituents were based not only on the product ion scan, which provided unique fragmentation information of a selected molecular ion, but also on the specific fragmentation of multiple reaction monitoring (MRM) data, which confirmed the retention times of LC chromatographic peaks. The method was applied in the analysis of human plasma samples in the presence of silymarin and appeared to be suitable for the pharmacokinetic studies in which the discrimination of silymarin constituents is essential.

The application of NMR and MS methods for detection of adulteration of wine, fruit juices, and olive oil. A review.

PubMed

Ogrinc, N; Kosir, I J; Spangenberg, J E; Kidric, J

2003-06-01

This review covers two important techniques, high resolution nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS), used to characterize food products and detect possible adulteration of wine, fruit juices, and olive oil, all important products of the Mediterranean Basin. Emphasis is placed on the complementary use of SNIF-NMR (site-specific natural isotopic fractionation nuclear magnetic resonance) and IRMS (isotope-ratio mass spectrometry) in association with chemometric methods for detecting the adulteration.

Processing of copper converter slag for metals reclamation: Part II: mineralogical study.

PubMed

Deng, Tong; Ling, Yunhan

2004-10-01

Chemical and mineralogical characterizations of a copper converter slag, and its products obtained by curing with strong sulphuric acid and leaching with hot water, were carried out using ore microscopy, scanning electronic microscopy with energy dispersive spectrometry, wave-length dispersive X-ray fluorescence spectrometry, X-ray diffractometry and chemical phase analysis, which provided necessary information to develop a new process for treating such slag and further understanding of the chemical and mineralogical changes in the process.

Understanding Coatings that Protect Plasmonic Structures for Materials Characterization and Detection and Identification of Chemical, Biological and Explosive Agents

DTIC Science & Technology

2013-04-11

in the top monomolecular layer of a blend film using mass spectrometry. This technique we call Surface Layer-Matrix Assisted Laser Desorption...C., Foster, M.D. “Probing Surface Concentration of Cyclic/linear Blend Films Using Surface MALDI-TOF Mass Spectrometry,” Dept. of Polymer Science...Isotopically Labeled Species in a Polymer Blend Using Tip Enhanced Raman Spectroscopy, ACS Macro Letters (11 2012) TOTAL: 2 Books Number of Manuscripts

Metaproteomics: Harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities

PubMed Central

Hettich, Robert L.; Pan, Chongle; Chourey, Karuna; Giannone, Richard J.

2013-01-01

Summary The availability of extensive genome information for many different microbes, including unculturable species in mixed communities from environmental samples, has enabled systems-biology interrogation by providing a means to access genomic, transcriptomic, and proteomic information. To this end, metaproteomics exploits the power of high performance mass spectrometry for extensive characterization of the complete suite of proteins expressed by a microbial community in an environmental sample. PMID:23469896

Final Report

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

McLuckey, Scott

2016-08-30

The overall objectives of this research effort were to expand the capabilities of spectroscopic and ion chemistry tools for the structural characterization of polyatomic ions of relevance to the broad mission of the Department of Energy. Mass spectrometry currently plays an important role in virtually all of the molecular sciences by virtue of the value of the accurate measurement of mass and the structural information that can be derived from various structural probes based on, for example, ion chemistry, ion mobility, and ion spectroscopy. Mass spectrometry has long played important roles in supporting the missions of the Department of Energymore » and its predecessor agencies, particularly in the area of isotopic analysis of nuclides. Molecular mass spectrometry has played increasingly important roles is many aspects of the production and use of energy as the nation has diversified its energy portfolio. There is an ongoing need for the expansion of the measurement capabilities associated with molecular mass spectrometry that involves both technological developments as well as improved understanding of the chemical and physical processes that take place upon ionization and ion analysis in a mass spectrometer. Advances in mass spectrometry have impacted science broadly and further advances will be required to meet the needs of current energy and environmental research. This program has historically focused on the structural characterization of polyatomic ions, usually within the context of a tandem mass spectrometry experiment. A wide variety of physical and chemical processes can take place within a mass spectrometer and advantage can be taken of such processes to enhance the quality and quantity of information that can be derived for a given chemical system of interest. For example, ions can undergo interactions with neutral molecules/atoms, light, surfaces, electrons, or oppositely charged ions. The outcomes of all such interactions can be sensitive to the structures of the ions and are therefore candidates for probes of ion structure. This program has historically focused on the chemistry and physics associated with ion/neutral interactions at both low and high translational energies, and ion/ion reactions. The former area has involved the study of ion/molecule reactions at thermal energies and the extensive study of collisional activation under a wide variety of conditions. A major area of emphasis has been collisional activation in electrodynamic ion traps. The study of gas-phase ion/ion reactions within the context of tandem mass spectrometry was initiated in this program and has grown to be a major research area in this group. Most of the focus in ion/ion chemistry has been on proton transfer and electron transfer reactions and some of the work in the previous budget period was directed, in particular, to fundamental aspects of electron transfer. Recently, the discovery of selective covalent ion/ion reactions has opened up new vistas for research that will expand significantly the capabilities of tandem mass spectrometry for the structural characterization of polyatomic ions.« less

Spatiotemporal characterization of ultrashort optical vortex pulses

NASA Astrophysics Data System (ADS)

Miranda, Miguel; Kotur, Marija; Rudawski, Piotr; Guo, Chen; Harth, Anne; L'Huillier, Anne; Arnold, Cord L.

2017-12-01

We use a spiral phase plate to generate few-cycle optical vortices from an ultrafast titanium:sapphire oscillator and characterize them in the spatiotemporal domain with a recently introduced technique based on spatially resolved Fourier transform spectrometry. The performance of this simple approach to the generation of optical vortices is analysed from a wavelength-dependent perspective as well as in the spatiotemporal domain, allowing us to characterize ultrashort vortex pulses in space, frequency and time.

Evaluation of comprehensive multidimensional separations using reversed-phase, reversed-phase liquid chromatography/mass spectrometry for shotgun proteomics.

PubMed

Nakamura, Tatsuji; Kuromitsu, Junro; Oda, Yoshiya

2008-03-01

Two-dimensional liquid-chromatographic (LC) separation followed by mass spectrometric (MS) analysis was examined for the identification of peptides in complex mixtures as an alternative to widely used two-dimensional gel electrophoresis followed by MS analysis for use in proteomics. The present method involves the off-line coupling of a narrow-bore, polymer-based, reversed-phase column using an acetonitrile gradient in an alkaline mobile phase in the first dimension with octadecylsilanized silica (ODS)-based nano-LC/MS in the second dimension. After the first separation, successive fractions were acidified and dried off-line, then loaded on the second dimension column. Both columns separate peptides according to hydrophobicity under different pH conditions, but more peptides were identified than with the conventional technique for shotgun proteomics, that is, the combination of a strong cation exchange column with an ODS column, and the system was robust because no salts were included in the mobile phases. The suitability of the method for proteomics measurements was evaluated.

The potential use of cuticular hydrocarbons and multivariate analysis to age empty puparial cases of Calliphora vicina and Lucilia sericata.

PubMed

Moore, Hannah E; Pechal, Jennifer L; Benbow, M Eric; Drijfhout, Falko P

2017-05-16

Cuticular hydrocarbons (CHC) have been successfully used in the field of forensic entomology for identifying and ageing forensically important blowfly species, primarily in the larval stages. However in older scenes where all other entomological evidence is no longer present, Calliphoridae puparial cases can often be all that remains and therefore being able to establish the age could give an indication of the PMI. This paper examined the CHCs present in the lipid wax layer of insects, to determine the age of the cases over a period of nine months. The two forensically important species examined were Calliphora vicina and Lucilia sericata. The hydrocarbons were chemically extracted and analysed using Gas Chromatography - Mass Spectrometry. Statistical analysis was then applied in the form of non-metric multidimensional scaling analysis (NMDS), permutational multivariate analysis of variance (PERMANOVA) and random forest models. This study was successful in determining age differences within the empty cases, which to date, has not been establish by any other technique.

Noninvasive diagnosis of intraamniotic infection: proteomic biomarkers in vaginal fluid.

PubMed

Hitti, Jane; Lapidus, Jodi A; Lu, Xinfang; Reddy, Ashok P; Jacob, Thomas; Dasari, Surendra; Eschenbach, David A; Gravett, Michael G; Nagalla, Srinivasa R

2010-07-01

We analyzed the vaginal fluid proteome to identify biomarkers of intraamniotic infection among women in preterm labor. Proteome analysis was performed on vaginal fluid specimens from women with preterm labor, using multidimensional liquid chromatography, tandem mass spectrometry, and label-free quantification. Enzyme immunoassays were used to quantify candidate proteins. Classification accuracy for intraamniotic infection (positive amniotic fluid bacterial culture and/or interleukin-6 >2 ng/mL) was evaluated using receiver-operator characteristic curves obtained by logistic regression. Of 170 subjects, 30 (18%) had intraamniotic infection. Vaginal fluid proteome analysis revealed 338 unique proteins. Label-free quantification identified 15 proteins differentially expressed in intraamniotic infection, including acute-phase reactants, immune modulators, high-abundance amniotic fluid proteins and extracellular matrix-signaling factors; these findings were confirmed by enzyme immunoassay. A multi-analyte algorithm showed accurate classification of intraamniotic infection. Vaginal fluid proteome analyses identified proteins capable of discriminating between patients with and without intraamniotic infection. Copyright (c) 2010 Mosby, Inc. All rights reserved.

Characterization of fast pyrolysis products generated from several western USA woody species

Treesearch

Jacqueline M. Jarvis; Deborah S. Page-Dumroese; Nathaniel M. Anderson; Yuri Corilo; Ryan P. Rodgers

2014-01-01

Woody biomass has the potential to be utilized at an alternative fuel source through its pyrolytic conversion. Here, fast pyrolysis bio-oils derived from several western USA woody species are characterized by negative-ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS) to determine molecular-level composition. The...

Multidimensional Knowledge Structures.

ERIC Educational Resources Information Center

Schuh, Kathy L.

Multidimensional knowledge structures, described from a constructivist perspective and aligned with the "Mind as Rhizome" metaphor, provide support for constructivist learning strategies. This qualitative study was conducted to seek empirical support for a description of multidimensional knowledge structures, focusing on the…

Multidimensional quantum entanglement with large-scale integrated optics.

PubMed

Wang, Jianwei; Paesani, Stefano; Ding, Yunhong; Santagati, Raffaele; Skrzypczyk, Paul; Salavrakos, Alexia; Tura, Jordi; Augusiak, Remigiusz; Mančinska, Laura; Bacco, Davide; Bonneau, Damien; Silverstone, Joshua W; Gong, Qihuang; Acín, Antonio; Rottwitt, Karsten; Oxenløwe, Leif K; O'Brien, Jeremy L; Laing, Anthony; Thompson, Mark G

2018-04-20

The ability to control multidimensional quantum systems is central to the development of advanced quantum technologies. We demonstrate a multidimensional integrated quantum photonic platform able to generate, control, and analyze high-dimensional entanglement. A programmable bipartite entangled system is realized with dimensions up to 15 × 15 on a large-scale silicon photonics quantum circuit. The device integrates more than 550 photonic components on a single chip, including 16 identical photon-pair sources. We verify the high precision, generality, and controllability of our multidimensional technology, and further exploit these abilities to demonstrate previously unexplored quantum applications, such as quantum randomness expansion and self-testing on multidimensional states. Our work provides an experimental platform for the development of multidimensional quantum technologies. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Recent applications of gas chromatography with high-resolution mass spectrometry.

PubMed

Špánik, Ivan; Machyňáková, Andrea

2018-01-01

Gas chromatography coupled to high-resolution mass spectrometry is a powerful analytical method that combines excellent separation power of gas chromatography with improved identification based on an accurate mass measurement. These features designate gas chromatography with high-resolution mass spectrometry as the first choice for identification and structure elucidation of unknown volatile and semi-volatile organic compounds. Gas chromatography with high-resolution mass spectrometry quantitative analyses was previously focused on the determination of dioxins and related compounds using magnetic sector type analyzers, a standing requirement of many international standards. The introduction of a quadrupole high-resolution time-of-flight mass analyzer broadened interest in this method and novel applications were developed, especially for multi-target screening purposes. This review is focused on the development and the most interesting applications of gas chromatography coupled to high-resolution mass spectrometry towards analysis of environmental matrices, biological fluids, and food safety since 2010. The main attention is paid to various approaches and applications of gas chromatography coupled to high-resolution mass spectrometry for non-target screening to identify contaminants and to characterize the chemical composition of environmental, food, and biological samples. The most interesting quantitative applications, where a significant contribution of gas chromatography with high-resolution mass spectrometry over the currently used methods is expected, will be discussed as well. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An improved method for the analysis of 2-aminoacetophenone in wine based on headspace solid-phase microextraction and heart-cut multidimensional gas chromatography with selective detection by tandem mass spectrometry.

PubMed

Schmarr, Hans-Georg; Keiser, Jutta; Krautwald, Susann

2016-12-16

Heart-cut multidimensional gas chromatography coupled to selective mass spectrometric detection (H/C MDGC-MS-MS) was shown to be a suitable combination for analysis of the key component for the wine off-flavor named "atypical aging off-flavor" (german: "Untypische Alterungsnote", UTA), 2-aminoacetophenone (2-AAP). Headspace solid phase microextraction (HS-SPME) was applied as an easy to automate sample preparation step suiting routine control situations. During method development two critical aspects were found, of which one is the chemical degradation of the neat substance, leading to signal reduction and a false response behavior. A second aspect is the pH stability of the deuterated isotopologue 1-(2-aminophenyl)-2,2,2-trideuterio-ethanone (2-AAP-d3) used for quantification via a stable isotope dilution assay. Despite an earlier suggestion to increase the extractable amount of 2-AAP and its isotopic standard in the headspace, alkalization of 2-AAP-d3 containing aqueous samples were found to be critical. In such a milieu a deuterium exchange can then cause erroneous quantitative results. The method proposed in our study thus uses native wine pH conditions and proved to be suitable for routine control with respect to the detection of the "atypical aging off-flavor" in wine at concentration levels below its sensory threshold of about 1μgL -1 . Good linearity was obtained in the calibrated range from 0.1-8μgL -1 (y=1,2338x+0,1029, R=0,9985) with limits of detection or quantification being 0.01 and 0.14μg/L, respectively. Copyright © 2016 Elsevier B.V. All rights reserved.

Fundamental studies of gas phase ionic reactions by ion mobility spectrometry

NASA Technical Reports Server (NTRS)

Giles, K.; Knighton, W. B.; Sahlstrom, K. E.; Grimsrud, E. P.

1995-01-01

Ion mobility spectrometry (IMS) provides a promising approach to the study of gas phase ionic reactions in buffer gases at unusually high pressures. This point is illustrated here by studies of the Sn2 nucleophilic displacement reaction, Cl(-) + CH3Br yields Br + CH3Br, using IMS at atmospheric pressure. The equilibrium clustering reaction, Cl(-)(CHCI3)(n - 1) + CHCI3 yields Cl(-)(CHCI3)(n), where n = 1 and 2, and the effect of clustering on the Sn2 reaction with CH3Br have also been characterized by this IMS-based kinetic method. Present problems and anticipated improvements in the application of ion mobility spectrometry to studies of other gas phase ionic processes are discussed.

Profiling Changes in Histone Post-translational Modifications by Top-Down Mass Spectrometry.

PubMed

Zhou, Mowei; Wu, Si; Stenoien, David L; Zhang, Zhaorui; Connolly, Lanelle; Freitag, Michael; Paša-Tolić, Ljiljana

2017-01-01

Top-down mass spectrometry is a valuable tool for understanding gene expression through characterization of combinatorial histone post-translational modifications (i.e., histone code). In this protocol, we describe a top-down workflow that employs liquid chromatography (LC) coupled to mass spectrometry (MS), for fast global profiling of changes in histone proteoforms, and apply LCMS top-down approach for comparative analysis of a wild-type and a mutant fungal species. The proteoforms exhibiting differential abundances can be subjected to further targeted studies by other MS or orthogonal (e.g., biochemical) assays. This method can be generally adapted for screening of changes in histone modifications between samples such as wild type vs. mutant or healthy vs. diseased.

Membrane protein separation and analysis by supercritical fluid chromatography-mass spectrometry.

PubMed

Zhang, Xu; Scalf, Mark; Westphall, Michael S; Smith, Lloyd M

2008-04-01

Membrane proteins comprise 25-30% of the human genome and play critical roles in a wide variety of important biological processes. However, their hydrophobic nature has compromised efforts at structural characterization by both X-ray crystallography and mass spectrometry. The detergents that are generally used to solubilize membrane proteins interfere with the crystallization process essential to X-ray studies and cause severe ion suppression effects that hinder mass spectrometric analysis. In this report, the use of supercritical fluid chromatography-mass spectrometry for the separation and analysis of integral membrane proteins and hydrophobic peptides is investigated. It is shown that detergents are rapidly and effectively separated from the proteins and peptides, yielding them in a state suitable for direct mass spectrometric analysis.

Multidimensional Perfectionism and the Self

ERIC Educational Resources Information Center

Ward, Andrew M.; Ashby, Jeffrey S.

2008-01-01

This study examined multidimensional perfectionism and self-development. Two hundred seventy-one undergraduates completed a measure of multidimensional perfectionism and two Kohutian measures designed to measure aspects of self-development including social connectedness, social assurance, goal instability (idealization), and grandiosity. The…

Chemical space visualization: transforming multidimensional chemical spaces into similarity-based molecular networks.

PubMed

de la Vega de León, Antonio; Bajorath, Jürgen

2016-09-01

The concept of chemical space is of fundamental relevance for medicinal chemistry and chemical informatics. Multidimensional chemical space representations are coordinate-based. Chemical space networks (CSNs) have been introduced as a coordinate-free representation. A computational approach is presented for the transformation of multidimensional chemical space into CSNs. The design of transformation CSNs (TRANS-CSNs) is based upon a similarity function that directly reflects distance relationships in original multidimensional space. TRANS-CSNs provide an immediate visualization of coordinate-based chemical space and do not require the use of dimensionality reduction techniques. At low network density, TRANS-CSNs are readily interpretable and make it possible to evaluate structure-activity relationship information originating from multidimensional chemical space.

Characterization of Athabasca lean oil sands and mixed surficial materials: Comparison of capillary electrophoresis/low-resolution mass spectrometry and high-resolution mass spectrometry.

PubMed

MacLennan, Matthew S; Peru, Kerry M; Swyngedouw, Chris; Fleming, Ian; Chen, David D Y; Headley, John V

2018-05-15

Oil sands mining in Alberta, Canada, requires removal and stockpiling of considerable volumes of near-surface overburden material. This overburden includes lean oil sands (LOS) which cannot be processed economically but contain sparingly soluble petroleum hydrocarbons and naphthenic acids, which can leach into environmental waters. In order to measure and track the leaching of dissolved constituents and distinguish industrially derived organics from naturally occurring organics in local waters, practical methods were developed for characterizing multiple sources of contaminated water leakage. Capillary electrophoresis/positive-ion electrospray ionization low-resolution time-of-flight mass spectrometry (CE/LRMS), high-resolution negative-ion electrospray ionization Orbitrap mass spectrometry (HRMS) and conventional gas chromatography/flame ionization detection (GC/FID) were used to characterize porewater samples collected from within Athabasca LOS and mixed surficial materials. GC/FID was used to measure total petroleum hydrocarbon and HRMS was used to measure total naphthenic acid fraction components (NAFCs). HRMS and CE/LRMS were used to characterize samples according to source. The amounts of total petroleum hydrocarbon in each sample as measured by GC/FID ranged from 0.1 to 15.1 mg/L while the amounts of NAFCs as measured by HRMS ranged from 5.3 to 82.3 mg/L. Factors analysis (FA) on HRMS data visually demonstrated clustering according to sample source and was correlated to molecular formula. LRMS coupled to capillary electrophoresis separation (CE/LRMS) provides important information on NAFC isomers by adding analyte migration time data to m/z and peak intensity. Differences in measured amounts of total petroleum hydrocarbons by GC/FID and NAFCs by HRMS indicate that the two methods provide complementary information about the nature of dissolved organic species in a soil or water leachate samples. NAFC molecule class O x S y is a possible tracer for LOS seepage. CE/LRMS provides complementary information and is a feasible and practical option for source evaluation of NAFCs in water. Copyright © 2018 John Wiley & Sons, Ltd.

Multidimensional poverty and catastrophic health spending in the mountainous regions of Myanmar, Nepal and India.

PubMed

Mohanty, Sanjay K; Agrawal, Nand Kishor; Mahapatra, Bidhubhusan; Choudhury, Dhrupad; Tuladhar, Sabarnee; Holmgren, E Valdemar

2017-01-18

Economic burden to households due to out-of-pocket expenditure (OOPE) is large in many Asian countries. Though studies suggest increasing household poverty due to high OOPE in developing countries, studies on association of multidimensional poverty and household health spending is limited. This paper tests the hypothesis that the multidimensionally poor are more likely to incur catastrophic health spending cutting across countries. Data from the Poverty and Vulnerability Assessment (PVA) Survey carried out by the International Center for Integrated Mountain Development (ICIMOD) has been used in the analyses. The PVA survey was a comprehensive household survey that covered the mountainous regions of India, Nepal and Myanmar. A total of 2647 households from India, 2310 households in Nepal and 4290 households in Myanmar covered under the PVA survey. Poverty is measured in a multidimensional framework by including the dimensions of education, income and energy, water and sanitation using the Alkire and Foster method. Health shock is measured using the frequency of illness, family sickness and death of any family member in a reference period of one year. Catastrophic health expenditure is defined as 40% above the household's capacity to pay. Results suggest that about three-fifths of the population in Myanmar, two-fifths of the population in Nepal and one-third of the population in India are multidimensionally poor. About 47% of the multidimensionally poor in India had incurred catastrophic health spending compared to 35% of the multidimensionally non-poor and the pattern was similar in both Nepal and Myanmar. The odds of incurring catastrophic health spending was 56% more among the multidimensionally poor than among the multidimensionally non-poor [95% CI: 1.35-1.76]. While health shocks to households are consistently significant predictors of catastrophic health spending cutting across country of residence, the educational attainment of the head of the household is not significant. The multidimensionally poor in the poorer regions are more likely to face health shocks and are less likely to afford professional health services. Increasing government spending on health and increasing households' access to health insurance can reduce catastrophic health spending and multidimensional poverty.

The effects of context on multidimensional spatial cognitive models. Ph.D. Thesis - Arizona Univ.

NASA Technical Reports Server (NTRS)

Dupnick, E. G.

1979-01-01

Spatial cognitive models obtained by multidimensional scaling represent cognitive structure by defining alternatives as points in a coordinate space based on relevant dimensions such that interstimulus dissimilarities perceived by the individual correspond to distances between the respective alternatives. The dependence of spatial models on the context of the judgments required of the individual was investigated. Context, which is defined as a perceptual interpretation and cognitive understanding of a judgment situation, was analyzed and classified with respect to five characteristics: physical environment, social environment, task definition, individual perspective, and temporal setting. Four experiments designed to produce changes in the characteristics of context and to test the effects of these changes upon individual cognitive spaces are described with focus on experiment design, objectives, statistical analysis, results, and conclusions. The hypothesis is advanced that an individual can be characterized as having a master cognitive space for a set of alternatives. When the context changes, the individual appears to change the dimension weights to give a new spatial configuration. Factor analysis was used in the interpretation and labeling of cognitive space dimensions.

Multidimensional In Vivo Hazard Assessment Using Zebrafish

PubMed Central

Tanguay, Robert L.

2014-01-01

There are tens of thousands of man-made chemicals in the environment; the inherent safety of most of these chemicals is not known. Relevant biological platforms and new computational tools are needed to prioritize testing of chemicals with limited human health hazard information. We describe an experimental design for high-throughput characterization of multidimensional in vivo effects with the power to evaluate trends relating to commonly cited chemical predictors. We evaluated all 1060 unique U.S. EPA ToxCast phase 1 and 2 compounds using the embryonic zebrafish and found that 487 induced significant adverse biological responses. The utilization of 18 simultaneously measured endpoints means that the entire system serves as a robust biological sensor for chemical hazard. The experimental design enabled us to describe global patterns of variation across tested compounds, evaluate the concordance of the available in vitro and in vivo phase 1 data with this study, highlight specific mechanisms/value-added/novel biology related to notochord development, and demonstrate that the developmental zebrafish detects adverse responses that would be missed by less comprehensive testing strategies. PMID:24136191

Multi-dimensional spatial light communication made with on-chip InGaN photonic integration

NASA Astrophysics Data System (ADS)

Yang, Yongchao; Zhu, Bingcheng; Shi, Zheng; Wang, Jinyuan; Li, Xin; Gao, Xumin; Yuan, Jialei; Li, Yuanhang; Jiang, Yan; Wang, Yongjin

2017-04-01

Here, we propose, fabricate and characterize suspended photonic integration of InGaN multiple-quantum-well light-emitting diode (MQW-LED), waveguide and InGaN MQW-photodetector on a single chip. The unique light emission property of InGaN MQW-LED makes it feasible to establish multi-dimensional spatial data transmission using visible light. The in-plane light communication system is comprised of InGaN MQW-LED, waveguide and InGaN MQW-photodetector, and the out-of-plane data transmission is realized by detecting the free-space light emission via a commercial photodiode module. Moreover, a full-duplex light communication is experimentally demonstrated at a data transmission rate of 50 Mbps when both InGaN MQW-diodes operate under simultaneous light emission and detection mode. The in-plane superimposed signals are able to be extracted through the self-interference cancellation method, and the out-of-plane superimposed signals are in good agreement with the calculated signals according to the extracted transmitted signals. These results are promising for the development of on-chip InGaN photonic integration for diverse applications.

PACE-90 water and solute transport calculations for 0.01, 0.1, and 0. 5 mm/yr infiltration into Yucca Mountain; Yucca Mountain Site Characterization Project

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

Dykhuizen, R.C.; Eaton, R.R.; Hopkins, P.L.

1991-12-01

Numerical results are presented for the Performance Assessment Calculational Exercise (PACE-90). One- and two-dimensional water and solute transport are presented for steady infiltration into Yucca Mountain. Evenly distributed infiltration rates of 0.01, 0.1, and 0.5 mm/yr were considered. The calculations of solute transport show that significant amounts of radionuclides can reach the water table over 100,000 yr at the 0.5 mm/yr rate. For time periods less than 10,000 yr or infiltrations less than 0.1 mm/yr very little solute reaches the water table. The numerical simulations clearly demonstrate that multi-dimensional effects can result in significant decreases in the travel time ofmore » solute through the modeled domain. Dual continuum effects are shown to be negligible for the low steady state fluxes considered. However, material heterogeneities may cause local amplification of the flux level in multi-dimensional flows. These higher flux levels may then require modeling of a dual continuum porous medium.« less

Neural Correlates of Lyrical Improvisation: An fMRI Study of Freestyle Rap

PubMed Central

Liu, Siyuan; Chow, Ho Ming; Xu, Yisheng; Erkkinen, Michael G.; Swett, Katherine E.; Eagle, Michael W.; Rizik-Baer, Daniel A.; Braun, Allen R.

2012-01-01

The neural correlates of creativity are poorly understood. Freestyle rap provides a unique opportunity to study spontaneous lyrical improvisation, a multidimensional form of creativity at the interface of music and language. Here we use functional magnetic resonance imaging to characterize this process. Task contrast analyses indicate that improvised performance is characterized by dissociated activity in medial and dorsolateral prefrontal cortices, providing a context in which stimulus-independent behaviors may unfold in the absence of conscious monitoring and volitional control. Connectivity analyses reveal widespread improvisation-related correlations between medial prefrontal, cingulate motor, perisylvian cortices and amygdala, suggesting the emergence of a network linking motivation, language, affect and movement. Lyrical improvisation appears to be characterized by altered relationships between regions coupling intention and action, in which conventional executive control may be bypassed and motor control directed by cingulate motor mechanisms. These functional reorganizations may facilitate the initial improvisatory phase of creative behavior. PMID:23155479

Neural correlates of lyrical improvisation: an FMRI study of freestyle rap.

PubMed

Liu, Siyuan; Chow, Ho Ming; Xu, Yisheng; Erkkinen, Michael G; Swett, Katherine E; Eagle, Michael W; Rizik-Baer, Daniel A; Braun, Allen R

2012-01-01

The neural correlates of creativity are poorly understood. Freestyle rap provides a unique opportunity to study spontaneous lyrical improvisation, a multidimensional form of creativity at the interface of music and language. Here we use functional magnetic resonance imaging to characterize this process. Task contrast analyses indicate that improvised performance is characterized by dissociated activity in medial and dorsolateral prefrontal cortices, providing a context in which stimulus-independent behaviors may unfold in the absence of conscious monitoring and volitional control. Connectivity analyses reveal widespread improvisation-related correlations between medial prefrontal, cingulate motor, perisylvian cortices and amygdala, suggesting the emergence of a network linking motivation, language, affect and movement. Lyrical improvisation appears to be characterized by altered relationships between regions coupling intention and action, in which conventional executive control may be bypassed and motor control directed by cingulate motor mechanisms. These functional reorganizations may facilitate the initial improvisatory phase of creative behavior.

Diagnostic ion filtering to characterize ginseng saponins by rapid liquid chromatography with time-of-flight mass spectrometry.

PubMed

Qi, Lian-Wen; Wang, Huai-You; Zhang, Hui; Wang, Chong-Zhi; Li, Ping; Yuan, Chun-Su

2012-03-23

As one of the most commonly used medicinal plants, ginseng has been an attractive model herb for study. A wide range of analytical methods has been used to characterize its constituents. However, less effort has been devoted to the rare ginseng saponins, especially their isomers and sugar linkages. In this study, we used segmental monitoring and diagnostic ion filtering to characterize ginseng saponins by rapid liquid chromatography with time-of-flight mass spectrometry (LC-TOF-MS). By using selected diagnostic ions, specific groups of ginseng saponins were readily extracted from the complicated matrix. 20(R) and 20(S) stereo-saponins were differentiated using the peak abundance ratio of [M-H(2)O+H](+) to [M-2H(2)O+H](+). The fragmentation behavior of ginsenosides was first reported in negative ion mode by MS/MS with high-energy collision-induced dissociation, producing rules to determine sugar numbers, positions and linkages. Using the rules, we identified and compared the nontarget ginseng saponin profiling of raw and steamed American ginseng roots and berries. We characterized 70 saponins in the samples. Our strategy can be extended to screen and characterize other rare ginseng saponins and their metabolites. Copyright © 2012 Elsevier B.V. All rights reserved.

An introduction to multidimensional measurement using Rasch models.

PubMed

Briggs, Derek C; Wilson, Mark

2003-01-01

The act of constructing a measure requires a number of important assumptions. Principle among these assumptions is that the construct is unidimensional. In practice there are many instances when the assumption of unidimensionality does not hold, and where the application of a multidimensional measurement model is both technically appropriate and substantively advantageous. In this paper we illustrate the usefulness of a multidimensional approach to measurement with the Multidimensional Random Coefficient Multinomial Logit (MRCML) model, an extension of the unidimensional Rasch model. An empirical example is taken from a collection of embedded assessments administered to 541 students enrolled in middle school science classes with a hands-on science curriculum. Student achievement on these assessments are multidimensional in nature, but can also be treated as consecutive unidimensional estimates, or as is most common, as a composite unidimensional estimate. Structural parameters are estimated for each model using ConQuest, and model fit is compared. Student achievement in science is also compared across models. The multidimensional approach has the best fit to the data, and provides more reliable estimates of student achievement than under the consecutive unidimensional approach. Finally, at an interpretational level, the multidimensional approach may well provide richer information to the classroom teacher about the nature of student achievement.

Ultra high performance liquid chromatography coupled with electrospray ionization/quadrupole time-of-flight mass spectrometry for the rapid analysis of constituents in the traditional Chinese medicine formula Wu Ji Bai Feng Pill.

PubMed

Duan, Shengnan; Qi, Wen; Zhang, Siwen; Huang, Kunkun; Yuan, Dan

2017-10-01

An ultra high performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight mass spectrometry method in both positive and negative ion modes was established in order to comprehensively investigate the major constituents in Wu Ji Bai Feng Pill. Briefly, a Waters ACQUITY UPLC HSS C 18 column was used to separate the aqueous extract of Wu Ji Bai Feng Pill. A total of 0.1% formic acid in acetonitrile and 0.1% aqueous formic acid v/v were used as the mobile phase. All analytes were determined using quadrupole time-of-flight mass spectrometry with electrospray ionization source in positive and negative ion modes. At length, a total of 173 components including flavones and their glycosides, monoterpene glycosides, triterpene saponins, phenethylalchohol glycosides, iridoid glycosides, phthalides, tanshinones, phenolic acids, sesquiterpenoids and cyclopeptides were identified or tentatively characterized in Wu Ji Bai Feng Pill in an analysis of 16.0 min based on the accurate mass and tandem mass spectrometry behaviors. The developed method is rapid and highly sensitive to characterize the chemical constituents of Wu Ji Bai Feng Pill, which could not only be used for chemical standardization and quality control of Wu Ji Bai Feng Pill, but also be helpful for further study in vivo metabolism of Wu Ji Bai Feng Pill. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Glycomics expression analysis of sulfated glycosaminoglycans of human colorectal cancer tissues and non-neoplastic mucosa by electrospray ionization mass spectrometry.

PubMed

Marolla, Ana Paula Cleto; Waisberg, Jaques; Saba, Gabriela Tognini; Waisberg, Daniel Reis; Margeotto, Fernando Beani; Pinhal, Maria Aparecida da Silva

2015-01-01

To determine the presence of glycosaminoglycans in the extracellular matrix of connective tissue from neoplastic and non-neoplastic colorectal tissues, since it has a central role in tumor development and progression. Tissue samples from neoplastic and non-neoplastic colorectal tissues were obtained from 64 operated patients who had colorectal carcinoma with no distant metastases. Expressions of heparan sulphate, chondroitin sulphate, dermatan sulphate and their fragments were analyzed by electrospray ionization mass spectrometry, with the technique for extraction and quantification of glycosaminoglycans after proteolysis and electrophoresis. The statistical analysis included mean, standard deviation, and Student'st test. The glycosaminoglycans extracted from colorectal tissue showed three electrophoretic bands in agarose gel. Electrospray ionization mass spectrometry showed characteristic disaccharide fragments from glycosaminoglycans, indicating their structural characterization in the tissues analyzed. Some peaks in the electrospray ionization mass spectrometry were not characterized as fragments of sugars, indicating the presence of fragments of the protein structure of proteoglycans generated during the glycosaminoglycan purification. The average amount of chondroitin and dermatan increased in the neoplastic tissue compared to normal tissue (p=0.01). On the other hand, the average amount of heparan decreased in the neoplastic tissue compared to normal tissue (p= 0.03). The method allowed the determination of the glycosaminoglycans structural profile in colorectal tissue from neoplastic and non-neoplastic colorectal tissue. Neoplastic tissues showed greater amounts of chondroitin sulphate and dermatan sulphate compared to non-neoplastic tissues, while heparan sulphate was decreased in neoplastic tissues.

Authenticity of Benin metalworks evaluated by inductively coupled plasma mass spectrometry and lead isotope analyses

NASA Astrophysics Data System (ADS)

Fabbri, E.; Soffritti, C.; Merlin, M.; Vaccaro, C.; Garagnani, G. L.

2017-05-01

Two metal plaques and a cock statuette belonging to a private collection and stylistically consistent with the Royal Art of Benin (Nigeria) were investigated in order to verify their authenticity. The characterization of alloys and patinas were carried out by inductively coupled plasma mass spectrometry, optical microscopy, scanning electron microscopy and energy dispersion spectroscopy, and X-Ray diffraction spectrometry. Furthermore, thermal ionization mass spectrometry was used to assess the abundances of lead isotopes and to attempt a dating by the measurement of 210Pb/204Pb ratio. The results showed that all three artefacts were mainly composed of low lead-brass alloys, with relatively high concentrations of zinc, antimony, cadmium and aluminum in the solid copper solution. Microstructures were mostly dendritic, typical of as-cast brasses, and characterized by recrystallized non-homogeneous twinned grains in areas corresponding to surface decorations, probably due to multiple hammering steps followed by partial annealing treatments. The matrix was composed of a cored α-Cu solid solution together with non-metallic inclusions, lead globules and Sn-rich precipitates in interdendritic spaces. On the surface of all metalworks, both copper and zinc oxides, a non-continuous layer of sulphur-containing contaminants and chloride-containing compounds, were identified. The lead isotope results were consistent with brasses produced shortly before or after 1900 CE. Overall, the data obtained by different techniques supported the hypothesis that the three artefacts were not authentic.

Identification of carbohydrate anomers using ion mobility-mass spectrometry.

PubMed

Hofmann, J; Hahm, H S; Seeberger, P H; Pagel, K

2015-10-08

Carbohydrates are ubiquitous biological polymers that are important in a broad range of biological processes. However, owing to their branched structures and the presence of stereogenic centres at each glycosidic linkage between monomers, carbohydrates are harder to characterize than are peptides and oligonucleotides. Methods such as nuclear magnetic resonance spectroscopy can be used to characterize glycosidic linkages, but this technique requires milligram amounts of material and cannot detect small amounts of coexisting isomers. Mass spectrometry, on the other hand, can provide information on carbohydrate composition and connectivity for even small amounts of sample, but it cannot be used to distinguish between stereoisomers. Here, we demonstrate that ion mobility-mass spectrometry--a method that separates molecules according to their mass, charge, size, and shape--can unambiguously identify carbohydrate linkage-isomers and stereoisomers. We analysed six synthetic carbohydrate isomers that differ in composition, connectivity, or configuration. Our data show that coexisting carbohydrate isomers can be identified, and relative concentrations of the minor isomer as low as 0.1 per cent can be detected. In addition, the analysis is rapid, and requires no derivatization and only small amounts of sample. These results indicate that ion mobility-mass spectrometry is an effective tool for the analysis of complex carbohydrates. This method could have an impact on the field of carbohydrate synthesis similar to that of the advent of high-performance liquid chromatography on the field of peptide assembly in the late 1970s.

Identification of carbohydrate anomers using ion mobility-mass spectrometry

NASA Astrophysics Data System (ADS)

Hofmann, J.; Hahm, H. S.; Seeberger, P. H.; Pagel, K.

2015-10-01

Carbohydrates are ubiquitous biological polymers that are important in a broad range of biological processes. However, owing to their branched structures and the presence of stereogenic centres at each glycosidic linkage between monomers, carbohydrates are harder to characterize than are peptides and oligonucleotides. Methods such as nuclear magnetic resonance spectroscopy can be used to characterize glycosidic linkages, but this technique requires milligram amounts of material and cannot detect small amounts of coexisting isomers. Mass spectrometry, on the other hand, can provide information on carbohydrate composition and connectivity for even small amounts of sample, but it cannot be used to distinguish between stereoisomers. Here, we demonstrate that ion mobility-mass spectrometry--a method that separates molecules according to their mass, charge, size, and shape--can unambiguously identify carbohydrate linkage-isomers and stereoisomers. We analysed six synthetic carbohydrate isomers that differ in composition, connectivity, or configuration. Our data show that coexisting carbohydrate isomers can be identified, and relative concentrations of the minor isomer as low as 0.1 per cent can be detected. In addition, the analysis is rapid, and requires no derivatization and only small amounts of sample. These results indicate that ion mobility-mass spectrometry is an effective tool for the analysis of complex carbohydrates. This method could have an impact on the field of carbohydrate synthesis similar to that of the advent of high-performance liquid chromatography on the field of peptide assembly in the late 1970s.

Structural characterization of arginine-vasopressin and lysine-vasopressin by Fourier- transform ion cyclotron resonance mass spectrometry and infrared multiphoton dissociation.

PubMed

Bianco, Giuliana; Battista, Fabio; Buchicchio, Alessandro; Amarena, Concetta G; Schmitt-Kopplin, Philippe; Guerrieri, Antonio

2015-01-01

Arginine-vasopressin (AVP) and lysine-vasopressin (LVP) were analyzed by reversed-phase liquid chromatography/mass spectrometry (LC-MS) using Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) electrospray ionization (ESI) in the positive ion mode. LVP and AVP exhibited the protonated adduct [M+H](+) as the predominant ion at m/z 1056.43965 and at m/z 1084.44561, respectively. Infrared multiphoton dissociation (IRMPD), using a CO(2) laser source at a wavelength of 10.6 μm, was applied to protonated vasopressin molecules. The IRMPD mass spectra presented abundant mass fragments essential for a complete structural information. Several fragment ions, shared between two target molecules, are discussed in detail. Some previously unpublished fragments were identified unambiguously utilizing the high resolution and accurate mass information provided by the FT-ICR mass spectrometer. The opening of the disulfide loop and the cleavage of the peptide bonds within the ring were observed even under low-energy fragmentation conditions. Coupling the high-performance FT-ICR mass spectrometer with IRMPD as a contemporary fragmentation technique proved to be very promising for the structural characterization of vasopressin.

Structural characterization and chemical classification of some bryophytes found in Latvia.

PubMed

Maksimova, Viktorija; Klavina, Laura; Bikovens, Oskars; Zicmanis, Andris; Purmalis, Oskars

2013-07-01

Bryophytes are the second largest taxonomic group in the plant kingdom; yet, studies conducted to better understand their chemical composition are rare. The aim of this study was to characterize the chemical composition of bryophytes common in Northern Europe by using elemental, spectral, and non-destructive analytical methods, such as Fourier transform IR spectrometry (FT-IR), solid-phase (13) C-NMR spectrometry, and pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS), for the purpose of investigating their chemotaxonomic relationships on the basis of chemical-composition data. The results of all these analyses showed that bryophytes consist mainly of carbohydrates. Judging by FT-IR spectra, the OH groups in combination of CO groups were the most abundant groups. The (13) C-NMR spectra provided information on the presence of such compounds as phenolics and lipids. It was found that the amount of phenolic compounds in bryophytes is relatively small. This finding definitely confirmed the absence of lignin in the studied bryophytes. Cluster analysis was used to better understand differences in the chemical composition of bryophyte samples and to evaluate possible usage of these methods in the chemotaxonomy of bryophytes. Copyright © 2013 Verlag Helvetica Chimica Acta AG, Zürich.

Rapid separation and characterization of diterpenoid alkaloids in processed roots of Aconitum carmichaeli using ultra high performance liquid chromatography coupled with hybrid linear ion trap-Orbitrap tandem mass spectrometry.

PubMed

Xu, Wen; Zhang, Jing; Zhu, Dayuan; Huang, Juan; Huang, Zhihai; Bai, Junqi; Qiu, Xiaohui

2014-10-01

The lateral root of Aconitum carmichaeli, a popular traditional Chinese medicine, has been widely used to treat rheumatic diseases. For decades, diterpenoid alkaloids have dominated the phytochemical and biomedical research on this plant. In this study, a rapid and sensitive method based on ultra high performance liquid chromatography coupled with linear ion trap-Orbitrap tandem mass spectrometry was developed to characterize the diterpenoid alkaloids in Aconitum carmichaeli. Based on an optimized chromatographic condition, more than 120 diterpenoid alkaloids were separated with good resolution. Using a systematic strategy that combines high resolution separation, highly accurate mass measurements and a good understanding of the diagnostic fragment-based fragmentation patterns, these diterpenoid alkaloids were identified or tentatively identified. The identification of these chemicals provided essential data for further phytochemical studies and toxicity research of Aconitum carmichaeli. Moreover, the ultra high performance liquid chromatography with linear ion trap-Orbitrap mass spectrometry platform was an effective and accurate tool for rapid qualitative analysis of secondary metabolite productions from natural resources. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Systematic chemical profiling of a multicomponent Chinese herbal formula Huo Luo Xiao Ling Dan by ultra high performance liquid chromatography coupled with electrospray ionization quadrupoletime-of-flight mass spectrometry.

PubMed

Wang, Fenrong; Ai, Yu; Wu, Yun; Ma, Wen; Bian, Qiaoxia; Lee, David Y-W; Dai, Ronghua

2015-03-01

Huo Luo Xiao Ling Dan, a Chinese herbal formula consisting of 11 different herbs, has been used in folk medicine for the treatment of arthritis and other chronic inflammatory diseases. However, the chemical compositions of Huo Luo Xiao Ling Dan are not completely characterized. In the present study, an ultra high performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight mass spectrometry method in positive and negative ion modes was employed to identify biochemical constitutes in Huo Luo Xiao Ling Dan. As a result, a total of 76 compounds including alkaloids, monoterpene glycosides, iridoids, phenolic acids, and tanshinones, coumarins, lactones, flavones, and their glycosides, triterpenes, and triterpene saponins were characterized by comparing the retention time and mass spectrometry data with reference standards within 5 ppm error or by reference to the reference literature. These results would provide the basis for a further in vivo study of Huo Luo Xiao Ling Dan and information for potential new drug candidates for treating arthritis and other chronic inflammatory diseases. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Easy ambient sonic-spray ionization mass spectrometry combined with thin-layer chromatography.

PubMed

Haddad, Renato; Milagre, Humberto M S; Catharino, Rodrigo Ramos; Eberlin, Marcos N

2008-04-15

On-spot detection and analyte characterization on thin-layer chromatography (TLC) plates is performed via ambient desorption/ionization and (tandem) mass spectrometry detection, that is, via easy ambient sonic spray ionization mass spectrometry (EASI-MS). As proof-of-principle cases, mixtures of semipolar nitrogenated compounds as well as pharmaceutical drugs and vegetable oils have been tested. The technique has also been applied to monitor a chemical reaction of synthetic importance. EASI is the simplest and gentlest ambient ionization technique currently available, assisted solely by N2 (or air). It uses no voltages, no electrical discharges; no UV or laser beams, and no high temperature and is most easily implemented in all API mass spectrometers. TLC is also the simplest, fastest, and most easily performed chromatographic technique. TLC plus EASI-MS therefore provide a simple and advantageous combination of chromatographic separation and sensitive detection of the TLC spots as well as on-spot MS or MS/MS characterization. The favorable characteristics of TLC-EASI-MS indicate advantageous applications in several areas such as drug and oil analysis, phytochemistry and synthetic chemistry, forensics via reliable counterfeit detection, and quality control.

Analytical characterization of bioactive N-benzyl-substituted phenethylamines and 5-methoxytryptamines.

PubMed

Brandt, Simon D; Elliott, Simon P; Kavanagh, Pierce V; Dempster, Nicola M; Meyer, Markus R; Maurer, Hans H; Nichols, David E

2015-04-15

Substances based on the N-(2-methoxybenzyl)phenethylamine template ('NBOMe' derivatives) play an important role in medicinal research but some of these derivatives have also appeared as 'research chemicals' for recreational use which has attracted attention worldwide. A major challenge associated with newly emerging substances includes the lack of analytical data and the ability to correctly identify positional isomers. Six N-benzylphenethylamines based on the 2,5-dimethoxy-4-iodophenethylamine structure ('25I') and twelve substituted N-benzyl-5-methoxytryptamines ('5MT') have been prepared and extensively characterized. Techniques used for characterization were gas chromatography/ion trap mass spectrometry in electron and chemical ionization mode, liquid chromatography/diode array detection (DAD), infrared spectroscopy, electrospray high mass accuracy quadrupole time-of-flight tandem mass spectrometry, and triple quadrupole tandem mass spectrometry. The characterization of 18 'NBOMe' compounds provided a comprehensive collection of chromatographic and spectral data. Four groups of three positional isomers, i.e. 25I-NB2OMe, 25I-NB3OMe, 25I-NB4OMe, 25I-NB2B, 25I-NB3B, 25I-NB4B and their 5-methoxytryptamine counterparts, were included and assessed for ability to obtain differentiation. Six meta-substituted N-benzyl derivatives of 5-methoxytryptamine (CF3, F, CH3, Cl, I, SCH3) were also studied. The implementation of mass spectral techniques was helpful for the differentiation between isomers, for example, when considering the difference in a number of ion ratios. This was considered beneficial in cases where chromatographic separation was only partially achieved under liquid chromatography (LC) conditions. The use of LC/DAD analysis was also found to be valuable for this particular purpose, which confirmed the integrative value of complementary techniques used in areas related to forensic toxicology. Copyright © 2015 John Wiley & Sons, Ltd.

Cancer vaccine characterization: from bench to clinic.

PubMed

de la Luz-Hernández, K; Rabasa, Y; Montesinos, R; Fuentes, D; Santo-Tomás, J F; Morales, O; Aguilar, Y; Pacheco, B; Castillo, A

2014-05-19

The development of safe, effective, and affordable vaccines has become a global effort due to its vast impact on overall world health conditions. A brief overview of vaccine characterization techniques, especially in the area of high-resolution mass spectrometry, is presented. It is highly conceivable that the proper use of advanced technologies such as high-resolution mass spectrometry, along with the appropriate chemical and physical property evaluations, will yield tremendous in-depth scientific understanding for the characterization of vaccines in various stages of vaccine development. This work presents the physicochemical and biological characterization of cancer vaccine Racotumomab/alumina, a murine anti-idiotypic antibody that mimics N-glycolyl-GM3 gangliosides. This antibody has been tested as an anti-idiotypic cancer vaccine, adjuvated in Al(OH)3, in several clinical trials for melanoma, breast, and lung cancer. Racotumomab was obtained from ascites fluid, transferred to fermentation in stirred tank at 10 L and followed to a scale up to 41 L. The mass spectrometry was used for the determination of intact molecule, light and heavy chains masses; amino acids sequence analysis, N- and C-terminal, glycosylation and posttranslational modifications. Also we used the DLS for the size distribution and zeta potential analysis. The biological analyses were performed in mice and chickens. We observed differences in glycosylation pattern, charge heterogeneity and structural stability between in vivo-produced and bioreactor-obtained Racotumomab products. Interestingly, these modifications had no significant impact on the immune responses elicited in two different animal models. We are demonstrated that this approach could potentially be more efficient and effective for supporting vaccine research and development. Copyright © 2014. Published by Elsevier Ltd.

Improving Analytical Characterization of Glycoconjugate Vaccines through Combined High-Resolution MS and NMR: Application to Neisseria meningitidis Serogroup B Oligosaccharide-Peptide Glycoconjugates.

PubMed

Yu, Huifeng; An, Yanming; Battistel, Marcos D; Cipollo, John F; Freedberg, Darón I

2018-04-17

Conjugate vaccines are highly heterogeneous in terms of glycosylation sites and linked oligosaccharide length. Therefore, the characterization of conjugate vaccines' glycosylation state is challenging. However, improved product characterization can lead to enhancements in product control and product quality. Here, we present a synergistic combination of high-resolution mass spectrometry (MS) and nuclear magnetic resonance spectroscopy (NMR) for the analysis of glycoconjugates. We use the power of this strategy to characterize model polysaccharide conjugates and to demonstrate a detailed level of glycoproteomic analysis. These are first steps on model compounds that will help untangle the details of complex product characterization in conjugate vaccines. Ultimately, this strategy can be applied to enhance the characterization of polysaccharide conjugate vaccines. In this study, we lay the groundwork for the analysis of conjugate vaccines. To begin this effort, oligosaccharide-peptide conjugates were synthesized by periodate oxidation of an oligosaccharide of a defined length, α,2-8 sialic acid trimer, followed by a reductive amination, and linking the trimer to an immunogenic peptide from tetanus toxoid. Combined mass spectrometry and nuclear magnetic resonance were used to monitor each reaction and conjugation products. Complete NMR peak assignment and detailed MS information on oxidized oligosialic acid and conjugates are reported. These studies provide a deeper understanding of the conjugation chemistry process and products, which can lead to a better controlled production process.

Mass spectrometry-based metabolomics: Targeting the crosstalk between gut microbiota and brain in neurodegenerative disorders.

PubMed

Luan, Hemi; Wang, Xian; Cai, Zongwei

2017-11-12

Metabolomics seeks to take a "snapshot" in a time of the levels, activities, regulation and interactions of all small molecule metabolites in response to a biological system with genetic or environmental changes. The emerging development in mass spectrometry technologies has shown promise in the discovery and quantitation of neuroactive small molecule metabolites associated with gut microbiota and brain. Significant progress has been made recently in the characterization of intermediate role of small molecule metabolites linked to neural development and neurodegenerative disorder, showing its potential in understanding the crosstalk between gut microbiota and the host brain. More evidence reveals that small molecule metabolites may play a critical role in mediating microbial effects on neurotransmission and disease development. Mass spectrometry-based metabolomics is uniquely suitable for obtaining the metabolic signals in bidirectional communication between gut microbiota and brain. In this review, we summarized major mass spectrometry technologies including liquid chromatography-mass spectrometry, gas chromatography-mass spectrometry, and imaging mass spectrometry for metabolomics studies of neurodegenerative disorders. We also reviewed the recent advances in the identification of new metabolites by mass spectrometry and metabolic pathways involved in the connection of intestinal microbiota and brain. These metabolic pathways allowed the microbiota to impact the regular function of the brain, which can in turn affect the composition of microbiota via the neurotransmitter substances. The dysfunctional interaction of this crosstalk connects neurodegenerative diseases, including Parkinson's disease, Alzheimer's disease and Huntington's disease. The mass spectrometry-based metabolomics analysis provides information for targeting dysfunctional pathways of small molecule metabolites in the development of the neurodegenerative diseases, which may be valuable for the investigation of underlying mechanism of therapeutic strategies. © 2017 Wiley Periodicals, Inc.

Condensed tannins from acacia mangium bark: Characterization by spot tests and FTIR

NASA Astrophysics Data System (ADS)

Bharudin, Muhammad Azizi; Zakaria, Sarani; Chia, Chin Hua

2013-11-01

This paper describes the adaptation and evaluation of one chemical tests for tannins characterization in acacia mangium bark. Acid butanol test developed to identify respectively condensed tannins is described. The two traditional tests used for tannin characterization namely ferric test and vanillin test were also performed and their functional also discussed. Condensed tannins were extracted from acacia mangium bark using water medium in presence of three different concentration basic reagent of NaOH(5%,10% and 15%) and were characterized by FT-IR spectrometry.

One-step multiple component isolation from the oil of Crinitaria tatarica (Less.) Sojak. by preparative capillary gas with characterization by spectroscopic and spectrometric techniques and evaluation of biological activity

USDA-ARS?s Scientific Manuscript database

In the present work multiple component isolation from the oil of Crinitaria tatarica (Less.) Sojak. by Preparative Capillary Gas Chromatography (PCGC) with characterization by mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy have been carried out. Gas chromatography (GC-FID) ...

High-resolution gas chromatography/mas spectrometry method for characterization and quantitative analysis of ginkgolic acids in ginkgo biloba plants, extracts, and dietary supplements

USDA-ARS?s Scientific Manuscript database

A high resolution GC/MS with Selected Ion Monitor (SIM) method focusing on the characterization and quantitative analysis of ginkgolic acids (GAs) in Ginkgo biloba L. plant materials, extracts and commercial products was developed and validated. The method involved sample extraction with (1:1) meth...

Comprehensive characterization of C-glycosyl flavones in wheat (Triticum aestivum L.) germ using UPLC-PDA-ESI/HRMSn and mass defect filtering

USDA-ARS?s Scientific Manuscript database

A comprehensive characterization of C-glycosyl flavones in wheat germ has been conducted using multi-stage high resolution mass spectrometry (HRMS) combined with mass defect filter (MDF). MDF performed the initial search of raw data with defined mass ranges and mass defect windows to generate the n...

Characterization of constituents in Stellera chamaejasme L. by rapid-resolution liquid chromatography-diode array detection and electrospray ionization time-of-flight mass spectrometry.

PubMed

Zhao, Liang; Lou, Zi-Yang; Zhu, Zhen-Yu; Zhang, Guo-Qing; Chai, Yi-Feng

2008-01-01

A reliable and rapid method based on rapid-resolution liquid chromatography-diode array detection (RRLC-DAD) and electrospray ionization time-of-flight mass spectrometry (ESI-TOF/MS) has been developed for the isolation and characterization of multiple constituents in the root of Stellera chamaejasme L., which was extracted by sonication with methanol in an optimized procedure. Separation of the multiple constituents was achieved on an Agilent Zorbax XDB-C18 (50x3.0 mm i.d.; 1.8 microm) column using a gradient elution at a flow rate of 0.4 mL/min. The detection wavelength was 210 nm. Mass spectra were acquired in both positive and negative modes. A formula database of the known chemical constituents in the root of Stellera chamaejasme L. was established by an Agilent software. Twenty-two obvious peaks appeared in the total ion chromatogram and nine of them were characterized by TOF/MS. The RRLC-DAD and ESI-TOF/MS method with ultrasonic extraction would be useful for rapid and effective characterization of chemical constituents in the root of Stellera chamaejasme L. Copyright (c) 2007 John Wiley & Sons, Ltd.

Advances and unresolved challenges in the structural characterization of isomeric lipids.

PubMed

Hancock, Sarah E; Poad, Berwyck L J; Batarseh, Amani; Abbott, Sarah K; Mitchell, Todd W

2017-05-01

As the field of lipidomics grows and its application becomes wide and varied it is important that we don't forget its foundation, i.e. the identification and measurement of molecular lipids. Advances in liquid chromatography and the emergence of ion mobility as a useful tool in lipid analysis are allowing greater separation of lipid isomers than ever before. At the same time, novel ion activation techniques, such as ozone-induced dissociation, are pushing lipid structural characterization by mass spectrometry to new levels. Nevertheless, the quantitative capacity of these techniques is yet to be proven and further refinements are required to unravel the high level of lipid complexity found in biological samples. At present there is no one technique capable of providing full structural characterization of lipids from a biological sample. There are however, numerous techniques now available (as discussed in this review) that could be deployed in a targeted approach. Moving forward, the combination of advanced separation and ion activation techniques is likely to provide mass spectrometry-based lipidomics with its best opportunity to achieve complete molecular-level lipid characterization and measurement from complex mixtures. Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.

Biogenic manganese oxide nanoparticle formation by a multimeric multicopper oxidase Mnx.

PubMed

Romano, Christine A; Zhou, Mowei; Song, Yang; Wysocki, Vicki H; Dohnalkova, Alice C; Kovarik, Libor; Paša-Tolić, Ljiljana; Tebo, Bradley M

2017-09-29

Bacteria that produce Mn oxides are extraordinarily skilled engineers of nanomaterials that contribute significantly to global biogeochemical cycles. Their enzyme-based reaction mechanisms may be genetically tailored for environmental remediation applications or bioenergy production. However, significant challenges exist for structural characterization of the enzymes responsible for biomineralization. The active Mn oxidase in Bacillus sp. PL-12, Mnx, is a complex composed of a multicopper oxidase (MCO), MnxG, and two accessory proteins, MnxE and MnxF. MnxG shares sequence similarity with other, structurally characterized MCOs. MnxE and MnxF have no similarity to any characterized proteins. The ~200 kDa complex has been recalcitrant to crystallization, so its structure is unknown. Here, we show that native mass spectrometry defines the subunit topology and copper binding of Mnx, while high-resolution electron microscopy visualizes the protein and nascent Mn oxide minerals. These data provide critical structural information for understanding Mn biomineralization by such unexplored enzymes.Significant challenges exist for structural characterization of enzymes responsible for biomineralization. Here the authors show that native mass spectrometry and high resolution electron microscopy can define the subunit topology and copper binding of a manganese oxidizing complex, and describe early stage formation of its mineral products.

Identifying cancer biomarkers by mass spectrometry-based glycomics

PubMed Central

Mechref, Yehia; Hu, Yunli; Garcia, Aldo; Hussein, Ahmed

2013-01-01

Correlations between aberrant glycosylation and cancer have been established for decades. The major advances in mass spectrometry (MS) and separation science have rapidly advanced detailed characterization of the changes associated with cancer development and progression. Over the past 10 years, many reports have described MS-based glycomic methods directed toward comparing the glycomic profiles of different human specimens collected from disease-free individuals and patients with cancers. Glycomic profiling of glycoproteins isolated from human specimens originating from disease-free individuals and patients with cancers have also been performed. Profiling of native, labeled, and permethylated glycans has been acquired using MALDI-MS and LC-MS. This review focuses on describing, discussing, and evaluating the different glycomic methods employed to characterize and quantify glycomic changes associated with cancers of different organs, including breast, colon, esophagus, liver, ovarian, pancreas, and prostate. PMID:22740464

Lysozyme oxidation by singlet molecular oxygen: Peptide characterization using [18 O]-labeling oxygen and nLC-MS/MS.

PubMed

Marques, Emerson Finco; Medeiros, Marisa H G; Di Mascio, Paolo

2017-11-01

Singlet molecular oxygen ( 1 O 2 ) is generated in biological systems and reacts with different biomolecules. Proteins are a major target for 1 O 2 , and His, Tyr, Met, Cys, and Trp are oxidized at physiological pH. In the present study, the modification of lysozyme protein by 1 O 2 was investigated using mass spectrometry approaches. The experimental findings showed methionine, histidine, and tryptophan oxidation. The experiments were achieved using [ 18 O]-labeled 1 O 2 released from thermolabile endoperoxides in association with nano-scale liquid chromatography coupled to electrospray ionization mass spectrometry. The structural characterization by nLC-MS/MS of the amino acids in the tryptic peptides of the proteins showed addition of [ 18 O]-labeling atoms in different amino acids. Copyright © 2017 John Wiley & Sons, Ltd.

Metabolite characterization of a novel sedative drug, remimazolam in human plasma and urine using ultra high-performance liquid chromatography coupled with synapt high-definition mass spectrometry.

PubMed

Zhou, Ying; Hu, Pei; Jiang, Ji

2017-04-15

Remimazolam is a new chemical entity belonging to the benzodiazepine class of sedative drugs, which shows faster-acting onset and recovery than currently available short-acting sedatives. In the present study, ultra high performance liquid chromatography with synapt high-definition mass spectrometry method combined with MassLynx software was established to characterize metabolites of remimazolam in human plasma and urine. In total, 5 human metabolites were detected, including 3 phase I and 2 phase II metabolites. There was no novel human metabolite detected compared to that in rat. Hydrolysis, glucuronidation and oxidation were the major metabolic reactions. To our knowledge, this is the first report of the human metabolic profile of remimazolam. Copyright © 2017 Elsevier B.V. All rights reserved.

Characterization of dilute species within CVD-grown silicon nanowires doped using trimethylboron: protected lift-out specimen preparation for atom probe tomography.

PubMed

Prosa, T J; Alvis, R; Tsakalakos, L; Smentkowski, V S

2010-08-01

Three-dimensional quantitative compositional analysis of nanowires is a challenge for standard techniques such as secondary ion mass spectrometry because of specimen size and geometry considerations; however, it is precisely the size and geometry of nanowires that makes them attractive candidates for analysis via atom probe tomography. The resulting boron composition of various trimethylboron vapour-liquid-solid grown silicon nanowires were measured both with time-of-flight secondary ion mass spectrometry and pulsed-laser atom probe tomography. Both characterization techniques yielded similar results for relative composition. Specialized specimen preparation for pulsed-laser atom probe tomography was utilized and is described in detail whereby individual silicon nanowires are first protected, then lifted out, trimmed, and finally wet etched to remove the protective layer for subsequent three-dimensional analysis.

Secondary ion mass spectrometry: The application in the analysis of atmospheric particulate matter

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

Huang, Di; Hua, Xin; Xiu, Guang-Li

Currently, considerable attention has been paid to atmospheric particulate matter (PM) investigation due to its importance in human health and global climate change. Surface characterization of PM is important since the chemical heterogeneity between the surface and bulk may vary its impact on the environment and human being. Secondary ion mass spectrometry (SIMS) is a surface technique with high surface sensitivity, capable of high spatial chemical imaging and depth profiling. Recent research shows that SIMS holds great potential in analyzing both surface and bulk chemical information of PM. In this review, we presented the working principal of SIMS in PMmore » characterization, summarized recent applications in PM analysis from different sources, discussed its advantages and limitations, and proposed the future development of this technique with a perspective in environmental sciences.« less

The Chilean Rural Practitioner Programme: a multidimensional strategy to attract and retain doctors in rural areas

PubMed Central

Peña, Sebastian; Ramirez, Jorge; Becerra, Carlos; Carabantes, Jorge

2010-01-01

Abstract Developing countries currently face internal and external migration of their health workforce and interventions are needed to attract and retain health professionals in rural areas. Evidence of multidimensional interventions, however, is scarce. This study explores a long-standing strategy to attract and retain doctors to rural areas in Chile: the Rural Practitioner Programme. The main objective is to describe the programme, characterize its multidimensional set of incentives and appraise preliminary programme outcomes. Retrospective national data were employed to examine recruitment, retention and incentives provided to extend the length of stay and motivate non-clinical work. The programme has successfully recruited a large number of applicants, with acceptance rates close to 100%. Retention rates are nearly 100% (drop-outs are exceptional), but only 58% of participants stay for the maximum period. Areas with greater work difficulty are attracting the best-ranked applicants, but incentives to engage in community projects, management responsibilities, continuous medical education and research have achieved mixed results. Rural doctors are satisfied with their experience and 70% plan to practise as specialists in a referral hospital. The programme has successfully matched the interests of physicians in specialization with the country’s need for rural doctors. However, a gap might be forming between the demand for certain specialties and what the programme can offer. There is a need to conciliate both parties, which will require a more refined strategy than before. This should be grounded in robust knowledge based on programme outcomes and evidence of the interests and motivations of health professionals. PMID:20461139

The Tunneling Method for Global Optimization in Multidimensional Scaling.

ERIC Educational Resources Information Center

Groenen, Patrick J. F.; Heiser, Willem J.

1996-01-01

A tunneling method for global minimization in multidimensional scaling is introduced and adjusted for multidimensional scaling with general Minkowski distances. The method alternates a local search step with a tunneling step in which a different configuration is sought with the same STRESS implementation. (SLD)

Multidimensional Poverty and Health Status as a Predictor of Chronic Income Poverty.

PubMed

Callander, Emily J; Schofield, Deborah J

2015-12-01

Longitudinal analysis of Wave 5 to 10 of the nationally representative Household, Income and Labour Dynamics in Australia dataset was undertaken to assess whether multidimensional poverty status can predict chronic income poverty. Of those who were multidimensionally poor (low income plus poor health or poor health and insufficient education attainment) in 2007, and those who were in income poverty only (no other forms of disadvantage) in 2007, a greater proportion of those in multidimensional poverty continued to be in income poverty for the subsequent 5 years through to 2012. People who were multidimensionally poor in 2007 had 2.17 times the odds of being in income poverty each year through to 2012 than those who were in income poverty only in 2005 (95% CI: 1.23-3.83). Multidimensional poverty measures are a useful tool for policymakers to identify target populations for policies aiming to improve equity and reduce chronic disadvantage. Copyright © 2014 John Wiley & Sons, Ltd.

Multidimensional upwind hydrodynamics on unstructured meshes using graphics processing units - I. Two-dimensional uniform meshes

NASA Astrophysics Data System (ADS)

Paardekooper, S.-J.

2017-08-01

We present a new method for numerical hydrodynamics which uses a multidimensional generalization of the Roe solver and operates on an unstructured triangular mesh. The main advantage over traditional methods based on Riemann solvers, which commonly use one-dimensional flux estimates as building blocks for a multidimensional integration, is its inherently multidimensional nature, and as a consequence its ability to recognize multidimensional stationary states that are not hydrostatic. A second novelty is the focus on graphics processing units (GPUs). By tailoring the algorithms specifically to GPUs, we are able to get speedups of 100-250 compared to a desktop machine. We compare the multidimensional upwind scheme to a traditional, dimensionally split implementation of the Roe solver on several test problems, and we find that the new method significantly outperforms the Roe solver in almost all cases. This comes with increased computational costs per time-step, which makes the new method approximately a factor of 2 slower than a dimensionally split scheme acting on a structured grid.

Ion Mobility Spectrometry-Mass Spectrometry Coupled with Gas-Phase Hydrogen/Deuterium Exchange for Metabolomics Analyses

NASA Astrophysics Data System (ADS)

Maleki, Hossein; Karanji, Ahmad K.; Majuta, Sandra; Maurer, Megan M.; Valentine, Stephen J.

2018-02-01

Ion mobility spectrometry-mass spectrometry (IMS-MS) in combination with gas-phase hydrogen/deuterium exchange (HDX) and collision-induced dissociation (CID) is evaluated as an analytical method for small-molecule standard and mixture characterization. Experiments show that compound ions exhibit unique HDX reactivities that can be used to distinguish different species. Additionally, it is shown that gas-phase HDX kinetics can be exploited to provide even further distinguishing capabilities by using different partial pressures of reagent gas. The relative HDX reactivity of a wide variety of molecules is discussed in light of the various molecular structures. Additionally, hydrogen accessibility scoring (HAS) and HDX kinetics modeling of candidate ( in silico) ion structures is utilized to estimate the relative ion conformer populations giving rise to specific HDX behavior. These data interpretation methods are discussed with a focus on developing predictive tools for HDX behavior. Finally, an example is provided in which ion mobility information is supplemented with HDX reactivity data to aid identification efforts of compounds in a metabolite extract.

Autonomous Metabolomics for Rapid Metabolite Identification in Global Profiling

DOE PAGES

Benton, H. Paul; Ivanisevic, Julijana; Mahieu, Nathaniel G.; ...

2014-12-12

An autonomous metabolomic workflow combining mass spectrometry analysis with tandem mass spectrometry data acquisition was designed to allow for simultaneous data processing and metabolite characterization. Although previously tandem mass spectrometry data have been generated on the fly, the experiments described herein combine this technology with the bioinformatic resources of XCMS and METLIN. We can analyze large profiling datasets and simultaneously obtain structural identifications, as a result of this unique integration. Furthermore, validation of the workflow on bacterial samples allowed the profiling on the order of a thousand metabolite features with simultaneous tandem mass spectra data acquisition. The tandem mass spectrometrymore » data acquisition enabled automatic search and matching against the METLIN tandem mass spectrometry database, shortening the current workflow from days to hours. Overall, the autonomous approach to untargeted metabolomics provides an efficient means of metabolomic profiling, and will ultimately allow the more rapid integration of comparative analyses, metabolite identification, and data analysis at a systems biology level.« less

Characterization of Compounds in Psoralea corylifolia Using High-Performance Liquid Chromatography Diode Array Detection, Time-of-Flight Mass Spectrometry and Quadrupole Ion Trap Mass Spectrometry.

PubMed

Tan, Guangguo; Yang, Tiehong; Miao, Huayan; Chen, Hao; Chai, Yifeng; Wu, Hong

2015-10-01

High-performance liquid chromatography with diode array detection (HPLC-DAD), time-of-flight mass spectrometry (HPLC-TOFMS) and quadrupole ion trap mass spectrometry (HPLC-QITMS) were used for separation and identification of multi-components in Psoralea corylifolia. Benefiting from combining the accurate mass measurement of HPLC-TOFMS to generate elemental compositions, the complementary multilevel structural information provided by HPLC-QITMS and the characteristic UV spectra obtained from HPLC-DAD, 24 components in P. corylifolia were identified. The five groups of isomers were differentiated based on the fragmentation behaviors in QITMS and UV spectra. It can be concluded that an effective method based on the combination of HPLC-DAD, HPLC-TOFMS and HPLC-QITMS for identification of chemical components in P. corylifolia was established. The results provide essential data for further pharmacological and clinical studies of P. corylifolia and facilitate the rapid quality control of the crude drug. © Crown copyright 2015.

Detection of trace ink compounds in erased handwritings using electrospray-assisted laser desorption ionization mass spectrometry.

PubMed

Kao, Yi-Ying; Cheng, Sy-Chyi; Cheng, Chu-Nian; Shiea, Jentaie; Ho, Hsiu-O

2014-06-01

Writings made with erasable pens on paper surfaces can either be rubbed off with an eraser or rendered invisible by changing the temperature of the ink. However, trace ink compounds still remain in the paper fibers even after rubbing or rendering. The detection of these ink compounds from erased handwritings will be helpful in knowing the written history of the paper. In this study, electrospray-assisted laser desorption ionization/mass spectrometry was used to characterize trace ink compounds remaining in visible and invisible ink lines. The ink compounds were desorbed from the paper surface by irradiating the handwritings with a pulsed laser beam; the desorbed analytes were subsequently ionized in an electrospray plume and detected by a quadrupole time-of-flight mass spectrometry mass analyzer. Because of the high spatial resolution of the laser beam, electrospray-assisted laser desorption ionization/mass spectrometry analysis resulted in minimal damage to the sample documents. Copyright © 2014 John Wiley & Sons, Ltd.

Detection of new emerging type-A trichothecenes by untargeted mass spectrometry.

PubMed

González-Jartín, Jesús M; Alfonso, Amparo; Sainz, María J; Vieytes, Mercedes R; Botana, Luis M

2018-02-01

Mycotoxins occur naturally as agricultural contaminants all over the world. The toxic effects of some of their metabolites are known and their presence regulated in food and feed. This paper describes two methods for the detection of toxins of type-A trichothecenes group, and their modified forms, using mass spectrometry. Ultra-performance liquid chromatography coupled to mass spectrometry-ion trap-time of flight (UPLC-MS-IT-TOF) was employed to characterize the fragmentation pathways of 10 type-A trichothecenes, and characteristic ions were tentatively identified in scan mode through their accurate masses. Unknown signals were detected in a F. sporotrichioides extract, which afterwards were identified as seven modified forms of neosolaniol (NEO) and T-2 toxin. Then, UPLC coupled to tandem mass spectrometry (MS/MS) was employed to develop a precursor ion scanning method that can be used as a screening tool to detect any modified type-A trichothecenes. Copyright © 2017 Elsevier B.V. All rights reserved.

Inductively coupled plasma mass spectrometry and electrospray mass spectrometry for speciation analysis: applications and instrumentation

NASA Astrophysics Data System (ADS)

Rosen, Amy L.; Hieftje, Gary M.

2004-02-01

To gain an understanding of the function, toxicity and distribution of trace elements, it is necessary to determine not only the presence and concentration of the elements of interest, but also their speciation, by identifying and characterizing the compounds within which each is present. For sensitive detection of compounds containing elements of interest, inductively coupled plasma mass spectrometry (ICP-MS) is a popular method, and for identification of compounds via determination of molecular weight, electrospray ionization mass spectrometry (ESI-MS) is gaining increasing use. ICP-MS and ESI-MS, usually coupled to a separation technique such as chromatography or capillary electrophoresis, have already been applied to a large number of research problems in such diverse fields as environmental chemistry, nutritional science, and bioinorganic chemistry, but a great deal of work remains to be completed. Current areas of research to which ICP-MS and ESI-MS have been applied are discussed, and the existing instrumentation used to solve speciation problems is described.

Structural Elucidation of Enzymatically Synthesized Galacto-oligosaccharides Using Ion-Mobility Spectrometry-Tandem Mass Spectrometry.

PubMed

Carević, Milica; Bezbradica, Dejan; Banjanac, Katarina; Milivojević, Ana; Fanuel, Mathieu; Rogniaux, Hélène; Ropartz, David; Veličković, Dušan

2016-05-11

Galacto-oligosaccharides (GOS) represent a diverse group of well-characterized prebiotic ingredients derived from lactose in a reaction catalyzed with β-galactosidases. Enzymatic transgalactosylation results in a mixture of compounds of various degrees of polymerization and types of linkages. Because structure plays an important role in terms of prebiotic activity, it is of crucial importance to provide an insight into the mechanism of transgalactosylation reaction and occurrence of different types of β-linkages during GOS synthesis. Our study proved that a novel one-step method, based on ion-mobility spectrometry-tandem mass spectrometry (IMS-MS/MS), enables complete elucidation of GOS structure. It has been shown that β-galactosidase from Aspergillus oryzae has the highest affinity toward formation of β-(1→3) or β-(1→6) linkages. Additionally, it was observed that the occurrence of different linkages varies during the reaction course, indicating that tailoring favorable GOS structures with improved prebiotic activity can be achieved by adequate control of enzymatic synthesis.

Enhancing Student Motivation and Engagement: The Effects of a Multidimensional Intervention

ERIC Educational Resources Information Center

Martin, Andrew J.

2008-01-01

The present study sought to investigate the effects of a multidimensional educational intervention on high school students' motivation and engagement. The intervention incorporated: (a) multidimensional targets of motivation and engagement, (b) empirically derived intervention methodology, (c) research-based risk and protective factors, (d)…

Characterization of on-target generated tryptic peptides from Giberella zeae conidia spore proteins by means of matrix-assisted laser desorption/ionization mass spectrometry.

PubMed

Dong, Hongjuan; Marchetti-Deschmann, Martina; Allmaier, Günter

2014-01-01

Traditionally characterization of microbial proteins is performed by a complex sequence of steps with the final step to be either Edman sequencing or mass spectrometry, which generally takes several weeks or months to be complete. In this work, we proposed a strategy for the characterization of tryptic peptides derived from Giberella zeae (anamorph: Fusarium graminearum) proteins in parallel to intact cell mass spectrometry (ICMS) in which no complicated and time-consuming steps were needed. Experimentally, after a simple washing treatment of the spores, the aliquots of the intact G. zeae macro conidia spores solution, were deposited two times onto one MALDI (matrix-assisted laser desorption ionization) mass spectrometry (MS) target (two spots). One spot was used for ICMS and the second spot was subject to a brief on-target digestion with bead-immobilized or non-immobilized trypsin. Subsequently, one spot was analyzed immediately by MALDI MS in the linear mode (ICMS) whereas the second spot containing the digested material was investigated by MALDI MS in the reflectron mode ("peptide mass fingerprint") followed by protonated peptide selection for MS/MS (post source decay (PSD) fragment ion) analysis. Based on the formed fragment ions of selected tryptic peptides a complete or partial amino acid sequence was generated by manual de novo sequencing. These sequence data were used for homology search for protein identification. Finally four different peptides of varying abundances have been identified successfully allowing the verification that our desorbed/ionized surface compounds were indeed derived from proteins. The presence of three different proteins could be found unambiguously. Interestingly, one of these proteins is belonging to the ribosomal superfamily which indicates that not only surface-associated proteins were digested. This strategy minimized the amount of time and labor required for obtaining deeper information on spore preparations within the nowadays widely used ICMS approach. Copyright © 2013 Elsevier Ltd. All rights reserved.

Manganese oxide nanoparticle-assisted laser desorption/ionization mass spectrometry for medical applications

NASA Astrophysics Data System (ADS)

Taira, Shu; Kitajima, Kenji; Katayanagi, Hikaru; Ichiishi, Eiichiro; Ichiyanagi, Yuko

2009-06-01

We prepared and characterized manganese oxide magnetic nanoparticles (d =5.6 nm) and developed nanoparticle-assited laser desorption/ionization (nano-PALDI) mass spectrometry. The nanoparticles had MnO2 and Mn2O3 cores conjugated with hydroxyl and amino groups, and showed paramagnetism at room temperature. The nanoparticles worked as an ionization assisting reagent in mass spectroscopy. The mass spectra showed no background in the low m/z. The nanoparticles could ionize samples of peptide, drug and proteins (approx. 5000 Da) without using matrix, i.e., 2,5-dihydroxybenzoic acid (DHB), 4-hydroxy-α-cinnamic acid (CHCA) and liquid matrix, as conventional ionization assisting reagents. Post source decay spectra by nano-PALDI mass spectrometry will yield information of the chemical structure of analytes.

Challenges in the quality assurance of elemental and isotopic analyses in the nuclear domain benefitting from high resolution ICP-OES and sector field ICP-MS.

PubMed

Krachler, Michael; Alvarez-Sarandes, Rafael; Van Winckel, Stefaan

Accurate analytical data reinforces fundamentally the meaningfulness of nuclear fuel performance assessments and nuclear waste characterization. Regularly lacking matrix-matched certified reference materials, quality assurance of elemental and isotopic analysis of nuclear materials remains a challenging endeavour. In this context, this review highlights various dedicated experimental approaches envisaged at the European Commission-Joint Research Centre-Institute for Transuranium Elements to overcome this limitation, mainly focussing on the use of high resolution-inductively coupled plasma-optical emission spectrometry (HR-ICP-OES) and sector field-inductively coupled plasma-mass spectrometry (SF-ICP-MS). However, also α- and γ-spectrometry are included here to help characterise extensively the investigated actinide solutions for their actual concentration, potential impurities and isotopic purity.

Separation and identification of corticosterone metabolites by liquid chromatography--electrospray ionization mass spectrometry.

PubMed

Miksík, I; Vylitová, M; Pácha, J; Deyl, Z

1999-04-16

High-performance liquid chromatography coupled to atmospheric pressure ionization-electrospray ionization mass spectrometry (API-ESI-MS) was investigated for the analysis of corticosterone metabolites; their characterization was obtained by combining the separation on Zorbax Eclipse XDB C18 column (eluted with a methanol-water-acetic acid gradient) with identification using positive ion mode API-ESI-MS and selected ion analysis. The applicability of this method was verified by monitoring the activity of steroid converting enzymes (20beta-hydroxysteroid dehydrogenase and 11beta-hydroxysteroid dehydrogenase) in avian intestines.

The on-line characterization of a radium slurry by gamma-ray spectrometry.

PubMed

Philips, S; Croft, S

2005-01-01

We have developed an in-line monitor to directly measure the (226)Ra concentration in a nuclear waste stream using quantitative gamma-ray spectrometry applied to the 186keV emission. The waste stream is in the form of a slurry composed of the solid waste material mixed with water. The concentration measurement includes a self-attenuation correction factor determined from a transmission measurement using the 122keV gamma from (57)Co. Presented here is the model for the measurement system and results from some initial tests.

Mass Determination of Entire Amyloid Fibrils by Using Mass Spectrometry.

PubMed

Doussineau, Tristan; Mathevon, Carole; Altamura, Lucie; Vendrely, Charlotte; Dugourd, Philippe; Forge, Vincent; Antoine, Rodolphe

2016-02-12

Amyloid fibrils are self-assembled protein structures with important roles in biology (either pathogenic or physiological), and are attracting increasing interest in nanotechnology. However, because of their high aspect ratio and the presence of some polymorphism, that is, the possibility to adopt various structures, their characterization is challenging and basic information such as their mass is unknown. Here we show that charge-detection mass spectrometry, recently developed for large self-assembled systems such as viruses, provides such information in a straightforward manner. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Characterization of low-molecular weight iodine-terminated polyethylenes by gas chromatography/mass spectrometry and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry with the use of derivatization.

PubMed

Zaikin, Vladimir G; Borisov, Roman S; Polovkov, Nikolai Yu; Zhilyaev, Dmitry I; Vinogradov, Aleksei A; Ivanyuk, Aleksei V

2013-01-01

Gas chromatography/mass spectrometry (GC/MS) and matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) mass spectrometry, in conjunction with various derivatization approaches, have been applied to structure determination of individual oligomers and molecular-mass distributions (MMD) in low-molecular mass polyethylene having an iodine terminus. Direct GC/MS analysis has shown that the samples under investigation composed of polyethyelene-iodides (major components) and n-alkanes. Exchange reaction with methanol in the presence of NaOH gave rise to methoxy-derivatives and n-alkenes. Electron ionization mass spectra have shown that the former contained terminal methoxy groups indicating the terminal position of the iodine atom in the initial oligomers. MMD parameters have been determined with the aid of MALDI mass spectrometry followed by preliminary derivatization-formation of covalently bonded charge through the reaction of iodides with triphenylphosphine, trialkylamines, pyridine or quinoline. The mass spectra revealed well-resolved peaks for cationic parts of derivatized oligomers allowing the determination of MMD. The latter values have been compared with those calculated from GC/MS data.

Analysis of metal-binding proteins separated by non-denaturating gel electrophoresis using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS).

PubMed

Becker, J Susanne; Mounicou, Sandra; Zoriy, Miroslav V; Becker, J Sabine; Lobinski, Ryszard

2008-09-15

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) have become established as very efficient and sensitive biopolymer and elemental mass spectrometric techniques for studying metal-binding proteins (metalloproteins) in life sciences. Protein complexes present in rat tissues (liver and kidney) were separated in their native state in the first dimension by blue native gel electrophoresis (BN-PAGE). Essential and toxic metals, such as zinc, copper, iron, nickel, chromium, cadmium and lead, were detected by scanning the gel bands using quadrupole LA-ICP-MS with and without collision cell as a microanalytical technique. Several proteins were identified by using MALDI-TOF-MS together with a database search. For example, on one protein band cut from the BN-PAGE gel and digested with the enzyme trypsin, two different proteins - protein FAM44B and cathepsin B precursor - were identified. By combining biomolecular and elemental mass spectrometry, it was possible to characterize and identify selected metal-binding rat liver and kidney tissue proteins.

Heteronuclear Multidimensional Protein NMR in a Teaching Laboratory

ERIC Educational Resources Information Center

Wright, Nathan T.

2016-01-01

Heteronuclear multidimensional NMR techniques are commonly used to study protein structure, function, and dynamics, yet they are rarely taught at the undergraduate level. Here, we describe a senior undergraduate laboratory where students collect, process, and analyze heteronuclear multidimensional NMR experiments using an unstudied Ig domain (Ig2…

Compressed Continuous Computation v. 12/20/2016

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

Gorodetsky, Alex

2017-02-17

A library for performing numerical computation with low-rank functions. The (C3) library enables performing continuous linear and multilinear algebra with multidimensional functions. Common tasks include taking "matrix" decompositions of vector- or matrix-valued functions, approximating multidimensional functions in low-rank format, adding or multiplying functions together, integrating multidimensional functions.

The Discriminating Power of Items that Measure More than One Dimension.

ERIC Educational Resources Information Center

Reckase, Mark D.

The work presented in this paper defined conceptually the concepts of multidimensional discrimination and information, derived mathematical expressions for the concepts for a particular multidimensional item response theory (IRT) model, and applied the concepts to actual test data. Multidimensional discrimination was defined as a function of the…

Multidimensional Computerized Adaptive Testing for Indonesia Junior High School Biology

ERIC Educational Resources Information Center

Kuo, Bor-Chen; Daud, Muslem; Yang, Chih-Wei

2015-01-01

This paper describes a curriculum-based multidimensional computerized adaptive test that was developed for Indonesia junior high school Biology. In adherence to the Indonesian curriculum of different Biology dimensions, 300 items was constructed, and then tested to 2238 students. A multidimensional random coefficients multinomial logit model was…

Supervised and Unsupervised Learning of Multidimensional Acoustic Categories

ERIC Educational Resources Information Center

Goudbeek, Martijn; Swingley, Daniel; Smits, Roel

2009-01-01

Learning to recognize the contrasts of a language-specific phonemic repertoire can be viewed as forming categories in a multidimensional psychophysical space. Research on the learning of distributionally defined visual categories has shown that categories defined over 1 dimension are easy to learn and that learning multidimensional categories is…

Health, Wealth and Wisdom: Exploring Multidimensional Inequality in a Developing Country

ERIC Educational Resources Information Center

Nilsson, Therese

2010-01-01

Despite a broad theoretical literature on multidimensional inequality and a widespread belief that welfare is not synonymous to income--not the least in a developing context--empirical inequality examinations rarely includes several welfare attributes. We explore three techniques on how to evaluate multidimensional inequality using Zambian…

Multidimensional Physical Self-Concept of Athletes with Physical Disabilities

ERIC Educational Resources Information Center

Shapiro, Deborah R.; Martin, Jeffrey J.

2010-01-01

The purposes of this investigation were first to predict reported PA (physical activity) behavior and self-esteem using a multidimensional physical self-concept model and second to describe perceptions of multidimensional physical self-concept (e.g., strength, endurance, sport competence) among athletes with physical disabilities. Athletes (N =…

Method of data mining including determining multidimensional coordinates of each item using a predetermined scalar similarity value for each item pair

DOEpatents

Meyers, Charles E.; Davidson, George S.; Johnson, David K.; Hendrickson, Bruce A.; Wylie, Brian N.

1999-01-01

A method of data mining represents related items in a multidimensional space. Distance between items in the multidimensional space corresponds to the extent of relationship between the items. The user can select portions of the space to perceive. The user also can interact with and control the communication of the space, focusing attention on aspects of the space of most interest. The multidimensional spatial representation allows more ready comprehension of the structure of the relationships among the items.

A Conceptual Model for Multidimensional Analysis of Documents

NASA Astrophysics Data System (ADS)

Ravat, Franck; Teste, Olivier; Tournier, Ronan; Zurlfluh, Gilles

Data warehousing and OLAP are mainly used for the analysis of transactional data. Nowadays, with the evolution of Internet, and the development of semi-structured data exchange format (such as XML), it is possible to consider entire fragments of data such as documents as analysis sources. As a consequence, an adapted multidimensional analysis framework needs to be provided. In this paper, we introduce an OLAP multidimensional conceptual model without facts. This model is based on the unique concept of dimensions and is adapted for multidimensional document analysis. We also provide a set of manipulation operations.

A review of snapshot multidimensional optical imaging: measuring photon tags in parallel

PubMed Central

Gao, Liang; Wang, Lihong V.

2015-01-01

Multidimensional optical imaging has seen remarkable growth in the past decade. Rather than measuring only the two-dimensional spatial distribution of light, as in conventional photography, multidimensional optical imaging captures light in up to nine dimensions, providing unprecedented information about incident photons’ spatial coordinates, emittance angles, wavelength, time, and polarization. Multidimensional optical imaging can be accomplished either by scanning or parallel acquisition. Compared with scanning-based imagers, parallel acquisition—also dubbed snapshot imaging—has a prominent advantage in maximizing optical throughput, particularly when measuring a datacube of high dimensions. Here, we first categorize snapshot multidimensional imagers based on their acquisition and image reconstruction strategies, then highlight the snapshot advantage in the context of optical throughput, and finally we discuss their state-of-the-art implementations and applications. PMID:27134340

A multidimensional subdiffusion model: An arbitrage-free market

NASA Astrophysics Data System (ADS)

Li, Guo-Hua; Zhang, Hong; Luo, Mao-Kang

2012-12-01

To capture the subdiffusive characteristics of financial markets, the subordinated process, directed by the inverse α-stale subordinator Sα(t) for 0 < α < 1, has been employed as the model of asset prices. In this article, we introduce a multidimensional subdiffusion model that has a bond and K correlated stocks. The stock price process is a multidimensional subdiffusion process directed by the inverse α-stable subordinator. This model describes the period of stagnation for each stock and the behavior of the dependency between multiple stocks. Moreover, we derive the multidimensional fractional backward Kolmogorov equation for the subordinated process using the Laplace transform technique. Finally, using a martingale approach, we prove that the multidimensional subdiffusion model is arbitrage-free, and also gives an arbitrage-free pricing rule for contingent claims associated with the martingale measure.

Progress in multi-dimensional upwind differencing

NASA Technical Reports Server (NTRS)

Vanleer, Bram

1992-01-01

Multi-dimensional upwind-differencing schemes for the Euler equations are reviewed. On the basis of the first-order upwind scheme for a one-dimensional convection equation, the two approaches to upwind differencing are discussed: the fluctuation approach and the finite-volume approach. The usual extension of the finite-volume method to the multi-dimensional Euler equations is not entirely satisfactory, because the direction of wave propagation is always assumed to be normal to the cell faces. This leads to smearing of shock and shear waves when these are not grid-aligned. Multi-directional methods, in which upwind-biased fluxes are computed in a frame aligned with a dominant wave, overcome this problem, but at the expense of robustness. The same is true for the schemes incorporating a multi-dimensional wave model not based on multi-dimensional data but on an 'educated guess' of what they could be. The fluctuation approach offers the best possibilities for the development of genuinely multi-dimensional upwind schemes. Three building blocks are needed for such schemes: a wave model, a way to achieve conservation, and a compact convection scheme. Recent advances in each of these components are discussed; putting them all together is the present focus of a worldwide research effort. Some numerical results are presented, illustrating the potential of the new multi-dimensional schemes.

Minimum Action Path Theory Reveals the Details of Stochastic Transitions Out of Oscillatory States

NASA Astrophysics Data System (ADS)

de la Cruz, Roberto; Perez-Carrasco, Ruben; Guerrero, Pilar; Alarcon, Tomas; Page, Karen M.

2018-03-01

Cell state determination is the outcome of intrinsically stochastic biochemical reactions. Transitions between such states are studied as noise-driven escape problems in the chemical species space. Escape can occur via multiple possible multidimensional paths, with probabilities depending nonlocally on the noise. Here we characterize the escape from an oscillatory biochemical state by minimizing the Freidlin-Wentzell action, deriving from it the stochastic spiral exit path from the limit cycle. We also use the minimized action to infer the escape time probability density function.

Minimum Action Path Theory Reveals the Details of Stochastic Transitions Out of Oscillatory States.

PubMed

de la Cruz, Roberto; Perez-Carrasco, Ruben; Guerrero, Pilar; Alarcon, Tomas; Page, Karen M

2018-03-23

Cell state determination is the outcome of intrinsically stochastic biochemical reactions. Transitions between such states are studied as noise-driven escape problems in the chemical species space. Escape can occur via multiple possible multidimensional paths, with probabilities depending nonlocally on the noise. Here we characterize the escape from an oscillatory biochemical state by minimizing the Freidlin-Wentzell action, deriving from it the stochastic spiral exit path from the limit cycle. We also use the minimized action to infer the escape time probability density function.

LC-MS of Metmyoglobin at pH = 2: Separation and Characterization of Apomyoglobin and Heme by ESI-MS and UV-Vis

ERIC Educational Resources Information Center

Stynes, Helen Cleary; Layo, Araceli; Smith, Richard W.

2004-01-01

The protein species of apomyoglobin (apoMb) and heme are freed and segregated from the aqueous protein solution of metmyoglobin by liquid chromatography, and are distinguished by UV-Vis absorption or electrospray ionization mass spectrometry (ESI-MS). This is an ingenious and effective approach to characterize apomyoglobin and heme, while students…

Identification of candidate angiogenic inhibitors processed by matrix metalloproteinase 2 (MMP-2) in cell-based proteomic screens: disruption of vascular endothelial growth factor (VEGF)/heparin affin regulatory peptide (pleiotrophin) and VEGF/Connective tissue growth factor angiogenic inhibitory complexes by MMP-2 proteolysis.

PubMed

Dean, Richard A; Butler, Georgina S; Hamma-Kourbali, Yamina; Delbé, Jean; Brigstock, David R; Courty, José; Overall, Christopher M

2007-12-01

Matrix metalloproteinases (MMPs) exert both pro- and antiangiogenic functions by the release of cytokines or proteolytically generated angiogenic inhibitors from extracellular matrix and basement membrane remodeling. In the Mmp2-/- mouse neovascularization is greatly reduced, but the mechanistic aspects of this remain unclear. Using isotope-coded affinity tag labeling of proteins analyzed by multidimensional liquid chromatography and tandem mass spectrometry we explored proteome differences between Mmp2-/- cells and those rescued by MMP-2 transfection. Proteome signatures that are hallmarks of proteolysis revealed cleavage of many known MMP-2 substrates in the cellular context. Proteomic evidence of MMP-2 processing of novel substrates was found. Insulin-like growth factor binding protein 6, follistatin-like 1, and cystatin C protein cleavage by MMP-2 was biochemically confirmed, and the cleavage sites in heparin affin regulatory peptide (HARP; pleiotrophin) and connective tissue growth factor (CTGF) were sequenced by matrix-assisted laser desorption ionization-time of flight mass spectrometry. MMP-2 processing of HARP and CTGF released vascular endothelial growth factor (VEGF) from angiogenic inhibitory complexes. The cleaved HARP N-terminal domain increased HARP-induced cell proliferation, whereas the HARP C-terminal domain was antagonistic and decreased cell proliferation and migration. Hence the unmasking of cytokines, such as VEGF, by metalloproteinase processing of their binding proteins is a new mechanism in the control of cytokine activation and angiogenesis.

Editorial overview: Omics

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

Barran, Perdita; Baker, Erin

The great complexity of biological systems and their environment poses similarly vast challenges for accurate analytical evaluations of their identity, structure and quantity. Post genomic science, has predicted much regarding the static populations of biological systems, but a further challenge for analysis is to test the accuracy of these predictions, as well as provide a better representation of the transient nature of the molecules of life. Accurate measurements of biological systems have wide applications for biological, forensic, biotechnological and healthcare fields. Therefore, the holy grail is to find a technique which can identify and quantify biological molecules with high throughput,more » sensitivity and robustness, as well evaluate molecular structure(s) in order to understand how the specific molecules interact and function. While wrapping all of these characteristics into one platform may sound difficult, ion mobility spectrometry (IMS) is addressing all of these challenges. Over the last decade, the number of analytical studies utilizing IMS for the evaluation of complex biological and environmental samples has greatly increased. In most cases IMS is coupled with mass spectrometry (IM-MS), but even alone IMS provides the unique capability of rapidly assessing a molecule’s structure, which can be extremely difficult with other techniques. The robustness of the IMS measurement is bourne out by its widespread use in security, environmental and military applications. The multidimensional IM-MS measurements however have been proven to be ever more powerful, as applied to complex mixtures as they enable the evaluation of both the structure and mass of every molecular component in a sample during a single measurement, without the need for continual reference calibration.« less

Identification of Candidate Angiogenic Inhibitors Processed by Matrix Metalloproteinase 2 (MMP-2) in Cell-Based Proteomic Screens: Disruption of Vascular Endothelial Growth Factor (VEGF)/Heparin Affin Regulatory Peptide (Pleiotrophin) and VEGF/Connective Tissue Growth Factor Angiogenic Inhibitory Complexes by MMP-2 Proteolysis▿ †

PubMed Central

Dean, Richard A.; Butler, Georgina S.; Hamma-Kourbali, Yamina; Delbé, Jean; Brigstock, David R.; Courty, José; Overall, Christopher M.

2007-01-01

Matrix metalloproteinases (MMPs) exert both pro- and antiangiogenic functions by the release of cytokines or proteolytically generated angiogenic inhibitors from extracellular matrix and basement membrane remodeling. In the Mmp2−/− mouse neovascularization is greatly reduced, but the mechanistic aspects of this remain unclear. Using isotope-coded affinity tag labeling of proteins analyzed by multidimensional liquid chromatography and tandem mass spectrometry we explored proteome differences between Mmp2−/− cells and those rescued by MMP-2 transfection. Proteome signatures that are hallmarks of proteolysis revealed cleavage of many known MMP-2 substrates in the cellular context. Proteomic evidence of MMP-2 processing of novel substrates was found. Insulin-like growth factor binding protein 6, follistatin-like 1, and cystatin C protein cleavage by MMP-2 was biochemically confirmed, and the cleavage sites in heparin affin regulatory peptide (HARP; pleiotrophin) and connective tissue growth factor (CTGF) were sequenced by matrix-assisted laser desorption ionization-time of flight mass spectrometry. MMP-2 processing of HARP and CTGF released vascular endothelial growth factor (VEGF) from angiogenic inhibitory complexes. The cleaved HARP N-terminal domain increased HARP-induced cell proliferation, whereas the HARP C-terminal domain was antagonistic and decreased cell proliferation and migration. Hence the unmasking of cytokines, such as VEGF, by metalloproteinase processing of their binding proteins is a new mechanism in the control of cytokine activation and angiogenesis. PMID:17908800

Recent development in mass spectrometry and its hyphenated techniques for the analysis of medicinal plants.

PubMed

Zhu, Ming-Zhi; Chen, Gui-Lin; Wu, Jian-Lin; Li, Na; Liu, Zhong-Hua; Guo, Ming-Quan

2018-04-23

Medicinal plants are gaining increasing attention worldwide due to their empirical therapeutic efficacy and being a huge natural compound pool for new drug discovery and development. The efficacy, safety and quality of medicinal plants are the main concerns, which are highly dependent on the comprehensive analysis of chemical components in the medicinal plants. With the advances in mass spectrometry (MS) techniques, comprehensive analysis and fast identification of complex phytochemical components have become feasible, and may meet the needs, for the analysis of medicinal plants. Our aim is to provide an overview on the latest developments in MS and its hyphenated technique and their applications for the comprehensive analysis of medicinal plants. Application of various MS and its hyphenated techniques for the analysis of medicinal plants, including but not limited to one-dimensional chromatography, multiple-dimensional chromatography coupled to MS, ambient ionisation MS, and mass spectral database, have been reviewed and compared in this work. Recent advancs in MS and its hyphenated techniques have made MS one of the most powerful tools for the analysis of complex extracts from medicinal plants due to its excellent separation and identification ability, high sensitivity and resolution, and wide detection dynamic range. To achieve high-throughput or multi-dimensional analysis of medicinal plants, the state-of-the-art MS and its hyphenated techniques have played, and will continue to play a great role in being the major platform for their further research in order to obtain insight into both their empirical therapeutic efficacy and quality control. Copyright © 2018 John Wiley & Sons, Ltd.

Mass Spectrometry Imaging for the Investigation of Intratumor Heterogeneity.

PubMed

Balluff, B; Hanselmann, M; Heeren, R M A

2017-01-01

One of the big clinical challenges in the treatment of cancer is the different behavior of cancer patients under guideline therapy. An important determinant for this phenomenon has been identified as inter- and intratumor heterogeneity. While intertumor heterogeneity refers to the differences in cancer characteristics between patients, intratumor heterogeneity refers to the clonal and nongenetic molecular diversity within a patient. The deciphering of intratumor heterogeneity is recognized as key to the development of novel therapeutics or treatment regimens. The investigation of intratumor heterogeneity is challenging since it requires an untargeted molecular analysis technique that accounts for the spatial and temporal dynamics of the tumor. So far, next-generation sequencing has contributed most to the understanding of clonal evolution within a cancer patient. However, it falls short in accounting for the spatial dimension. Mass spectrometry imaging (MSI) is a powerful tool for the untargeted but spatially resolved molecular analysis of biological tissues such as solid tumors. As it provides multidimensional datasets by the parallel acquisition of hundreds of mass channels, multivariate data analysis methods can be applied for the automated annotation of tissues. Moreover, it integrates the histology of the sample, which enables studying the molecular information in a histopathological context. This chapter will illustrate how MSI in combination with statistical methods and histology has been used for the description and discovery of intratumor heterogeneity in different cancers. This will give evidence that MSI constitutes a unique tool for the investigation of intratumor heterogeneity, and could hence become a key technology in cancer research. © 2017 Elsevier Inc. All rights reserved.

A Mass Spectrometry Study of Isotope Separation in the Laser Plume

NASA Astrophysics Data System (ADS)

Suen, Timothy Wu

Accurate quantification of isotope ratios is critical for both preventing the development of illicit weapons programs in nuclear safeguards and identifying the source of smuggled material in nuclear forensics. While isotope analysis has traditionally been performed by mass spectrometry, the need for in situ measurements has prompted the development of optical techniques, such as laser-induced breakdown spectroscopy (LIBS) and laser ablation molecular isotopic spectrometry (LAMIS). These optical measurements rely on laser ablation for direct solid sampling, but several past studies have suggested that the distribution of isotopes in the ablation plume is not uniform. This study seeks to characterize isotope separation in the laser plume through the use of orthogonal-acceleration time-of-flight mass spectrometry. A silver foil was ablated with a Nd:YAG at 355 nm at an energy of 50 muJ with a spot size of 71 mum, for a fluence of 1.3 J/cm2 and an irradiance of 250 MW/cm2. Flat-plate repellers were used to sample the plume, and a temporal profile of the ions was obtained by varying the time delay on the high-voltage pulse. A spatial profile along the axis of the plume was generated by changing the position of the sample, which yielded snapshots of the isotopic composition with time. In addition, the reflectron time-of-flight system was used as an energy filter in conjunction with the repellers to sample slices of the laser plasma orthogonal to the plume axis. Mass spectrometry of the plume revealed a fast ion distribution and a slow ion distribution. Measurements taken across the entire plume showed the fast 109Ag ions slightly ahead in both space and time, causing the 107Ag fraction to drop to 0.34 at 3 mus, 4 mm from the sample surface. Although measurements centered on the near side of the plume did not show isotope separation, the slow ions on the far side of the plume included much more 109Ag than 107Ag. In addition to examining the isotope content of the ablation plume, this study has developed a mass spectrometry characterization technique that may be useful for investigating chemical reactions during laser ablation.

Multivariate proteomic profiling identifies novel accessory proteins of coated vesicles

PubMed Central

Antrobus, Robin; Hirst, Jennifer; Bhumbra, Gary S.; Kozik, Patrycja; Jackson, Lauren P.; Sahlender, Daniela A.

2012-01-01

Despite recent advances in mass spectrometry, proteomic characterization of transport vesicles remains challenging. Here, we describe a multivariate proteomics approach to analyzing clathrin-coated vesicles (CCVs) from HeLa cells. siRNA knockdown of coat components and different fractionation protocols were used to obtain modified coated vesicle-enriched fractions, which were compared by stable isotope labeling of amino acids in cell culture (SILAC)-based quantitative mass spectrometry. 10 datasets were combined through principal component analysis into a “profiling” cluster analysis. Overall, 136 CCV-associated proteins were predicted, including 36 new proteins. The method identified >93% of established CCV coat proteins and assigned >91% correctly to intracellular or endocytic CCVs. Furthermore, the profiling analysis extends to less well characterized types of coated vesicles, and we identify and characterize the first AP-4 accessory protein, which we have named tepsin. Finally, our data explain how sequestration of TACC3 in cytosolic clathrin cages causes the severe mitotic defects observed in auxilin-depleted cells. The profiling approach can be adapted to address related cell and systems biological questions. PMID:22472443

Selective ionization of dissolved organic nitrogen by positive ion atmospheric pressure photoionization coupled with Fourier transform ion cyclotron resonance mass spectrometry.

PubMed

Podgorski, David C; McKenna, Amy M; Rodgers, Ryan P; Marshall, Alan G; Cooper, William T

2012-06-05

Dissolved organic nitrogen (DON) comprises a heterogeneous family of organic compounds that includes both well-known biomolecules such as urea or amino acids and more complex, less characterized compounds such as humic and fulvic acids. Typically, DON represents only a small fraction of the total dissolved organic carbon pool and therefore presents inherent problems for chemical analysis and characterization. Here, we demonstrate that DON may be selectively ionized by atmospheric pressure photionization (APPI) and characterized at the molecular level by Fourier transform ion cyclotron resonance mass spectrometry. Unlike electrospray ionization (ESI), APPI ionizes polar and nonpolar compounds, and ionization efficiency is not determined by polarity. APPI is tolerant to salts, due to the thermal treatment inherent to nebulization, and thus avoids salt-adduct formation that can complicate ESI mass spectra. Here, for dissolved organic matter from various aquatic environments, we selectively ionize DON species that are not efficiently ionized by other ionization techniques and demonstrate significant signal-to-noise increase for nitrogen species by use of APPI relative to ESI.

Characterization of carotenoids and carotenoid esters in red pepper pods (Capsicum annuum L.) by high-performance liquid chromatography/atmospheric pressure chemical ionization mass spectrometry.

PubMed

Schweiggert, Ute; Kammerer, Dietmar R; Carle, Reinhold; Schieber, Andreas

2005-01-01

Carotenoids and carotenoid esters were extracted from red pepper pods (Capsicum annuum L.) without saponification. Among the 42 compounds detected, 4 non-esterified, 11 mono- and 17 diesters were characterized based on their retention times, UV/Vis spectra and their fragmentation patterns in collision-induced dissociation experiments in atmospheric pressure chemical ionization mass spectrometry (APCI-MS). Positive and negative ion mode measurements were used for the characterization of major and minor carotenoids and their esters. Capsanthin esterified with lauric, palmitic and myristic acids represented the predominant compounds in the red pepper extracts. Additionally, three beta-cryptoxanthin and one zeaxanthin monoester were tentatively identified in red pepper pods for the first time. Furthermore, the specific fragmentation patterns of capsanthin-laurate-myristate and capsanthin-myristate-palmitate were used for the distinction of both regioisomers. The results obtained from LC-DAD-APCI-MSn experiments demonstrated that the carotenoid profile of red pepper pods is considerably more complex than considered hitherto. Copyright (c) 2005 John Wiley & Sons, Ltd.

Unravelling the mysteries of sub-second biochemical processes using time-resolved mass spectrometry.

PubMed

Lento, Cristina; Wilson, Derek J

2017-05-21

Many important chemical and biochemical phenomena proceed on sub-second time scales before entering equilibrium. In this mini-review, we explore the history and recent advancements of time-resolved mass spectrometry (TRMS) for the characterization of millisecond time-scale chemical reactions and biochemical processes. TRMS allows for the simultaneous tracking of multiple reactants, intermediates and products with no chromophoric species required, high sensitivity and temporal resolution. The method has most recently been used for the characterization of several short-lived reaction intermediates in rapid chemical reactions. Most of the reactions that occur in living organisms are accelerated by enzymes, with pre-steady state kinetics only attainable using time-resolved methods. TRMS has been increasingly used to monitor the conversion of substrates to products and the resulting changes to the enzyme during catalytic turnover. Early events in protein folding systems have also been elucidated, along with the characterization of dynamics and transient secondary structures in intrinsically disordered proteins. In this review, we will highlight representative examples where TRMS has been applied to study these phenomena.

Characterizing plant cell wall derived oligosaccharides using hydrophilic interaction chromatography with mass spectrometry detection.

PubMed

Leijdekkers, A G M; Sanders, M G; Schols, H A; Gruppen, H

2011-12-23

Analysis of complex mixtures of plant cell wall derived oligosaccharides is still challenging and multiple analytical techniques are often required for separation and characterization of these mixtures. In this work it is demonstrated that hydrophilic interaction chromatography coupled with evaporative light scattering and mass spectrometry detection (HILIC-ELSD-MS(n)) is a valuable tool for identification of a wide range of neutral and acidic cell wall derived oligosaccharides. The separation potential for acidic oligosaccharides observed with HILIC is much better compared to other existing techniques, like capillary electrophoresis, reversed phase and porous-graphitized carbon chromatography. Important structural information, such as presence of methyl esters and acetyl groups, is retained during analysis. Separation of acidic oligosaccharides with equal charge yet with different degrees of polymerization can be obtained. The efficient coupling of HILIC with ELSD and MS(n)-detection enables characterization and quantification of many different oligosaccharide structures present in complex mixtures. This makes HILIC-ELSD-MS(n) a versatile and powerful additional technique in plant cell wall analysis. Copyright © 2011 Elsevier B.V. All rights reserved.

Optimization of microwave-assisted extraction for the characterization of olive leaf phenolic compounds by using HPLC-ESI-TOF-MS/IT-MS(2).

PubMed

Taamalli, Amani; Arráez-Román, David; Ibañez, Elena; Zarrouk, Mokhtar; Segura-Carretero, Antonio; Fernández-Gutiérrez, Alberto

2012-01-25

In the present work, a simple and rapid method for the extraction of phenolic compounds from olive leaves, using microwave-assisted extraction (MAE) technique, has been developed. The experimental variables that affect the MAE process, such as the solvent type and composition, microwave temperature, and extraction time, were optimized using a univariate method. The obtained extracts were analyzed by using high-performance liquid chromatography (HPLC) coupled to electrospray time-of-flight mass spectrometry (ESI-TOF-MS) and electrospray ion trap tandem mass spectrometry (ESI-IT-MS(2)) to prove the MAE extraction efficiency. The optimal MAE conditions were methanol:water (80:20, v/v) as extracting solvent, at a temperature equal to 80 °C for 6 min. Under these conditions, several phenolic compounds could be characterized by HPLC-ESI-MS/MS(2). As compared to the conventional method, MAE can be used as an alternative extraction method for the characterization of phenolic compounds from olive leaves due to its efficiency and speed.

Characterization of isochlorogenic acid A metabolites in rats using high-performance liquid chromatography/quadrupole time-of-flight mass spectrometry.

PubMed

Wang, Jing; Cao, Guoxiu; Wang, Hong; Ye, Hui; Zhong, Yunxi; Wang, Guangji; Hao, Haiping

2017-08-01

Isochlorogenic acid A is widely present in fruits, vegetables and herbal medicines, and is characterized by anti-inflammatory, hepatoprotective and antiviral properties. However, little is known about its metabolic fate and pharmacokinetic properties. This study is thus designed to investigate the metabolic fate of isochlorogenic acid A. An analytical method based on high-performance liquid chromatography/quadrupole time-of-flight mass spectrometry (HPLC/Q-TOF MS) was established to characterize the metabolites of isochlorogenic acid A in the plasma, urine and feces of rats. A total of 32 metabolites were identified. The metabolic pathways mainly include hydrolyzation, dehydroxylation, hydrogenation and conjugation with methyl, glucuronic acid, glycine, sulfate, glutathione and cysteine. Moreover, the pharmacokinetic profiles of all the circulating metabolites were investigated. M11 resulting from hydrolyzation, dehydroxylation and hydrogenation was the dominant circulating metabolite after the intragastric administration of isochlorogenic acid A. The results obtained will be useful for further study of elucidating potential bioactive metabolites which can provide better explanation of the pharmacological and/or toxicological effects of this compound. Copyright © 2017 John Wiley & Sons, Ltd.

Equating Multidimensional Tests under a Random Groups Design: A Comparison of Various Equating Procedures

ERIC Educational Resources Information Center

Lee, Eunjung

2013-01-01

The purpose of this research was to compare the equating performance of various equating procedures for the multidimensional tests. To examine the various equating procedures, simulated data sets were used that were generated based on a multidimensional item response theory (MIRT) framework. Various equating procedures were examined, including…

Effect Size Measures for Differential Item Functioning in a Multidimensional IRT Model

ERIC Educational Resources Information Center

Suh, Youngsuk

2016-01-01

This study adapted an effect size measure used for studying differential item functioning (DIF) in unidimensional tests and extended the measure to multidimensional tests. Two effect size measures were considered in a multidimensional item response theory model: signed weighted P-difference and unsigned weighted P-difference. The performance of…

On Multidimensional Item Response Theory: A Coordinate-Free Approach. Research Report. ETS RR-07-30

ERIC Educational Resources Information Center

Antal, Tamás

2007-01-01

A coordinate-free definition of complex-structure multidimensional item response theory (MIRT) for dichotomously scored items is presented. The point of view taken emphasizes the possibilities and subtleties of understanding MIRT as a multidimensional extension of the classical unidimensional item response theory models. The main theorem of the…

The Definition of Difficulty and Discrimination for Multidimensional Item Response Theory Models.

ERIC Educational Resources Information Center

Reckase, Mark D.; McKinley, Robert L.

A study was undertaken to develop guidelines for the interpretation of the parameters of three multidimensional item response theory models and to determine the relationship between the parameters and traditional concepts of item difficulty and discrimination. The three models considered were multidimensional extensions of the one-, two-, and…

Bifactor Approach to Modeling Multidimensionality of Physical Self-Perception Profile

ERIC Educational Resources Information Center

Chung, ChihMing; Liao, Xiaolan; Song, Hairong; Lee, Taehun

2016-01-01

The multi-dimensionality of Physical Self-Perception Profile (PSPP) has been acknowledged by the use of correlated-factor model and second-order model. In this study, the authors critically endorse the bifactor model, as a substitute to address the multi-dimensionality of PSPP. To cross-validate the models, analyses are conducted first in…

Item Vector Plots for the Multidimensional Three-Parameter Logistic Model

ERIC Educational Resources Information Center

Bryant, Damon; Davis, Larry

2011-01-01

This brief technical note describes how to construct item vector plots for dichotomously scored items fitting the multidimensional three-parameter logistic model (M3PLM). As multidimensional item response theory (MIRT) shows promise of being a very useful framework in the test development life cycle, graphical tools that facilitate understanding…

Deriving Multidimensional Poverty Indicators: Methodological Issues and an Empirical Analysis for Italy

ERIC Educational Resources Information Center

Coromaldi, Manuela; Zoli, Mariangela

2012-01-01

Theoretical and empirical studies have recently adopted a multidimensional concept of poverty. There is considerable debate about the most appropriate degree of multidimensionality to retain in the analysis. In this work we add to the received literature in two ways. First, we derive indicators of multiple deprivation by applying a particular…

Evaluating Item Fit for Multidimensional Item Response Models

ERIC Educational Resources Information Center

Zhang, Bo; Stone, Clement A.

2008-01-01

This research examines the utility of the s-x[superscript 2] statistic proposed by Orlando and Thissen (2000) in evaluating item fit for multidimensional item response models. Monte Carlo simulation was conducted to investigate both the Type I error and statistical power of this fit statistic in analyzing two kinds of multidimensional test…

A Multidimensional Scaling Approach to Dimensionality Assessment for Measurement Instruments Modeled by Multidimensional Item Response Theory

ERIC Educational Resources Information Center

Toro, Maritsa

2011-01-01

The statistical assessment of dimensionality provides evidence of the underlying constructs measured by a survey or test instrument. This study focuses on educational measurement, specifically tests comprised of items described as multidimensional. That is, items that require examinee proficiency in multiple content areas and/or multiple cognitive…

Perceptual Salience and Children's Multidimensional Problem Solving

ERIC Educational Resources Information Center

Odom, Richard D.; Corbin, David W.

1973-01-01

Uni- and multidimensional processing of 6- to 9-year olds was studied using recall tasks in which an array of stimuli was reconstructed to match a model array. Results indicated that both age groups were able to solve multidimensional problems, but that solution rate was retarded by the unidimensional processing of highly salient dimensions.…

The Multidimensional Attitudes Scale toward Persons with Disabilities (MAS): Construction and Validation

ERIC Educational Resources Information Center

Findler, Liora; Vilchinsky, Noa; Werner, Shirli

2007-01-01

This study presents the development of a new instrument, the "Multidimensional Attitudes Scale Toward Persons With Disabilities" (MAS). Based on the multidimensional approach, it posits that attitudes are composed of three dimensions: affect, cognition, and behavior. The scale was distributed to a sample of 132 people along with a…

Covalent Organic Frameworks as a Platform for Multidimensional Polymerization.

PubMed

Bisbey, Ryan P; Dichtel, William R

2017-06-28

The simultaneous polymerization and crystallization of monomers featuring directional bonding designs provides covalent organic frameworks (COFs), which are periodic polymer networks with robust covalent bonds arranged in two- or three-dimensional topologies. The range of properties characterized in COFs has rapidly expanded to include those of interest for heterogeneous catalysis, energy storage and photovoltaic devices, and proton-conducting membranes. Yet many of these applications will require materials quality, morphological control, and synthetic efficiency exceeding the capabilities of contemporary synthetic methods. This level of control will emerge from an improved fundamental understanding of COF nucleation and growth processes. More powerful characterization of structure and defects, improved syntheses guided by mechanistic understanding, and accessing diverse isolated forms, ranging from single crystals to thin films to colloidal suspensions, remain important frontier problems.

Covalent Organic Frameworks as a Platform for Multidimensional Polymerization

PubMed Central

2017-01-01

The simultaneous polymerization and crystallization of monomers featuring directional bonding designs provides covalent organic frameworks (COFs), which are periodic polymer networks with robust covalent bonds arranged in two- or three-dimensional topologies. The range of properties characterized in COFs has rapidly expanded to include those of interest for heterogeneous catalysis, energy storage and photovoltaic devices, and proton-conducting membranes. Yet many of these applications will require materials quality, morphological control, and synthetic efficiency exceeding the capabilities of contemporary synthetic methods. This level of control will emerge from an improved fundamental understanding of COF nucleation and growth processes. More powerful characterization of structure and defects, improved syntheses guided by mechanistic understanding, and accessing diverse isolated forms, ranging from single crystals to thin films to colloidal suspensions, remain important frontier problems. PMID:28691064

The Extraction of One-Dimensional Flow Properties from Multi-Dimensional Data Sets

NASA Technical Reports Server (NTRS)

Baurle, Robert A.; Gaffney, Richard L., Jr.

2007-01-01

The engineering design and analysis of air-breathing propulsion systems relies heavily on zero- or one-dimensional properties (e.g. thrust, total pressure recovery, mixing and combustion efficiency, etc.) for figures of merit. The extraction of these parameters from experimental data sets and/or multi-dimensional computational data sets is therefore an important aspect of the design process. A variety of methods exist for extracting performance measures from multi-dimensional data sets. Some of the information contained in the multi-dimensional flow is inevitably lost when any one-dimensionalization technique is applied. Hence, the unique assumptions associated with a given approach may result in one-dimensional properties that are significantly different than those extracted using alternative approaches. The purpose of this effort is to examine some of the more popular methods used for the extraction of performance measures from multi-dimensional data sets, reveal the strengths and weaknesses of each approach, and highlight various numerical issues that result when mapping data from a multi-dimensional space to a space of one dimension.

The Art of Extracting One-Dimensional Flow Properties from Multi-Dimensional Data Sets

NASA Technical Reports Server (NTRS)

Baurle, R. A.; Gaffney, R. L.

2007-01-01

The engineering design and analysis of air-breathing propulsion systems relies heavily on zero- or one-dimensional properties (e:g: thrust, total pressure recovery, mixing and combustion efficiency, etc.) for figures of merit. The extraction of these parameters from experimental data sets and/or multi-dimensional computational data sets is therefore an important aspect of the design process. A variety of methods exist for extracting performance measures from multi-dimensional data sets. Some of the information contained in the multi-dimensional flow is inevitably lost when any one-dimensionalization technique is applied. Hence, the unique assumptions associated with a given approach may result in one-dimensional properties that are significantly different than those extracted using alternative approaches. The purpose of this effort is to examine some of the more popular methods used for the extraction of performance measures from multi-dimensional data sets, reveal the strengths and weaknesses of each approach, and highlight various numerical issues that result when mapping data from a multi-dimensional space to a space of one dimension.