Mass spectrometry-based proteomics: from cancer biology to protein biomarkers, drug targets, and clinical applications.

PubMed

Jimenez, Connie R; Verheul, Henk M W

2014-01-01

Proteomics is optimally suited to bridge the gap between genomic information on the one hand and biologic functions and disease phenotypes at the other, since it studies the expression and/or post-translational modification (especially phosphorylation) of proteins--the major cellular players bringing about cellular functions--at a global level in biologic specimens. Mass spectrometry technology and (bio)informatic tools have matured to the extent that they can provide high-throughput, comprehensive, and quantitative protein inventories of cells, tissues, and biofluids in clinical samples at low level. In this article, we focus on next-generation proteomics employing nanoliquid chromatography coupled to high-resolution tandem mass spectrometry for in-depth (phospho)protein profiling of tumor tissues and (proximal) biofluids, with a focus on studies employing clinical material. In addition, we highlight emerging proteogenomic approaches for the identification of tumor-specific protein variants, and targeted multiplex mass spectrometry strategies for large-scale biomarker validation. Below we provide a discussion of recent progress, some research highlights, and challenges that remain for clinical translation of proteomic discoveries.

Insights on the distribution of substitutions in spruce galactoglucomannan and its derivatives using integrated chemo-enzymatic deconstruction, chromatography and mass spectrometry.

PubMed

Liu, Jun; Leppänen, Ann-Sofie; Kisonen, Victor; Willför, Stefan; Xu, Chunlin; Vilaplana, Francisco

2018-06-01

Accurate determination of the distribution of substitutions in the primary molecular structure of heteropolysaccharides and their derivatives is a prerequisite for their increasing application in the pharmaceutical and biomedical fields, which is unfortunately hindered due to the lack of effective analytical techniques. Acetylated galactoglucomannan (GGM) is an abundant plant polysaccharide as the main hemicellulose in softwoods, and therefore constitutes an important renewable resource from lignocellulosic biomass for the development of bioactive and functional materials. Here we present a methodology for profiling the intramolecular structure of spruce GGM and its chemical derivatives (cationic, anionic, and benzoylated) by combining chemo-enzymatic hydrolysis, liquid chromatography, and mass spectrometry. Fast identification and qualitative mass profiling of GGM and its derivatives was conducted using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF-MS) and electrospray ionization mass spectrometry (ESI-MS). Tandem mass fragmentation analysis and its hyphenation with hydrophilic interaction liquid chromatography (HILIC-ESI-MS/MS) provide further insights on the substitution placement of the GGM oligosaccharides and its derivatives. This method will be useful in understanding the structure-function relationships of native GGM and their derivatives, and therefore facilitate their potential application. Copyright © 2018 Elsevier B.V. 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.

Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry: Mechanistic Studies and Methods for Improving the Structural Identification of Carbohydrates

PubMed Central

Lai, Yin-Hung; Wang, Yi-Sheng

2017-01-01

Although matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is one of the most widely used soft ionization methods for biomolecules, the lack of detailed understanding of ionization mechanisms restricts its application in the analysis of carbohydrates. Structural identification of carbohydrates achieved by MALDI mass spectrometry helps us to gain insights into biological functions and pathogenesis of disease. In this review, we highlight mechanistic details of MALDI, including both ionization and desorption. Strategies to improve the ion yield of carbohydrates are also reviewed. Furthermore, commonly used fragmentation methods to identify the structure are discussed. PMID:28959517

Cross-Linking and Mass Spectrometry Methodologies to Facilitate Structural Biology: Finding a Path through the Maze

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

Merkley, Eric D.; Cort, John R.; Adkins, Joshua N.

2013-09-01

Multiprotein complexes, rather than individual proteins, make up a large part of the biological macromolecular machinery of a cell. Understanding the structure and organization of these complexes is critical to understanding cellular function. Chemical cross-linking coupled with mass spectrometry is emerging as a complementary technique to traditional structural biology methods and can provide low-resolution structural information for a multitude of purposes, such as distance constraints in computational modeling of protein complexes. In this review, we discuss the experimental considerations for successful application of chemical cross-linking-mass spectrometry in biological studies and highlight three examples of such studies from the recent literature.more » These examples (as well as many others) illustrate the utility of a chemical cross-linking-mass spectrometry approach in facilitating structural analysis of large and challenging complexes.« less

Efficient Enrichment and Analysis of Vicinal-Diol-Containing Flavonoid Molecules Using Boronic-Acid-Functionalized Particles and Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry.

PubMed

Kim, Eunjin; Kang, Hyunook; Choi, Insung; Song, Jihyeon; Mok, Hyejung; Jung, Woong; Yeo, Woon-Seok

2018-05-09

Detection and quantitation of flavonoids are relatively difficult compared to those of other small-molecule analytes because flavonoids undergo rapid metabolic processes, resulting in their elimination from the body. Here, we report an efficient enrichment method for facilitating the analysis of vicinal-diol-containing flavonoid molecules using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. In our strategy, boronic-acid-functionalized polyacrylamide particles were used, where boronic acids bound to vicinal diols to form boronate monoesters at basic pH. This complex remained intact during the enrichment processes, and the vicinal-diol-containing flavonoids were easily separated by centrifugation and subsequent acidic treatments. The selectivity and limit of detection of our strategy were confirmed by mass spectrometry analysis, and the validity was assessed by performing the detection and quantitation of quercetin in mouse organs.

Structural characterisation of medically relevant protein assemblies by integrating mass spectrometry with computational modelling.

PubMed

Politis, Argyris; Schmidt, Carla

2018-03-20

Structural mass spectrometry with its various techniques is a powerful tool for the structural elucidation of medically relevant protein assemblies. It delivers information on the composition, stoichiometries, interactions and topologies of these assemblies. Most importantly it can deal with heterogeneous mixtures and assemblies which makes it universal among the conventional structural techniques. In this review we summarise recent advances and challenges in structural mass spectrometric techniques. We describe how the combination of the different mass spectrometry-based methods with computational strategies enable structural models at molecular levels of resolution. These models hold significant potential for helping us in characterizing the function of protein assemblies related to human health and disease. In this review we summarise the techniques of structural mass spectrometry often applied when studying protein-ligand complexes. We exemplify these techniques through recent examples from literature that helped in the understanding of medically relevant protein assemblies. We further provide a detailed introduction into various computational approaches that can be integrated with these mass spectrometric techniques. Last but not least we discuss case studies that integrated mass spectrometry and computational modelling approaches and yielded models of medically important protein assembly states such as fibrils and amyloids. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

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.

A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra.

PubMed

Kou, Qiang; Wu, Si; Tolic, Nikola; Paša-Tolic, Ljiljana; Liu, Yunlong; Liu, Xiaowen

2017-05-01

Although proteomics has rapidly developed in the past decade, researchers are still in the early stage of exploring the world of complex proteoforms, which are protein products with various primary structure alterations resulting from gene mutations, alternative splicing, post-translational modifications, and other biological processes. Proteoform identification is essential to mapping proteoforms to their biological functions as well as discovering novel proteoforms and new protein functions. Top-down mass spectrometry is the method of choice for identifying complex proteoforms because it provides a 'bird's eye view' of intact proteoforms. The combinatorial explosion of various alterations on a protein may result in billions of possible proteoforms, making proteoform identification a challenging computational problem. We propose a new data structure, called the mass graph, for efficient representation of proteoforms and design mass graph alignment algorithms. We developed TopMG, a mass graph-based software tool for proteoform identification by top-down mass spectrometry. Experiments on top-down mass spectrometry datasets showed that TopMG outperformed existing methods in identifying complex proteoforms. http://proteomics.informatics.iupui.edu/software/topmg/. xwliu@iupui.edu. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Joining Forces: Integrating Proteomics and Cross-linking with the Mass Spectrometry of Intact Complexes*

PubMed Central

Stengel, Florian; Aebersold, Ruedi; Robinson, Carol V.

2012-01-01

Protein assemblies are critical for cellular function and understanding their physical organization is the key aim of structural biology. However, applying conventional structural biology approaches is challenging for transient, dynamic, or polydisperse assemblies. There is therefore a growing demand for hybrid technologies that are able to complement classical structural biology methods and thereby broaden our arsenal for the study of these important complexes. Exciting new developments in the field of mass spectrometry and proteomics have added a new dimension to the study of protein-protein interactions and protein complex architecture. In this review, we focus on how complementary mass spectrometry-based techniques can greatly facilitate structural understanding of protein assemblies. PMID:22180098

Stability of high-mass molecular libraries: the role of the oligoporphyrin core

PubMed Central

Sezer, Uĝur; Schmid, Philipp; Felix, Lukas; Mayor, Marcel; Arndt, Markus

2015-01-01

Molecular beam techniques are a key to many experiments in physical chemistry and quantum optics. In particular, advanced matter-wave experiments with high-mass molecules profit from the availability of slow, neutral and mass-selected molecular beams that are sufficiently stable to remain intact during laser heating and photoionization mass spectrometry. We present experiments on the photostability with molecular libraries of tailored oligoporphyrins with masses up to 25 000 Da. We compare two fluoroalkylsulfanyl-functionalized libraries based on two different molecular cores that offer the same number of anchor points for functionalization but differ in their geometry and electronic properties. A pentaporphyrin core stabilizes a library of chemically well-defined molecules with more than 1600 atoms. They can be neutrally desorbed with velocities as low as 20 m/s and efficiently analyzed in photoionization mass spectrometry. Copyright © 2015 John Wiley & Sons, Ltd. PMID:25601698

[Identification and analysis of the proteins interacted with Prestin in cochlear outer hair cells of guinea pig].

PubMed

Luo, X; Wang, J Y; Zhang, F L; Xia, Y

2018-01-07

Objective: To explore the regulation and mechanism of Prestin protein by identifying the proteins interacted with Prestin in cochlear outer hair cell(OHC) and analyzing their biological function. Methods: Co-immunoprecipitation combined mass spectrometry technology was used to isolate and identify the proteins interacted with Prestin protein of OHC, bioinformatics was used to construct Prestin protein interaction network. The proteins interacted with Prestin in OHC of guinea pig were determined by matching primary interaction mass spectrometry with protein interaction network, and annotated their functions. Results: The results of co-immunoprecipitation combined with mass spectrometry showed that 116 kinds of credible proteins could interact with Prestin. By constructing Prestin protein interaction network, matching the results of mass spectrometry and analyzing of sub-cellular localization, eight kinds of proteins were confirmed that they interacted with Prestin directly, namely EEF2, HSP90AB1, FN1, FLNA, EEF1A1, HSP90B1, ATP5A1, and ERH, respectively, which were mainly involved in the synthesis and transportation, transmembrane folding and localization, structural stability and signal transduction of Prestin protein. Conclusion: EEF2, HSP90AB1, FN1, FLNA, EEF1A1, HSP90B1, ATP5A1 and ERH provide molecular basis for sensory amplification function of OHCs by participating in biotransformation, transmembrane folding and localization, signal transduction and other biological processes of Prestin protein.

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.

Recent advances in applying mass spectrometry and systems biology to determine brain dynamics.

PubMed

Scifo, Enzo; Calza, Giulio; Fuhrmann, Martin; Soliymani, Rabah; Baumann, Marc; Lalowski, Maciej

2017-06-01

Neurological disorders encompass various pathologies which disrupt normal brain physiology and function. Poor understanding of their underlying molecular mechanisms and their societal burden argues for the necessity of novel prevention strategies, early diagnostic techniques and alternative treatment options to reduce the scale of their expected increase. Areas covered: This review scrutinizes mass spectrometry based approaches used to investigate brain dynamics in various conditions, including neurodegenerative and neuropsychiatric disorders. Different proteomics workflows for isolation/enrichment of specific cell populations or brain regions, sample processing; mass spectrometry technologies, for differential proteome quantitation, analysis of post-translational modifications and imaging approaches in the brain are critically deliberated. Future directions, including analysis of cellular sub-compartments, targeted MS platforms (selected/parallel reaction monitoring) and use of mass cytometry are also discussed. Expert commentary: Here, we summarize and evaluate current mass spectrometry based approaches for determining brain dynamics in health and diseases states, with a focus on neurological disorders. Furthermore, we provide insight on current trends and new MS technologies with potential to improve this analysis.

Study of oxygen/tetraethoxysilane plasmas in a helicon reactor using optical emission spectroscopy and mass spectrometry

NASA Astrophysics Data System (ADS)

Aumaille, K.; Granier, A.; Schmidt, M.; Grolleau, B.; Vallée, C.; Turban, G.

2000-08-01

Oxygen/tetraethoxysilane (O2/TEOS) plasmas created in a low-pressure (2 mTorr) rf helicon reactor have been studied by optical emission spectroscopy and mass spectrometry as a function of the rf (13.56 MHz) power injected into the plasma, which is varied from 25 to 300 W. Complementary measurements for the interpretation of the mass spectrometric data have also been carried out using the threshold ionization mass spectrometry technique. It is shown that valuable information on the parent molecules is obtained by both optical emission spectroscopy and threshold ionization mass spectrometry techniques. At low rf power TEOS molecules and organic compounds like hydrocarbons (CH4, C2H2) and alcohols (CH3CH2OH) as well as H2, H2O, CO, O2, CO2 are observed. At high rf power TEOS and O2 molecules are totally or mostly depleted, the share of hydrocarbons decreases and carbon monoxide, carbon dioxide, water and hydrogen become the essential parts of the gas phase.

Mass Spectrometry Analysis of Spatial Protein Networks by Colocalization Analysis (COLA).

PubMed

Mardakheh, Faraz K

2017-01-01

A major challenge in systems biology is comprehensive mapping of protein interaction networks. Crucially, such interactions are often dynamic in nature, necessitating methods that can rapidly mine the interactome across varied conditions and treatments to reveal change in the interaction networks. Recently, we described a fast mass spectrometry-based method to reveal functional interactions in mammalian cells on a global scale, by revealing spatial colocalizations between proteins (COLA) (Mardakheh et al., Mol Biosyst 13:92-105, 2017). As protein localization and function are inherently linked, significant colocalization between two proteins is a strong indication for their functional interaction. COLA uses rapid complete subcellular fractionation, coupled with quantitative proteomics to generate a subcellular localization profile for each protein quantified by the mass spectrometer. Robust clustering is then applied to reveal significant similarities in protein localization profiles, indicative of colocalization.

Capillary electrophoresis-high resolution sector field inductively coupled plasma mass spectrometry.

PubMed

Sonke, Jeroen E; Salters, Vincent J M

2007-08-03

The background and applications of high resolution sector field inductively coupled plasma mass spectrometry (HR-ICP-MS) as a detector for capillary (CE) and gel electrophoretic separations are reviewed. Notable progress has been made in the fields of bioinorganic and environmental (geo-) chemistry. Metallomics, the study of metal species interactions and functions in biological systems, puts substantial technical demands on speciation analysis. The combination of high species resolving power (CE) and high sensitivity-high mass resolving power (HR-ICP-MS) provides a solid base to meet such demands.

A Phytochemical-Sensing Strategy Based on Mass Spectrometry Imaging and Metabolic Profiling for Understanding the Functionality of the Medicinal Herb Green Tea.

PubMed

Fujimura, Yoshinori; Miura, Daisuke; Tachibana, Hirofumi

2017-09-27

Low-molecular-weight phytochemicals have health benefits and reduce the risk of diseases, but the mechanisms underlying their activities have remained elusive because of the lack of a methodology that can easily visualize the exact behavior of such small molecules. Recently, we developed an in situ label-free imaging technique, called mass spectrometry imaging, for visualizing spatially-resolved biotransformations based on simultaneous mapping of the major bioactive green tea polyphenol and its phase II metabolites. In addition, we established a mass spectrometry-based metabolic profiling technique capable of evaluating the bioactivities of diverse green tea extracts, which contain multiple phytochemicals, by focusing on their compositional balances. This methodology allowed us to simultaneously evaluate the relative contributions of the multiple compounds present in a multicomponent system to its bioactivity. This review highlights small molecule-sensing techniques for visualizing the complex behaviors of herbal components and linking such information to an enhanced understanding of the functionalities of multicomponent medicinal herbs.

Laser ablation synthesis of arsenic-phosphide Asm Pn clusters from As-P mixtures. Laser desorption ionisation with quadrupole ion trap time-of-flight mass spectrometry: The mass spectrometer as a synthesizer.

PubMed

Kubáček, Pavel; Prokeš, Lubomír; Pamreddy, Annapurna; Peña-Méndez, Eladia María; Conde, José Elias; Alberti, Milan; Havel, Josef

2018-05-30

Only a few arsenic phosphides are known. A high potential for the generation of new compounds is offered by Laser Ablation Synthesis (LAS) and when Laser Desorption Ionization (LDI) is coupled with simultaneous Time-Of-Flight Mass Spectrometry (TOFMS), immediate identification of the clusters can be achieved. LAS was used for the generation of arsenic phosphides via laser ablation of phosphorus-arsenic mixtures while quadrupole ion trap time-of-flight mass spectrometry (QIT-TOFMS) was used to acquire the mass spectra. Many new As m P n ± clusters (479 binary and 369 mono-elemental) not yet described in the literature were generated in the gas phase and their stoichiometry determined. The likely structures for some of the observed clusters arbitrary selected (20) were computed by density functional theory (DFT) optimization. LAS is an advantageous approach for the generation of new As m P n clusters, while mass spectrometry was found to be an efficient technique for the determination of cluster stoichiometry. The results achieved might inspire the synthesis of new materials. Copyright © 2018 John Wiley & Sons, Ltd.

Functionalizing Microporous Membranes for Protein Purification and Protein Digestion

NASA Astrophysics Data System (ADS)

Dong, Jinlan; Bruening, Merlin L.

2015-07-01

This review examines advances in the functionalization of microporous membranes for protein purification and the development of protease-containing membranes for controlled protein digestion prior to mass spectrometry analysis. Recent studies confirm that membranes are superior to bead-based columns for rapid protein capture, presumably because convective mass transport in membrane pores rapidly brings proteins to binding sites. Modification of porous membranes with functional polymeric films or TiO2 nanoparticles yields materials that selectively capture species ranging from phosphopeptides to His-tagged proteins, and protein-binding capacities often exceed those of commercial beads. Thin membranes also provide a convenient framework for creating enzyme-containing reactors that afford control over residence times. With millisecond residence times, reactors with immobilized proteases limit protein digestion to increase sequence coverage in mass spectrometry analysis and facilitate elucidation of protein structures. This review emphasizes the advantages of membrane-based techniques and concludes with some challenges for their practical application.

Functionalizing Microporous Membranes for Protein Purification and Protein Digestion.

PubMed

Dong, Jinlan; Bruening, Merlin L

2015-01-01

This review examines advances in the functionalization of microporous membranes for protein purification and the development of protease-containing membranes for controlled protein digestion prior to mass spectrometry analysis. Recent studies confirm that membranes are superior to bead-based columns for rapid protein capture, presumably because convective mass transport in membrane pores rapidly brings proteins to binding sites. Modification of porous membranes with functional polymeric films or TiO₂ nanoparticles yields materials that selectively capture species ranging from phosphopeptides to His-tagged proteins, and protein-binding capacities often exceed those of commercial beads. Thin membranes also provide a convenient framework for creating enzyme-containing reactors that afford control over residence times. With millisecond residence times, reactors with immobilized proteases limit protein digestion to increase sequence coverage in mass spectrometry analysis and facilitate elucidation of protein structures. This review emphasizes the advantages of membrane-based techniques and concludes with some challenges for their practical application.

Carboxylic acid functional group analysis using constant neutral loss scanning-mass spectrometry.

PubMed

Dron, Julien; Eyglunent, Gregory; Temime-Roussel, Brice; Marchand, Nicolas; Wortham, Henri

2007-12-12

The present study describes the development of a new analytical technique for the functional group determination of the carboxylic moiety using atmospheric pressure chemical ionization-mass spectrometry (APCI-MS/MS) operated in the constant neutral loss scanning (CNLS) mode. Carboxylic groups were first derivatized into their corresponding methyl esters by reacting with BF3/methanol mix and the reaction mixture was then directly injected into the APCI chamber. The loss of methanol (m/z = 32 amu) resulting from the fragmentation of the protonated methyl esters was then monitored. Applying this method together with a statistical approach to reference mixtures containing 31 different carboxylic acids at randomly calculated concentrations demonstrated its suitability for quantitative functional group measurements with relative standard deviations below 15% and a detection limit of 0.005 mmol L(-1). Its applicability to environmental matrices was also shown through the determination of carboxylic acid concentrations inside atmospheric aerosol samples. To the best of our knowledge, it is the first time that the tandem mass spectrometry was successfully applied to functional group analysis, offering great perspectives in the characterization of complex mixtures which are prevailing in the field of environmental analysis as well as in the understanding of the chemical processes occurring in these matrices.

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

Application of mass spectrometry technologies for the discovery of low-molecular weight modulators of enzymes and protein-protein interactions.

PubMed

Zehender, Hartmut; Mayr, Lorenz M

2007-10-01

In recent years, mass spectrometry has gained widespread use as an assay and screening technology in drug discovery because it enables sensitive, label-free detection of low-molecular weight modulators of biomolecules as well as sensitive and accurate detection of high-molecular weight modifications of biomolecules. Electrospray and matrix-assisted laser desorption ionization are the most widely used ionization techniques to identify chemical compounds interfering with enzymatic function, receptor-ligand binding or molecules modulating a protein-protein interaction of interest. Mass spectrometry based techniques are no longer restricted to screening in biochemical assay systems but have now become also applicable to imaging of biomolecules and chemical compounds in cell-based assay systems and even in highly complex tissue sections.

Silver Coating for High-Mass-Accuracy Imaging Mass Spectrometry of Fingerprints on Nanostructured Silicon.

PubMed

Guinan, Taryn M; Gustafsson, Ove J R; McPhee, Gordon; Kobus, Hilton; Voelcker, Nicolas H

2015-11-17

Nanostructure imaging mass spectrometry (NIMS) using porous silicon (pSi) is a key technique for molecular imaging of exogenous and endogenous low molecular weight compounds from fingerprints. However, high-mass-accuracy NIMS can be difficult to achieve as time-of-flight (ToF) mass analyzers, which dominate the field, cannot sufficiently compensate for shifts in measured m/z values. Here, we show internal recalibration using a thin layer of silver (Ag) sputter-coated onto functionalized pSi substrates. NIMS peaks for several previously reported fingerprint components were selected and mass accuracy was compared to theoretical values. Mass accuracy was improved by more than an order of magnitude in several cases. This straightforward method should form part of the standard guidelines for NIMS studies for spatial characterization of small molecules.

Phonon-assisted field emission in silicon nanomembranes for time-of-flight mass spectrometry of proteins.

PubMed

Park, Jonghoo; Aksamija, Zlatan; Shin, Hyun-Cheol; Kim, Hyunseok; Blick, Robert H

2013-06-12

Time-of-flight (TOF) mass spectrometry has been considered as the method of choice for mass analysis of large intact biomolecules, which are ionized in low charge states by matrix-assisted-laser-desorption/ionization (MALDI). However, it remains predominantly restricted to the mass analysis of biomolecules with a mass below about 50,000 Da. This limitation mainly stems from the fact that the sensitivity of the standard detectors decreases with increasing ion mass. We describe here a new principle for ion detection in TOF mass spectrometry, which is based upon suspended silicon nanomembranes. Impinging ion packets on one side of the suspended silicon nanomembrane generate nonequilibrium phonons, which propagate quasi-diffusively and deliver thermal energy to electrons within the silicon nanomembrane. This enhances electron emission from the nanomembrane surface with an electric field applied to it. The nonequilibrium phonon-assisted field emission in the suspended nanomembrane connected to an effective cooling of the nanomembrane via field emission allows mass analysis of megadalton ions with high mass resolution at room temperature. The high resolution of the detector will give better insight into high mass proteins and their functions.

Computational analyses of spectral trees from electrospray multi-stage mass spectrometry to aid metabolite identification.

PubMed

Cao, Mingshu; Fraser, Karl; Rasmussen, Susanne

2013-10-31

Mass spectrometry coupled with chromatography has become the major technical platform in metabolomics. Aided by peak detection algorithms, the detected signals are characterized by mass-over-charge ratio (m/z) and retention time. Chemical identities often remain elusive for the majority of the signals. Multi-stage mass spectrometry based on electrospray ionization (ESI) allows collision-induced dissociation (CID) fragmentation of selected precursor ions. These fragment ions can assist in structural inference for metabolites of low molecular weight. Computational investigations of fragmentation spectra have increasingly received attention in metabolomics and various public databases house such data. We have developed an R package "iontree" that can capture, store and analyze MS2 and MS3 mass spectral data from high throughput metabolomics experiments. The package includes functions for ion tree construction, an algorithm (distMS2) for MS2 spectral comparison, and tools for building platform-independent ion tree (MS2/MS3) libraries. We have demonstrated the utilization of the package for the systematic analysis and annotation of fragmentation spectra collected in various metabolomics platforms, including direct infusion mass spectrometry, and liquid chromatography coupled with either low resolution or high resolution mass spectrometry. Assisted by the developed computational tools, we have demonstrated that spectral trees can provide informative evidence complementary to retention time and accurate mass to aid with annotating unknown peaks. These experimental spectral trees once subjected to a quality control process, can be used for querying public MS2 databases or de novo interpretation. The putatively annotated spectral trees can be readily incorporated into reference libraries for routine identification of metabolites.

POTAMOS mass spectrometry calculator: computer aided mass spectrometry to the post-translational modifications of proteins. A focus on histones.

PubMed

Vlachopanos, A; Soupsana, E; Politou, A S; Papamokos, G V

2014-12-01

Mass spectrometry is a widely used technique for protein identification and it has also become the method of choice in order to detect and characterize the post-translational modifications (PTMs) of proteins. Many software tools have been developed to deal with this complication. In this paper we introduce a new, free and user friendly online software tool, named POTAMOS Mass Spectrometry Calculator, which was developed in the open source application framework Ruby on Rails. It can provide calculated mass spectrometry data in a time saving manner, independently of instrumentation. In this web application we have focused on a well known protein family of histones whose PTMs are believed to play a crucial role in gene regulation, as suggested by the so called "histone code" hypothesis. The PTMs implemented in this software are: methylations of arginines and lysines, acetylations of lysines and phosphorylations of serines and threonines. The application is able to calculate the kind, the number and the combinations of the possible PTMs corresponding to a given peptide sequence and a given mass along with the full set of the unique primary structures produced by the possible distributions along the amino acid sequence. It can also calculate the masses and charges of a fragmented histone variant, which carries predefined modifications already implemented. Additional functionality is provided by the calculation of the masses of fragments produced upon protein cleavage by the proteolytic enzymes that are most widely used in proteomics studies. Copyright © 2014 Elsevier Ltd. All rights reserved.

Ranked solutions to a class of combinatorial optimizations—with applications in mass spectrometry based peptide sequencing and a variant of directed paths in random media

NASA Astrophysics Data System (ADS)

Doerr, Timothy P.; Alves, Gelio; Yu, Yi-Kuo

2005-08-01

Typical combinatorial optimizations are NP-hard; however, for a particular class of cost functions the corresponding combinatorial optimizations can be solved in polynomial time using the transfer matrix technique or, equivalently, the dynamic programming approach. This suggests a way to efficiently find approximate solutions-find a transformation that makes the cost function as similar as possible to that of the solvable class. After keeping many high-ranking solutions using the approximate cost function, one may then re-assess these solutions with the full cost function to find the best approximate solution. Under this approach, it is important to be able to assess the quality of the solutions obtained, e.g., by finding the true ranking of the kth best approximate solution when all possible solutions are considered exhaustively. To tackle this statistical issue, we provide a systematic method starting with a scaling function generated from the finite number of high-ranking solutions followed by a convergent iterative mapping. This method, useful in a variant of the directed paths in random media problem proposed here, can also provide a statistical significance assessment for one of the most important proteomic tasks-peptide sequencing using tandem mass spectrometry data. For directed paths in random media, the scaling function depends on the particular realization of randomness; in the mass spectrometry case, the scaling function is spectrum-specific.

Use of high-throughput mass spectrometry to elucidate host pathogen interactions in Salmonella

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

Rodland, Karin D.; Adkins, Joshua N.; Ansong, Charles

Capabilities in mass spectrometry are evolving rapidly, with recent improvements in sensitivity, data analysis, and most important, from the standpoint of this review, much higher throughput allowing analysis of many samples in a single day. This short review describes how these improvements in mass spectrometry can be used to dissect host-pathogen interactions using Salmonella as a model system. This approach enabled direct identification of the majority of annotated Salmonella proteins, quantitation of expression changes under various in vitro growth conditions, and new insights into virulence and expression of Salmonella proteins within host cell cells. One of the most significant findingsmore » is that a very high percentage of the all annotated genes (>20%) in Salmonella are regulated post-transcriptionally. In addition, new and unexpected interactions have been identified for several Salmonella virulence regulators that involve protein-protein interactions, suggesting additional functions of these regulators in coordinating virulence expression. Overall high throughput mass spectrometry provides a new view of pathogen-host interactions emphasizing the protein products and defining how protein interactions determine the outcome of infection.« less

Native Mass Spectrometry: What is in the Name?

NASA Astrophysics Data System (ADS)

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

2017-01-01

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

DC Potentials Applied to an End-cap Electrode of a 3-D Ion Trap for Enhanced MSn Functionality

PubMed Central

Prentice, Boone M.; Xu, Wei; Ouyang, Zheng; McLuckey, Scott A.

2010-01-01

The effects of the application of various DC magnitudes and polarities to an end-cap of a 3-D quadrupole ion trap throughout a mass spectrometry experiment were investigated. Application of a monopolar DC field was achieved by applying a DC potential to the exit end-cap electrode, while maintaining the entrance end-cap electrode at ground potential. Control over the monopolar DC magnitude and polarity during time periods associated with ion accumulation, mass analysis, ion isolation, ion/ion reaction, and ion activation can have various desirable effects. Included amongst these are increased ion capture efficiency, increased ion ejection efficiency during mass analysis, effective isolation of ions using lower AC resonance ejection amplitudes, improved temporal control of the overlap of oppositely charged ion populations, and the performance of “broad-band” collision induced dissociation (CID). These results suggest general means to improve the performance of the 3-D ion trap in a variety of mass spectrometry and tandem mass spectrometry experiments. PMID:21927573

Identification of Methanococcus Jannaschii Proteins in 2-D Gel Electrophoresis Patterns by Mass Spectrometry

DOE R&D Accomplishments Database

Liang, X.

1998-06-10

The genome of Methanococcus jannaschii has been sequenced completely and has been found to contain approximately 1,770 predicted protein-coding regions. When these coding regions are expressed and how their expression is regulated, however, remain open questions. In this work, mass spectrometry was combined with two-dimensional gel electrophoresis to identify which proteins the genes produce under different growth conditions, and thus investigate the regulation of genes responsible for functions characteristic of this thermophilic representative of the methanogenic Archaea.

Identification of the Phenol Functionality in Deprotonated Monomeric and Dimeric Lignin Degradation Products via Tandem Mass Spectrometry Based on Ion-Molecule Reactions with Diethylmethoxyborane

NASA Astrophysics Data System (ADS)

Zhu, Hanyu; Max, Joann P.; Marcum, Christopher L.; Luo, Hao; Abu-Omar, Mahdi M.; Kenttämaa, Hilkka I.

2016-11-01

Conversion of lignin into smaller molecules provides a promising alternate and sustainable source for the valuable chemicals currently derived from crude oil. Better understanding of the chemical composition of the resulting product mixtures is essential for the optimization of such conversion processes. However, these mixtures are complex and contain isomeric molecules with a wide variety of functionalities, which makes their characterization challenging. Tandem mass spectrometry based on ion-molecule reactions has proven to be a powerful tool in functional group identification and isomer differentiation for previously unknown compounds. This study demonstrates that the identification of the phenol functionality, the most commonly observed functionality in lignin degradation products, can be achieved via ion-molecule reactions between diethylmethoxyborane (DEMB) and the deprotonated analyte in the absence of strongly electron-withdrawing substituents in the ortho- and para-positions. Either a stable DEMB adduct or an adduct that has lost a methanol molecule (DEMB adduct-MeOH) is formed for these ions. Deprotonated phenols with an adjacent phenol or hydroxymethyl functionality or a conjugated carboxylic acid functionality can be identified based on the formation of DEMB adduct-MeOH. Deprotonated compounds not containing the phenol functionality and phenols containing an electron-withdrawing ortho- or para-substituent were found to be unreactive toward diethylmethoxyborane. Hence, certain deprotonated isomeric compounds with phenol and carboxylic acid, aldehyde, carboxylic acid ester, or nitro functionalities can be differentiated via these reactions. The above mass spectrometry method was successfully coupled with high-performance liquid chromatography for the analysis of a complex biomass degradation mixture.

Determination of atomic hydrogen in non-thermal hydrogen plasmas by means of molecular beam threshold ionization mass spectrometry.

PubMed

Wang, Wei-Guo; Xu, Yong; Yang, Xue-Feng; Wang, Wen-Chun; Zhu, Ai-Min

2005-01-01

Atomic hydrogen plays important roles in chemical vapor deposition of functional materials, plasma etching and new approaches to chemical synthesis of hydrogen-containing compounds. The present work reports experimental determinations of atomic hydrogen near the grounded electrode in medium-pressure dielectric barrier discharge hydrogen plasmas by means of molecular beam threshold ionization mass spectrometry (MB-TIMS). At certain discharge conditions (a.c. frequency of 24 kHz, 28 kV of peak-to-peak voltage), the measured hydrogen dissociation fraction is decreased from approximately 0.83% to approximately 0.14% as the hydrogen pressure increases from 2.0 to 14.0 Torr. A simulation method for extraction of the approximate electron beam energy distribution function in the mass spectrometer ionizer and a semi-quantitative approach to calibrate the mass discrimination effect caused by the supersonic beam formation and the mass spectrometer measurement are reported. Copyright 2005 John Wiley & Sons, Ltd.

Counting Molecules by Desorption Ionization and Mass Spectrometry/Mass Spectrometry.

ERIC Educational Resources Information Center

Cooks, R. G.; Busch, K. L.

1982-01-01

Discusses two newer methods in mass spectrometry and shows how they can increase signal and signal-to-noise ratios, respectively. The first method, desorption ionization (DI), increases sensitivity while the second method, mass spectrometry/mass spectrometry (MS/MS), increases specificity. Together, the two methods offer improved analytical…

Mass Spectrometry-based Approaches to Understand the Molecular Basis of Memory

NASA Astrophysics Data System (ADS)

Pontes, Arthur; de Sousa, Marcelo

2016-10-01

The central nervous system is responsible for an array of cognitive functions such as memory, learning, language and attention. These processes tend to take place in distinct brain regions; yet, they need to be integrated to give rise to adaptive or meaningful behavior. Since cognitive processes result from underlying cellular and molecular changes, genomics and transcriptomics assays have been applied to human and animal models to understand such events. Nevertheless, genes and RNAs are not the end products of most biological functions. In order to gain further insights toward the understanding of brain processes, the field of proteomics has been of increasing importance in the past years. Advancements in liquid chromatography-tandem mass spectrometry (LC-MS/MS) have enable the identification and quantification of thousand of proteins with high accuracy and sensitivity, fostering a revolution in the neurosciences. Herein, we review the molecular bases of explicit memory in the hippocampus. We outline the principles of mass spectrometry (MS)-based proteomics, highlighting the use of this analytical tool to study memory formation. In addition, we discuss MS-based targeted approaches as the future of protein analysis.

SILAC-Based Comparative Proteomic Analysis of Lysosomes from Mammalian Cells Using LC-MS/MS.

PubMed

Thelen, Melanie; Winter, Dominic; Braulke, Thomas; Gieselmann, Volkmar

2017-01-01

Mass spectrometry-based proteomics of lysosomal proteins has led to significant advances in understanding lysosomal function and pathology. The ever-increasing sensitivity and resolution of mass spectrometry in combination with labeling procedures which allow comparative quantitative proteomics can be applied to shed more light on the steadily increasing range of lysosomal functions. In addition, investigation of alterations in lysosomal protein composition in the many lysosomal storage diseases may yield further insights into the molecular pathology of these disorders. Here, we describe a protocol which allows to determine quantitative differences in the lysosomal proteome of cells which are genetically and/or biochemically different or have been exposed to certain stimuli. The method is based on stable isotope labeling of amino acids in cell culture (SILAC). Cells are exposed to superparamagnetic iron oxide particles which are endocytosed and delivered to lysosomes. After homogenization of cells, intact lysosomes are rapidly enriched by passing the cell homogenates over a magnetic column. Lysosomes are eluted after withdrawal of the magnetic field and subjected to mass spectrometry.

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.

Mass Spectrometry Imaging and GC-MS Profiling of the Mammalian Peripheral Sensory-Motor Circuit

NASA Astrophysics Data System (ADS)

Rubakhin, Stanislav S.; Ulanov, Alexander; Sweedler, Jonathan V.

2015-06-01

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) has evolved to become an effective discovery tool in science and clinical diagnostics. Here, chemical imaging approaches are applied to well-defined regions of the mammalian peripheral sensory-motor system, including the dorsal root ganglia (DRG) and adjacent nerves. By combining several MSI approaches, analyte coverage is increased and 195 distinct molecular features are observed. Principal component analysis suggests three chemically different regions within the sensory-motor system, with the DRG and adjacent nerve regions being the most distinct. Investigation of these regions using gas chromatography-mass spectrometry corroborate these findings and reveal important metabolic markers related to the observed differences. The heterogeneity of the structurally, physiologically, and functionally connected regions demonstrates the intricate chemical and spatial regulation of their chemical composition.

Characterizing virus-induced gene silencing at the cellular level with in situ multimodal imaging

DOE PAGES

Burkhow, Sadie J.; Stephens, Nicole M.; Mei, Yu; ...

2018-05-25

Reverse genetic strategies, such as virus-induced gene silencing, are powerful techniques to study gene function. Currently, there are few tools to study the spatial dependence of the consequences of gene silencing at the cellular level. Here, we report the use of multimodal Raman and mass spectrometry imaging to study the cellular-level biochemical changes that occur from silencing the phytoene desaturase ( pds) gene using a Foxtail mosaic virus (FoMV) vector in maize leaves. The multimodal imaging method allows the localized carotenoid distribution to be measured and reveals differences lost in the spatial average when analyzing a carotenoid extraction of themore » whole leaf. The nature of the Raman and mass spectrometry signals are complementary: silencing pds reduces the downstream carotenoid Raman signal and increases the phytoene mass spectrometry signal.« less

Sample collection and preparation of biofluids and extracts for gas chromatography-mass spectrometry.

PubMed

Emwas, Abdul-Hamid M; Al-Talla, Zeyad A; Kharbatia, Najeh M

2015-01-01

To maximize the utility of gas chromatography-mass spectrometry (GC-MS) in metabonomics research, all stages of the experimental design should be standardized, including sample collection, storage, preparation, and sample separation. Moreover, the prerequisite for any GC-MS analysis is that a compound must be volatile and thermally stable if it is to be analyzed using this technique. Since many metabolites are nonvolatile and polar in nature, they are not readily amenable to analysis by GC-MS and require initial chemical derivatization of the polar functional groups in order to reduce the polarity and to increase the thermal stability and volatility of the analytes. In this chapter, an overview is presented of the optimum approach to sample collection, storage, and preparation for gas chromatography-mass spectrometry-based metabonomics with particular focus on urine samples as example of biofluids.

Characterizing virus-induced gene silencing at the cellular level with in situ multimodal imaging

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

Burkhow, Sadie J.; Stephens, Nicole M.; Mei, Yu

Reverse genetic strategies, such as virus-induced gene silencing, are powerful techniques to study gene function. Currently, there are few tools to study the spatial dependence of the consequences of gene silencing at the cellular level. Here, we report the use of multimodal Raman and mass spectrometry imaging to study the cellular-level biochemical changes that occur from silencing the phytoene desaturase ( pds) gene using a Foxtail mosaic virus (FoMV) vector in maize leaves. The multimodal imaging method allows the localized carotenoid distribution to be measured and reveals differences lost in the spatial average when analyzing a carotenoid extraction of themore » whole leaf. The nature of the Raman and mass spectrometry signals are complementary: silencing pds reduces the downstream carotenoid Raman signal and increases the phytoene mass spectrometry signal.« less

Laser Ablation-Aerosol Mass Spectrometry-Chemical Ionization Mass Spectrometry for Ambient Surface Imaging

DOE PAGES

Berry, Jennifer L.; Day, Douglas A.; Elseberg, Tim; ...

2018-02-20

Mass spectrometry imaging is becoming an increasingly common analytical technique due to its ability to provide spatially resolved chemical information. In this paper, we report a novel imaging approach combining laser ablation with two mass spectrometric techniques, aerosol mass spectrometry and chemical ionization mass spectrometry, separately and in parallel. Both mass spectrometric methods provide the fast response, rapid data acquisition, low detection limits, and high-resolution peak separation desirable for imaging complex samples. Additionally, the two techniques provide complementary information with aerosol mass spectrometry providing near universal detection of all aerosol molecules and chemical ionization mass spectrometry with a heated inletmore » providing molecular-level detail of both gases and aerosols. The two techniques operate with atmospheric pressure interfaces and require no matrix addition for ionization, allowing for samples to be investigated in their native state under ambient pressure conditions. We demonstrate the ability of laser ablation-aerosol mass spectrometry-chemical ionization mass spectrometry (LA-AMS-CIMS) to create 2D images of both standard compounds and complex mixtures. Finally, the results suggest that LA-AMS-CIMS, particularly when combined with advanced data analysis methods, could have broad applications in mass spectrometry imaging applications.« less

Laser Ablation-Aerosol Mass Spectrometry-Chemical Ionization Mass Spectrometry for Ambient Surface Imaging

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

Berry, Jennifer L.; Day, Douglas A.; Elseberg, Tim

Mass spectrometry imaging is becoming an increasingly common analytical technique due to its ability to provide spatially resolved chemical information. In this paper, we report a novel imaging approach combining laser ablation with two mass spectrometric techniques, aerosol mass spectrometry and chemical ionization mass spectrometry, separately and in parallel. Both mass spectrometric methods provide the fast response, rapid data acquisition, low detection limits, and high-resolution peak separation desirable for imaging complex samples. Additionally, the two techniques provide complementary information with aerosol mass spectrometry providing near universal detection of all aerosol molecules and chemical ionization mass spectrometry with a heated inletmore » providing molecular-level detail of both gases and aerosols. The two techniques operate with atmospheric pressure interfaces and require no matrix addition for ionization, allowing for samples to be investigated in their native state under ambient pressure conditions. We demonstrate the ability of laser ablation-aerosol mass spectrometry-chemical ionization mass spectrometry (LA-AMS-CIMS) to create 2D images of both standard compounds and complex mixtures. Finally, the results suggest that LA-AMS-CIMS, particularly when combined with advanced data analysis methods, could have broad applications in mass spectrometry imaging applications.« less

Clinical, biopsy, and mass spectrometry findings of renal gelsolin amyloidosis.

PubMed

Sethi, Sanjeev; Dasari, Surendra; Amin, Md Shahrier; Vrana, Julie A; Theis, Jason D; Alexander, Mariam P; Kurtin, Paul J

2017-04-01

Gelsolin amyloidosis is a rare type of amyloidosis typically involving the cranial and peripheral nerves, but rarely the kidney. Here we report the clinical, kidney biopsy, and mass spectrometry findings in 12 cases of renal gelsolin amyloidosis. Of the 12 patients, five were men and seven were women with mean age at diagnosis of 63.8 years. Gelsolin amyloidosis was most common in Caucasians (six patients) and Asians (four patients), and included one each African-American and Hispanic patients. Nephrotic syndrome was the most common cause of biopsy, although most patients also had progressive loss of kidney function. Hematological and serological evaluation was negative in 11 patients, while one patient had a monoclonal gammopathy. The renal biopsy showed large amounts of pale eosinophilic Congo red-positive amyloid deposits typically restricted to the glomeruli. Immunofluorescence studies were negative for immunoglobulins in nine cases with three cases of smudgy glomerular staining for IgG. Electron microscopy showed mostly random arrangement of amyloid fibrils with focally parallel bundles/sheets of amyloid fibrils present. Laser microdissection of the amyloid deposits followed by mass spectrometry showed large spectra numbers for gelsolin, serum amyloid P component, and apolipoproteins E and AIV. Furthermore, the p. Asn211Lys gelsolin mutation on mass spectrometry studies was detected in three patients by mass spectrometry, which appears to represent a renal-limited form of gelsolin amyloidosis. Thus, renal gelsolin amyloidosis is seen in older patients, presents with nephrotic syndrome and progressive chronic kidney disease, and histologically exhibits glomerular involvement. The diagnosis can be confirmed by mass spectrometry studies. Copyright © 2016 International Society of Nephrology. Published by Elsevier Inc. All rights reserved.

Neuropeptide modulation of pattern-generating systems in crustaceans: comparative studies and approaches.

PubMed

Dickinson, Patsy S; Qu, Xuan; Stanhope, Meredith E

2016-12-01

Central pattern generators are subject to modulation by peptides, allowing for flexibility in patterned output. Current techniques used to characterize peptides include mass spectrometry and transcriptomics. In recent years, hundreds of neuropeptides have been sequenced from crustaceans; mass spectrometry has been used to identify peptides and to determine their levels and locations, setting the stage for comparative studies investigating the physiological roles of peptides. Such studies suggest that there is some evolutionary conservation of function, but also divergence of function even within a species. With current baseline data, it should be possible to begin using comparative approaches to ask fundamental questions about why peptides are encoded the way that they are and how this affects nervous system function. Copyright © 2016 Elsevier Ltd. All rights reserved.

Mass spectrometry.

NASA Technical Reports Server (NTRS)

Burlingame, A. L.; Johanson, G. A.

1972-01-01

Review of the current state of mass spectrometry, indicating its unique importance for advanced scientific research. Mass spectrometry applications in computer techniques, gas chromatography, ion cyclotron resonance, molecular fragmentation and ionization, and isotope labeling are covered. Details are given on mass spectrometry applications in bio-organic chemistry and biomedical research. As the subjects of these applications are indicated alkaloids, carbohydrates, lipids, terpenes, quinones, nucleic acid components, peptides, antibiotics, and human and animal metabolisms. Particular attention is given to the mass spectra of organo-inorganic compounds, inorganic mass spectrometry, surface phenomena such as secondary ion and electron emission, and elemental and isotope analysis. Further topics include mass spectrometry in organic geochemistry, applications in geochronology and cosmochemistry, and organic mass spectrometry.

Identification of ortho-Substituted Benzoic Acid/Ester Derivatives via the Gas-Phase Neighboring Group Participation Effect in (+)-ESI High Resolution Mass Spectrometry.

PubMed

Blincoe, William D; Rodriguez-Granillo, Agustina; Saurí, Josep; Pierson, Nicholas A; Joyce, Leo A; Mangion, Ian; Sheng, Huaming

2018-04-01

Benzoic acid/ester/amide derivatives are common moieties in pharmaceutical compounds and present a challenge in positional isomer identification by traditional tandem mass spectrometric analysis. A method is presented for exploiting the gas-phase neighboring group participation (NGP) effect to differentiate ortho-substituted benzoic acid/ester derivatives with high resolution mass spectrometry (HRMS 1 ). Significant water/alcohol loss (>30% abundance in MS 1 spectra) was observed for ortho-substituted nucleophilic groups; these fragment peaks are not observable for the corresponding para and meta-substituted analogs. Experiments were also extended to the analysis of two intermediates in the synthesis of suvorexant (Belsomra) with additional analysis conducted with nuclear magnetic resonance (NMR), density functional theory (DFT), and ion mobility spectrometry-mass spectrometry (IMS-MS) studies. Significant water/alcohol loss was also observed for 1-substituted 1, 2, 3-triazoles but not for the isomeric 2-substituted 1, 2, 3-triazole analogs. IMS-MS, NMR, and DFT studies were conducted to show that the preferred orientation of the 2-substituted triazole rotamer was away from the electrophilic center of the reaction, whereas the 1-subtituted triazole was oriented in close proximity to the center. Abundance of NGP product was determined to be a product of three factors: (1) proton affinity of the nucleophilic group; (2) steric impact of the nucleophile; and (3) proximity of the nucleophile to carboxylic acid/ester functional groups. Graphical Abstract ᅟ.

Mapping Cellular Polarity Networks Using Mass Spectrometry-based Strategies.

PubMed

Daulat, Avais M; Puvirajesinghe, Tania M; Camoin, Luc; Borg, Jean-Paul

2018-05-18

Cell polarity is a vital biological process involved in the building, maintenance and normal functioning of tissues in invertebrates and vertebrates. Unsurprisingly, molecular defects affecting polarity organization and functions have a strong impact on tissue homeostasis, embryonic development and adult life, and may directly or indirectly lead to diseases. Genetic studies have demonstrated the causative effect of several polarity genes in diseases; however, much remains to be clarified before a comprehensive view of the molecular organization and regulation of the protein networks associated with polarity proteins is obtained. This challenge can be approached head-on using proteomics to identify protein complexes involved in cell polarity and their modifications in a spatio-temporal manner. We review the fundamental basics of mass spectrometry techniques and provide an in-depth analysis of how mass spectrometry has been instrumental in understanding the complex and dynamic nature of some cell polarity networks at the tissue (apico-basal and planar cell polarities) and cellular (cell migration, ciliogenesis) levels, with the fine dissection of the interconnections between prototypic cell polarity proteins and signal transduction cascades in normal and pathological situations. This review primarily focuses on epithelial structures which are the fundamental building blocks for most metazoan tissues, used as the archetypal model to study cellular polarity. This field offers broad perspectives thanks to the ever-increasing sensitivity of mass spectrometry and its use in combination with recently developed molecular strategies able to probe in situ proteomic networks. Copyright © 2018 Elsevier Ltd. All rights reserved.

Identification of ortho-Substituted Benzoic Acid/Ester Derivatives via the Gas-Phase Neighboring Group Participation Effect in (+)-ESI High Resolution Mass Spectrometry

NASA Astrophysics Data System (ADS)

Blincoe, William D.; Rodriguez-Granillo, Agustina; Saurí, Josep; Pierson, Nicholas A.; Joyce, Leo A.; Mangion, Ian; Sheng, Huaming

2018-02-01

Benzoic acid/ester/amide derivatives are common moieties in pharmaceutical compounds and present a challenge in positional isomer identification by traditional tandem mass spectrometric analysis. A method is presented for exploiting the gas-phase neighboring group participation (NGP) effect to differentiate ortho-substituted benzoic acid/ester derivatives with high resolution mass spectrometry (HRMS1). Significant water/alcohol loss (>30% abundance in MS1 spectra) was observed for ortho-substituted nucleophilic groups; these fragment peaks are not observable for the corresponding para and meta-substituted analogs. Experiments were also extended to the analysis of two intermediates in the synthesis of suvorexant (Belsomra) with additional analysis conducted with nuclear magnetic resonance (NMR), density functional theory (DFT), and ion mobility spectrometry-mass spectrometry (IMS-MS) studies. Significant water/alcohol loss was also observed for 1-substituted 1, 2, 3-triazoles but not for the isomeric 2-substituted 1, 2, 3-triazole analogs. IMS-MS, NMR, and DFT studies were conducted to show that the preferred orientation of the 2-substituted triazole rotamer was away from the electrophilic center of the reaction, whereas the 1-subtituted triazole was oriented in close proximity to the center. Abundance of NGP product was determined to be a product of three factors: (1) proton affinity of the nucleophilic group; (2) steric impact of the nucleophile; and (3) proximity of the nucleophile to carboxylic acid/ester functional groups. [Figure not available: see fulltext.

Matrix-assisted laser desorption ionization time-of-flight mass spectrometric analysis of degradation products after treatment of methylene blue aqueous solution with three-dimensionally integrated microsolution plasma

NASA Astrophysics Data System (ADS)

Shirafuji, Tatsuru; Nomura, Ayano; Hayashi, Yui; Tanaka, Kenji; Goto, Motonobu

2016-01-01

Methylene blue can be degraded in three-dimensionally integrated microsolution plasma. The degradation products have been analyzed by matrix-assisted laser desorption ionization time-of-flight (MALDI TOF) mass spectrometry to understand the degradation mechanisms. The results of MALDI TOF mass spectrometry have shown that sulfoxide is formed at the first stage of the oxidation. Then, partial oxidation proceeds on the methyl groups left on the sulfoxide. The sulfoxide is subsequently separated to two benzene derivatives. Finally, weak functional groups are removed from the benzene derivatives.

Functionalized graphene quantum dots loaded with free radicals combined with liquid chromatography and tandem mass spectrometry to screen radical scavenging natural antioxidants from Licorice and Scutellariae.

PubMed

Wang, Guoying; Niu, XiuLi; Shi, Gaofeng; Chen, Xuefu; Yao, Ruixing; Chen, Fuwen

2014-12-01

A novel screening method was developed for the detection and identification of radical scavenging natural antioxidants based on a free radical reaction combined with liquid chromatography with tandem mass spectrometry. Functionalized graphene quantum dots were prepared for loading free radicals in the complex screening system. The detection was performed with and without a preliminary exposure of the samples to specific free radicals on the functionalized graphene quantum dots, which can facilitate charge transfer between free radicals and antioxidants. The difference in chromatographic peak areas was used to identify potential antioxidants. This is a novel approach to simultaneously evaluate the antioxidant power of a component versus a free radical, and to identify it in a vegetal matrix. The structures of the antioxidants in the samples were identified using tandem mass spectrometry and comparison with standards. Fourteen compounds were found to possess potential antioxidant activity, and their free radical scavenging capacities were investigated. The order of scavenging capacity of 14 compounds was compared according to their free radical scavenging rate. 4',5,6,7-Tetrahydroxyflavone (radical scavenging rate: 0.05253 mL mg(-1) s(-1) ) showed the strongest capability for scavenging free radicals. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mass Spectrometry Based Proteomic Analysis of Salivary Glands of Urban Malaria Vector Anopheles stephensi

PubMed Central

Vijay, Sonam

2014-01-01

Salivary gland proteins of Anopheles mosquitoes offer attractive targets to understand interactions with sporozoites, blood feeding behavior, homeostasis, and immunological evaluation of malaria vectors and parasite interactions. To date limited studies have been carried out to elucidate salivary proteins of An. stephensi salivary glands. The aim of the present study was to provide detailed analytical attributives of functional salivary gland proteins of urban malaria vector An. stephensi. A proteomic approach combining one-dimensional electrophoresis (1DE), ion trap liquid chromatography mass spectrometry (LC/MS/MS), and computational bioinformatic analysis was adopted to provide the first direct insight into identification and functional characterization of known salivary proteins and novel salivary proteins of An. stephensi. Computational studies by online servers, namely, MASCOT and OMSSA algorithms, identified a total of 36 known salivary proteins and 123 novel proteins analysed by LC/MS/MS. This first report describes a baseline proteomic catalogue of 159 salivary proteins belonging to various categories of signal transduction, regulation of blood coagulation cascade, and various immune and energy pathways of An. stephensi sialotranscriptome by mass spectrometry. Our results may serve as basis to provide a putative functional role of proteins in concept of blood feeding, biting behavior, and other aspects of vector-parasite host interactions for parasite development in anopheline mosquitoes. PMID:25126571

Mass spectrometry based proteomic analysis of salivary glands of urban malaria vector Anopheles stephensi.

PubMed

Vijay, Sonam; Rawat, Manmeet; Sharma, Arun

2014-01-01

Salivary gland proteins of Anopheles mosquitoes offer attractive targets to understand interactions with sporozoites, blood feeding behavior, homeostasis, and immunological evaluation of malaria vectors and parasite interactions. To date limited studies have been carried out to elucidate salivary proteins of An. stephensi salivary glands. The aim of the present study was to provide detailed analytical attributives of functional salivary gland proteins of urban malaria vector An. stephensi. A proteomic approach combining one-dimensional electrophoresis (1DE), ion trap liquid chromatography mass spectrometry (LC/MS/MS), and computational bioinformatic analysis was adopted to provide the first direct insight into identification and functional characterization of known salivary proteins and novel salivary proteins of An. stephensi. Computational studies by online servers, namely, MASCOT and OMSSA algorithms, identified a total of 36 known salivary proteins and 123 novel proteins analysed by LC/MS/MS. This first report describes a baseline proteomic catalogue of 159 salivary proteins belonging to various categories of signal transduction, regulation of blood coagulation cascade, and various immune and energy pathways of An. stephensi sialotranscriptome by mass spectrometry. Our results may serve as basis to provide a putative functional role of proteins in concept of blood feeding, biting behavior, and other aspects of vector-parasite host interactions for parasite development in anopheline mosquitoes.

Parallel Exploration of Interaction Space by BioID and Affinity Purification Coupled to Mass Spectrometry.

PubMed

Hesketh, Geoffrey G; Youn, Ji-Young; Samavarchi-Tehrani, Payman; Raught, Brian; Gingras, Anne-Claude

2017-01-01

Complete understanding of cellular function requires knowledge of the composition and dynamics of protein interaction networks, the importance of which spans all molecular cell biology fields. Mass spectrometry-based proteomics approaches are instrumental in this process, with affinity purification coupled to mass spectrometry (AP-MS) now widely used for defining interaction landscapes. Traditional AP-MS methods are well suited to providing information regarding the temporal aspects of soluble protein-protein interactions, but the requirement to maintain protein-protein interactions during cell lysis and AP means that both weak-affinity interactions and spatial information is lost. A more recently developed method called BioID employs the expression of bait proteins fused to a nonspecific biotin ligase, BirA*, that induces in vivo biotinylation of proximal proteins. Coupling this method to biotin affinity enrichment and mass spectrometry negates many of the solubility and interaction strength issues inherent in traditional AP-MS methods, and provides unparalleled spatial context for protein interactions. Here we describe the parallel implementation of both BioID and FLAG AP-MS allowing simultaneous exploration of both spatial and temporal aspects of protein interaction networks.

Coupling flash liquid chromatography with mass spectrometry for enrichment and isolation of milk oligosaccharides for functional studies.

PubMed

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

2012-05-15

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

Parsimonious Charge Deconvolution for Native Mass Spectrometry

PubMed Central

2018-01-01

Charge deconvolution infers the mass from mass over charge (m/z) measurements in electrospray ionization mass spectra. When applied over a wide input m/z or broad target mass range, charge-deconvolution algorithms can produce artifacts, such as false masses at one-half or one-third of the correct mass. Indeed, a maximum entropy term in the objective function of MaxEnt, the most commonly used charge deconvolution algorithm, favors a deconvolved spectrum with many peaks over one with fewer peaks. Here we describe a new “parsimonious” charge deconvolution algorithm that produces fewer artifacts. The algorithm is especially well-suited to high-resolution native mass spectrometry of intact glycoproteins and protein complexes. Deconvolution of native mass spectra poses special challenges due to salt and small molecule adducts, multimers, wide mass ranges, and fewer and lower charge states. We demonstrate the performance of the new deconvolution algorithm on a range of samples. On the heavily glycosylated plasma properdin glycoprotein, the new algorithm could deconvolve monomer and dimer simultaneously and, when focused on the m/z range of the monomer, gave accurate and interpretable masses for glycoforms that had previously been analyzed manually using m/z peaks rather than deconvolved masses. On therapeutic antibodies, the new algorithm facilitated the analysis of extensions, truncations, and Fab glycosylation. The algorithm facilitates the use of native mass spectrometry for the qualitative and quantitative analysis of protein and protein assemblies. PMID:29376659

A theoretical and mass spectrometry study of the fragmentation of mycosporine-like amino acids

NASA Astrophysics Data System (ADS)

Cardozo, Karina H. M.; Vessecchi, Ricardo; Carvalho, Valdemir M.; Pinto, Ernani; Gates, Paul J.; Colepicolo, Pio; Galembeck, Sérgio E.; Lopes, Norberto P.

2008-06-01

In the present study, the mycosporine-like amino acids (MAAs) were isolated from the marine red alga Gracilaria tenuistipitata and analysed by high-resolution accurate-mass sequential mass spectrometry (MSn). In addition to the proposed fragmentation mechanism based on the MSn analysis, it is clearly demonstrated that the elimination of mass 15 is a radical processes taking place at the methoxyl substituent of the double bond. This characteristic loss of a methyl radical was studied by theoretical calculations and the homolytic cleavage of the OC bond is suggested to be dependent on the bond weakening. The protonation site of the MAAs was indicated by analysis of the Fukui functions and the relative Gibbs energies of the several possible protonated forms.

Current Status and Future Perspectives of Mass Spectrometry Imaging

PubMed Central

Nimesh, Surendra; Mohottalage, Susantha; Vincent, Renaud; Kumarathasan, Prem

2013-01-01

Mass spectrometry imaging is employed for mapping proteins, lipids and metabolites in biological tissues in a morphological context. Although initially developed as a tool for biomarker discovery by imaging the distribution of protein/peptide in tissue sections, the high sensitivity and molecular specificity of this technique have enabled its application to biomolecules, other than proteins, even in cells, latent finger prints and whole organisms. Relatively simple, with no requirement for labelling, homogenization, extraction or reconstitution, the technique has found a variety of applications in molecular biology, pathology, pharmacology and toxicology. By discriminating the spatial distribution of biomolecules in serial sections of tissues, biomarkers of lesions and the biological responses to stressors or diseases can be better understood in the context of structure and function. In this review, we have discussed the advances in the different aspects of mass spectrometry imaging processes, application towards different disciplines and relevance to the field of toxicology. PMID:23759983

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.

Diamond nanowires for highly sensitive matrix-free mass spectrometry analysis of small molecules.

PubMed

Coffinier, Yannick; Szunerits, Sabine; Drobecq, Hervé; Melnyk, Oleg; Boukherroub, Rabah

2012-01-07

This paper reports on the use of boron-doped diamond nanowires (BDD NWs) as an inorganic substrate for matrix-free laser desorption/ionization mass spectrometry (LDI-MS) analysis of small molecules. The diamond nanowires are prepared by reactive ion etching (RIE) with oxygen plasma of highly boron-doped (the boron level is 10(19) B cm(-3)) or undoped nanocrystalline diamond substrates. The resulting diamond nanowires are coated with a thin silicon oxide layer that confers a superhydrophilic character to the surface. To minimize droplet spreading, the nanowires were chemically functionalized with octadecyltrichlorosilane (OTS) and then UV/ozone treated to reach a final water contact angle of 120°. The sub-bandgap absorption under UV laser irradiation and the heat confinement inside the nanowires allowed desorption/ionization, most likely via a thermal mechanism, and mass spectrometry analysis of small molecules. A detection limit of 200 zeptomole for verapamil was demonstrated.

Isolation and Preparation of Extracellular Proteins from Lignocellulose Degrading Fungi for Comparative Proteomic Studies Using Mass Spectrometry.

PubMed

Gruninger, Robert J; Tsang, Adrian; McAllister, Tim A

2017-01-01

Fungi utilize a unique mechanism of nutrient acquisition involving extracellular digestion. To understand the biology of these microbes, it is important to identify and characterize the function of proteins that are secreted and involved in this process. Mass spectrometry-based proteomics is a powerful tool to study complex mixtures of proteins and understand how the proteins produced by an organism change in response to different conditions. Many fungi are efficient decomposers of plant cell wall, and anaerobic fungi are well recognized for their ability to digest lignocellulose. Here, we outline a protocol for the enrichment and isolation of proteins secreted by anaerobic fungi after growth on simple (glucose) and complex (straw and alfalfa hay) carbon sources. We provide detailed instruction on generating protein fragments and preparing these for proteomic analysis using reversed phase chromatography and mass spectrometry.

Data Analysis Methods for Synthetic Polymer Mass Spectrometry: Autocorrelation

PubMed Central

Wallace, William E.; Guttman, Charles M.

2002-01-01

Autocorrelation is shown to be useful in describing the periodic patterns found in high- resolution mass spectra of synthetic polymers. Examples of this usefulness are described for a simple linear homopolymer to demonstrate the method fundamentals, a condensation polymer to demonstrate its utility in understanding complex spectra with multiple repeating patterns on different mass scales, and a condensation copolymer to demonstrate how it can elegantly and efficiently reveal unexpected phenomena. It is shown that using autocorrelation to determine where the signal devolves into noise can be useful in determining molecular mass distributions of synthetic polymers, a primary focus of the NIST synthetic polymer mass spectrometry effort. The appendices describe some of the effects of transformation from time to mass space when time-of-flight mass separation is used, as well as the effects of non-trivial baselines on the autocorrelation function. PMID:27446716

MASS SPECTROMETRY IN ENVIRONMENTAL SCIENCES

EPA Science Inventory

This review covers applications of mass spectrometry to the environmental sciences. From the early applications of mass spectrometry to environmental research in the 1960s and 1970s, mass spectrometry has played an important role in aiding our understanding of environmental poll...

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

Hands-on Electrospray Ionization-Mass Spectrometry for Upper-Level Undergraduate and Graduate Students

ERIC Educational Resources Information Center

Stock, Naomi L.; March, Raymond E.

2014-01-01

Electrospray ionization-mass spectrometry (ESI-MS) is a powerful technique for the detection, identification, and quantification of organic compounds. As mass spectrometers have become more user-friendly and affordable, many students--often with little experience in mass spectrometry--find themselves needing to incorporate mass spectrometry into…

The association of low-molecular-weight hydrophobic compounds with native casein micelles in bovine milk

PubMed Central

Cheema, M.; Mohan, M. S.; Campagna, S. R.; Jurat-Fuentes, J. L.; Harte, F. M.

2015-01-01

The agreed biological function of the casein micelles in milk is to carry minerals (calcium, magnesium, and phosphorus) from mother to young along with amino acids for growth and development. Recently, native and modified casein micelles were used as encapsulating and delivery agents for various hydrophobic low-molecular-weight probes. The ability of modified casein micelles to bind certain probes may derive from the binding affinity of native casein micelles. Hence, a study with milk from single cows was conducted to further elucidate the association of hydrophobic molecules into native casein micelles and further understand their biological function. Hydrophobic and hydrophilic extraction followed by ultraperformance liquid chromatography-high resolution mass spectrometry analysis were performed over protein fractions obtained from size exclusion fractionation of raw skim milk. Hydrophobic compounds, including phosphatidylcholine, lyso-phosphatidylcholine, phosphatidylethanolamine, and sphingomyelin, showed strong association exclusively to casein micelles as compared with whey proteins, whereas hydrophilic compounds did not display any preference for their association among milk proteins. Further analysis using liquid chromatography-tandem mass spectrometry detected 42 compounds associated solely with the casein-micelles fraction. Mass fragments in tandem mass spectrometry identified 4 of these compounds as phosphatidylcholine with fatty acid composition of 16:0/18:1, 14:0/16:0, 16:0/16:0, and 18:1/18:0. These results support that transporting low-molecular-weight hydrophobic molecules is also a biological function of the casein micelles in milk. PMID:26074238

Mass spectrometry as a quantitative tool in plant metabolomics

PubMed Central

Jorge, Tiago F.; Mata, Ana T.

2016-01-01

Metabolomics is a research field used to acquire comprehensive information on the composition of a metabolite pool to provide a functional screen of the cellular state. Studies of the plant metabolome include the analysis of a wide range of chemical species with very diverse physico-chemical properties, and therefore powerful analytical tools are required for the separation, characterization and quantification of this vast compound diversity present in plant matrices. In this review, challenges in the use of mass spectrometry (MS) as a quantitative tool in plant metabolomics experiments are discussed, and important criteria for the development and validation of MS-based analytical methods provided. This article is part of the themed issue ‘Quantitative mass spectrometry’. PMID:27644967

Time-Resolved Molecular Characterization of Limonene/Ozone Aerosol using High-Resolution Electrospray Ionization Mass Spectrometry

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

Bateman, Adam P.; Nizkorodov, Serguei; Laskin, Julia

2009-09-09

Molecular composition of limonene/O3 secondary organic aerosol (SOA) was investigated using high-resolution electrospray ionization mass spectrometry (HR-ESI-MS) as a function of reaction time. SOA was generated by ozonation of D-limonene in a reaction chamber and sampled at different time intervals using a cascade impactor. The SOA samples were extracted into acetonitrile and analyzed using a HR-ESI-MS instrument with a resolving power of 100,000 (m/Δm). The resulting mass spectra provided detailed information about the extent of oxidation inferred from the O:C ratios, double bond equivalency (DBE) factors, and aromaticity indexes (AI) in hundreds of identified individual SOA species.

Advancements in mass spectrometry for biological samples: Protein chemical cross-linking and metabolite analysis of plant tissues

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

Klein, Adam

2015-01-01

This thesis presents work on advancements and applications of methodology for the analysis of biological samples using mass spectrometry. Included in this work are improvements to chemical cross-linking mass spectrometry (CXMS) for the study of protein structures and mass spectrometry imaging and quantitative analysis to study plant metabolites. Applications include using matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) to further explore metabolic heterogeneity in plant tissues and chemical interactions at the interface between plants and pests. Additional work was focused on developing liquid chromatography-mass spectrometry (LC-MS) methods to investigate metabolites associated with plant-pest interactions.

Mass spectrometry-based proteomics for translational research: a technical overview.

PubMed

Paulo, Joao A; Kadiyala, Vivek; Banks, Peter A; Steen, Hanno; Conwell, Darwin L

2012-03-01

Mass spectrometry-based investigation of clinical samples enables the high-throughput identification of protein biomarkers. We provide an overview of mass spectrometry-based proteomic techniques that are applicable to the investigation of clinical samples. We address sample collection, protein extraction and fractionation, mass spectrometry modalities, and quantitative proteomics. Finally, we examine the limitations and further potential of such technologies. Liquid chromatography fractionation coupled with tandem mass spectrometry is well suited to handle mixtures of hundreds or thousands of proteins. Mass spectrometry-based proteome elucidation can reveal potential biomarkers and aid in the development of hypotheses for downstream investigation of the molecular mechanisms of disease.

Mass Spectrometry-Based Proteomics for Translational Research: A Technical Overview

PubMed Central

Paulo, Joao A.; Kadiyala, Vivek; Banks, Peter A.; Steen, Hanno; Conwell, Darwin L.

2012-01-01

Mass spectrometry-based investigation of clinical samples enables the high-throughput identification of protein biomarkers. We provide an overview of mass spectrometry-based proteomic techniques that are applicable to the investigation of clinical samples. We address sample collection, protein extraction and fractionation, mass spectrometry modalities, and quantitative proteomics. Finally, we examine the limitations and further potential of such technologies. Liquid chromatography fractionation coupled with tandem mass spectrometry is well suited to handle mixtures of hundreds or thousands of proteins. Mass spectrometry-based proteome elucidation can reveal potential biomarkers and aid in the development of hypotheses for downstream investigation of the molecular mechanisms of disease. PMID:22461744

Enrichment of peptides in serum by C(8)-functionalized magnetic nanoparticles for direct matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis.

PubMed

Yao, Ning; Chen, Hemei; Lin, Huaqing; Deng, Chunhui; Zhang, Xiangmin

2008-03-21

Human serum contains a complex array of proteolytically derived peptides (serum peptidome), which contain biomarkers of preclinical screening and disease diagnosis. Recently, commercial C(8)-functionalized magnetic beads (1-10 microm) were widely applied to the separation and enrichment of peptides in human serum, prior to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analysis. In this work, laboratory-prepared C(8)-functionalized magnetic nanoparticles (about 50 nm) were prepared and applied to the fast separation and the enrichment of peptides from serum. At first, the C(8)-magnetic nanoparticles were synthesized by modifying amine-functionalized magnetic nanoparticles with chlorodimethyloctylsilane. These synthesized C(8)-amine-functionalized magnetic particles have excellent magnetic responsibility, high dispersibility and large surface area. Finally, the C(8)-magnetic nanoparticles were successfully applied to fast and efficient enrichment of low-abundance peptides from protein tryptic digestion and human serum followed by MALDI-TOF-MS analysis.

Identification of fatty acids and fatty acid amides in human meibomian gland secretions.

PubMed

Nichols, Kelly K; Ham, Bryan M; Nichols, Jason J; Ziegler, Corrie; Green-Church, Kari B

2007-01-01

The complex superficial lipid layer of the tear film functions to prevent evaporation and maintain tear stability. Although classes of lipids found in the tear film have been reported, individual lipid species are currently being studied with more sophisticated. The purpose of this work was to show the identification of fatty acids and the fatty acid amides in human meibomian gland secretions by using electrospray mass spectrometry. methods. Human meibomian gland secretions (meibum) were analyzed by electrospray quadrupole time-of-flight mass spectrometry (positive- and negative-ion mode). Accurate mass determination and collision-induced dissociation of meibum, and lipid standards were used to identify lipid species. Mass analysis of meibum in an acidic chloroform-methanol solution in positive-ion mode revealed a mass peak of m/z 282.3, which was identified as the protonated molecule of oleamide [C(18)H(35)NO+H](+). The high-resolution mass analysis of the m/z 282.2788 peak (oleamide) demonstrated a mass accuracy of 3.2 parts per million (ppm). Collision-induced dissociation of this species from meibum, compared with an oleamide standard, confirmed its identification. Myristic, palmitic, stearic, and oleic free fatty acids were identified in a similar manner, as were the other fatty acid amides (myristamide, palmitamide, stearamide, and erucamide). The findings indicate that oleamide (cis-9-octadecenamide), an endogenous fatty acid primary amide, is a predominant component of meibum when examined by electrospray mass spectrometry. The novel finding of oleamide and other members of the fatty acid amide family in the tear film could lead to additional insights into the role of fatty acid amide activity in human biological systems and may indicate a new function for this lipid class of molecules in ocular surface signaling and/or in the maintenance of the complex tear film.

Identification of Unknown Contaminants in Water Samples from ISS Employing Liquid Chromatography/Mass Spectrometry/Mass Spectrometry

NASA Technical Reports Server (NTRS)

Rutz, Jeffrey A.; Schultz, John R.

2008-01-01

Mass Spectrometry/Mass Spectrometry (MS/MS) is a powerful technique for identifying unknown organic compounds. For non-volatile or thermally unstable unknowns dissolved in liquids, liquid chromatography/mass spectrometry/mass spectrometry (LC/MS/MS) is often the variety of MS/MS used for the identification. One type of LC/MS/MS that is rapidly becoming popular is time-of-flight (TOF) mass spectrometry. This technique is now in use at the Johnson Space Center for identification of unknown nonvolatile organics in water samples from the space program. An example of the successful identification of one unknown is reviewed in detail in this paper. The advantages of time-of-flight instrumentation are demonstrated through this example as well as the strategy employed in using time-of-flight data to identify unknowns.

Mono-isotope Prediction for Mass Spectra Using Bayes Network.

PubMed

Li, Hui; Liu, Chunmei; Rwebangira, Mugizi Robert; Burge, Legand

2014-12-01

Mass spectrometry is one of the widely utilized important methods to study protein functions and components. The challenge of mono-isotope pattern recognition from large scale protein mass spectral data needs computational algorithms and tools to speed up the analysis and improve the analytic results. We utilized naïve Bayes network as the classifier with the assumption that the selected features are independent to predict mono-isotope pattern from mass spectrometry. Mono-isotopes detected from validated theoretical spectra were used as prior information in the Bayes method. Three main features extracted from the dataset were employed as independent variables in our model. The application of the proposed algorithm to publicMo dataset demonstrates that our naïve Bayes classifier is advantageous over existing methods in both accuracy and sensitivity.

Chemometrics comparison of gas chromatography with mass spectrometry and comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry Daphnia magna metabolic profiles exposed to salinity.

PubMed

Parastar, Hadi; Garreta-Lara, Elba; Campos, Bruno; Barata, Carlos; Lacorte, Silvia; Tauler, Roma

2018-06-01

The performances of gas chromatography with mass spectrometry and of comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry are examined through the comparison of Daphnia magna metabolic profiles. Gas chromatography with mass spectrometry and comprehensive two-dimensional gas chromatography with mass spectrometry were used to compare the concentration changes of metabolites under saline conditions. In this regard, a chemometric strategy based on wavelet compression and multivariate curve resolution-alternating least squares is used to compare the performances of gas chromatography with mass spectrometry and comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry for the untargeted metabolic profiling of Daphnia magna in control and salinity-exposed samples. Examination of the results confirmed the outperformance of comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry over gas chromatography with mass spectrometry for the detection of metabolites in D. magna samples. The peak areas of multivariate curve resolution-alternating least squares resolved elution profiles in every sample analyzed by comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry were arranged in a new data matrix that was then modeled by partial least squares discriminant analysis. The control and salt-exposed daphnids samples were discriminated and the most relevant metabolites were estimated using variable importance in projection and selectivity ratio values. Salinity de-regulated 18 metabolites from metabolic pathways involved in protein translation, transmembrane cell transport, carbon metabolism, secondary metabolism, glycolysis, and osmoregulation. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mass spectrometry imaging under ambient conditions.

PubMed

Wu, Chunping; Dill, Allison L; Eberlin, Livia S; Cooks, R Graham; Ifa, Demian R

2013-01-01

Mass spectrometry imaging (MSI) has emerged as an important tool in the last decade and it is beginning to show potential to provide new information in many fields owing to its unique ability to acquire molecularly specific images and to provide multiplexed information, without the need for labeling or staining. In MSI, the chemical identity of molecules present on a surface is investigated as a function of spatial distribution. In addition to now standard methods involving MSI in vacuum, recently developed ambient ionization techniques allow MSI to be performed under atmospheric pressure on untreated samples outside the mass spectrometer. Here we review recent developments and applications of MSI emphasizing the ambient ionization techniques of desorption electrospray ionization (DESI), laser ablation electrospray ionization (LAESI), probe electrospray ionization (PESI), desorption atmospheric pressure photoionization (DAPPI), femtosecond laser desorption ionization (fs-LDI), laser electrospray mass spectrometry (LEMS), infrared laser ablation metastable-induced chemical ionization (IR-LAMICI), liquid microjunction surface sampling probe mass spectrometry (LMJ-SSP MS), nanospray desorption electrospray ionization (nano-DESI), and plasma sources such as the low temperature plasma (LTP) probe and laser ablation coupled to flowing atmospheric-pressure afterglow (LA-FAPA). Included are discussions of some of the features of ambient MSI for example the ability to implement chemical reactions with the goal of providing high abundance ions characteristic of specific compounds of interest and the use of tandem mass spectrometry to either map the distribution of targeted molecules with high specificity or to provide additional MS information on the structural identification of compounds. We also describe the role of bioinformatics in acquiring and interpreting the chemical and spatial information obtained through MSI, especially in biological applications for tissue diagnostic purposes. Finally, we discuss the challenges in ambient MSI and include perspectives on the future of the field. Copyright © 2012 Wiley Periodicals, Inc.

Mass Spectrometry Imaging under Ambient Conditions

PubMed Central

Wu, Chunping; Dill, Allison L.; Eberlin, Livia S.; Cooks, R. Graham; Ifa, Demian R.

2012-01-01

Mass spectrometry imaging (MSI) has emerged as an important tool in the last decade and it is beginning to show potential to provide new information in many fields owing to its unique ability to acquire molecularly specific images and to provide multiplexed information, without the need for labeling or staining. In MSI, the chemical identity of molecules present on a surface is investigated as a function of spatial distribution. In addition to now standard methods involving MSI in vacuum, recently developed ambient ionization techniques allow MSI to be performed under atmospheric pressure on untreated samples outside the mass spectrometer. Here we review recent developments and applications of MSI emphasizing the ambient ionization techniques of desorption electrospray ionization (DESI), laser ablation electrospray ionization (LAESI), probe electrospray ionization (PESI), desorption atmospheric pressure photoionization (DAPPI), femtosecond laser desorption ionization (fs-LDI), laser electrospray mass spectrometry (LEMS), infrared laser ablation metastable-induced chemical ionization (IR-LAMICI), liquid microjunction surface sampling probe mass spectrometry (LMJ-SSP MS), nanospray desorption electrospray ionization (nano-DESI), and plasma sources such as the low temperature plasma (LTP) probe and laser ablation coupled to flowing atmospheric-pressure afterglow (LA-FAPA). Included are discussions of some of the features of ambient MSI including the ability to implement chemical reactions with the goal of providing high abundance ions characteristic of specific compounds of interest and the use of tandem mass spectrometry to either map the distribution of targeted molecules with high specificity or to provide additional MS information in the structural identification of compounds. We also describe the role of bioinformatics in acquiring and interpreting the chemical and spatial information obtained through MSI, especially in biological applications for tissue diagnostic purposes. Finally, we discuss the challenges in ambient MSI and include perspectives on the future of the field. PMID:22996621

Electronic drive and acquisition system for mass spectrometry

NASA Technical Reports Server (NTRS)

Schaefer, Rembrandt Thomas (Inventor); Chutjian, Ara (Inventor); Tran, Tuan (Inventor); Madzunkov, Stojan M. (Inventor); Thomas, John L. (Inventor); Mojarradi, Mohammad (Inventor); MacAskill, John (Inventor); Blaes, Brent R. (Inventor); Darrach, Murray R. (Inventor); Burke, Gary R. (Inventor)

2010-01-01

The present invention discloses a mixed signal RF drive electronics board that offers small, low power, reliable, and customizable method for driving and generating mass spectra from a mass spectrometer, and for control of other functions such as electron ionizer, ion focusing, single-ion detection, multi-channel data accumulation and, if desired, front-end interfaces such as pumps, valves, heaters, and columns.

The Area between Exchange Curves as a Measure of Conformational Differences in Hydrogen-Deuterium Exchange Mass Spectrometry Studies

PubMed Central

Mazur, Sharlyn J.; Weber, Daniel P.

2018-01-01

Hydrogen-deuterium exchange mass spectrometry (HDX-MS) provides information about protein conformational mobility under native conditions. The area between exchange curves, Abec, a functional data analysis concept, was adapted to the interpretation of HDX-MS data and provides a useful measure of exchange curve dissimilarity for tests of significance. Importantly, for most globular proteins under native conditions, Abec values provide an estimate of the log ratio of exchange-competent fractions in the two states, and thus are related to differences in the free energy of microdomain unfolding. PMID:28236290

pymzML--Python module for high-throughput bioinformatics on mass spectrometry data.

PubMed

Bald, Till; Barth, Johannes; Niehues, Anna; Specht, Michael; Hippler, Michael; Fufezan, Christian

2012-04-01

pymzML is an extension to Python that offers (i) an easy access to mass spectrometry (MS) data that allows the rapid development of tools, (ii) a very fast parser for mzML data, the standard data format in MS and (iii) a set of functions to compare or handle spectra. pymzML requires Python2.6.5+ and is fully compatible with Python3. The module is freely available on http://pymzml.github.com or pypi, is published under LGPL license and requires no additional modules to be installed. christian@fufezan.net.

Bile acids: analysis in biological fluids and tissues

PubMed Central

Griffiths, William J.; Sjövall, Jan

2010-01-01

The formation of bile acids/bile alcohols is of major importance for the maintenance of cholesterol homeostasis. Besides their functions in lipid absorption, bile acids/bile alcohols are regulatory molecules for a number of metabolic processes. Their effects are structure-dependent, and numerous metabolic conversions result in a complex mixture of biologically active and inactive forms. Advanced methods are required to characterize and quantify individual bile acids in these mixtures. A combination of such analyses with analyses of the proteome will be required for a better understanding of mechanisms of action and nature of endogenous ligands. Mass spectrometry is the basic detection technique for effluents from chromatographic columns. Capillary liquid chromatography-mass spectrometry with electrospray ionization provides the highest sensitivity in metabolome analysis. Classical gas chromatography-mass spectrometry is less sensitive but offers extensive structure-dependent fragmentation increasing the specificity in analyses of isobaric isomers of unconjugated bile acids. Depending on the nature of the bile acid/bile alcohol mixture and the range of concentration of individuals, different sample preparation sequences, from simple extractions to group separations and derivatizations, are applicable. We review the methods currently available for the analysis of bile acids in biological fluids and tissues, with emphasis on the combination of liquid and gas phase chromatography with mass spectrometry. PMID:20008121

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.

Protonation Sites, Tandem Mass Spectrometry and Computational Calculations of o-Carbonyl Carbazolequinone Derivatives.

PubMed

Martínez-Cifuentes, Maximiliano; Clavijo-Allancan, Graciela; Zuñiga-Hormazabal, Pamela; Aranda, Braulio; Barriga, Andrés; Weiss-López, Boris; Araya-Maturana, Ramiro

2016-07-05

A series of a new type of tetracyclic carbazolequinones incorporating a carbonyl group at the ortho position relative to the quinone moiety was synthesized and analyzed by tandem electrospray ionization mass spectrometry (ESI/MS-MS), using Collision-Induced Dissociation (CID) to dissociate the protonated species. Theoretical parameters such as molecular electrostatic potential (MEP), local Fukui functions and local Parr function for electrophilic attack as well as proton affinity (PA) and gas phase basicity (GB), were used to explain the preferred protonation sites. Transition states of some main fragmentation routes were obtained and the energies calculated at density functional theory (DFT) B3LYP level were compared with the obtained by ab initio quadratic configuration interaction with single and double excitation (QCISD). The results are in accordance with the observed distribution of ions. The nature of the substituents in the aromatic ring has a notable impact on the fragmentation routes of the molecules.

Protonation Sites, Tandem Mass Spectrometry and Computational Calculations of o-Carbonyl Carbazolequinone Derivatives

PubMed Central

Martínez-Cifuentes, Maximiliano; Clavijo-Allancan, Graciela; Zuñiga-Hormazabal, Pamela; Aranda, Braulio; Barriga, Andrés; Weiss-López, Boris; Araya-Maturana, Ramiro

2016-01-01

A series of a new type of tetracyclic carbazolequinones incorporating a carbonyl group at the ortho position relative to the quinone moiety was synthesized and analyzed by tandem electrospray ionization mass spectrometry (ESI/MS-MS), using Collision-Induced Dissociation (CID) to dissociate the protonated species. Theoretical parameters such as molecular electrostatic potential (MEP), local Fukui functions and local Parr function for electrophilic attack as well as proton affinity (PA) and gas phase basicity (GB), were used to explain the preferred protonation sites. Transition states of some main fragmentation routes were obtained and the energies calculated at density functional theory (DFT) B3LYP level were compared with the obtained by ab initio quadratic configuration interaction with single and double excitation (QCISD). The results are in accordance with the observed distribution of ions. The nature of the substituents in the aromatic ring has a notable impact on the fragmentation routes of the molecules. PMID:27399676

Clinical Mass Spectrometry: Achieving Prominence in Laboratory Medicine

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

Annesley, Thomas M.; Cooks, Robert G.; Herold, David A.

Each year the journal Clinical Chemistry publishes a January special issue on a topic that is relevant to the laboratory medicine community. In January 2016 the topic is mass spectrometry, and the issue is entitled “Clinical Mass Spectrometry: Achieving Prominence in Laboratory Medicine”. One popular feature in our issues is a Q&A on a topic, clearly in this case mass spectrometry. The journal is assembling a panel of 5-6 experts from various areas of mass spectrometry ranging from instrument manufacturing to practicing clinical chemists. Dick Smith is one of the scientist requested to participate in this special issue Q&A onmore » Mass Spectrometry. The Q&A Transcript is attached« less

Mass spectrometry of atmospheric aerosols--recent developments and applications. Part II: On-line mass spectrometry techniques.

PubMed

Pratt, Kerri A; Prather, Kimberly A

2012-01-01

Many of the significant advances in our understanding of atmospheric particles can be attributed to the application of mass spectrometry. Mass spectrometry provides high sensitivity with fast response time to probe chemically complex particles. This review focuses on recent developments and applications in the field of mass spectrometry of atmospheric aerosols. In Part II of this two-part review, we concentrate on real-time mass spectrometry techniques, which provide high time resolution for insight into brief events and diurnal changes while eliminating the potential artifacts acquired during long-term filter sampling. In particular, real-time mass spectrometry has been shown recently to provide the ability to probe the chemical composition of ambient individual particles <30 nm in diameter to further our understanding of how particles are formed through nucleation in the atmosphere. Further, transportable real-time mass spectrometry techniques are now used frequently on ground-, ship-, and aircraft-based studies around the globe to further our understanding of the spatial distribution of atmospheric aerosols. In addition, coupling aerosol mass spectrometry techniques with other measurements in series has allowed the in situ determination of chemically resolved particle effective density, refractive index, volatility, and cloud activation properties. Copyright © 2011 Wiley Periodicals, Inc.

multiplierz v2.0: A Python-based ecosystem for shared access and analysis of native mass spectrometry data.

PubMed

Alexander, William M; Ficarro, Scott B; Adelmant, Guillaume; Marto, Jarrod A

2017-08-01

The continued evolution of modern mass spectrometry instrumentation and associated methods represents a critical component in efforts to decipher the molecular mechanisms which underlie normal physiology and understand how dysregulation of biological pathways contributes to human disease. The increasing scale of these experiments combined with the technological diversity of mass spectrometers presents several challenges for community-wide data access, analysis, and distribution. Here we detail a redesigned version of multiplierz, our Python software library which leverages our common application programming interface (mzAPI) for analysis and distribution of proteomic data. New features include support for a wider range of native mass spectrometry file types, interfaces to additional database search engines, compatibility with new reporting formats, and high-level tools to perform post-search proteomic analyses. A GUI desktop environment, mzDesktop, provides access to multiplierz functionality through a user friendly interface. multiplierz is available for download from: https://github.com/BlaisProteomics/multiplierz; and mzDesktop is available for download from: https://sourceforge.net/projects/multiplierz/. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Halobacterium salinarum NRC-1 PeptideAtlas: strategies for targeted proteomics

PubMed Central

Van, Phu T.; Schmid, Amy K.; King, Nichole L.; Kaur, Amardeep; Pan, Min; Whitehead, Kenia; Koide, Tie; Facciotti, Marc T.; Goo, Young-Ah; Deutsch, Eric W.; Reiss, David J.; Mallick, Parag; Baliga, Nitin S.

2009-01-01

The relatively small numbers of proteins and fewer possible posttranslational modifications in microbes provides a unique opportunity to comprehensively characterize their dynamic proteomes. We have constructed a Peptide Atlas (PA) for 62.7% of the predicted proteome of the extremely halophilic archaeon Halobacterium salinarum NRC-1 by compiling approximately 636,000 tandem mass spectra from 497 mass spectrometry runs in 88 experiments. Analysis of the PA with respect to biophysical properties of constituent peptides, functional properties of parent proteins of detected peptides, and performance of different mass spectrometry approaches has helped highlight plausible strategies for improving proteome coverage and selecting signature peptides for targeted proteomics. Notably, discovery of a significant correlation between absolute abundances of mRNAs and proteins has helped identify low abundance of proteins as the major limitation in peptide detection. Furthermore we have discovered that iTRAQ labeling for quantitative proteomic analysis introduces a significant bias in peptide detection by mass spectrometry. Therefore, despite identifying at least one proteotypic peptide for almost all proteins in the PA, a context-dependent selection of proteotypic peptides appears to be the most effective approach for targeted proteomics. PMID:18652504

Direct analysis of phycobilisomal antenna proteins and metabolites in small cyanobacterial populations by laser ablation electrospray ionization mass spectrometry.

PubMed

Parsiegla, Goetz; Shrestha, Bindesh; Carrière, Frédéric; Vertes, Akos

2012-01-03

Due to their significance in energy and environmental and natural product research, as well as their large genetic diversity, rapid in situ analysis of cyanobacteria is of increasing interest. Metabolic profiles and the composition of energy harvesting antenna protein complexes are needed to understand how environmental factors affect the functioning of these microorganisms. Here, we show that laser ablation electrospray ionization (LAESI) mass spectrometry enables the direct analysis of phycobilisomal antenna proteins and report on numerous metabolites from intact cyanobacteria. Small populations (n < 616 ± 76) of vegetative Anabaena sp. PCC7120 cyanobacterial cells are analyzed by LAESI mass spectrometry. The spectra reveal the ratio of phycocyanin (C-PC) and allophycocyanin (APC) in the antenna complex, the subunit composition of the phycobiliproteins, and the tentative identity of over 30 metabolites and lipids. Metabolites are tentatively identified by accurate mass measurements, isotope distribution patterns, and literature searches. The rapid simultaneous analysis of abundant proteins and diverse metabolites enables the evaluation of the environmental response and metabolic adaptation of cyanobacteria and other microorganisms. © 2011 American Chemical Society

Effect of Genetic Database Comprehensiveness on Fractional Proteomics of Escherichia coli O157:H7

DTIC Science & Technology

2014-01-01

proteins would be observed in the extracellular fraction. 15. SUBJECT TERMS Escherichia coli O157:H7 Liquid chromatography Mass spectrometry...Preparation ...............1 2.2 Liquid Chromatography /Mass Spectrometry Sample Preparation ....................2 2.3 Liquid Chromatography /Mass... Chromatography /Mass Spectrometry Sample Preparation. Samples were prepared for liquid chromatography tandem mass spectrometry (LC-MS/MS) in a similar

The association of low-molecular-weight hydrophobic compounds with native casein micelles in bovine milk.

PubMed

Cheema, M; Mohan, M S; Campagna, S R; Jurat-Fuentes, J L; Harte, F M

2015-08-01

The agreed biological function of the casein micelles in milk is to carry minerals (calcium, magnesium, and phosphorus) from mother to young along with amino acids for growth and development. Recently, native and modified casein micelles were used as encapsulating and delivery agents for various hydrophobic low-molecular-weight probes. The ability of modified casein micelles to bind certain probes may derive from the binding affinity of native casein micelles. Hence, a study with milk from single cows was conducted to further elucidate the association of hydrophobic molecules into native casein micelles and further understand their biological function. Hydrophobic and hydrophilic extraction followed by ultraperformance liquid chromatography-high resolution mass spectrometry analysis were performed over protein fractions obtained from size exclusion fractionation of raw skim milk. Hydrophobic compounds, including phosphatidylcholine, lyso-phosphatidylcholine, phosphatidylethanolamine, and sphingomyelin, showed strong association exclusively to casein micelles as compared with whey proteins, whereas hydrophilic compounds did not display any preference for their association among milk proteins. Further analysis using liquid chromatography-tandem mass spectrometry detected 42 compounds associated solely with the casein-micelles fraction. Mass fragments in tandem mass spectrometry identified 4 of these compounds as phosphatidylcholine with fatty acid composition of 16:0/18:1, 14:0/16:0, 16:0/16:0, and 18:1/18:0. These results support that transporting low-molecular-weight hydrophobic molecules is also a biological function of the casein micelles in milk. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

A novel route to recognizing quaternary ammonium cations using electrospray mass spectrometry.

PubMed

Shackman, Holly M; Ding, Wei; Bolgar, Mark S

2015-01-01

Characterizing and elucidating structures is a commonplace and necessary activity in the pharmaceutical industry with mass spectrometry and NMR being the primary tools for analysis. Although many functional groups are readily identifiable, quaternary ammonium cations have proven to be difficult to unequivocally identify using these techniques. Due to the lack of an N-H bond, quaternary ammonium groups can only be detected in the (1)H NMR spectra by weak signals generated from long-range (14)N-H coupling, which by themselves are inconclusive evidence of a quaternary ammonium functional group. Due to their low intensity, these signals are frequently not detected. Additionally, ions cannot be differentiated in a mass spectrum as an M(+) or [M + H](+) ion without prior knowledge of the compound's structure. In order to utilize mass spectrometry as a tool for determining this functionality, ion cluster formation of quaternary ammonium cations and non-quaternary amines was studied using electrospray ionization. Several mobile phase modifiers were compared; however, the addition of small amounts of trifluoroacetic acid proved superior in producing characteristic and intense [M +2TFA](-) clusters for compounds containing quaternary ammonium cations when using negative electrospray. By fragmenting this characteristic ion using CID, nearly all compounds studied could be unambiguously identified as containing a quaternary ammonium cation or a non-quaternary amine attributable to the presence (non-quaternary amine) or absence (quaternary ammonium cation) of the resulting [2TFA + H](-) ion in the product spectra. This method of analysis provides a rapid, novel, and reliable technique for indicating the presence of quaternary ammonium cations in order to aid in structural elucidation.

The expanding role of mass spectrometry in the field of vaccine development.

PubMed

Sharma, Vaneet Kumar; Sharma, Ity; Glick, James

2018-05-31

Biological mass spectrometry has evolved as a core analytical technology in the last decade mainly because of its unparalleled ability to perform qualitative as well as quantitative profiling of enormously complex biological samples with high mass accuracy, sensitivity, selectivity and specificity. Mass spectrometry-based techniques are also routinely used to assess glycosylation and other post-translational modifications, disulfide bond linkage, and scrambling as well as for the detection of host cell protein contaminants in the field of biopharmaceuticals. The role of mass spectrometry in vaccine development has been very limited but is now expanding as the landscape of global vaccine development is shifting towards the development of recombinant vaccines. In this review, the role of mass spectrometry in vaccine development is presented, some of the ongoing efforts to develop vaccines for diseases with global unmet medical need are discussed and the regulatory challenges of implementing mass spectrometry techniques in a quality control laboratory setting are highlighted. © 2018 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc.

Imaging mass spectrometry statistical analysis.

PubMed

Jones, Emrys A; Deininger, Sören-Oliver; Hogendoorn, Pancras C W; Deelder, André M; McDonnell, Liam A

2012-08-30

Imaging mass spectrometry is increasingly used to identify new candidate biomarkers. This clinical application of imaging mass spectrometry is highly multidisciplinary: expertise in mass spectrometry is necessary to acquire high quality data, histology is required to accurately label the origin of each pixel's mass spectrum, disease biology is necessary to understand the potential meaning of the imaging mass spectrometry results, and statistics to assess the confidence of any findings. Imaging mass spectrometry data analysis is further complicated because of the unique nature of the data (within the mass spectrometry field); several of the assumptions implicit in the analysis of LC-MS/profiling datasets are not applicable to imaging. The very large size of imaging datasets and the reporting of many data analysis routines, combined with inadequate training and accessible reviews, have exacerbated this problem. In this paper we provide an accessible review of the nature of imaging data and the different strategies by which the data may be analyzed. Particular attention is paid to the assumptions of the data analysis routines to ensure that the reader is apprised of their correct usage in imaging mass spectrometry research. Copyright © 2012 Elsevier B.V. All rights reserved.

Traceless Immobilization of Analytes for High-Throughput Experiments with SAMDI Mass Spectrometry.

PubMed

Helal, Kazi Y; Alamgir, Azmain; Berns, Eric J; Mrksich, Milan

2018-06-21

Label-free assays, and particularly those based on the combination of mass spectroscopy with surface chemistries, enable high-throughput experiments of a broad range of reactions. However, these methods can still require the incorporation of functional groups that allow immobilization of reactants and products to surfaces prior to analysis. In this paper, we report a traceless method for attaching molecules to a self-assembled monolayer for matrix-assisted laser desorption and ionization (SAMDI) mass spectrometry. This method uses monolayers that are functionalized with a 3-trifluoromethyl-3-phenyl-diazirine group that liberates nitrogen when irradiated and gives a carbene that inserts into a wide range of bonds to covalently immobilize molecules. Analysis of the monolayer with SAMDI then reveals peaks for each of the adducts formed from molecules in the sample. This method is applied to characterize a P450 drug metabolizing enzyme and to monitor a Suzuki-Miyaura coupling chemical reaction and is important because modification of the substrates with a functional group would alter their activities. This method will be important for high-throughput experiments in many areas, including reaction discovery and optimization.

Illustrating the Concepts of Isotopes and Mass Spectrometry in Introductory Courses: A MALDI-TOF Mass Spectrometry Laboratory Experiment

ERIC Educational Resources Information Center

Dopke, Nancy Carter; Lovett, Timothy Neal

2007-01-01

Mass spectrometry is a widely used and versatile tool for scientists in many different fields. Soft ionization techniques such as matrix-assisted laser desorption/ionization (MALDI) allow for the analysis of biomolecules, polymers, and clusters. This article describes a MALDI mass spectrometry experiment designed for students in introductory…

End-group characterisation of poly(propylene glycol)s by means of electrospray ionisation-tandem mass spectrometry (ESI-MS/MS).

PubMed

Jackson, Anthony T; Slade, Susan E; Thalassinos, Konstantinos; Scrivens, James H

2008-10-01

The end-group functionalisation of a series of poly(propylene glycol)s has been characterised by means of electrospray ionisation-tandem mass spectrometry (ESI-MS/MS). A series of peaks with mass-to-charge ratios that are close to that of the precursor ion were used to generate information on the end-group functionalities of the poly(propylene glycol)s. Fragment ions resulting from losses of both of the end groups were noted from some of the samples. An example is presented of how software can be used to significantly reduce the length of time involved in data interpretation (which is typically the most time-consuming part of the analysis).

Collaborative Undergraduate HBCU Student Summer Training Program Award

DTIC Science & Technology

2012-06-01

facultyTab The Wright Labo ratory is focuse d on defining the composition, activity, and overall cellul ar function of protein complexes in...overall cellul ar function of protein complexes in higher organisms. We utilize quantitative mass spectrometry as a platform to study protein

Time to face the fats: what can mass spectrometry reveal about the structure of lipids and their interactions with proteins?

PubMed

Brown, Simon H J; Mitchell, Todd W; Oakley, Aaron J; Pham, Huong T; Blanksby, Stephen J

2012-09-01

Since the 1950s, X-ray crystallography has been the mainstay of structural biology, providing detailed atomic-level structures that continue to revolutionize our understanding of protein function. From recent advances in this discipline, a picture has emerged of intimate and specific interactions between lipids and proteins that has driven renewed interest in the structure of lipids themselves and raised intriguing questions as to the specificity and stoichiometry in lipid-protein complexes. Herein we demonstrate some of the limitations of crystallography in resolving critical structural features of ligated lipids and thus determining how these motifs impact protein binding. As a consequence, mass spectrometry must play an important and complementary role in unraveling the complexities of lipid-protein interactions. We evaluate recent advances and highlight ongoing challenges towards the twin goals of (1) complete structure elucidation of low, abundant, and structurally diverse lipids by mass spectrometry alone, and (2) assignment of stoichiometry and specificity of lipid interactions within protein complexes.

Time to Face the Fats: What Can Mass Spectrometry Reveal about the Structure of Lipids and Their Interactions with Proteins?

NASA Astrophysics Data System (ADS)

Brown, Simon H. J.; Mitchell, Todd W.; Oakley, Aaron J.; Pham, Huong T.; Blanksby, Stephen J.

2012-09-01

Since the 1950s, X-ray crystallography has been the mainstay of structural biology, providing detailed atomic-level structures that continue to revolutionize our understanding of protein function. From recent advances in this discipline, a picture has emerged of intimate and specific interactions between lipids and proteins that has driven renewed interest in the structure of lipids themselves and raised intriguing questions as to the specificity and stoichiometry in lipid-protein complexes. Herein we demonstrate some of the limitations of crystallography in resolving critical structural features of ligated lipids and thus determining how these motifs impact protein binding. As a consequence, mass spectrometry must play an important and complementary role in unraveling the complexities of lipid-protein interactions. We evaluate recent advances and highlight ongoing challenges towards the twin goals of (1) complete structure elucidation of low, abundant, and structurally diverse lipids by mass spectrometry alone, and (2) assignment of stoichiometry and specificity of lipid interactions within protein complexes.

Improved Steroids Detection and Evidence for Their Regiospecific Decompositions Using Anion Attachment Mass Spectrometry.

PubMed

Dumont, Quentin; Bárcenas, Mariana; Dossmann, Héloïse; Bailloux, Isabelle; Buisson, Corinne; Mechin, Nathalie; Molina, Adeline; Lasne, Françoise; Rannulu, Nalaka S; Cole, Richard B

2016-04-05

Nonpolar anabolic steroids are doping agents that typically do not provide strong signals by electrospray ionization-mass spectrometry (ESI-MS) owing especially to the low polarity of the functional groups present. We have investigated the addition of anions, in ammonium salt form, to anabolic steroid samples as ionization enhancers and have confirmed that lower instrumental limits of detection (as low as 10 ng/mL for fluoxymesterone-M) are obtained by fluoride anion attachment mass spectrometry, as compared to ESI(+)/(-) or atmospheric pressure photoionization (APPI)(+). Moreover, collision-induced decomposition (CID) spectra of precursor fluoride adducts of the bifunctional steroid "reduced pregnenolone" (containing two hydroxyl groups) and its d4-analogue provide evidence of regiospecific decompositions after attachment of fluoride anion to a specific hydroxyl group of the steroid. This type of charting of specific CID reaction pathways can offer value to selected reaction monitoring experiments (SRM) as it may result in a gain in selectivity in detection as well as in improvements in quantification.

Regional differences in brain glucose metabolism determined by imaging mass spectrometry.

PubMed

Kleinridders, André; Ferris, Heather A; Reyzer, Michelle L; Rath, Michaela; Soto, Marion; Manier, M Lisa; Spraggins, Jeffrey; Yang, Zhihong; Stanton, Robert C; Caprioli, Richard M; Kahn, C Ronald

2018-06-01

Glucose is the major energy substrate of the brain and crucial for normal brain function. In diabetes, the brain is subject to episodes of hypo- and hyperglycemia resulting in acute outcomes ranging from confusion to seizures, while chronic metabolic dysregulation puts patients at increased risk for depression and Alzheimer's disease. In the present study, we aimed to determine how glucose is metabolized in different regions of the brain using imaging mass spectrometry (IMS). To examine the relative abundance of glucose and other metabolites in the brain, mouse brain sections were subjected to imaging mass spectrometry at a resolution of 100 μm. This was correlated with immunohistochemistry, qPCR, western blotting and enzyme assays of dissected brain regions to determine the relative contributions of the glycolytic and pentose phosphate pathways to regional glucose metabolism. In brain, there are significant regional differences in glucose metabolism, with low levels of hexose bisphosphate (a glycolytic intermediate) and high levels of the pentose phosphate pathway (PPP) enzyme glucose-6-phosphate dehydrogenase (G6PD) and PPP metabolite hexose phosphate in thalamus compared to cortex. The ratio of ATP to ADP is significantly higher in white matter tracts, such as corpus callosum, compared to less myelinated areas. While the brain is able to maintain normal ratios of hexose phosphate, hexose bisphosphate, ATP, and ADP during fasting, fasting causes a large increase in cortical and hippocampal lactate. These data demonstrate the importance of direct measurement of metabolic intermediates to determine regional differences in brain glucose metabolism and illustrate the strength of imaging mass spectrometry for investigating the impact of changing metabolic states on brain function at a regional level with high resolution. Copyright © 2018 The Authors. Published by Elsevier GmbH.. All rights reserved.

Time‐of‐flight secondary ion mass spectrometry imaging of biological samples with delayed extraction for high mass and high spatial resolutions

PubMed Central

Vanbellingen, Quentin P.; Elie, Nicolas; Eller, Michael J.; Della‐Negra, Serge; Touboul, David

2015-01-01

Rationale In Time‐of‐Flight Secondary Ion Mass Spectrometry (TOF‐SIMS), pulsed and focused primary ion beams enable mass spectrometry imaging, a method which is particularly useful to map various small molecules such as lipids at the surface of biological samples. When using TOF‐SIMS instruments, the focusing modes of the primary ion beam delivered by liquid metal ion guns can provide either a mass resolution of several thousand or a sub‐µm lateral resolution, but the combination of both is generally not possible. Methods With a TOF‐SIMS setup, a delayed extraction applied to secondary ions has been studied extensively on rat cerebellum sections in order to compensate for the effect of long primary ion bunches. Results The use of a delayed extraction has been proven to be an efficient solution leading to unique features, i.e. a mass resolution up to 10000 at m/z 385.4 combined with a lateral resolution of about 400 nm. Simulations of ion trajectories confirm the experimental determination of optimal delayed extraction and allow understanding of the behavior of ions as a function of their mass‐to‐charge ratio. Conclusions Although the use of a delayed extraction has been well known for many years and is very popular in MALDI, it is much less used in TOF‐SIMS. Its full characterization now enables secondary ion images to be recorded in a single run with a submicron spatial resolution and with a mass resolution of several thousand. This improvement is very useful when analyzing lipids on tissue sections, or rare, precious, or very small size samples. © 2015 The Authors. Rapid Communications in Mass Spectrometry published by John Wiley & Sons Ltd. PMID:26395603

Single-protein nanomechanical mass spectrometry in real time

PubMed Central

Hanay, M.S.; Kelber, S.; Naik, A.K.; Chi, D.; Hentz, S.; Bullard, E.C.; Colinet, E.; Duraffourg, L.; Roukes, M.L.

2012-01-01

Nanoelectromechanical systems (NEMS) resonators can detect mass with exceptional sensitivity. Previously, mass spectra from several hundred adsorption events were assembled in NEMS-based mass spectrometry using statistical analysis. Here, we report the first realization of single-molecule NEMS-based mass spectrometry in real time. As each molecule in the sample adsorbs upon the NEMS resonator, its mass and the position-of-adsorption are determined by continuously tracking two driven vibrational modes of the device. We demonstrate the potential of multimode NEMS-based mass spectrometry by analyzing IgM antibody complexes in real-time. NEMS-MS is a unique and promising new form of mass spectrometry: it can resolve neutral species, provides resolving power that increases markedly for very large masses, and allows acquisition of spectra, molecule-by-molecule, in real-time. PMID:22922541

Comparison of analytical performances of inductively coupled plasma mass spectrometry and inductively coupled plasma atomic emission spectrometry for trace analysis of bismuth and bismuth oxide

NASA Astrophysics Data System (ADS)

Medvedev, Nickolay S.; Shaverina, Anastasiya V.; Tsygankova, Alphiya R.; Saprykin, Anatoly I.

2018-04-01

The paper presents а comparison of analytical performances of inductively coupled plasma mass spectrometry (ICP-MS) and inductively coupled plasma atomic emission spectrometry (ICP-AES) for trace analysis of high purity bismuth and bismuth oxide. Matrix effects in the ICP-MS and ICP-AES methods were studied as a function of Bi concentration, ICP power and nebulizer flow rate. For ICP-MS the strong dependence of the matrix effects versus the atomic mass of analytes was observed. For ICP-AES the minimal matrix effects were achieved for spectral lines of analytes with low excitation potentials. The optimum degree of sample dilution providing minimum values of the limits of detection (LODs) was chosen. Both methods let us to reach LODs from n·10-7 to n·10-4 wt% for more than 50 trace elements. For most elements the LODs of ICP-MS were lower in comparison to ICP-AES. Validation of accuracy of the developed techniques was performed by "added-found" experiments and by comparison of the results of ICP-MS and ICP-AES analysis of high-purity bismuth oxide.

Characterization of polyesters by matrix-assisted laser desorption/ionization and Fourier transform mass spectrometry.

PubMed

Mize, Todd H; Simonsick, William J; Amster, I Jonathan

2003-01-01

Two homopolyesters, poly(neopentyl glycol-alt-isophthalic acid) and poly(hexanediol-alt-azelaic acid), and two copolyesters, poly(dipropoxylated bisphenol-A-alt-(isophthalic acid-co-adipic acid)) and poly(neopentyl glycol-alt-(adipic acid-co-isophthalic acid)) were analyzed by internal source matrix assisted laser desorption/ionization Fourier transform mass spectrometry (MALDI-FTMS). The high resolution and high mass accuracy provided by FTMS greatly facilitate the characterization of the polyester and copolyester samples. Isobaric resolution allows the ion abundances of overlapping isotopic envelopes to be assessed. Repeat units were confirmed and end functionality assigned. Single shot mass spectra of the entire polymeric distribution demonstrate that the dynamic range of this internal MALDI source instrument and the analyzer cell exceeds performance of those previously reported for higher field instruments. Corrections of space charge mass shift effects are demonstrated for the analytes using an external calibrant and (subsequent to confirmation of structure) via internal calibration which removes ambiguity due to space charge differences in calibrant and analyte spectra. Capillary gel permeation chromatography was used to prepare low polydispersity samples from a high polydispersity polyester, improving the measurement of molecular weight distribution two-fold while retaining the benefits of high resolution mass spectrometry for elucidation of oligomer identity.

The life sciences mass spectrometry research unit.

PubMed

Hopfgartner, Gérard; Varesio, Emmanuel

2012-01-01

The Life Sciences Mass Spectrometry (LSMS) research unit focuses on the development of novel analytical workflows based on innovative mass spectrometric and software tools for the analysis of low molecular weight compounds, peptides and proteins in complex biological matrices. The present article summarizes some of the recent work of the unit: i) the application of matrix-assisted laser desorption/ionization (MALDI) for mass spectrometry imaging (MSI) of drug of abuse in hair, ii) the use of high resolution mass spectrometry for simultaneous qualitative/quantitative analysis in drug metabolism and metabolomics, and iii) the absolute quantitation of proteins by mass spectrometry using the selected reaction monitoring mode.

The allure of mass spectrometry: From an earlyday chemist's perspective.

PubMed

Tőkés, László

2017-07-01

This reminiscing review article is an account of the author's fascination and involvements with mass spectrometry from the perspective of an organic chemist with an interest in natural product chemistry. It covers a period from 1961 through the mid 1990s as mass spectrometry evolved form a novelty technique to become a most widely used analytical technique. Following a brief synopsis of my pathway to mass spectrometry, my research efforts in this field are presented with a focus mainly on evolving principles and technologies which I had personal involvements with. To provide historical perspectives, discussions of these developments are accompanied by brief outlines of the relevant state-of-the-art, shedding light on the technical and conceptual challenges encountered during those early days in mass spectrometry. Examples are presented of my involvements with basic and applied research in mass spectrometry during graduate studies at Stanford University and close to three decade tenure in pharmaceutical research at Syntex Research. My basic research interests focused mainly on principles of electron ionization induced fragmentation mechanisms, with an emphasis on steroids and other model compounds. Extensive deuterium labeling evidence was used to determine the fragmentation mechanisms of the diagnostically significant ions in the spectra of numerous model compounds, uncovering examples of wide-ranging hydrogen transfers, skeletal rearrangements, methyl and phenyl migrations, stereoselective fragmentations and low and high energy fragmentation processes. Depiction of the industrial research phase of my career includes comments on the pivotal role mass spectrometry played on advancing modern pharmaceutical research. Examples are presented of involvements with instrumental developments and a few select cases of applied research, including studies of bile mechanisms in vertebrates, identification of bisphenol-A leaching from sterilized polycarbonate containers, high sensitivity TCDD analyses and other projects. Reflecting on my services for the mass spectrometry society, involvements with the co-founding and 12 year chairing of the Asilomar Conference on Mass Spectrometry and founding of the Bay Area Mass Spectrometry regional MS discussion group, as part of my services for the mass spectrometry community, are presented in some detail. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:520-542, 2017. © 2016 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc.

Identification of Fatty Acids, Phospholipids, and Their Oxidation Products Using Matrix-Assisted Laser Desorption Ionization Mass Spectrometry and Electrospray Ionization Mass Spectrometry

ERIC Educational Resources Information Center

Harmon, Christopher W.; Mang, Stephen A.; Greaves, John; Finlayson-Pitts, Barbara J.

2010-01-01

Electrospray ionization mass spectrometry (ESI-MS) and matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) have found increasing application in the analysis of biological samples. Using these techniques to solve problems in analytical chemistry should be an essential component of the training of undergraduate chemists. We…

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.

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.

Mass Spectrometry Imaging of Biological Tissue: An Approach for Multicenter Studies

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

Rompp, Andreas; Both, Jean-Pierre; Brunelle, Alain

2015-03-01

Mass spectrometry imaging has become a popular tool for probing the chemical complexity of biological surfaces. This led to the development of a wide range of instrumentation and preparation protocols. It is thus desirable to evaluate and compare the data output from different methodologies and mass spectrometers. Here, we present an approach for the comparison of mass spectrometry imaging data from different laboratories (often referred to as multicenter studies). This is exemplified by the analysis of mouse brain sections in five laboratories in Europe and the USA. The instrumentation includes matrix-assisted laser desorption/ionization (MALDI)-time-of-flight (TOF), MALDI-QTOF, MALDIFourier transform ion cyclotronmore » resonance (FTICR), atmospheric-pressure (AP)-MALDI-Orbitrap, and cluster TOF-secondary ion mass spectrometry (SIMS). Experimental parameters such as measurement speed, imaging bin width, and mass spectrometric parameters are discussed. All datasets were converted to the standard data format imzML and displayed in a common open-source software with identical parameters for visualization, which facilitates direct comparison of MS images. The imzML conversion also allowed exchange of fully functional MS imaging datasets between the different laboratories. The experiments ranged from overview measurements of the full mouse brain to detailed analysis of smaller features (depending on spatial resolution settings), but common histological features such as the corpus callosum were visible in all measurements. High spatial resolution measurements of AP-MALDI-Orbitrap and TOF-SIMS showed comparable structures in the low-micrometer range. We discuss general considerations for planning and performing multicenter studies in mass spectrometry imaging. This includes details on the selection, distribution, and preparation of tissue samples as well as on data handling. Such multicenter studies in combination with ongoing activities for reporting guidelines, a common data format (imzML) and a public data repository can contribute to more reliability and transparency of MS imaging studies.« less

Imaging mass spectrometry in drug development and toxicology.

PubMed

Karlsson, Oskar; Hanrieder, Jörg

2017-06-01

During the last decades, imaging mass spectrometry has gained significant relevance in biomedical research. Recent advances in imaging mass spectrometry have paved the way for in situ studies on drug development, metabolism and toxicology. In contrast to whole-body autoradiography that images the localization of radiolabeled compounds, imaging mass spectrometry provides the possibility to simultaneously determine the discrete tissue distribution of the parent compound and its metabolites. In addition, imaging mass spectrometry features high molecular specificity and allows comprehensive, multiplexed detection and localization of hundreds of proteins, peptides and lipids directly in tissues. Toxicologists traditionally screen for adverse findings by histopathological examination. However, studies of the molecular and cellular processes underpinning toxicological and pathologic findings induced by candidate drugs or toxins are important to reach a mechanistic understanding and an effective risk assessment strategy. One of IMS strengths is the ability to directly overlay the molecular information from the mass spectrometric analysis with the tissue section and allow correlative comparisons of molecular and histologic information. Imaging mass spectrometry could therefore be a powerful tool for omics profiling of pharmacological/toxicological effects of drug candidates and toxicants in discrete tissue regions. The aim of the present review is to provide an overview of imaging mass spectrometry, with particular focus on MALDI imaging mass spectrometry, and its use in drug development and toxicology in general.

Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts

PubMed Central

Frenkel-Morgenstern, Milana; Lacroix, Vincent; Ezkurdia, Iakes; Levin, Yishai; Gabashvili, Alexandra; Prilusky, Jaime; del Pozo, Angela; Tress, Michael; Johnson, Rory; Guigo, Roderic; Valencia, Alfonso

2012-01-01

Chimeric RNAs comprise exons from two or more different genes and have the potential to encode novel proteins that alter cellular phenotypes. To date, numerous putative chimeric transcripts have been identified among the ESTs isolated from several organisms and using high throughput RNA sequencing. The few corresponding protein products that have been characterized mostly result from chromosomal translocations and are associated with cancer. Here, we systematically establish that some of the putative chimeric transcripts are genuinely expressed in human cells. Using high throughput RNA sequencing, mass spectrometry experimental data, and functional annotation, we studied 7424 putative human chimeric RNAs. We confirmed the expression of 175 chimeric RNAs in 16 human tissues, with an abundance varying from 0.06 to 17 RPKM (Reads Per Kilobase per Million mapped reads). We show that these chimeric RNAs are significantly more tissue-specific than non-chimeric transcripts. Moreover, we present evidence that chimeras tend to incorporate highly expressed genes. Despite the low expression level of most chimeric RNAs, we show that 12 novel chimeras are translated into proteins detectable in multiple shotgun mass spectrometry experiments. Furthermore, we confirm the expression of three novel chimeric proteins using targeted mass spectrometry. Finally, based on our functional annotation of exon organization and preserved domains, we discuss the potential features of chimeric proteins with illustrative examples and suggest that chimeras significantly exploit signal peptides and transmembrane domains, which can alter the cellular localization of cognate proteins. Taken together, these findings establish that some chimeric RNAs are translated into potentially functional proteins in humans. PMID:22588898

Characterization of drug-eluting stent (DES) materials with cluster secondary ion mass spectrometry (SIMS)

NASA Astrophysics Data System (ADS)

Mahoney, Christine M.; Patwardhan, Dinesh V.; Ken McDermott, M.

2006-07-01

Secondary ion mass spectrometry (SIMS) employing an SF 5+ polyatomic primary ion source was utilized to analyze several materials commonly used in drug-eluting stents (DES). Poly(ethylene- co-vinyl acetate) (PEVA), poly(lactic- co-glycolic acid) (PLGA) and various poly(urethanes) were successfully depth profiled using SF 5+ bombardment. The resultant molecular depth profiles obtained from these polymeric films showed very little degradation in molecular signal as a function of increasing SF 5+ primary ion dose when experiments were performed at low temperatures (signal was maintained for doses up to ˜5 × 10 15 ions/cm 2). Temperature was determined to be an important parameter in both the success of the depth profiles and the mass spectral analysis of the polymers. In addition to the pristine polymer films, paclitaxel (drug released in Taxus™ stent) containing PLGA films were also characterized, where it was confirmed that both drug and polymer signals could be monitored as a function of depth at lower paclitaxel concentrations (10 wt%).

Protein Structural Analysis via Mass Spectrometry-Based Proteomics

PubMed Central

Artigues, Antonio; Nadeau, Owen W.; Rimmer, Mary Ashley; Villar, Maria T.; Du, Xiuxia; Fenton, Aron W.; Carlson, Gerald M.

2017-01-01

Modern mass spectrometry (MS) technologies have provided a versatile platform that can be combined with a large number of techniques to analyze protein structure and dynamics. These techniques include the three detailed in this chapter: 1) hydrogen/deuterium exchange (HDX), 2) limited proteolysis, and 3) chemical crosslinking (CX). HDX relies on the change in mass of a protein upon its dilution into deuterated buffer, which results in varied deuterium content within its backbone amides. Structural information on surface exposed, flexible or disordered linker regions of proteins can be achieved through limited proteolysis, using a variety of proteases and only small extents of digestion. CX refers to the covalent coupling of distinct chemical species and has been used to analyze the structure, function and interactions of proteins by identifying crosslinking sites that are formed by small multi-functional reagents, termed crosslinkers. Each of these MS applications is capable of revealing structural information for proteins when used either with or without other typical high resolution techniques, including NMR and X-ray crystallography. PMID:27975228

Role of Mass Spectrometry in Clinical Endocrinology.

PubMed

Ketha, Siva S; Singh, Ravinder J; Ketha, Hemamalini

2017-09-01

The advent of mass spectrometry into the clinical laboratory has led to an improvement in clinical management of several endocrine diseases. Liquid chromatography tandem mass spectrometry found some of its first clinical applications in the diagnosis of inborn errors of metabolism, in quantitative steroid analysis, and in drug analysis laboratories. Mass spectrometry assays offer analytical sensitivity and specificity that is superior to immunoassays for many analytes. This article highlights several areas of clinical endocrinology that have witnessed the use of liquid chromatography tandem mass spectrometry to improve clinical outcomes. Copyright © 2017 Elsevier Inc. All rights reserved.

Recent advances in lipid separations and structural elucidation using mass spectrometry combined with ion mobility spectrometry, ion-molecule reactions and fragmentation approaches

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

Zheng, Xueyun; Smith, Richard D.; Baker, Erin S.

Lipids are a vital class of molecules that play important and varied roles in biological processes. Fully understanding lipid roles, however, is extremely difficult since the number and diversity of lipid species is immense, with cells expressing hundreds of enzymes that synthesize tens of thousands of different lipids. While recent advances in chromatography and high resolution mass spectrometry have greatly progressed the understanding of lipid species and functions, effectively separating many lipids still remains problematic. Isomeric lipids have made lipid characterization especially difficult and occur due to subclasses having the same chemical composition, or species having multiple acyl chains connectivitiesmore » (sn-1, sn-2, or sn-3), double bond positions and orientations (cis or trans), and functional group stereochemistry (R versus S). Fully understanding the roles of lipids in biological processes therefore requires separating and evaluating how isomers change in biological and environmental samples. To address this challenge, ion mobility spectrometry separations, ion-molecule reactions and fragmentation techniques have increasingly been added to lipid analysis workflows to improve identifications. In this manuscript, we review the current state of these approaches and their capabilities for improving the identification of specific lipid species.« less

Advances in imaging secondary ion mass spectrometry for biological samples

DOE PAGES

Boxer, Steven G.; Kraft, Mary L.; Weber, Peter K.

2008-12-16

Imaging mass spectrometry combines the power of mass spectrometry to identify complex molecules based on mass with sample imaging. Recent advances in secondary ion mass spectrometry have improved sensitivity and spatial resolution, so that these methods have the potential to bridge between high-resolution structures obtained by X-ray crystallography and cyro-electron microscopy and ultrastructure visualized by conventional light microscopy. Following background information on the method and instrumentation, we address the key issue of sample preparation. Because mass spectrometry is performed in high vacuum, it is essential to preserve the lateral organization of the sample while removing bulk water, and this hasmore » been a major barrier for applications to biological systems. Furthermore, recent applications of imaging mass spectrometry to cell biology, microbial communities, and biosynthetic pathways are summarized briefly, and studies of biological membrane organization are described in greater depth.« less

Crux: Rapid Open Source Protein Tandem Mass Spectrometry Analysis

PubMed Central

2015-01-01

Efficiently and accurately analyzing big protein tandem mass spectrometry data sets requires robust software that incorporates state-of-the-art computational, machine learning, and statistical methods. The Crux mass spectrometry analysis software toolkit (http://cruxtoolkit.sourceforge.net) is an open source project that aims to provide users with a cross-platform suite of analysis tools for interpreting protein mass spectrometry data. PMID:25182276

TUBEs-Mass Spectrometry for Identification and Analysis of the Ubiquitin-Proteome.

PubMed

Azkargorta, Mikel; Escobes, Iraide; Elortza, Felix; Matthiesen, Rune; Rodríguez, Manuel S

2016-01-01

Mass spectrometry (MS) has become the method of choice for the large-scale analysis of protein ubiquitylation. There exist a number of proposed methods for mapping ubiquitin sites, each with different pros and cons. We present here a protocol for the MS analysis of the ubiquitin-proteome captured by TUBEs and subsequent data analysis. Using dedicated software and algorithms, specific information on the presence of ubiquitylated peptides can be obtained from the MS search results. In addition, a quantitative and functional analysis of the ubiquitylated proteins and their interacting partners helps to unravel the biological and molecular processes they are involved in.

Direct Analysis in Real Time (DART) of an Organothiophosphate at Ultrahigh Resolution by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry and Tandem Mass Spectrometry

PubMed Central

Prokai, Laszlo; Stevens, Stanley M.

2016-01-01

Direct analysis in real time (DART) is a recently developed ambient ionization technique for mass spectrometry to enable rapid and sensitive analyses with little or no sample preparation. After swab-based field sampling, the organothiophosphate malathion was analyzed using DART-Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) and tandem mass spectrometry (MS/MS). Mass resolution was documented to be over 800,000 in full-scan MS mode and over 1,000,000 for an MS/MS product ion produced by collision-induced dissociation of the protonated analyte. Mass measurement accuracy below 1 ppm was obtained for all DART-generated ions that belonged to the test compound in the mass spectra acquired using only external mass calibration. This high mass measurement accuracy, achievable at present only through FTMS, was required for unequivocal identification of the corresponding molecular formulae. PMID:26784186

Direct Analysis in Real Time (DART) of an Organothiophosphate at Ultrahigh Resolution by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry and Tandem Mass Spectrometry.

PubMed

Prokai, Laszlo; Stevens, Stanley M

2016-01-16

Direct analysis in real time (DART) is a recently developed ambient ionization technique for mass spectrometry to enable rapid and sensitive analyses with little or no sample preparation. After swab-based field sampling, the organothiophosphate malathion was analyzed using DART-Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) and tandem mass spectrometry (MS/MS). Mass resolution was documented to be over 800,000 in full-scan MS mode and over 1,000,000 for an MS/MS product ion produced by collision-induced dissociation of the protonated analyte. Mass measurement accuracy below 1 ppm was obtained for all DART-generated ions that belonged to the test compound in the mass spectra acquired using only external mass calibration. This high mass measurement accuracy, achievable at present only through FTMS, was required for unequivocal identification of the corresponding molecular formulae.

Characterization of Long-Chain Fatty Acid as N-(4-Aminomethylphenyl) Pyridinium Derivative by MALDI LIFT-TOF/TOF Mass Spectrometry

NASA Astrophysics Data System (ADS)

Frankfater, Cheryl; Jiang, Xuntian; Hsu, Fong-Fu

2018-05-01

Charge remote fragmentation (CRF) elimination of CnH2n+2 residues along the aliphatic tail of long chain fatty acid is hall mark of keV high-energy CID fragmentation process. It is an important fragmentation pathway leading to structural characterization of biomolecules by CID tandem mass spectrometry. In this report, we describe MALDI LIFT TOF-TOF mass spectrometric approach to study a wide variety of fatty acids (FAs), which were derivatized to N-(4-aminomethylphenyl) pyridinium (AMPP) derivative, and desorbed as M+ ions by laser with or without matrix. The high-energy MALDI LIFT TOF-TOF mass spectra of FA-AMPP contain fragment ions mainly deriving from CRF cleavages of CnH2n+2 residues, as expected. These ions together with ions from specific cleavages of the bond(s) involving the functional group within the molecule provide more complete structural identification than those produced by low-energy CID/HCD using a linear ion-trap instrument. However, this LIFT TOF-TOF mass spectrometric approach inherits low sensitivity, a typical feature of high-energy CID tandem mass spectrometry. Because of the lack of unit mass precursor ion selection with sufficient sensitivity of the current LIFT TOF-TOF technology, product ion spectra from same chain length fatty acids with difference in one or two double bonds in a mixture are not distinguishable.

Functional phosphoproteomic mass spectrometry-based approaches

PubMed Central

2012-01-01

Mass Spectrometry (MS)-based phosphoproteomics tools are crucial for understanding the structure and dynamics of signaling networks. Approaches such as affinity purification followed by MS have also been used to elucidate relevant biological questions in health and disease. The study of proteomes and phosphoproteomes as linked systems, rather than research studies of individual proteins, are necessary to understand the functions of phosphorylated and un-phosphorylated proteins under spatial and temporal conditions. Phosphoproteome studies also facilitate drug target protein identification which may be clinically useful in the near future. Here, we provide an overview of general principles of signaling pathways versus phosphorylation. Likewise, we detail chemical phosphoproteomic tools, including pros and cons with examples where these methods have been applied. In addition, basic clues of electrospray ionization and collision induced dissociation fragmentation are detailed in a simple manner for successful phosphoproteomic clinical studies. PMID:23369623

Supported inhibitor for fishing lipases in complex biological media and mass spectrometry identification.

PubMed

Delorme, Vincent; Raux, Brigitt; Puppo, Rémy; Leclaire, Julien; Cavalier, Jean-François; Marc, Sylvain; Kamarajugadda, Pavan-Kumar; Buono, Gérard; Fotiadu, Frédéric; Canaan, Stéphane; Carrière, Frédéric

2014-12-01

A synthetic phosphonate inhibitor designed for lipase inhibition but displaying a broader range of activity was covalently immobilized on a solid support to generate a function-directed tool targeting serine hydrolases. To achieve this goal, straightforward and reliable analytical techniques were developed, allowing the monitoring of the solid support's chemical functionalization, enzyme capture processes and physisorption artifacts. This grafted inhibitor was tested on pure lipases and serine proteases from various origins, and assayed for the selective capture of lipases from several complex biological extracts. The direct identification of captured enzymes by mass spectrometry brought the proof of concept on the efficiency of this supported covalent inhibitor. The features and limitations of this "enzyme-fishing" proteomic tool provide new insight on solid-liquid inhibition process. Copyright © 2014. Published by Elsevier B.V.

The functional interactome landscape of the human histone deacetylase family

PubMed Central

Joshi, Preeti; Greco, Todd M; Guise, Amanda J; Luo, Yang; Yu, Fang; Nesvizhskii, Alexey I; Cristea, Ileana M

2013-01-01

Histone deacetylases (HDACs) are a diverse family of essential transcriptional regulatory enzymes, that function through the spatial and temporal recruitment of protein complexes. As the composition and regulation of HDAC complexes are only partially characterized, we built the first global protein interaction network for all 11 human HDACs in T cells. Integrating fluorescence microscopy, immunoaffinity purifications, quantitative mass spectrometry, and bioinformatics, we identified over 200 unreported interactions for both well-characterized and lesser-studied HDACs, a subset of which were validated by orthogonal approaches. We establish HDAC11 as a member of the survival of motor neuron complex and pinpoint a functional role in mRNA splicing. We designed a complementary label-free and metabolic-labeling mass spectrometry-based proteomics strategy for profiling interaction stability among different HDAC classes, revealing that HDAC1 interactions within chromatin-remodeling complexes are largely stable, while transcription factors preferentially exist in rapid equilibrium. Overall, this study represents a valuable resource for investigating HDAC functions in health and disease, encompassing emerging themes of HDAC regulation in cell cycle and RNA processing and a deeper functional understanding of HDAC complex stability. PMID:23752268

Modification of Keap1 Cysteine Residues by Sulforaphane

PubMed Central

Hu, Chenqi; Eggler, Aimee L.; Mesecar, Andrew D.; van Breemen, Richard B.

2011-01-01

Activation of the transcription factor NF-E2-related factor-2 (Nrf2) through modification of Kelch-like ECH-associated protein 1 (Keap1) cysteines, leading to up-regulation of the antioxidant response element (ARE), is an important mechanism of cellular defense against reactive oxygen species and xenobiotic electrophiles. Sulforaphane, occurring in cruciferous vegetables such as broccoli, is a potent natural ARE activator that functions by modifying Keap1 cysteine residues, but there are conflicting in vitro and in vivo data regarding which of these cysteine residues react. Although most biological data indicate that modification of C151 is essential for sulforaphane action, some recent studies using mass spectrometry have failed to identify C151 as a site of Keap1 sulforaphane reaction. We have reconciled these conflicting data using mass spectrometry with a revised sample preparation protocol and confirmed that C151 is indeed among the most readily modified cysteines of Keap1 by sulforaphane. Previous mass spectrometry-based studies used iodoacetamide during sample preparation to derivatize free cysteine sulfhydryl groups causing loss of sulforaphane from highly reactive and reversible cysteine residues on Keap1 including C151. By omitting iodoacetamide from the protocol and reducing sample preparation time, our mass spectrometry-based studies now confirm previous cell-based studies which showed that sulforaphane reacts with at least four cysteine residues of Keap1 including C151. PMID:21391649

A novel sidestream ultrasonic flow sensor for multiple breath washout in children.

PubMed

Fuchs, Susanne I; Sturz, J; Junge, S; Ballmann, M; Gappa, M

2008-08-01

Inert gas multiple breath washout (MBW) for measuring Lung Clearance Index using mass spectrometry and 4% sulfur hexafluoride (SF(6)) as the tracer gas has been shown to be sensitive for detecting early Cystic Fibrosis (CF) lung disease. However, mass spectrometry requires bulky equipment and is expensive to buy and maintain. A novel sidestream ultrasonic device may overcome this problem. The aims of this study were to assess the feasibility and clinical validity of measuring lung volume (functional residual capacity, FRC) and the LCI using the sidestream ultrasonic flow sensor in children and adolescents with CF in relation to spirometry and plain chest radiographs. MBW using the sidestream ultrasonic device and conventional spirometry were performed in 26 patients with CF and 22 healthy controls. In the controls (4.7-17.7 years) LCI was similar to that reported using mass spectrometry (mean (SD) 6.7 (0.5)). LCI was elevated in 77% of the CF children (6.8-18.9 years), whereas spirometry was abnormal in only 38.5%, 61.5%, and 26.9% for FEV(1), MEF(25), and FEV(1)/FVC, respectively. This was more marked in children <10 years. LCI correlated with the Crispin-Norman score, whereas FEV(1) did not. Sidestream ultrasonic MBW is a valid and simple alternative to mass spectrometry for assessing ventilation homogeneity in children. (c) 2008 Wiley-Liss, Inc.

Binomial probability distribution model-based protein identification algorithm for tandem mass spectrometry utilizing peak intensity information.

PubMed

Xiao, Chuan-Le; Chen, Xiao-Zhou; Du, Yang-Li; Sun, Xuesong; Zhang, Gong; He, Qing-Yu

2013-01-04

Mass spectrometry has become one of the most important technologies in proteomic analysis. Tandem mass spectrometry (LC-MS/MS) is a major tool for the analysis of peptide mixtures from protein samples. The key step of MS data processing is the identification of peptides from experimental spectra by searching public sequence databases. Although a number of algorithms to identify peptides from MS/MS data have been already proposed, e.g. Sequest, OMSSA, X!Tandem, Mascot, etc., they are mainly based on statistical models considering only peak-matches between experimental and theoretical spectra, but not peak intensity information. Moreover, different algorithms gave different results from the same MS data, implying their probable incompleteness and questionable reproducibility. We developed a novel peptide identification algorithm, ProVerB, based on a binomial probability distribution model of protein tandem mass spectrometry combined with a new scoring function, making full use of peak intensity information and, thus, enhancing the ability of identification. Compared with Mascot, Sequest, and SQID, ProVerB identified significantly more peptides from LC-MS/MS data sets than the current algorithms at 1% False Discovery Rate (FDR) and provided more confident peptide identifications. ProVerB is also compatible with various platforms and experimental data sets, showing its robustness and versatility. The open-source program ProVerB is available at http://bioinformatics.jnu.edu.cn/software/proverb/ .

Mass spectrometry in grape and wine chemistry. Part II: The consumer protection.

PubMed

Flamini, Riccardo; Panighel, Annarita

2006-01-01

Controls in food industry are fundamental to protect the consumer health. For products of high quality, warranty of origin and identity is required and analytical control is very important to prevent frauds. In this article, the "state of art" of mass spectrometry in enological chemistry as a consumer safety contribute is reported. Gas chromatography-mass spectrometry (GC/MS) and liquid-chromatography-mass spectrometry (LC/MS) methods have been developed to determine pesticides, ethyl carbamate, and compounds from the yeast and bacterial metabolism in wine. The presence of pesticides in wine is mainly linked to the use of dicarboxyimide fungicides on vineyard shortly before the harvest to prevent the Botrytis cinerea attack of grape. Pesticide residues are regulated at maximum residue limits in grape of low ppm levels, but significantly lower levels in wine have to be detected, and mass spectrometry offers effective and sensitive methods. Moreover, mass spectrometry represent an advantageous alternative to the radioactive-source-containing electron capture detector commonly used in GC analysis of pesticides. Analysis of ochratoxin A (OTA) in wine by LC/MS and multiple mass spectrometry (MS/MS) permits to confirm the toxin presence without the use of expensive immunoaffinity columns, or time and solvent consuming sample derivatization procedures. Inductively coupled plasma-mass spectrometry (ICP/MS) is used to control heavy metals contamination in wine, and to verify the wine origin and authenticity. Isotopic ratio-mass spectrometry (IRMS) is applied to reveal wine watering and sugar additions, and to determine the product origin and traceability.

Analysis of GAA/TTC DNA triplexes using nuclear magnetic resonance and electrospray ionization mass spectrometry.

PubMed

Mariappan, S V Santhana; Cheng, Xun; van Breemen, Richard B; Silks, Louis A; Gupta, Goutam

2004-11-15

The formation of a GAA/TTC DNA triplex has been implicated in Friedreich's ataxia. The destabilization of GAA/TTC DNA triplexes either by pH or by binding to appropriate ligands was analyzed by nuclear magnetic resonance (NMR) and positive-ion electrospray mass spectrometry. The triplexes and duplexes were identified by changes in the NMR chemical shifts of H8, H1, H4, 15N7, and 15N4. The lowest pH at which the duplex is detectable depends upon the overall stability and the relative number of Hoogsteen C composite function G to T composite function A basepairs. A melting pH (pHm) of 7.6 was observed for the destabilization of the (GAA)2T4(TTC)2T4(CTT)2 triplex to the corresponding Watson-Crick duplex and the T4(CTT)2 overhang. The mass spectrometric analyses of (TTC)6.(GAA)6 composite function(TTC)6 triplex detected ions due to both triplex and single-stranded oligonucleotides under acidic conditions. The triplex ions disappeared completely at alkaline pH. Duplex and single strands were detectable only at neutral and alkaline pH values. Mass spectrometric analyses also showed that minor groove-binding ligands berenil, netropsin, and distamycin and the intercalating ligand acridine orange destabilize the (TTC)6.(GAA)6 composite function (TTC)6 triplex. These NMR and mass spectrometric methods may function as screening assays for the discovery of agents that destabilize GAA/TTC triplexes and as general methods for the characterization of structure, dynamics, and stability of DNA and DNA-ligand complexes.

Identification and Quantification of Pesticides in Environmental Waters With Solid Phase Microextraction and Analysis Using Field-Portable Gas Chromatography-Mass Spectrometry

DTIC Science & Technology

2004-06-10

Microextraction and Analysis using Field-Portable Gas Chromatography-Mass Spectrometry Name of Candidate: CPT Michael J. Nack...and Analysis using Field-Portable Gas Chromatography-Mass Spectrometry Beyond brief excerpts is with the permission of the copyright owner, and...Pesticides in Environmental Waters with Solid Phase Microextraction and Analysis using Field-Portable Gas Chromatography-Mass Spectrometry

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.

Cracking the Sugar Code by Mass Spectrometry - An Invited Perspective in Honor of Dr. Catherine E. Costello, Recipient of the 2017 ASMS Distinguished Contribution Award

NASA Astrophysics Data System (ADS)

Mirgorodskaya, Ekaterina; Karlsson, Niclas G.; Sihlbom, Carina; Larson, Göran; Nilsson, Carol L.

2018-04-01

The structural study of glycans and glycoconjugates is essential to assign their roles in homeostasis, health, and disease. Once dominated by nuclear magnetic resonance spectroscopy, mass spectrometric methods have become the preferred toolbox for the determination of glycan structures at high sensitivity. The patterns of such structures in different cellular states now allow us to interpret the sugar codes in health and disease, based on structure-function relationships. Dr. Catherine E. Costello was the 2017 recipient of the American Society for Mass Spectrometry's Distinguished Contribution Award. In this Perspective article, we describe her seminal work in a historical and geographical context and review the impact of her research accomplishments in the field. 8[Figure not available: see fulltext.

Analysis of Glycosaminoglycans Using Mass Spectrometry

PubMed Central

Staples, Gregory O.; Zaia, Joseph

2015-01-01

The glycosaminoglycans (GAGs) are linear polysaccharides expressed on animal cell surfaces and in extracellular matrices. Their biosynthesis is under complex control and confers a domain structure that is essential to their ability to bind to protein partners. Key to understanding the functions of GAGs are methods to determine accurately and rapidly patterns of sulfation, acetylation and uronic acid epimerization that correlate with protein binding or other biological activities. Mass spectrometry (MS) is particularly suitable for the analysis of GAGs for biomedical purposes. Using modern ionization techniques it is possible to accurately determine molecular weights of GAG oligosaccharides and their distributions within a mixture. Methods for direct interfacing with liquid chromatography have been developed to permit online mass spectrometric analysis of GAGs. New tandem mass spectrometric methods for fine structure determination of GAGs are emerging. This review summarizes MS-based approaches for analysis of GAGs, including tissue extraction and chromatographic methods compatible with LC/MS and tandem MS. PMID:25705143

Differentiation of regioisomeric aromatic ketocarboxylic acids by atmospheric pressure chemical ionization CAD tandem mass spectrometry in a linear quadrupole ion trap mass spectrometer

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

Amundson, Lucas M.; Owen, Ben C.; Gallardo, Vanessa A.

2011-01-01

Positive-mode atmospheric pressure chemical ionization tandem mass spectrometry (APCI-MS n ) was tested for the differentiation of regioisomeric aromatic ketocarboxylic acids. Each analyte forms exclusively an abundant protonated molecule upon ionization via positive-mode APCI in a commercial linear quadrupole ion trap (LQIT) mass spectrometer. Energy-resolved collision-activated dissociation (CAD) experiments carried out on the protonated analytes revealed fragmentation patterns that varied based on the location of the functional groups. Unambiguous differentiation between the regioisomers was achieved in each case by observing different fragmentation patterns, different relative abundances of ion-molecule reaction products, or different relative abundances of fragment ions formed at differentmore » collision energies. The mechanisms of some of the reactions were examined by H/D exchange reactions and molecular orbital calculations.« less

The allure of mass spectrometry: From an earlyday chemist's perspective

PubMed Central

2016-01-01

1 This reminiscing review article is an account of the author's fascination and involvements with mass spectrometry from the perspective of an organic chemist with an interest in natural product chemistry. It covers a period from 1961 through the mid 1990s as mass spectrometry evolved form a novelty technique to become a most widely used analytical technique. Following a brief synopsis of my pathway to mass spectrometry, my research efforts in this field are presented with a focus mainly on evolving principles and technologies which I had personal involvements with. To provide historical perspectives, discussions of these developments are accompanied by brief outlines of the relevant state‐of‐the‐art, shedding light on the technical and conceptual challenges encountered during those early days in mass spectrometry. Examples are presented of my involvements with basic and applied research in mass spectrometry during graduate studies at Stanford University and close to three decade tenure in pharmaceutical research at Syntex Research. My basic research interests focused mainly on principles of electron ionization induced fragmentation mechanisms, with an emphasis on steroids and other model compounds. Extensive deuterium labeling evidence was used to determine the fragmentation mechanisms of the diagnostically significant ions in the spectra of numerous model compounds, uncovering examples of wide‐ranging hydrogen transfers, skeletal rearrangements, methyl and phenyl migrations, stereoselective fragmentations and low and high energy fragmentation processes. Depiction of the industrial research phase of my career includes comments on the pivotal role mass spectrometry played on advancing modern pharmaceutical research. Examples are presented of involvements with instrumental developments and a few select cases of applied research, including studies of bile mechanisms in vertebrates, identification of bisphenol‐A leaching from sterilized polycarbonate containers, high sensitivity TCDD analyses and other projects. Reflecting on my services for the mass spectrometry society, involvements with the co‐founding and 12 year chairing of the Asilomar Conference on Mass Spectrometry and founding of the Bay Area Mass Spectrometry regional MS discussion group, as part of my services for the mass spectrometry community, are presented in some detail. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:520–542, 2017 PMID:26999732

Stable isotope labelling methods in mass spectrometry-based quantitative proteomics.

PubMed

Chahrour, Osama; Cobice, Diego; Malone, John

2015-09-10

Mass-spectrometry based proteomics has evolved as a promising technology over the last decade and is undergoing a dramatic development in a number of different areas, such as; mass spectrometric instrumentation, peptide identification algorithms and bioinformatic computational data analysis. The improved methodology allows quantitative measurement of relative or absolute protein amounts, which is essential for gaining insights into their functions and dynamics in biological systems. Several different strategies involving stable isotopes label (ICAT, ICPL, IDBEST, iTRAQ, TMT, IPTL, SILAC), label-free statistical assessment approaches (MRM, SWATH) and absolute quantification methods (AQUA) are possible, each having specific strengths and weaknesses. Inductively coupled plasma mass spectrometry (ICP-MS), which is still widely recognised as elemental detector, has recently emerged as a complementary technique to the previous methods. The new application area for ICP-MS is targeting the fast growing field of proteomics related research, allowing absolute protein quantification using suitable elemental based tags. This document describes the different stable isotope labelling methods which incorporate metabolic labelling in live cells, ICP-MS based detection and post-harvest chemical label tagging for protein quantification, in addition to summarising their pros and cons. Copyright © 2015 Elsevier B.V. All rights reserved.

Application of Stable Isotope-Assisted Metabolomics for Cell Metabolism Studies

PubMed Central

You, Le; Zhang, Baichen; Tang, Yinjie J.

2014-01-01

The applications of stable isotopes in metabolomics have facilitated the study of cell metabolisms. Stable isotope-assisted metabolomics requires: (1) properly designed tracer experiments; (2) stringent sampling and quenching protocols to minimize isotopic alternations; (3) efficient metabolite separations; (4) high resolution mass spectrometry to resolve overlapping peaks and background noises; and (5) data analysis methods and databases to decipher isotopic clusters over a broad m/z range (mass-to-charge ratio). This paper overviews mass spectrometry based techniques for precise determination of metabolites and their isotopologues. It also discusses applications of isotopic approaches to track substrate utilization, identify unknown metabolites and their chemical formulas, measure metabolite concentrations, determine putative metabolic pathways, and investigate microbial community populations and their carbon assimilation patterns. In addition, 13C-metabolite fingerprinting and metabolic models can be integrated to quantify carbon fluxes (enzyme reaction rates). The fluxome, in combination with other “omics” analyses, may give systems-level insights into regulatory mechanisms underlying gene functions. More importantly, 13C-tracer experiments significantly improve the potential of low-resolution gas chromatography-mass spectrometry (GC-MS) for broad-scope metabolism studies. We foresee the isotope-assisted metabolomics to be an indispensable tool in industrial biotechnology, environmental microbiology, and medical research. PMID:24957020

Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage.

PubMed

Van, Phu T; Schmid, Amy K; King, Nichole L; Kaur, Amardeep; Pan, Min; Whitehead, Kenia; Koide, Tie; Facciotti, Marc T; Goo, Young Ah; Deutsch, Eric W; Reiss, David J; Mallick, Parag; Baliga, Nitin S

2008-09-01

The relatively small numbers of proteins and fewer possible post-translational modifications in microbes provide a unique opportunity to comprehensively characterize their dynamic proteomes. We have constructed a PeptideAtlas (PA) covering 62.7% of the predicted proteome of the extremely halophilic archaeon Halobacterium salinarum NRC-1 by compiling approximately 636 000 tandem mass spectra from 497 mass spectrometry runs in 88 experiments. Analysis of the PA with respect to biophysical properties of constituent peptides, functional properties of parent proteins of detected peptides, and performance of different mass spectrometry approaches has highlighted plausible strategies for improving proteome coverage and selecting signature peptides for targeted proteomics. Notably, discovery of a significant correlation between absolute abundances of mRNAs and proteins has helped identify low abundance of proteins as the major limitation in peptide detection. Furthermore, we have discovered that iTRAQ labeling for quantitative proteomic analysis introduces a significant bias in peptide detection by mass spectrometry. Therefore, despite identifying at least one proteotypic peptide for almost all proteins in the PA, a context-dependent selection of proteotypic peptides appears to be the most effective approach for targeted proteomics.

Evaluation of chemical labeling methods for identifying functional arginine residues of proteins by mass spectrometry.

PubMed

Wanigasekara, Maheshika S K; Chowdhury, Saiful M

2016-09-07

Arginine residues undergo several kinds of post-translational modifications (PTMs). These PTMs are associated with several inflammatory diseases, such as rheumatoid arthritis, atherosclerosis, and diabetes. Mass spectrometric studies of arginine modified proteins and peptides are very important, not only to identify the reactive arginine residues but also to understand the tandem mass spectrometry behavior of these peptides for assigning the sequences unambiguously. Herein, we utilize tandem mass spectrometry to report the performance of two widely used arginine labeling reagents, 1,2-cyclohexanedione (CHD) and phenylglyoxal (PG) with several arginine containing peptides and proteins. Time course labeling studies were performed to demonstrate the selectivity of the reagents in proteins or protein digests. Structural studies on the proteins were also explored to better understand the reaction sites and position of arginine residues. We found CHD showed better labeling efficiencies compared to phenylglyoxal. Reactive arginine profiling on a purified albumin protein clearly pointed out the cellular glycation modification site for this protein with high confidence. We believe these detailed mass-spectrometric studies will provide significant input to profile reactive arginine residues in large-scale studies; therefore, targeted proteomics can be performed to the short listed reactive sites for cellular arginine modifications. Copyright © 2016 Elsevier B.V. All rights reserved.

US Food and Drug Administration Perspectives on Clinical Mass Spectrometry.

PubMed

Lathrop, Julia Tait; Jeffery, Douglas A; Shea, Yvonne R; Scholl, Peter F; Chan, Maria M

2016-01-01

Mass spectrometry-based in vitro diagnostic devices that measure proteins and peptides are underutilized in clinical practice, and none has been cleared or approved by the Food and Drug Administration (FDA) for marketing or for use in clinical trials. One way to increase their utilization is through enhanced interactions between the FDA and the clinical mass spectrometry community to improve the validation and regulatory review of these devices. As a reference point from which to develop these interactions, this article surveys the FDA's regulation of mass spectrometry-based devices, explains how the FDA uses guidance documents and standards in the review process, and describes the FDA's previous outreach to stakeholders. Here we also discuss how further communication and collaboration with the clinical mass spectrometry communities can identify opportunities for the FDA to provide help in the development of mass spectrometry-based devices and enhance their entry into the clinic. © 2015 American Association for Clinical Chemistry.

Mass spectrometry-based biomarker discovery: toward a global proteome index of individuality.

PubMed

Hawkridge, Adam M; Muddiman, David C

2009-01-01

Biomarker discovery and proteomics have become synonymous with mass spectrometry in recent years. Although this conflation is an injustice to the many essential biomolecular techniques widely used in biomarker-discovery platforms, it underscores the power and potential of contemporary mass spectrometry. Numerous novel and powerful technologies have been developed around mass spectrometry, proteomics, and biomarker discovery over the past 20 years to globally study complex proteomes (e.g., plasma). However, very few large-scale longitudinal studies have been carried out using these platforms to establish the analytical variability relative to true biological variability. The purpose of this review is not to cover exhaustively the applications of mass spectrometry to biomarker discovery, but rather to discuss the analytical methods and strategies that have been developed for mass spectrometry-based biomarker-discovery platforms and to place them in the context of the many challenges and opportunities yet to be addressed.

Silver-109-based laser desorption/ionization mass spectrometry method for detection and quantification of amino acids.

PubMed

Arendowski, Adrian; Nizioł, Joanna; Ruman, Tomasz

2018-04-01

A new methodology applicable for both high-resolution laser desorption/ionization mass spectrometry and mass spectrometry imaging of amino acids is presented. The matrix-assisted laser desorption ionization-type target containing monoisotopic cationic 109 Ag nanoparticles ( 109 AgNPs) was used for rapid mass spectrometry measurements of 11 amino acids of different chemical properties. Amino acids were directly tested in 100,000-fold concentration change conditions ranging from 100 μg/mL to 1 ng/mL which equates to 50 ng to 500 fg of amino acid per measurement spot. Limit of detection values obtained suggest that presented method/target system is among the fastest and most sensitive ones in laser mass spectrometry. Mass spectrometry imaging of spots of human blood plasma spiked with amino acids showed their surface distribution allowing optimization of quantitative measurements. Copyright © 2018 John Wiley & Sons, Ltd.

Profiling of Arabidopsis secondary metabolites by capillary liquid chromatography coupled to electrospray ionization quadrupole time-of-flight mass spectrometry.

PubMed

von Roepenack-Lahaye, Edda; Degenkolb, Thomas; Zerjeski, Michael; Franz, Mathias; Roth, Udo; Wessjohann, Ludger; Schmidt, Jürgen; Scheel, Dierk; Clemens, Stephan

2004-02-01

Large-scale metabolic profiling is expected to develop into an integral part of functional genomics and systems biology. The metabolome of a cell or an organism is chemically highly complex. Therefore, comprehensive biochemical phenotyping requires a multitude of analytical techniques. Here, we describe a profiling approach that combines separation by capillary liquid chromatography with the high resolution, high sensitivity, and high mass accuracy of quadrupole time-of-flight mass spectrometry. About 2000 different mass signals can be detected in extracts of Arabidopsis roots and leaves. Many of these originate from Arabidopsis secondary metabolites. Detection based on retention times and exact masses is robust and reproducible. The dynamic range is sufficient for the quantification of metabolites. Assessment of the reproducibility of the analysis showed that biological variability exceeds technical variability. Tools were optimized or established for the automatic data deconvolution and data processing. Subtle differences between samples can be detected as tested with the chalcone synthase deficient tt4 mutant. The accuracy of time-of-flight mass analysis allows to calculate elemental compositions and to tentatively identify metabolites. In-source fragmentation and tandem mass spectrometry can be used to gain structural information. This approach has the potential to significantly contribute to establishing the metabolome of Arabidopsis and other model systems. The principles of separation and mass analysis of this technique, together with its sensitivity and resolving power, greatly expand the range of metabolic profiling.

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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

[Identification of mouse brain neuropeptides by high throughput mass spectrometry].

PubMed

Shao, Xianfeng; Ma, Min; Chen, Ruibing; Jia, Chenxi

2018-04-25

Neuropeptides play an important role in the physiological functions of the human body. The physiological activities such as pain, sleep, mood, learning and memory are affected by neuropeptides. Neuropeptides mainly exist in the nerve tissue of the body, and a small amount of them are distributed in body fluid and organs. At present, analysis of large-scale identification of neuropeptides in whole brain tissue is still challenging. Therefore, high-throughput detection of these neuropeptides is greatly significant to understand the composition and function of neuropeptides. In this study, 1 830 endogenous peptides and 99 novel putative neuropeptides were identified by extraction of endogenous peptides from whole brain tissue of mice by liquid phase tandem mass spectrometry (LC-MS / MS). The identification of these endogenous peptides provides not only a reference value in the treatment and mechanism studies of diseases and the development of drugs, but also the basis for the study of a new neuropeptides and their functions.

Newborn screening for sickling and other haemoglobin disorders using tandem mass spectrometry: A pilot study of methodology in laboratories in England.

PubMed

Daniel, Yvonne A; Henthorn, Joan

2016-12-01

To determine (i) if electrospray mass spectrometry-mass spectrometry with the SpOtOn Diagnostics Ltd reagent kit for sickle cell screening could be integrated into the English newborn screening programme, under routine screening conditions, and provide mass spectrometry-mass spectrometry results which match existing methods, and (ii) if common action values could be set for all manufacturers in the study, for all assessed haemoglobins, to indicate which samples require further investigation. Anonymised residual blood spots were analysed using the SpOtOn reagent kit as per manufacturer's instructions, in parallel with existing techniques at four laboratories. Mass spectrometry-mass spectrometry instrumentation at Laboratories A and B was AB Sciex (Warrington, UK) AP4000, and at Laboratories C and D, Waters Micromass (Manchester, UK), Xevo TQMS and Premier, respectively. There were 23,898 results accepted from the four laboratories. Excellent specificity at 100% sensitivity was observed for haemoglobin S, haemoglobin C, haemoglobin E and haemoglobin O Arab . A common action value was not possible for Hb C, but action values were set by manufacturer. The two haemoglobin D Punjab cases at Laboratory D were not detected using the common action value. Conversely, false-positive results with haemoglobin D Punjab were a problem at the remaining three laboratories. This multicentre study demonstrates that it is possible to implement mass spectrometry-mass spectrometry into an established screening programme while maintaining consistency with existing methods for haemoglobinopathy screening. However, one of the instruments investigated cannot be recommended for use with this application. © The Author(s) 2016.

ENVIRONMENTAL MASS SPECTROMETRY: EMERGING CONTAMINANTS AND CURRENT ISSUES

EPA Science Inventory

This review covers developments in environmental mass spectrometry over the period of 2000-2001. A few significant references that appeared between January and February 2002 are also included. The previous Environmental Mass Spectrometry review was very comprehensive, including...

Sampling and analyte enrichment strategies for ambient mass spectrometry.

PubMed

Li, Xianjiang; Ma, Wen; Li, Hongmei; Ai, Wanpeng; Bai, Yu; Liu, Huwei

2018-01-01

Ambient mass spectrometry provides great convenience for fast screening, and has showed promising potential in analytical chemistry. However, its relatively low sensitivity seriously restricts its practical utility in trace compound analysis. In this review, we summarize the sampling and analyte enrichment strategies coupled with nine modes of representative ambient mass spectrometry (desorption electrospray ionization, paper vhspray ionization, wooden-tip spray ionization, probe electrospray ionization, coated blade spray ionization, direct analysis in real time, desorption corona beam ionization, dielectric barrier discharge ionization, and atmospheric-pressure solids analysis probe) that have dramatically increased the detection sensitivity. We believe that these advances will promote routine use of ambient mass spectrometry. Graphical abstract Scheme of sampling stretagies for ambient mass spectrometry.

Re-investigation of the fragmentation of protonated carotenoids by electrospray ionization and nanospray tandem mass spectrometry.

PubMed

Neto, Fausto Carnevale; Guaratini, Thais; Costa-Lotufo, Letícia; Colepicolo, Pio; Gates, Paul J; Lopes, Norberto Peporine

2016-07-15

Carotenoids are polyene isoprenoids with an important role in photosynthesis and photoprotection. Their characterization in biological matrices is a crucial subject for biochemical research. In this work we report the full fragmentation of 16 polyenes (carotenes and xanthophylls) by electrospray ionization tandem mass spectrometry (ESI-CID-MS/MS) and nanospray tandem mass spectrometry (nanoESI-CID-MS/MS). Analyses were carried out on a quadrupole time-of-flight (QTOF) mass spectrometer coupled with a nanoESI source and on a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer with an ESI source. The formulae of the product ions were determined by accurate-mass measurements. It is demonstrated that the fragmentation routes observed for the protonated carotenoids derive essentially from charge-remote fragmentations and pericyclic rearrangements, such as electrocyclic and retro-ene eliminations (assisted or not by a sigmatropic hydrogen shift). All mechanisms are dependent on cis-trans isomerization through the formation of several conjugated polyene carbocation intermediates. Some specific ions for the carotenoid epoxides were justified through formation of cyclic oxonium ions. Complete fragmentation pathways of protonated carotenoids by ESI- and nanoESI-CID-MS/MS provided structural information about functional groups, polyene chain and double bonds, and contribute to identification of carotenoids based on MS/MS fragmentation patterns. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Derivatization of Dextran for Multiply Charged Ion Formation and Electrospray Ionization Time-of-Flight Mass Spectrometric Analysis

NASA Astrophysics Data System (ADS)

Tapia, Jesus B.; Hibbard, Hailey A. J.; Reynolds, Melissa M.

2017-10-01

We present the use of a simple, one-pot derivatization to allow the polysaccharide dextran to carry multiple positive charges, shifting its molecular weight distribution to a lower m/ z range. We performed this derivatization because molecular weight measurements of polysaccharides by mass spectrometry are challenging because of their lack of readily ionizable groups. The absence of ionizable groups limits proton abstraction and suppresses proton adduction during the ionization process, producing mass spectra with predominantly singly charged metal adduct ions, thereby limiting the detection of large polysaccharides. To address this challenge, we derivatized dextran T1 (approximately 1 kDa) by attaching ethylenediamine, giving dextran readily ionizable, terminal amine functional groups. The attached ethylenediamine groups facilitated proton adduction during the ionization process in positive ion mode. Using the low molecular weight dextran T1, we tracked the number of ethylenediamine attachments by measuring the mass shift from underivatized to derivatized dextran T1. Using electrospray ionization time-of-flight mass spectrometry, we observed derivatized dextran chains ranging from two to nine glucose residues with between one and four attachments/charges. Our success in shifting derivatized dextran T1 toward the low m/ z range suggests potential for this derivatization as a viable route for analysis of high molecular weight polysaccharides using electrospray ionization time-of-flight mass spectrometry. [Figure not available: see fulltext.

Current use of high-resolution mass spectrometry in drug screening relevant to clinical and forensic toxicology and doping control.

PubMed

Ojanperä, Ilkka; Kolmonen, Marjo; Pelander, Anna

2012-05-01

Clinical and forensic toxicology and doping control deal with hundreds or thousands of drugs that may cause poisoning or are abused, are illicit, or are prohibited in sports. Rapid and reliable screening for all these compounds of different chemical and pharmaceutical nature, preferably in a single analytical method, is a substantial effort for analytical toxicologists. Combined chromatography-mass spectrometry techniques with standardised reference libraries have been most commonly used for the purpose. In the last ten years, the focus has shifted from gas chromatography-mass spectrometry to liquid chromatography-mass spectrometry, because of progress in instrument technology and partly because of the polarity and low volatility of many new relevant substances. High-resolution mass spectrometry (HRMS), which enables accurate mass measurement at high resolving power, has recently evolved to the stage that is rapidly causing a shift from unit-resolution, quadrupole-dominated instrumentation. The main HRMS techniques today are time-of-flight mass spectrometry and Orbitrap Fourier-transform mass spectrometry. Both techniques enable a range of different drug-screening strategies that essentially rely on measuring a compound's or a fragment's mass with sufficiently high accuracy that its elemental composition can be determined directly. Accurate mass and isotopic pattern acts as a filter for confirming the identity of a compound or even identification of an unknown. High mass resolution is essential for improving confidence in accurate mass results in the analysis of complex biological samples. This review discusses recent applications of HRMS in analytical toxicology.

A comprehensive high-resolution mass spectrometry approach for characterization of metabolites by combination of ambient ionization, chromatography and imaging methods.

PubMed

Berisha, Arton; Dold, Sebastian; Guenther, Sabine; Desbenoit, Nicolas; Takats, Zoltan; Spengler, Bernhard; Römpp, Andreas

2014-08-30

An ideal method for bioanalytical applications would deliver spatially resolved quantitative information in real time and without sample preparation. In reality these requirements can typically not be met by a single analytical technique. Therefore, we combine different mass spectrometry approaches: chromatographic separation, ambient ionization and imaging techniques, in order to obtain comprehensive information about metabolites in complex biological samples. Samples were analyzed by laser desorption followed by electrospray ionization (LD-ESI) as an ambient ionization technique, by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging for spatial distribution analysis and by high-performance liquid chromatography/electrospray ionization mass spectrometry (HPLC/ESI-MS) for quantitation and validation of compound identification. All MS data were acquired with high mass resolution and accurate mass (using orbital trapping and ion cyclotron resonance mass spectrometers). Grape berries were analyzed and evaluated in detail, whereas wheat seeds and mouse brain tissue were analyzed in proof-of-concept experiments. In situ measurements by LD-ESI without any sample preparation allowed for fast screening of plant metabolites on the grape surface. MALDI imaging of grape cross sections at 20 µm pixel size revealed the detailed distribution of metabolites which were in accordance with their biological function. HPLC/ESI-MS was used to quantify 13 anthocyanin species as well as to separate and identify isomeric compounds. A total of 41 metabolites (amino acids, carbohydrates, anthocyanins) were identified with all three approaches. Mass accuracy for all MS measurements was better than 2 ppm (root mean square error). The combined approach provides fast screening capabilities, spatial distribution information and the possibility to quantify metabolites. Accurate mass measurements proved to be critical in order to reliably combine data from different MS techniques. Initial results on the mycotoxin deoxynivalenol (DON) in wheat seed and phospholipids in mouse brain as a model for mammalian tissue indicate a broad applicability of the presented workflow. Copyright © 2014 John Wiley & Sons, Ltd.

Clinical Application of Ambient Ionization Mass Spectrometry

PubMed Central

Li, Li-Hua; Hsieh, Hua-Yi; Hsu, Cheng-Chih

2017-01-01

Ambient ionization allows mass spectrometry analysis directly on the sample surface under atmospheric pressure with almost zero sample pretreatment. Since the development of desorption electrospray ionization (DESI) in 2004, many other ambient ionization techniques were developed. Due to their simplicity and low operation cost, rapid and on-site clinical mass spectrometry analysis becomes real. In this review, we will highlight some of the most widely used ambient ionization mass spectrometry approaches and their applications in clinical study. PMID:28337399

Identification of chemical components in Baidianling Capsule based on gas chromatography-mass spectrometry and high-performance liquid chromatography combined with Fourier transform ion cyclotron resonance mass spectrometry.

PubMed

Wu, Wenying; Chen, Yu; Wang, Binjie; Sun, Xiaoyang; Guo, Ping; Chen, Xiaohui

2017-08-01

Baidianling Capsule, which is made from 16 Chinese herbs, has been widely used for treating vitiligo clinically. In this study, the sensitive and rapid method has been developed for the analysis of chemical components in Baidianling Capsule by gas chromatography-mass spectrometry in combination with retention indices and high-performance liquid chromatography combined with Fourier transform ion cyclotron resonance mass spectrometry. Firstly, a total of 110 potential volatile compounds obtained from different extraction procedures including alkanes, alkenes, alkynes, ketones, ethers, aldehydes, alcohols, phenols, organic acids, esters, furans, pyrrole, acid amides, heterocycles, and oxides were detected from Baidianling Capsule by gas chromatography-mass spectrometry, of which 75 were identified by mass spectrometry in combination with the retention index. Then, a total of 124 components were tentatively identified by high-performance liquid chromatography combined with Fourier transform ion cyclotron resonance mass spectrometry. Fifteen constituents from Baidianling Capsule were accurately identified by comparing the retention times with those of reference compounds, others were identified by comparing the retention times and mass spectrometry data, as well as retrieving the reference literature. This study provides a practical strategy for rapidly screening and identifying the multiple constituents of a complex traditional Chinese medicine. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

"EMERGING" POLLUTANTS, MASS SPECTROMETRY, AND COMMUNICATING SCIENCE: PHARMACEUTICALS IN THE ENVIRONMENT

EPA Science Inventory

A foundation for Environmental Science - Mass Spectrometry: Historically fundamental to amassing our understanding of environmental processes and chemical pollution is the realm of mass spectrometry - the mainstay of analytical chemistry - the workhorse that supplies much of the...

Trimethylation enhancement using diazomethane (TrEnDi): rapid on-column quaternization of peptide amino groups via reaction with diazomethane significantly enhances sensitivity in mass spectrometry analyses via a fixed, permanent positive charge.

PubMed

Wasslen, Karl V; Tan, Le Hoa; Manthorpe, Jeffrey M; Smith, Jeffrey C

2014-04-01

Defining cellular processes relies heavily on elucidating the temporal dynamics of proteins. To this end, mass spectrometry (MS) is an extremely valuable tool; different MS-based quantitative proteomics strategies have emerged to map protein dynamics over the course of stimuli. Herein, we disclose our novel MS-based quantitative proteomics strategy with unique analytical characteristics. By passing ethereal diazomethane over peptides on strong cation exchange resin within a microfluidic device, peptides react to contain fixed, permanent positive charges. Modified peptides display improved ionization characteristics and dissociate via tandem mass spectrometry (MS(2)) to form strong a2 fragment ion peaks. Process optimization and determination of reactive functional groups enabled a priori prediction of MS(2) fragmentation patterns for modified peptides. The strategy was tested on digested bovine serum albumin (BSA) and successfully quantified a peptide that was not observable prior to modification. Our method ionizes peptides regardless of proton affinity, thus decreasing ion suppression and permitting predictable multiple reaction monitoring (MRM)-based quantitation with improved sensitivity.

Comparison of two cell lysis procedures for recovery of microcystins in water samples from silver lake in Dover, Delaware, with microcystin producing cyanobacterial accumulations

USGS Publications Warehouse

Loftin, Keith A.; Meyer, Michael T.; Rubio, Fernando; Kamp, Lisa; Humphries, Edythe; Whereat, Ed

2008-01-01

A collaboration was developed between Abraxis, LLC, the State of Delaware Department of Natural Resources and Environmental Control Division of Water Resources Environmental Laboratory, the University of Delaware, and the United States Geological Survey to investigate the efficacy of the QuikLyse procedure developed by Abraxis, LLC as an alternative cell-lysis technique suitable for use with an existing liquid chromatography/tandem mass spectrometry research method developed at the United States Geological Survey Organic Geochemistry Research Laboratory to analyze cyanotoxins. A comparison of three sequential freeze/thaw cycles versus QuikLyse, a proprietary chemical lysis procedure was conducted on four water samples collected from Silver Lake in Dover, Delaware. Results from the Abraxis Microcystins-DM enzyme-linked immunosorbent assay and liquid chromatography/tandem mass spectrometry were tabulated as a function of the cell lysis technique. Stastical comparison of percent relative standard deviations showed no significant difference (alpha = 0.05) between both cell-lysis techniques when measured by enzyme-linked immunosorbent assay or liquid chromatography/tandem mass spectrometry for three of the four samples.

Simulation of two dimensional electrophoresis and tandem mass spectrometry for teaching proteomics.

PubMed

Fisher, Amanda; Sekera, Emily; Payne, Jill; Craig, Paul

2012-01-01

In proteomics, complex mixtures of proteins are separated (usually by chromatography or electrophoresis) and identified by mass spectrometry. We have created 2DE Tandem MS, a computer program designed for use in the biochemistry, proteomics, or bioinformatics classroom. It contains two simulations-2D electrophoresis and tandem mass spectrometry. The two simulations are integrated together and are designed to teach the concept of proteome analysis of prokaryotic and eukaryotic organisms. 2DE-Tandem MS can be used as a freestanding simulation, or in conjunction with a wet lab, to introduce proteomics in the undergraduate classroom. 2DE Tandem MS is a free program available on Sourceforge at https://sourceforge.net/projects/jbf/. It was developed using Java Swing and functions in Mac OSX, Windows, and Linux, ensuring that every student sees a consistent and informative graphical user interface no matter the computer platform they choose. Java must be installed on the host computer to run 2DE Tandem MS. Example classroom exercises are provided in the Supporting Information. Copyright © 2012 Wiley Periodicals, Inc.

Efficient Analysis of Mass Spectrometry Data Using the Isotope Wavelet

NASA Astrophysics Data System (ADS)

Hussong, Rene; Tholey, Andreas; Hildebrandt, Andreas

2007-09-01

Mass spectrometry (MS) has become today's de-facto standard for high-throughput analysis in proteomics research. Its applications range from toxicity analysis to MS-based diagnostics. Often, the time spent on the MS experiment itself is significantly less than the time necessary to interpret the measured signals, since the amount of data can easily exceed several gigabytes. In addition, automated analysis is hampered by baseline artifacts, chemical as well as electrical noise, and an irregular spacing of data points. Thus, filtering techniques originating from signal and image analysis are commonly employed to address these problems. Unfortunately, smoothing, base-line reduction, and in particular a resampling of data points can affect important characteristics of the experimental signal. To overcome these problems, we propose a new family of wavelet functions based on the isotope wavelet, which is hand-tailored for the analysis of mass spectrometry data. The resulting technique is theoretically well-founded and compares very well with standard peak picking tools, since it is highly robust against noise spoiling the data, but at the same time sufficiently sensitive to detect even low-abundant peptides.

Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics

PubMed Central

Deutsch, Eric W.; Mendoza, Luis; Shteynberg, David; Slagel, Joseph; Sun, Zhi; Moritz, Robert L.

2015-01-01

Democratization of genomics technologies has enabled the rapid determination of genotypes. More recently the democratization of comprehensive proteomics technologies is enabling the determination of the cellular phenotype and the molecular events that define its dynamic state. Core proteomic technologies include mass spectrometry to define protein sequence, protein:protein interactions, and protein post-translational modifications. Key enabling technologies for proteomics are bioinformatic pipelines to identify, quantitate, and summarize these events. The Trans-Proteomics Pipeline (TPP) is a robust open-source standardized data processing pipeline for large-scale reproducible quantitative mass spectrometry proteomics. It supports all major operating systems and instrument vendors via open data formats. Here we provide a review of the overall proteomics workflow supported by the TPP, its major tools, and how it can be used in its various modes from desktop to cloud computing. We describe new features for the TPP, including data visualization functionality. We conclude by describing some common perils that affect the analysis of tandem mass spectrometry datasets, as well as some major upcoming features. PMID:25631240

INFRARED SPECTRUM OF POTASSIUM-CATIONIZED TRIETHYLPHOSPHATE GENERATED USING TANDEM MASS SPECTROMETRY AND INFRARED MULTIPLE PHOTON DISSOCIATION

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

Gary S. Groenewold; Christopher M. Leavitt; Ryan P. Dain

2009-09-01

Tandem mass spectrometry and wavelength selective infrared photodissociation was used to generate an infrared spectrum of gas-phase triethylphosphate cationized by attachment of K+. Prominent absorptions were observed in the region of 900 to 1300 cm-1 that are characteristic of phosphate P=O and P-O-R stretches. The relative positions and intensities of the IR absorptions were reproduced well by density functional theory (DFT) calculations performed using the B3LYP functional and the 6-31+g(d), 6-311+g(d,p) and 6-311++G(3df,2pd) basis sets. Because of good correspondence between experiment and theory for the cation, DFT was then used to generate a theoretical spectrum for neutral triethylphosphate, which inmore » turn accurately reproduces the IR spectrum of the neat liquid when solvent effects are included in the calculations.« less

Determination of Fusarium toxins in functional vegetable milks applying salting-out-assisted liquid-liquid extraction combined with ultra-high-performance liquid chromatography tandem mass spectrometry.

PubMed

Hamed, Ahmed M; Arroyo-Manzanares, Natalia; García-Campaña, Ana M; Gámiz-Gracia, Laura

2017-11-01

Vegetable milks are considered as functional foods due to their physiological benefits. Although the consumption of these products has significantly increased, they have received little attention in legislation with regard to contaminants. However, they may contain mycotoxins resulting from the use of contaminated raw materials. In this work, ultra-high-performance liquid chromatography tandem mass spectrometry has been proposed for the determination of the most relevant Fusarium toxins (fumonisin B 1 and B 2 , HT-2 and T-2 toxins, zearalenone, deoxynivalenol and fusarenon-X) in different functional beverages based on cereals, legumes and seeds. Sample treatment consisted of a simple salting-out-assisted liquid-liquid extraction with no further clean-up. The method provided limits of quantification between 3.2 and 57.7 µg L -1 , recoveries above 80% and precision with RSD lower than 12%. The method was also applied for studying the occurrence of these mycotoxins in market samples of vegetable functional beverages and deoxynivalenol was found in three oat-based commercial drinks.

Studying the Chemistry of Cationized Triacylglycerols Using Electrospray Ionization Mass Spectrometry and Density Functional Theory Computations

NASA Astrophysics Data System (ADS)

Grossert, J. Stuart; Herrera, Lisandra Cubero; Ramaley, Louis; Melanson, Jeremy E.

2014-08-01

Analysis of triacylglycerols (TAGs), found as complex mixtures in living organisms, is typically accomplished using liquid chromatography, often coupled to mass spectrometry. TAGs, weak bases not protonated using electrospray ionization, are usually ionized by adduct formation with a cation, including those present in the solvent (e.g., Na+). There are relatively few reports on the binding of TAGs with cations or on the mechanisms by which cationized TAGs fragment. This work examines binding efficiencies, determined by mass spectrometry and computations, for the complexation of TAGs to a range of cations (Na+, Li+, K+, Ag+, NH4 +). While most cations bind to oxygen, Ag+ binding to unsaturation in the acid side chains is significant. The importance of dimer formation, [2TAG + M]+ was demonstrated using several different types of mass spectrometers. From breakdown curves, it became apparent that two or three acid side chains must be attached to glycerol for strong cationization. Possible mechanisms for fragmentation of lithiated TAGs were modeled by computations on tripropionylglycerol. Viable pathways were found for losses of neutral acids and lithium salts of acids from different positions on the glycerol moiety. Novel lactone structures were proposed for the loss of a neutral acid from one position of the glycerol moiety. These were studied further using triple-stage mass spectrometry (MS3). These lactones can account for all the major product ions in the MS3 spectra in both this work and the literature, which should allow for new insights into the challenging analytical methods needed for naturally occurring TAGs.

Proteomic analysis of a decellularized human vocal fold mucosa scaffold using 2D electrophoresis and high-resolution mass spectrometry.

PubMed

Welham, Nathan V; Chang, Zhen; Smith, Lloyd M; Frey, Brian L

2013-01-01

Natural biologic scaffolds for tissue engineering are commonly generated by decellularization of tissues and organs. Despite some preclinical and clinical success, in vivo scaffold remodeling and functional outcomes remain variable, presumably due to the influence of unidentified bioactive molecules on the scaffold-host interaction. Here, we used 2D electrophoresis and high-resolution mass spectrometry-based proteomic analyses to evaluate decellularization effectiveness and identify potentially bioactive protein remnants in a human vocal fold mucosa model. We noted proteome, phosphoproteome and O-glycoproteome depletion post-decellularization, and identified >200 unique protein species within the decellularized scaffold. Gene ontology-based enrichment analysis revealed a dominant set of functionally-related ontology terms associated with extracellular matrix assembly, organization, morphology and patterning, consistent with preservation of a tissue-specific niche for later cell seeding and infiltration. We further identified a subset of ontology terms associated with bioactive (some of which are antigenic) cellular proteins, despite histological and immunohistochemical data indicating complete decellularization. These findings demonstrate the value of mass spectrometry-based proteomics in identifying agents potentially responsible for variation in host response to engineered tissues derived from decellularized scaffolds. This work has implications for the manufacturing of biologic scaffolds from any tissue or organ, as well as for prediction and monitoring of the scaffold-host interaction in vivo. Copyright © 2012 Elsevier Ltd. All rights reserved.

Formaldehyde cross-linking and structural proteomics: Bridging the gap.

PubMed

Srinivasa, Savita; Ding, Xuan; Kast, Juergen

2015-11-01

Proteins are dynamic entities constantly moving and altering their structures based on their functions and interactions inside and outside the cell. Formaldehyde cross-linking combined with mass spectrometry can accurately capture interactions of these rapidly changing biomolecules while maintaining their physiological surroundings. Even with its numerous established uses in biology and compatibility with mass spectrometry, formaldehyde has not yet been applied in structural proteomics. However, formaldehyde cross-linking is moving toward analyzing tertiary structure, which conventional cross-linkers have already accomplished. The purpose of this review is to describe the potential of formaldehyde cross-linking in structural proteomics by highlighting its applications, characteristics and current status in the field. Copyright © 2015 Elsevier Inc. All rights reserved.

LMJ Points Plus v2.6

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

Kertesz, Vilmos

Short summary of the software's functionality: • built-in scan feature to acquire optical image of the surface to be analyzed • click-and-point selection of points of interest on the surface • supporting standalone autosampler/HPLC/MS operation: creating independent batch files after points of interests are selected for LEAPShell (autosampler control software from Leap Technologies) and Analyst® (mass spectrometry (MS) software from AB Sciex) • supporting integrated autosampler/HPLC/MS operation: creating one batch file for all instruments controlled by Analyst® (mass spectrometry software from AB Sciex) after points of interests are selected •creating heatmaps of analytes of interests from collected MS files inmore » a hand-off fashion« less

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.

Optimization of Whole-Body Zebrafish Sectioning Methods for Mass Spectrometry Imaging

EPA Science Inventory

Mass spectrometry imaging methods and protocols have become widely adapted to a variety of tissues and species. However, the mass spectrometry imaging literature contains minimal information on whole-body cryosection preparation for the zebrafish (Danio rerio), a model organism ...

Mass spectrometry for the determination of fission products 135Cs, 137Cs and 90Sr: A review of methodology and applications

NASA Astrophysics Data System (ADS)

Bu, Wenting; Zheng, Jian; Liu, Xuemei; Long, Kaiming; Hu, Sheng; Uchida, Shigeo

2016-05-01

The radioactive fission products 135Cs, 137Cs and 90Sr have been released into the environment by human activities such as nuclear weapon tests, nuclear fuel reprocessing and nuclear power plant accidents. Monitoring of these radionuclides is important for dose assessment. Moreover, the 135Cs/137Cs isotopic ratio can be used as an important long-term fingerprint for radioactive source identification as it varies with weapon, reactor and fuel types. In recent years, mass spectrometry has become a powerful method for the determination of 135Cs, 137Cs and 90Sr in environmental samples. Mass spectrometry is characterized by the high sensitivity and low detection limit and the relatively shorter sample preparation and analysis times compared with radiometric methods. However, the mass spectrometric determination of radiocesium and 90Sr is affected by the peak tailings of the stable nuclides 133Cs and 88Sr, respectively, and the related isobaric and polyatomic interferences. Chemical separation and optimization of the mass spectrometry instrumental setup are strongly needed prior to the mass spectrometry detection. In this paper, we have reviewed the published works about the determination of 135Cs, 137Cs and 90Sr by mass spectrometry. The mass spectrometric techniques we cover are resonance ionization mass spectrometry (RIMS), thermal ionization mass spectrometry (TIMS), accelerator mass spectrometry (AMS) and inductively coupled plasma mass spectrometry (ICP-MS). For each technique, the principles or strategies used for the analysis of these radionuclides are discussed; these included the abundance sensitivity, ways to suppress the interference signals, and the instrumental setup. In particular, the chemical procedures for eliminating the interferences are also summarized. To date, triple quadrupole ICP-MS (ICP-QQQ) showed great ability for the analysis of these radionuclides and the detection limits were as low as 0.01 pg/mL levels. Finally, some investigations on the behaviors of radiocesium and radioactive source identifications are presented with the results of 135Cs/137Cs isotopic ratios measured in various environmental samples.

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

NASA Astrophysics Data System (ADS)

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

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

Differentiating Fragmentation Pathways of Cholesterol by Two-Dimensional Fourier Transform Ion Cyclotron Resonance Mass Spectrometry.

PubMed

van Agthoven, Maria A; Barrow, Mark P; Chiron, Lionel; Coutouly, Marie-Aude; Kilgour, David; Wootton, Christopher A; Wei, Juan; Soulby, Andrew; Delsuc, Marc-André; Rolando, Christian; O'Connor, Peter B

2015-12-01

Two-dimensional Fourier transform ion cyclotron resonance mass spectrometry is a data-independent analytical method that records the fragmentation patterns of all the compounds in a sample. This study shows the implementation of atmospheric pressure photoionization with two-dimensional (2D) Fourier transform ion cyclotron resonance mass spectrometry. In the resulting 2D mass spectrum, the fragmentation patterns of the radical and protonated species from cholesterol are differentiated. This study shows the use of fragment ion lines, precursor ion lines, and neutral loss lines in the 2D mass spectrum to determine fragmentation mechanisms of known compounds and to gain information on unknown ion species in the spectrum. In concert with high resolution mass spectrometry, 2D Fourier transform ion cyclotron resonance mass spectrometry can be a useful tool for the structural analysis of small molecules. Graphical Abstract ᅟ.

Structural Elucidation of cis / trans Dicaffeoylquinic Acid Photoisomerization Using Ion Mobility Spectrometry-Mass Spectrometry

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

Zheng, Xueyun; Renslow, Ryan S.; Makola, Mpho M.

Due to the recently uncovered health benefits and anti-HIV activities of dicaffeoylquinic acids (diCQAs), understanding their structures and functions is of great interest for drug discovery efforts. DiCQAs are analytically challenging to identify and quantify since they commonly exist as a diverse mixture of positional and geometric (cis/trans) isomers. In this work, we utilized ion mobility spectrometry coupled with mass spectrometry to separate the various isomers before and after UV irradiation. The experimental collision cross sections were then compared with theoretical structures to differentiate and identify the diCQA isomers. Our analyses found that naturally the diCQAs existed predominantly as trans/transmore » isomers, but after 3 h of UV irradiation, cis/cis, cis/trans, trans/cis, and trans/trans isomers were all present in the mixture. This is the first report of successful differentiation of cis/trans diCQA isomers individually, which shows the great promise of IMS coupled with theoretical calculations for determining the structure and activity relationships of different isomers in drug discovery studies.« less

Incorporating Biological Mass Spectrometry into Undergraduate Teaching Labs, Part 2: Peptide Identification via Molecular Mass Determination

ERIC Educational Resources Information Center

Arnquist, Isaac J.; Beussman, Douglas J.

2009-01-01

Mass spectrometry has become a routine analytical tool in the undergraduate curriculum in the form of GC-MS. While relatively few undergraduate programs have incorporated biological mass spectrometry into their programs, the importance of these techniques, as demonstrated by their recognition with the 2002 Nobel Prize, will hopefully lead to…

Fluorimetric and mass spectrometric study of the interaction of β-cyclodextrin and osthole

NASA Astrophysics Data System (ADS)

Zhang, Huarong; Zhang, Hanqi; Qu, Chenling; Bai, Lifei; Ding, Lan

2007-11-01

The inclusion complex of β-cyclodextrin (β-CD) and osthole was studied by the electrospray ionization mass spectrometry (ESI-MS) and fluorescence spectrometry. From the mass spectrum, the 1:1 stoichiometric inclusion complex of β-CD and osthole was observed. The tandem mass spectrum was performed. The fluorescence intensity of osthole increased in the present of β-CD. According to the 1:1 β-CD-osthole mode, the dissociation constant ( KD) was obtained by ESI-MS and fluorescence spectrometry. The KD of β-CD-osthole inclusion complex is 6.96 × 10 -3 mol L -1 obtained by mass spectrometry and that is 8.14 × 10 -3 mol L -1 obtained by fluorescence spectrometry, which is consistent with each other.

Supercritical fluid extraction and direct fluid injection mass spectrometry for the determination of trichothecene mycotoxins in wheat samples

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

Kalinoski, H.T.; Udseth, H.R.; Wright, B.W.

1986-10-01

The application of on-line supercritical fluid extraction with chemical ionization mass spectrometry and collision induced dissociation tandem mass spectrometry for the rapid identification of parts-per-million levels of several trichothecene mycotoxins is demonstrated. Supercritical carbon dioxide is shown to allow identification of mycotoxins with minimum sample handling in complex natural matrices (e.g., wheat). Tandem mass spectrometry techniques are employed for unambiguous identification of compounds of varying polarity, and false positives from isobaric compounds are avoided. Capillary column supercritical fluid chromatography-mass spectrometry of a supercritical fluid extract of the same sample was also performed and detection limits in the parts-per-billion range appearmore » feasible.« less

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.

Cluster secondary ion mass spectrometry microscope mode mass spectrometry imaging.

PubMed

Kiss, András; Smith, Donald F; Jungmann, Julia H; Heeren, Ron M A

2013-12-30

Microscope mode imaging for secondary ion mass spectrometry is a technique with the promise of simultaneous high spatial resolution and high-speed imaging of biomolecules from complex surfaces. Technological developments such as new position-sensitive detectors, in combination with polyatomic primary ion sources, are required to exploit the full potential of microscope mode mass spectrometry imaging, i.e. to efficiently push the limits of ultra-high spatial resolution, sample throughput and sensitivity. In this work, a C60 primary source was combined with a commercial mass microscope for microscope mode secondary ion mass spectrometry imaging. The detector setup is a pixelated detector from the Medipix/Timepix family with high-voltage post-acceleration capabilities. The system's mass spectral and imaging performance is tested with various benchmark samples and thin tissue sections. The high secondary ion yield (with respect to 'traditional' monatomic primary ion sources) of the C60 primary ion source and the increased sensitivity of the high voltage detector setup improve microscope mode secondary ion mass spectrometry imaging. The analysis time and the signal-to-noise ratio are improved compared with other microscope mode imaging systems, all at high spatial resolution. We have demonstrated the unique capabilities of a C60 ion microscope with a Timepix detector for high spatial resolution microscope mode secondary ion mass spectrometry imaging. Copyright © 2013 John Wiley & Sons, Ltd.

Fast Determination of Ingredients in Solid Pharmaceuticals by Microwave-Enhanced In-Source Decay of Microwave Plasma Torch Mass Spectrometry.

PubMed

Su, Rui; Wang, Xinchen; Hou, Changming; Yang, Meiling; Huang, Keke; Chen, Huanwen

2017-09-01

Rapid qualitative and quantitative analysis of solid samples (e.g., pharmaceutical preparations) by using a small and low-resolution mass spectrometer without MS/MS function is still a challenge in ambient pressure ionization mass spectrometric analysis. Herein, a practically efficient method termed microwave-enhanced in-source decay (MEISD) using microwave plasma torch desorption ionization coupled with time-of-flight mass spectrometry (MPTDI-TOF MS) was developed for fast analysis of pharmaceutical tablets using a miniature TOF mass spectrometer without tandem mass function. The intensity of ISD fragmentation was evaluated under different microwave power values. Several factors, including desorption distance and time that might affect the signal intensity and fragmentation, were systematically investigated. It was observed that both the protonated molecular ions and major fragment ions from the active ingredients in tablets could be found in the full-scan mass spectra in positive ion mode, which were comparable to those obtained by a commercial LTQ-XL ion trap mass spectrometer. The structures of the ingredients could be elucidated in detail using the MEISD method, which promotes our understanding of the desorption/ionization processes in microwave plasma torch (MPT). Quantitative analysis of 10 tablets was achieved by full-scan MPTDI-TOF MS with low limit of detection (LOD, 0.763 mg/g), acceptable relative standard deviation (RSD < 7.33%, n =10), and 10 s for each tablet, showing promising applications in high throughput screening of counterfeit drugs. Graphical Abstract ᅟ.

Fast Determination of Ingredients in Solid Pharmaceuticals by Microwave-Enhanced In-Source Decay of Microwave Plasma Torch Mass Spectrometry

NASA Astrophysics Data System (ADS)

Su, Rui; Wang, Xinchen; Hou, Changming; Yang, Meiling; Huang, Keke; Chen, Huanwen

2017-09-01

Rapid qualitative and quantitative analysis of solid samples (e.g., pharmaceutical preparations) by using a small and low-resolution mass spectrometer without MS/MS function is still a challenge in ambient pressure ionization mass spectrometric analysis. Herein, a practically efficient method termed microwave-enhanced in-source decay (MEISD) using microwave plasma torch desorption ionization coupled with time-of-flight mass spectrometry (MPTDI-TOF MS) was developed for fast analysis of pharmaceutical tablets using a miniature TOF mass spectrometer without tandem mass function. The intensity of ISD fragmentation was evaluated under different microwave power values. Several factors, including desorption distance and time that might affect the signal intensity and fragmentation, were systematically investigated. It was observed that both the protonated molecular ions and major fragment ions from the active ingredients in tablets could be found in the full-scan mass spectra in positive ion mode, which were comparable to those obtained by a commercial LTQ-XL ion trap mass spectrometer. The structures of the ingredients could be elucidated in detail using the MEISD method, which promotes our understanding of the desorption/ionization processes in microwave plasma torch (MPT). Quantitative analysis of 10 tablets was achieved by full-scan MPTDI-TOF MS with low limit of detection (LOD, 0.763 mg/g), acceptable relative standard deviation (RSD < 7.33%, n =10), and 10 s for each tablet, showing promising applications in high throughput screening of counterfeit drugs. [Figure not available: see fulltext.

Impact of comprehensive two-dimensional gas chromatography with mass spectrometry on food analysis.

PubMed

Tranchida, Peter Q; Purcaro, Giorgia; Maimone, Mariarosa; Mondello, Luigi

2016-01-01

Comprehensive two-dimensional gas chromatography with mass spectrometry has been on the separation-science scene for about 15 years. This three-dimensional method has made a great positive impact on various fields of research, and among these that related to food analysis is certainly at the forefront. The present critical review is based on the use of comprehensive two-dimensional gas chromatography with mass spectrometry in the untargeted (general qualitative profiling and fingerprinting) and targeted analysis of food volatiles; attention is focused not only on its potential in such applications, but also on how recent advances in comprehensive two-dimensional gas chromatography with mass spectrometry will potentially be important for food analysis. Additionally, emphasis is devoted to the many instances in which straightforward gas chromatography with mass spectrometry is a sufficiently-powerful analytical tool. Finally, possible future scenarios in the comprehensive two-dimensional gas chromatography with mass spectrometry food analysis field are discussed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Revealing Individual Lifestyles through Mass Spectrometry Imaging of Chemical Compounds in Fingerprints.

PubMed

Hinners, Paige; O'Neill, Kelly C; Lee, Young Jin

2018-03-26

Fingerprints, specifically the ridge details within the print, have long been used in forensic investigations for individual identification. Beyond the ridge detail, fingerprints contain useful chemical information. The study of fingerprint chemical information has become of interest, especially with mass spectrometry imaging technologies. Mass spectrometry imaging visualizes the spatial relationship of each compound detected, allowing ridge detail and chemical information in a single analysis. In this work, a range of exogenous fingerprint compounds that may reveal a personal lifestyle were studied using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). Studied chemical compounds include various brands of bug sprays and sunscreens, as well as food oils, alcohols, and citrus fruits. Brand differentiation and source determination were possible based on the active ingredients or exclusive compounds left in fingerprints. Tandem mass spectrometry was performed for the key compounds, so that these compounds could be confidently identified in a single multiplex mass spectrometry imaging data acquisition.

[Simultaneous determination of 16 flavonoids in the ginkgo dietary supplement tea by high performance liquid chromatography-tandem mass spectrometry].

PubMed

Jiang, Yalan; Huang, Fang; Wu, Fuhai; Wu, Huiqin; Huang, Xiaolan; Deng, Xin

2015-10-01

A method for the determination of 16 functional components of ginkgo dietary supplement tea such as catechin, vitexin, puerarin, isoflavoues aglycone, silymarin, quercetin, luteolin, apigenin, naringenin, hesperitin dihydrochalcone, kaempferol, hesperitin, isorhamnetin, baicalein, nobiletin and tangeretin by high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) was proposed. The conditions of chromatography and mass spectrometry were optimized. The 16 flavonoids were separated on a C18 chromatographic column with acetonitrile and water (additional 0.1% formic acid) as mobile phases under gradient elution at a flow rate of 0.25 mL/min. The determination was conducted by tandem mass spectrometry in positive ESI mode under multiple reaction monitoring (MRM) mode. Good linearities for all the compounds, with correlation coefficients over 0.996, were acquired. The recoveries were in the range of 70.9% to 100.0% (n = 6), while the relative standard deviations (RSDs) were less than 10%. The results showed that the nine flavonoids, which were kaempferol, quercetin, hesperitin, vitexin, luteolin, catechin, apigenin, naringenin and isorhamnetin, were higher in contents among the 16 flavonoids in real samples, and they constituted up to 99.6% of the total flavonoids. The contents of these nine flavonoids can be considered as the quality control index of the ginkgo dietary supplement tea. The method proved to be rapid, selective, sensitive and stable, and it can be applied to control the quality of the ginkgo dietary supplement tea.

PhosSA: Fast and accurate phosphorylation site assignment algorithm for mass spectrometry data.

PubMed

Saeed, Fahad; Pisitkun, Trairak; Hoffert, Jason D; Rashidian, Sara; Wang, Guanghui; Gucek, Marjan; Knepper, Mark A

2013-11-07

Phosphorylation site assignment of high throughput tandem mass spectrometry (LC-MS/MS) data is one of the most common and critical aspects of phosphoproteomics. Correctly assigning phosphorylated residues helps us understand their biological significance. The design of common search algorithms (such as Sequest, Mascot etc.) do not incorporate site assignment; therefore additional algorithms are essential to assign phosphorylation sites for mass spectrometry data. The main contribution of this study is the design and implementation of a linear time and space dynamic programming strategy for phosphorylation site assignment referred to as PhosSA. The proposed algorithm uses summation of peak intensities associated with theoretical spectra as an objective function. Quality control of the assigned sites is achieved using a post-processing redundancy criteria that indicates the signal-to-noise ratio properties of the fragmented spectra. The quality assessment of the algorithm was determined using experimentally generated data sets using synthetic peptides for which phosphorylation sites were known. We report that PhosSA was able to achieve a high degree of accuracy and sensitivity with all the experimentally generated mass spectrometry data sets. The implemented algorithm is shown to be extremely fast and scalable with increasing number of spectra (we report up to 0.5 million spectra/hour on a moderate workstation). The algorithm is designed to accept results from both Sequest and Mascot search engines. An executable is freely available at http://helixweb.nih.gov/ESBL/PhosSA/ for academic research purposes.

Non-invasive diagnosis of acute rejection in renal transplant patients using mass spectrometry of urine samples - a multicentre phase 3 diagnostic accuracy study.

PubMed

Zapf, Antonia; Gwinner, Wilfried; Karch, Annika; Metzger, Jochen; Haller, Hermann; Koch, Armin

2015-09-15

Reliable and timely detection of acute rejection in renal transplant patients is important to preserve the allograft function and to prevent premature allograft failure. The current gold standard for the rejection diagnosis is an allograft biopsy which is usually performed upon an unexplained decline in allograft function. Because of the invasiveness of the biopsy, non-invasive tests have been suggested to diagnose acute rejection including mass spectrometry analysis of urine samples. The aim of this study is to examine the diagnostic accuracy of mass spectrometry analysis in urine for the diagnosis of acute rejections using the biopsy as gold-standard. The study is an ongoing prospective, single-arm, multicentre, phase 3 diagnostic accuracy study. It started in October 2011 and will be concluded in December 2015. Patient within the first year after transplantation who are scheduled for a biopsy to clarify unexplained impairment of the allograft are consecutively recruited into the study. The overall sample size (n = 600) was calculated to demonstrate a sensitivity of 83 % and a specificity of 70 % for a one-sided type one error of 2.5 % and a power of 80 % per hypothesis. Biopsy evaluation and mass spectrometry analysis of urine samples (obtained immediately before biopsy) are performed independently by different readers without knowledge from the respective other assessment. The follow-up observation period is 6 months. For the primary analysis, the lower limits of the two-sided 95 % Wald confidence intervals for sensitivity and specificity will be compared with the pre-specified thresholds (83 % for sensitivity and 70 % for specificity). In secondary analyses the predictive values, the diagnostic measures in subgroups, and the clinical course will be assessed. Previous phase 2 diagnostic accuracy studies (in small selected study populations) provided sufficient evidence to suggest mass spectrometry on urine samples as a promising approach to detect acute rejections. This study determines the diagnostic performance of the test in the routine setting of post-transplant patient care, compared to the biopsy-based rejection diagnosis. The next step would be a randomized trial to compare the two diagnostic strategies (including the urine test or not) in relation to patient relevant endpoints. NCT01315067 ; March 14, 2011.

Mass spectrometry of long-lived radionuclides

NASA Astrophysics Data System (ADS)

Becker, Johanna Sabine

2003-10-01

The capability of determining element concentrations at the trace and ultratrace level and isotope ratios is a main feature of inorganic mass spectrometry. The precise and accurate determination of isotope ratios of long-lived natural and artificial radionuclides is required, e.g. for their environmental monitoring and health control, for studying radionuclide migration, for age dating, for determining isotope ratios of radiogenic elements in the nuclear industry, for quality assurance and determination of the burn-up of fuel material in a nuclear power plant, for reprocessing plants, nuclear material accounting and radioactive waste control. Inorganic mass spectrometry, especially inductively coupled plasma mass spectrometry (ICP-MS) as the most important inorganic mass spectrometric technique today, possesses excellent sensitivity, precision and good accuracy for isotope ratio measurements and practically no restriction with respect to the ionization potential of the element investigated—therefore, thermal ionization mass spectrometry (TIMS), which has been used as the dominant analytical technique for precise isotope ratio measurements of long-lived radionuclides for many decades, is being replaced increasingly by ICP-MS. In the last few years instrumental progress in improving figures of merit for the determination of isotope ratio measurements of long-lived radionuclides in ICP-MS has been achieved by the application of a multiple ion collector device (MC-ICP-MS) and the introduction of the collision cell interface in order to dissociate disturbing argon-based molecular ions, to reduce the kinetic energy of ions and neutralize the disturbing noble gas ions (e.g. of 129Xe + for the determination of 129I). The review describes the state of the art and the progress of different inorganic mass spectrometric techniques such as ICP-MS, laser ablation ICP-MS vs. TIMS, glow discharge mass spectrometry, secondary ion mass spectrometry, resonance ionization mass spectrometry and accelerator mass spectrometry for the determination of long-lived radionuclides in quite different materials.

Comparison of pulse glow discharge-ion mobility spectrometry and liquid chromatography with tandem mass spectrometry based on multiplug filtration cleanup for the analysis of tricaine mesylate residues in fish and water.

PubMed

Zou, Nan; Chen, Ronghua; Qin, Yuhong; Song, Shuangyu; Tang, Xinglin; Pan, Canping

2016-09-01

Analytical methods based on multiplug filtration cleanup coupled with pulse glow discharge-ion mobility spectrometry and liquid chromatography tandem mass spectrometry were developed for the analysis of tricaine mesylate residue in fish and fish-raising water samples. A silica fiber holder and an appropriate new interface were designed to make the direct introduction of the fiber into the pulse glow discharge-ion mobility spectrometry introduction mechanism. The multiplug filtration cleanup method with adsorption mixtures was optimized for the determination of tricaine mesylate in fish samples. Good linear relationships were obtained by the two methods. For fish samples, limits of detection were 6 and 0.6 μg/kg by ion mobility spectrometry and liquid chromatography with tandem mass spectrometry, respectively. The matrix effect of the established liquid chromatography tandem mass spectrometry method was negligible for fish samples but that of the ion mobility spectrometry method was not. The two methods were compared. The ion mobility spectrometry system could be used a rapid screening tool on site with the advantage of rapidity, simplicity, and portability, and the liquid chromatography tandem mass spectrometry system could be used for validation in laboratory conditions with the advantage of lower limit of detection, stability, and precision. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

MIPHENO: Data normalization for high throughput metabolic analysis.

EPA Science Inventory

High throughput methodologies such as microarrays, mass spectrometry and plate-based small molecule screens are increasingly used to facilitate discoveries from gene function to drug candidate identification. These large-scale experiments are typically carried out over the course...

Analysis of human plasma lipids by using comprehensive two-dimensional gas chromatography with dual detection and with the support of high-resolution time-of-flight mass spectrometry for structural elucidation.

PubMed

Salivo, Simona; Beccaria, Marco; Sullini, Giuseppe; Tranchida, Peter Q; Dugo, Paola; Mondello, Luigi

2015-01-01

The main focus of the present research is the analysis of the unsaponifiable lipid fraction of human plasma by using data derived from comprehensive two-dimensional gas chromatography with dual quadrupole mass spectrometry and flame ionization detection. This approach enabled us to attain both mass spectral information and analyte percentage data. Furthermore, gas chromatography coupled with high-resolution time-of-flight mass spectrometry was used to increase the reliability of identification of several unsaponifiable lipid constituents. The synergism between both the high-resolution gas chromatography and mass spectrometry processes enabled us to attain a more in-depth knowledge of the unsaponifiable fraction of human plasma. Additionally, information was attained on the fatty acid and triacylglycerol composition of the plasma samples, subjected to investigation by using comprehensive two-dimensional gas chromatography with dual quadrupole mass spectrometry and flame ionization detection and high-performance liquid chromatography with atmospheric pressure chemical ionization quadrupole mass spectrometry, respectively. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra.

PubMed

Tolić, Nikola; Liu, Yina; Liyu, Andrey; Shen, Yufeng; Tfaily, Malak M; Kujawinski, Elizabeth B; Longnecker, Krista; Kuo, Li-Jung; Robinson, Errol W; Paša-Tolić, Ljiljana; Hess, Nancy J

2017-12-05

Ultrahigh resolution mass spectrometry, such as Fourier transform ion cyclotron resonance mass spectrometry (FT ICR MS), can resolve thousands of molecular ions in complex organic matrices. A Compound Identification Algorithm (CIA) was previously developed for automated elemental formula assignment for natural organic matter (NOM). In this work, we describe software Formularity with a user-friendly interface for CIA function and newly developed search function Isotopic Pattern Algorithm (IPA). While CIA assigns elemental formulas for compounds containing C, H, O, N, S, and P, IPA is capable of assigning formulas for compounds containing other elements. We used halogenated organic compounds (HOC), a chemical class that is ubiquitous in nature as well as anthropogenic systems, as an example to demonstrate the capability of Formularity with IPA. A HOC standard mix was used to evaluate the identification confidence of IPA. Tap water and HOC spike in Suwannee River NOM were used to assess HOC identification in complex environmental samples. Strategies for reconciliation of CIA and IPA assignments were discussed. Software and sample databases with documentation are freely available.

Using ultrahigh-resolution mass spectrometry and toxicity identification techniques to characterize the toxicity of oil sands process-affected water: The case for classical naphthenic acids.

PubMed

Hughes, Sarah A; Mahaffey, Ashley; Shore, Bryon; Baker, Josh; Kilgour, Bruce; Brown, Christine; Peru, Kerry M; Headley, John V; Bailey, Howard C

2017-11-01

Previous assessments of oil sands process-affected water (OSPW) toxicity were hampered by lack of high-resolution analytical analysis, use of nonstandard toxicity methods, and variability between OSPW samples. We integrated ultrahigh-resolution mass spectrometry with a toxicity identification evaluation (TIE) approach to quantitatively identify the primary cause of acute toxicity of OSPW to rainbow trout (Oncorhynchus mykiss). The initial characterization of OSPW toxicity indicated that toxicity was associated with nonpolar organic compounds, and toxicant(s) were further isolated within a range of discrete methanol fractions that were then subjected to Orbitrap mass spectrometry to evaluate the contribution of naphthenic acid fraction compounds to toxicity. The results showed that toxicity was attributable to classical naphthenic acids, with the potency of individual compounds increasing as a function of carbon number. Notably, the mass of classical naphthenic acids present in OSPW was dominated by carbon numbers ≤16; however, toxicity was largely a function of classical naphthenic acids with ≥17 carbons. Additional experiments found that acute toxicity of the organic fraction was similar when tested at conductivities of 400 and 1800 μmhos/cm and that rainbow trout fry were more sensitive to the organic fraction than larval fathead minnows (Pimephales promelas). Collectively, the results will aid in developing treatment goals and targets for removal of OSPW toxicity in water return scenarios both during operations and on mine closure. Environ Toxicol Chem 2017;36:3148-3157. © 2017 SETAC. © 2017 SETAC.

Lipidomics in triacylglycerol and cholesteryl ester oxidation.

PubMed

Kuksis, Arnis

2007-05-01

Although direct mass spectrometry is capable of identification the major molecular species of lipids in crude total lipid extracts, prior chromatographic isolation is necessary for detection and identification of the minor components. This is especially important for the analysis of the oxolipids, which usually occur in trace amounts in the total lipid extract, and require prior isolation for detailed analysis. Both thin-layer chromatography and adsorption cartridges provide effective means for isolation and enrichment of lipid classes, while gas-liquid chromatography and high performance liquid chromatography with on-line mass spectrometry permit further separation and identification of molecular species. Prior chromatographic resolution is absolutely necessary for the identification of isobaric and chiral molecules, which mass spectrometry/mass spectrometry (MS/MS) cannot distinguish. Both gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry applications may require the preparation of derivatives in order to improve the chromatographic and mass spectrometric properties of the oxolipids which is a small inconvenience for securing analytical reliability. The following chapter reviews the advantages and necessity of combined chromatographic-mass spectrometric approaches to successful identification and quantification of molecular species of oxoacylglycerols and oxocholesteryl esters in in-vitro model studies of lipid peroxidation and in the analyses of oxolipids recovered from tissues.

Ranked solutions to a class of combinatorial optimizations - with applications in mass spectrometry based peptide sequencing

NASA Astrophysics Data System (ADS)

Doerr, Timothy; Alves, Gelio; Yu, Yi-Kuo

2006-03-01

Typical combinatorial optimizations are NP-hard; however, for a particular class of cost functions the corresponding combinatorial optimizations can be solved in polynomial time. This suggests a way to efficiently find approximate solutions - - find a transformation that makes the cost function as similar as possible to that of the solvable class. After keeping many high-ranking solutions using the approximate cost function, one may then re-assess these solutions with the full cost function to find the best approximate solution. Under this approach, it is important to be able to assess the quality of the solutions obtained, e.g., by finding the true ranking of kth best approximate solution when all possible solutions are considered exhaustively. To tackle this statistical issue, we provide a systematic method starting with a scaling function generated from the fininte number of high- ranking solutions followed by a convergent iterative mapping. This method, useful in a variant of the directed paths in random media problem proposed here, can also provide a statistical significance assessment for one of the most important proteomic tasks - - peptide sequencing using tandem mass spectrometry data.

Mass spectrometry. [in organic chemistry

NASA Technical Reports Server (NTRS)

Burlingame, A. L.; Shackleton, C. H. L.; Howe, I.; Chizhov, O. S.

1978-01-01

A review of mass spectrometry in organic chemistry is given, dealing with advances in instrumentation and computer techniques, selected topics in gas-phase ion chemistry, and applications in such fields as biomedicine, natural-product studies, and environmental pollution analysis. Innovative techniques and instrumentation are discussed, along with chromatographic-mass spectrometric on-line computer techniques, mass spectral interpretation and management techniques, and such topics in gas-phase ion chemistry as electron-impact ionization and decomposition, photoionization, field ionization and desorption, high-pressure mass spectrometry, ion cyclotron resonance, and isomerization reactions of organic ions. Applications of mass spectrometry are examined with respect to bio-oligomers and their constituents, biomedically important substances, microbiology, environmental organic analysis, and organic geochemistry.

Quantitation of mycotoxins using direct analysis in real time (DART)-mass spectrometry (MS)

USDA-ARS?s Scientific Manuscript database

Ambient ionization represents a new generation of mass spectrometry ion sources which is used for rapid ionization of small molecules under ambient conditions. The combination of ambient ionization and mass spectrometry allows analyzing multiple food samples with simple or no sample treatment, or in...

Focus on Advancing High Performance Mass Spectrometry, Honoring Dr. Richard D. Smith, Recipient of the 2013 Award for a Distinguished Contribution in Mass Spectrometry

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

Baker, Erin Shammel; Muddiman, David C.; Loo, Joseph

This special focus issue of the Journal of the American Society for Mass Spectrometry celebrates the accomplishments of Dr. Richard D. Smith, the recipient of the 2013ASMS Award for a Distinguished Contribution in Mass Spectrometry, and who serves as a Battelle Fellow, Chief Scientist in the Biological Sciences Division, and Director of Proteomics Research at Pacific Northwest National Laboratory (PNNL) in Richland, WA. The award is for his development of the electrodynamic ion funnel.

Chromatography - mass spectrometry in aerospace industry

NASA Astrophysics Data System (ADS)

Buryak, A. K.; Serdyuk, T. M.

2013-01-01

The applications of chromatography - mass spectrometry in aerospace industry are considered. The primary attention is devoted to the development of physicochemical grounds of the use of various chromatography - mass spectrometry procedures to solve topical problems of this industry. Various methods for investigation of the composition of rocket fuels, surfaces of structural materials and environmental media affected by aerospace activities are compared. The application of chromatography - mass spectrometry for the development and evaluation of processes for decontaminations of equipment, industrial wastes and soils from rocket fuel components is substantiated. The bibliography includes 135 references.

[Latest development in mass spectrometry for clinical application].

PubMed

Takino, Masahiko

2013-09-01

Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has seen enormous growth in special clinical chemistry laboratories. It significantly increases the analytic potential in clinical chemistry, especially in the field of low molecular weight biomarker analysis. This review summarizes the state of the art in mass spectrometry and related techniques for clinical application with a main focus on recent developments in LC-MS. Current trends in ionization techniques, automated online sample preparation techniques coupled with LC-MS, and ion mobility spectrometry are discussed. Emerging mass spectrometric approaches complementary to LC-MS are discussed as well.

Performance and cost analysis of matrix-assisted laser desorption ionization-time of flight mass spectrometry for routine identification of yeast.

PubMed

Dhiman, Neelam; Hall, Leslie; Wohlfiel, Sherri L; Buckwalter, Seanne P; Wengenack, Nancy L

2011-04-01

Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry was compared to phenotypic testing for yeast identification. MALDI-TOF mass spectrometry yielded 96.3% and 84.5% accurate species level identifications (spectral scores, ≥ 1.8) for 138 common and 103 archived strains of yeast. MALDI-TOF mass spectrometry is accurate, rapid (5.1 min of hands-on time/identification), and cost-effective ($0.50/sample) for yeast identification in the clinical laboratory.

Determination of stoichiometry and concentration of trace elements in thin BaxSr1-xTiO3 perovskite layers.

PubMed

Becker, J S; Boulyga, S F

2001-07-01

This paper describes an analytical procedure for determining the stoichiometry of BaxSr1-xTiO3 perovskite layers using inductively coupled plasma mass spectrometry (ICP-MS). The analytical results of mass spectrometry measurements are compared to those of X-ray fluorescence analysis (XRF). The performance and the limits of solid-state mass spectrometry analytical methods for the surface analysis of thin BaxSr1-xTiO3 perovskite layers sputtered neutral mass spectrometry (SNMS)--are investigated and discussed.

New isotope technologies in environmental physics

NASA Astrophysics Data System (ADS)

Povinec, P. P.; Betti, M.; Jull, A. J. T.; Vojtyla, P.

2008-02-01

As the levels of radionuclides observed at present in the environment are very low, high sensitive analytical systems are required for carrying out environmental investigations. We review recent progress which has been done in low-level counting techniques in both radiometrics and mass spectrometry sectors, with emphasis on underground laboratories, Monte Carlo (GEANT) simulation of background of HPGe detectors operating in various configurations, secondary ionisation mass spectrometry, and accelerator mass spectrometry. Applications of radiometrics and mass spectrometry techniques in radioecology and climate change studies are presented and discussed as well. The review should help readers in better orientation on recent developments in the field of low-level counting and spectrometry, and to advice on construction principles of underground laboratories, as well as on criteria how to choose low or high energy mass spectrometers for environmental investigations.

Native Liquid Extraction Surface Analysis Mass Spectrometry: Analysis of Noncovalent Protein Complexes Directly from Dried Substrates

NASA Astrophysics Data System (ADS)

Martin, Nicholas J.; Griffiths, Rian L.; Edwards, Rebecca L.; Cooper, Helen J.

2015-08-01

Liquid extraction surface analysis (LESA) mass spectrometry is a promising tool for the analysis of intact proteins from biological substrates. Here, we demonstrate native LESA mass spectrometry of noncovalent protein complexes of myoglobin and hemoglobin from a range of surfaces. Holomyoglobin, in which apomyoglobin is noncovalently bound to the prosthetic heme group, was observed following LESA mass spectrometry of myoglobin dried onto glass and polyvinylidene fluoride surfaces. Tetrameric hemoglobin [(αβ)2 4H] was observed following LESA mass spectrometry of hemoglobin dried onto glass and polyvinylidene fluoride (PVDF) surfaces, and from dried blood spots (DBS) on filter paper. Heme-bound dimers and monomers were also observed. The `contact' LESA approach was particularly suitable for the analysis of hemoglobin tetramers from DBS.

"EMERGING" POLLUTANTS, AND COMMUNICATING THE ...

EPA Pesticide Factsheets

This paper weaves a rnulti-dimensioned perspective of mass spectrometry as a career against the backdrop of mass spectrometry's key role in the past and future of environmental chemistry. Along the way, some insights are offered for better focusing the spotlight on the discipline of mass spectrometry. A Foundation for Environmental Science-Mass Spectrometry Historically fundamental to our understanding of environmental processes and chemical pollution is mass spectrometry. This branch of analytical chemistry is the workhorse which supplies much of the definitive data to environmental scientists and engineers for identifying the molecular compositions, and ultimately the structures, of chemicals. This is not to ignore the complementary and critical roles played by the adjunct practices of sample enrichment (e.g., to lower method detection limits via any of various means of selective extraction) and analyte separation (e.g., to lessen contaminant interferences via the myriad forms of chromatography and electrophoresis). While the power of mass spectrometry has long been highly visible to the practicing environmental chemist, it borders on continued obscurity to the lay public and most non-chemists. Even though mass spectrometry has played a long, historic and Largely invisible role in establishing or undergirding our existing knowledge about environmental processes and pollution, what recognition it does enjoy is usually relegated to that of a tool. It is usually

Through a Glass Darkly: Glimpses into the Future of Mass Spectrometry

PubMed Central

Cooks, R. Graham; Mueller, Thomas

2013-01-01

The paper has three parts, (i) a brief overview of the main achievements made using mass spectrometry across all the fields of science, (ii) a survey of some of the topics currently being pursued most activity, including both applications and fundamental studies, and (iii) some hints as to what the future of mass spectrometry might hold with particular emphasis on revolutionary changes in the subject. Emphasis is given to ambient methods of ionization and their use in disease diagnosis and to their use in combination with miniature mass spectrometers for in-situ measurements. Special attention goes to the chemical aspects of mass spectrometry, including its emerging role as a preparative method based on accelerated bimolecular reaction rates in solution and on ion soft landing as a means of surface tailoring. In summary, the paper covers the proud history, vibrant present and expansive future of mass spectrometry. PMID:24349920

Structure Elucidation of the Diagnostic Product Ion at m/z 97 Derived from Androst-4-en-3-One-Based Steroids by ESI-CID and IRMPD Spectroscopy

NASA Astrophysics Data System (ADS)

Thevis, Mario; Beuck, Simon; Höppner, Sebastian; Thomas, Andreas; Held, Joseph; Schäfer, Mathias; Oomens, Jos; Schänzer, Wilhelm

2012-03-01

Structure elucidation of steroids by mass spectrometry has been of great importance to various analytical arenas and numerous studies were conducted to provide evidence for the composition and origin of (tandem) mass spectrometry-derived product ions used to characterize and identify steroidal substances. The common product ion at m/z 97 generated from androst-4-ene-3-one analogs has been subject of various studies, including stable isotope-labeling and (high resolution/high accuracy) tandem mass spectrometry, but its gas-phase structure has never been confirmed. Using high resolution/high accuracy mass spectrometry and low resolution tandem mass spectrometry, density functional theory (DFT) calculation, and infrared multiple photon dissociation (IRMPD) spectroscopy employing a free electron laser, the structure of m/z 97 derived from testosterone was assigned to protonated 3-methyl-2-cyclopenten-1-one. This ion was identified in a set of six cyclic C6H9O+ isomers as computed at the B3LYP/6-311++G(2d,2p) level of theory (protonated 3-methyl-2-cyclopenten-1-one, 2-methyl-2-cyclopenten-1-one and 2-cyclohexen-1-one). Product ions of m/z 97 obtained from MS2 and MS3 experiments of protonated 3-methyl-2-cyclopenten-1-one, 2-methyl-2-cyclopenten-1-one, 2-cyclohexen-1-one, and testosterone corroborated the suggested gas-phase ion structure, which was eventually substantiated by IRMPD spectroscopy yielding a spectrum that convincingly matched the predicted counterpart. Finally, the dissociation pathway of the protonated molecule of testosterone to m/z 97 was revisited and an alternative pathway was suggested that considers the exclusion of C-10 along with the inclusion of C-5, which was experimentally demonstrated with stable isotope labeling.

A novel strategy for global mapping of O-GlcNAc proteins and peptides using selective enzymatic deglycosylation, HILIC enrichment and mass spectrometry identification.

PubMed

Shen, Bingquan; Zhang, Wanjun; Shi, Zhaomei; Tian, Fang; Deng, Yulin; Sun, Changqing; Wang, Guangshun; Qin, Weijie; Qian, Xiaohong

2017-07-01

O-GlcNAcylation is a kind of dynamic O-linked glycosylation of nucleocytoplasmic and mitochondrial proteins. It serves as a major nutrient sensor to regulate numerous biological processes including transcriptional regulation, cell metabolism, cellular signaling, and protein degradation. Dysregulation of cellular O-GlcNAcylated levels contributes to the etiologies of many diseases such as diabetes, neurodegenerative disease and cancer. However, deeper insight into the biological mechanism of O-GlcNAcylation is hampered by its extremely low stoichiometry and the lack of efficient enrichment approaches for large-scale identification by mass spectrometry. Herein, we developed a novel strategy for the global identification of O-GlcNAc proteins and peptides using selective enzymatic deglycosylation, HILIC enrichment and mass spectrometry analysis. Standard O-GlcNAc peptides can be efficiently enriched even in the presence of 500-fold more abundant non-O-GlcNAc peptides and identified by mass spectrometry with a low nanogram detection sensitivity. This strategy successfully achieved the first large-scale enrichment and characterization of O-GlcNAc proteins and peptides in human urine. A total of 474 O-GlcNAc peptides corresponding to 457 O-GlcNAc proteins were identified by mass spectrometry analysis, which is at least three times more than that obtained by commonly used enrichment methods. A large number of unreported O-GlcNAc proteins related to cell cycle, biological regulation, metabolic and developmental process were found in our data. The above results demonstrated that this novel strategy is highly efficient in the global enrichment and identification of O-GlcNAc peptides. These data provide new insights into the biological function of O-GlcNAcylation in human urine, which is correlated with the physiological states and pathological changes of human body and therefore indicate the potential of this strategy for biomarker discovery from human urine. Copyright © 2017. Published by Elsevier B.V.

Zero voltage mass spectrometry probes and systems

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

Cooks, Robert Graham; Wleklinski, Michael Stanley; Bag, Soumabha

The invention generally relates to zero volt mass spectrometry probes and systems. In certain embodiments, the invention provides a system including a mass spectrometry probe including a porous material, and a mass spectrometer (bench-top or miniature mass spectrometer). The system operates without an application of voltage to the probe. In certain embodiments, the probe is oriented such that a distal end faces an inlet of the mass spectrometer. In other embodiments, the distal end of the probe is 5 mm or less from an inlet of the mass spectrometer.

Improving mass measurement accuracy in mass spectrometry based proteomics by combining open source tools for chromatographic alignment and internal calibration.

PubMed

Palmblad, Magnus; van der Burgt, Yuri E M; Dalebout, Hans; Derks, Rico J E; Schoenmaker, Bart; Deelder, André M

2009-05-02

Accurate mass determination enhances peptide identification in mass spectrometry based proteomics. We here describe the combination of two previously published open source software tools to improve mass measurement accuracy in Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS). The first program, msalign, aligns one MS/MS dataset with one FTICRMS dataset. The second software, recal2, uses peptides identified from the MS/MS data for automated internal calibration of the FTICR spectra, resulting in sub-ppm mass measurement errors.

Fungal proteomics: from identification to function.

PubMed

Doyle, Sean

2011-08-01

Some fungi cause disease in humans and plants, while others have demonstrable potential for the control of insect pests. In addition, fungi are also a rich reservoir of therapeutic metabolites and industrially useful enzymes. Detailed analysis of fungal biochemistry is now enabled by multiple technologies including protein mass spectrometry, genome and transcriptome sequencing and advances in bioinformatics. Yet, the assignment of function to fungal proteins, encoded either by in silico annotated, or unannotated genes, remains problematic. The purpose of this review is to describe the strategies used by many researchers to reveal protein function in fungi, and more importantly, to consolidate the nomenclature of 'unknown function protein' as opposed to 'hypothetical protein' - once any protein has been identified by protein mass spectrometry. A combination of approaches including comparative proteomics, pathogen-induced protein expression and immunoproteomics are outlined, which, when used in combination with a variety of other techniques (e.g. functional genomics, microarray analysis, immunochemical and infection model systems), appear to yield comprehensive and definitive information on protein function in fungi. The relative advantages of proteomic, as opposed to transcriptomic-only, analyses are also described. In the future, combined high-throughput, quantitative proteomics, allied to transcriptomic sequencing, are set to reveal much about protein function in fungi. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Characteristics of food using Queso Fresco cheese as an example

USDA-ARS?s Scientific Manuscript database

Processing and aging affect food characteristics, such as rheology, functional properties, microstructure, and sensory traits. These effects are discussed using Queso Fresco, a popular Hispanic cheese variety, as an example. Gas chromatography-mass spectrometry data indicated that lipolysis occurr...

Exudate Chemical Profiles Derived from Lespedeza and Other Tallgrass Prairie Plant Species

DTIC Science & Technology

2017-05-01

assayed by liquid chromatography–tandem mass spec- trometry (LC-MS/MS) and gas chromatography/mass spectrometry (GC/MS). The objective was to elucidate...molecular weight compounds were identified via gas chromatography/mass spectrometry (GC/MS) and tentatively identified as benzophenone and 1,4...diacetylbenzene. Three higher molecular weight compounds were identified by liquid chromatography-electrospray ionization- mass spectrometry (LC-ESI-MS

Targeted Multiplex Imaging Mass Spectrometry in Transmission Geometry for Subcellular Spatial Resolution

PubMed Central

Lavenant, Gwendoline Thiery; Zavalin, Andrey I.; Caprioli, Richard M.

2013-01-01

Targeted multiplex Imaging Mass Spectrometry utilizes several different antigen-specific primary antibodies, each directly labeled with a unique photocleavable mass tag, to detect multiple antigens in a single tissue section. Each photocleavable mass tag bound to an antibody has a unique molecular weight and can be readily ionized by laser desorption ionization mass spectrometry. This manuscript describes a mass spectrometry method that allows imaging of targeted single cells within tissue using transmission geometry laser desorption ionization mass spectrometry. Transmission geometry focuses the laser beam on the back side of the tissue placed on a glass slide, providing a 2 μm diameter laser spot irradiating the biological specimen. This matrix-free method enables simultaneous localization at the sub-cellular level of multiple antigens using specific tagged antibodies. We have used this technology to visualize the co-expression of synaptophysin and two major hormones peptides, insulin and somatostatin, in duplex assays in beta and delta cells contained in a human pancreatic islet. PMID:23397138

Targeted Multiplex Imaging Mass Spectrometry in Transmission Geometry for Subcellular Spatial Resolution

NASA Astrophysics Data System (ADS)

Thiery-Lavenant, Gwendoline; Zavalin, Andre I.; Caprioli, Richard M.

2013-04-01

Targeted multiplex imaging mass spectrometry utilizes several different antigen-specific primary antibodies, each directly labeled with a unique photocleavable mass tag, to detect multiple antigens in a single tissue section. Each photocleavable mass tag bound to an antibody has a unique molecular weight and can be readily ionized by laser desorption ionization mass spectrometry. This article describes a mass spectrometry method that allows imaging of targeted single cells within tissue using transmission geometry laser desorption ionization mass spectrometry. Transmission geometry focuses the laser beam on the back side of the tissue placed on a glass slide, providing a 2 μm diameter laser spot irradiating the biological specimen. This matrix-free method enables simultaneous localization at the sub-cellular level of multiple antigens using specific tagged antibodies. We have used this technology to visualize the co-expression of synaptophysin and two major hormones peptides, insulin and somatostatin, in duplex assays in beta and delta cells contained in a human pancreatic islet.

Fourier transform mass spectrometry.

PubMed

Scigelova, Michaela; Hornshaw, Martin; Giannakopulos, Anastassios; Makarov, Alexander

2011-07-01

This article provides an introduction to Fourier transform-based mass spectrometry. The key performance characteristics of Fourier transform-based mass spectrometry, mass accuracy and resolution, are presented in the view of how they impact the interpretation of measurements in proteomic applications. The theory and principles of operation of two types of mass analyzer, Fourier transform ion cyclotron resonance and Orbitrap, are described. Major benefits as well as limitations of Fourier transform-based mass spectrometry technology are discussed in the context of practical sample analysis, and illustrated with examples included as figures in this text and in the accompanying slide set. Comparisons highlighting the performance differences between the two mass analyzers are made where deemed useful in assisting the user with choosing the most appropriate technology for an application. Recent developments of these high-performing mass spectrometers are mentioned to provide a future outlook.

Fourier Transform Mass Spectrometry

PubMed Central

Scigelova, Michaela; Hornshaw, Martin; Giannakopulos, Anastassios; Makarov, Alexander

2011-01-01

This article provides an introduction to Fourier transform-based mass spectrometry. The key performance characteristics of Fourier transform-based mass spectrometry, mass accuracy and resolution, are presented in the view of how they impact the interpretation of measurements in proteomic applications. The theory and principles of operation of two types of mass analyzer, Fourier transform ion cyclotron resonance and Orbitrap, are described. Major benefits as well as limitations of Fourier transform-based mass spectrometry technology are discussed in the context of practical sample analysis, and illustrated with examples included as figures in this text and in the accompanying slide set. Comparisons highlighting the performance differences between the two mass analyzers are made where deemed useful in assisting the user with choosing the most appropriate technology for an application. Recent developments of these high-performing mass spectrometers are mentioned to provide a future outlook. PMID:21742802

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.

Modeling of Plutonium Ionization Probabilities for Use in Nuclear Forensic Analysis by Resonance Ionization Mass Spectrometry

DTIC Science & Technology

2016-12-01

masses collide, they form a supercritical mass . Criticality refers to the neutron population within the system. A critical system is one that can...Spectrometry, no. 242, pp. 161–168, 2005. [9] S. Raeder, “Trace analysis of actinides in the environment by means of resonance ionization mass ...first ionization potential of actinide elements by resonance ionization mass spectrometry.” Spectrochimica Acta part B: Atomic Spectroscopy. vol. 52

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

Proteomics data repositories

PubMed Central

Riffle, Michael; Eng, Jimmy K.

2010-01-01

The field of proteomics, particularly the application of mass spectrometry analysis to protein samples, is well-established and growing rapidly. Proteomics studies generate large volumes of raw experimental data and inferred biological results. To facilitate the dissemination of these data, centralized data repositories have been developed that make the data and results accessible to proteomics researchers and biologists alike. This review of proteomics data repositories focuses exclusively on freely-available, centralized data resources that disseminate or store experimental mass spectrometry data and results. The resources chosen reflect a current “snapshot” of the state of resources available with an emphasis placed on resources that may be of particular interest to yeast researchers. Resources are described in terms of their intended purpose and the features and functionality provided to users. PMID:19795424

Application of visual basic in high-throughput mass spectrometry-directed purification of combinatorial libraries.

PubMed

Li, B; Chan, E C Y

2003-01-01

We present an approach to customize the sample submission process for high-throughput purification (HTP) of combinatorial parallel libraries using preparative liquid chromatography electrospray ionization mass spectrometry. In this study, Visual Basic and Visual Basic for Applications programs were developed using Microsoft Visual Basic 6 and Microsoft Excel 2000, respectively. These programs are subsequently applied for the seamless electronic submission and handling of data for HTP. Functions were incorporated into these programs where medicinal chemists can perform on-line verification of the purification status and on-line retrieval of postpurification data. The application of these user friendly and cost effective programs in our HTP technology has greatly increased our work efficiency by reducing paper work and manual manipulation of data.

Laser Engineered Graphene Paper for Mass Spectrometry Imaging

PubMed Central

Qian, Kun; Zhou, Liang; Liu, Jian; Yang, Jie; Xu, Hongyi; Yu, Meihua; Nouwens, Amanda; Zou, Jin; Monteiro, Michael J.; Yu, Chengzhong

2013-01-01

A pulsed laser engineering approach is developed to prepare novel functional graphene paper with graphitic nanospheres homogeneously decorated on the surface and the superior performance of engineered paper is revealed in matrix-free mass spectrometry (MS) detection and imaging. We demonstrate that the stability of graphene paper under intense irradiation can be dramatically increased through a designed laser engineering process by forming densely packed graphitic nanospheres on the paper surface. Moreover, the surface hydrophobicity is enhanced and electric conductivity is improved. The engineered graphene paper can image the invisible micro-patterns of trace amount molecules and increases the detection limit towards diverse molecules by over two orders of magnitude compared to the pristine graphene paper and commercial products in MS analysis. PMID:23475267

Quantification of phytochelatins in Chlamydomonas reinhardtii using ferrocene-based derivatization.

PubMed

Bräutigam, Anja; Bomke, Susanne; Pfeifer, Thorben; Karst, Uwe; Krauss, Gerd-Joachim; Wesenberg, Dirk

2010-08-01

A method for the identification and quantification of canonic and isoforms of phytochelatins (PCs) from Chlamydomonas reinhardtii was developed. After disulfide reduction with tris(2-carboxyethyl)phosphine (TCEP) PCs were derivatized with ferrocenecarboxylic acid (2-maleimidoyl)ethylamide (FMEA) in order to avoid oxidation of the free thiol functions during analysis. Liquid chromatography (LC) coupled to electrospray mass spectrometry (ESI-MS) and inductively coupled plasma-mass spectrometry (ICP-MS) was used for rapid and quantitative analysis of the precolumn derivatized PCs. PC(2-4), CysGSH, CysPC(2-4), CysPC(2)desGly, CysPC(2)Glu and CysPC(2)Ala were determined in the algal samples depending on the exposure of the cells to cadmium ions.

Quantitative identification of proteins that influence miRNA biogenesis by RNA pull-down-SILAC mass spectrometry (RP-SMS).

PubMed

Choudhury, Nila Roy; Michlewski, Gracjan

2018-06-08

RNA-binding proteins mediate and control gene expression. As some examples, they regulate pre-mRNA synthesis and processing; mRNA localisation, translation and decay; and microRNA (miRNA) biogenesis and function. Here, we present a detailed protocol for RNA pull-down coupled to stable isotope labelling by amino acids in cell culture (SILAC) mass spectrometry (RP-SMS) that enables quantitative, fast and specific detection of RNA-binding proteins that regulate miRNA biogenesis. In general, this method allows for the identification of RNA-protein complexes formed using in vitro or chemically synthesized RNAs and protein extracts derived from cultured cells. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Unexpected Crosslinking and Diglycation as Advanced Glycation End-Products from Glyoxal

NASA Astrophysics Data System (ADS)

Lopez-Clavijo, Andrea F.; Duque-Daza, Carlos A.; Soulby, Andrew; Canelon, Isolda Romero; Barrow, Mark; O'Connor, Peter B.

2014-12-01

Glyoxal-derived advanced glycation end-products (AGEs) are formed in physiological systems affecting protein/peptide function and structure. These AGEs are generated during aging and chronic diseases such as diabetes and are considered arginine glycating agents. Thus, the study of glyoxal-derived AGEs in lysine residues and amino acid competition is addressed here using acetylated and non-acetylated undecapeptides, with one arginine and one lysine residue available for glycation. Tandem mass spectrometry results from a Fourier transform ion cyclotron resonance mass spectrometer showed glycated species at both the arginine and lysine residues. One species with the mass addition of 116.01096 Da is formed at the arginine residue. A possible structure is proposed to explain this finding (Nδ-[2-(dihydroxymethyl)-2H,3aH,4H,6aH-[1, 3]dioxolo[5,6-d]imidazolin-5-yl]-L-ornithine-derived AGE). The second species corresponded to intramolecular crosslink involving the lysine residue and its presence is checked with ion-mobility mass spectrometry.

Fast quantitative detection of cocaine in beverages using nanoextractive electrospray ionization tandem mass spectrometry.

PubMed

Hu, Bin; Peng, Xuejiao; Yang, Shuiping; Gu, Haiwei; Chen, Huanwen; Huan, Yanfu; Zhang, Tingting; Qiao, Xiaolin

2010-02-01

Without any sample pretreatment, effervescent beverage fluids were manually sprayed into the primary ion plume created by using a nanoelectrospray ionization source for direct ionization, and the analyte ions of interest were guided into an ion trap mass spectrometer for tandem mass analysis. Functional ingredients (e.g., vitamins, taurine, and caffeine, etc.) and spiked impurity (e.g., cocaine) in various beverages, such as Red Bull energy drink, Coco-cola, and Pepsi samples were rapidly identified within 1.5 s. The limit of detection was found to be 7-15 fg (S/N = 3) for cocaine in different samples using the characteristic fragment (m/z 150) observed in the MS(3) experiments. Typical relative standard deviation and recovery of this method were 6.9%-8.6% and 104%-108% for direct analysis of three actual samples, showing that nanoextractive electrospray ionization tandem mass spectrometry is a useful technique for fast screening cocaine presence in beverages. 2010. Published by Elsevier Inc.

Label-Free Discovery Array Platform for the Characterization of Glycan Binding Proteins and Glycoproteins.

PubMed

Gray, Christopher J; Sánchez-Ruíz, Antonio; Šardzíková, Ivana; Ahmed, Yassir A; Miller, Rebecca L; Reyes Martinez, Juana E; Pallister, Edward; Huang, Kun; Both, Peter; Hartmann, Mirja; Roberts, Hannah N; Šardzík, Robert; Mandal, Santanu; Turnbull, Jerry E; Eyers, Claire E; Flitsch, Sabine L

2017-04-18

The identification of carbohydrate-protein interactions is central to our understanding of the roles of cell-surface carbohydrates (the glycocalyx), fundamental for cell-recognition events. Therefore, there is a need for fast high-throughput biochemical tools to capture the complexity of these biological interactions. Here, we describe a rapid method for qualitative label-free detection of carbohydrate-protein interactions on arrays of simple synthetic glycans, more complex natural glycosaminoglycans (GAG), and lectins/carbohydrate binding proteins using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. The platform can unequivocally identify proteins that are captured from either purified or complex sample mixtures, including biofluids. Identification of proteins bound to the functionalized array is achieved by analyzing either the intact protein mass or, after on-chip proteolytic digestion, the peptide mass fingerprint and/or tandem mass spectrometry of selected peptides, which can yield highly diagnostic sequence information. The platform described here should be a valuable addition to the limited analytical toolbox that is currently available for glycomics.

Boron nitride nanotubes matrix for signal enhancement in infrared laser desorption postionization mass spectrometry.

PubMed

Lu, Qiao; Hu, Yongjun; Chen, Jiaxin; Li, Yujian; Song, Wentao; Jin, Shan; Liu, Fuyi; Sheng, Liusi

2018-09-01

The nanomaterials function as the substrate to trap analytes, absorb energy from the laser irradiation and transfer energy to the analytes to facilitate the laser desorption process. In this work, the signal intensity and reproducibility of analytes with nanomaterials as matrices were explored by laser desorption postionization mass spectrometry (LDPI-MS). Herein, the desorbed neutral species were further ionized by vacuum ultraviolet (VUV, 118 nm) and analyzed by mass spectrometer. Compared with other nanomaterial matrices such as graphene and carbon nanotubes (CNTs), boron nitride nanotubes (BNNTs) exhibited much higher desorption efficiency under infrared (IR) light and produced no background signal in the whole mass range by LDPI-MS. Additionally, this method was successfully and firstly exploited to in situ detection and imaging for drugs of low concentration in intact tissues, which proved the utility, facility and convenience of this method applied in drug discovery and biomedical research. Copyright © 2018 Elsevier B.V. All rights reserved.

EMERGING POLLUTANTS, AND COMMUNICATING THE SCIENCE OF ENVIRONMENTAL CHEMISTRY AND MASS SPECTROMETRY: PHARMACEUTICALS IN THE ENVIRONMENT

EPA Science Inventory

This paper weaves a rnulti-dimensioned perspective of mass spectrometry as a career against the backdrop of mass spectrometry's key role in the past and future of environmental chemistry. Along the way, some insights are offered for better focusing the spotlight on the discipline...

Simulation of Two Dimensional Electrophoresis and Tandem Mass Spectrometry for Teaching Proteomics

ERIC Educational Resources Information Center

Fisher, Amanda; Sekera, Emily; Payne, Jill; Craig, Paul

2012-01-01

In proteomics, complex mixtures of proteins are separated (usually by chromatography or electrophoresis) and identified by mass spectrometry. We have created 2DE Tandem MS, a computer program designed for use in the biochemistry, proteomics, or bioinformatics classroom. It contains two simulations--2D electrophoresis and tandem mass spectrometry.…

"EMERGING" POLLUTANTS, AND COMMUNICATING THE SCIENCE OF ENVIRONMENTAL CHEMISTRY AND MASS SPECTROMETRY: PHARMACEUTICALS IN THE ENVIRONMENT

EPA Science Inventory

This paper weaves a rnulti-dimensioned perspective of mass spectrometry as a career against the backdrop of mass spectrometry's key role in the past and future of environmental chemistry. Along the way, some insights are offered for better focusing the spotlight on the discipline...

Accuracy of delta 18O isotope ratio measurements on the same sample by continuous-flow isotope-ratio mass spectrometry

USDA-ARS?s Scientific Manuscript database

The doubly labeled water method is considered the reference method to measure energy expenditure. Conventional mass spectrometry requires a separate aliquot of the same sample to be prepared and analyzed separately. With continuous-flow isotope-ratio mass spectrometry, the same sample could be analy...

Quantitation of aflatoxins from corn and other food related materials by direct analysis in real time - mass spectrometry (DART-MS)

USDA-ARS?s Scientific Manuscript database

Ambient ionization coupled to mass spectrometry continues to be applied to new analytical problems, facilitating the rapid and convenient analysis of a variety of analytes. Recently, demonstrations of ambient ionization mass spectrometry applied to quantitative analysis of mycotoxins have been shown...

21 CFR 862.1055 - Newborn screening test system for amino acids, free carnitine, and acylcarnitines using tandem...

Code of Federal Regulations, 2012 CFR

2012-04-01

... mass spectrometry is a device that consists of stable isotope internal standards, control materials..., free carnitine, and acylcarnitines using tandem mass spectrometry. 862.1055 Section 862.1055 Food and... screening test system for amino acids, free carnitine, and acylcarnitines using tandem mass spectrometry. (a...

21 CFR 862.1055 - Newborn screening test system for amino acids, free carnitine, and acylcarnitines using tandem...

Code of Federal Regulations, 2014 CFR

2014-04-01

... mass spectrometry is a device that consists of stable isotope internal standards, control materials..., free carnitine, and acylcarnitines using tandem mass spectrometry. 862.1055 Section 862.1055 Food and... screening test system for amino acids, free carnitine, and acylcarnitines using tandem mass spectrometry. (a...

Topographical and Chemical Imaging of a Phase Separated Polymer Using a Combined Atomic Force Microscopy/Infrared Spectroscopy/Mass Spectrometry Platform

DOE PAGES

Tai, Tamin; Karácsony, Orsolya; Bocharova, Vera; ...

2016-02-18

This article describes how the use of a hybrid atomic force microscopy/infrared spectroscopy/mass spectrometry imaging platform was demonstrated for the acquisition and correlation of nanoscale sample surface topography and chemical images based on infrared spectroscopy and mass spectrometry.

Next generation offline approaches to trace organic compound speciation: Approaching comprehensive speciation with soft ionization and very high resolution tandem mass spectrometry

NASA Astrophysics Data System (ADS)

Khare, P.; Marcotte, A.; Sheu, R.; Ditto, J.; Gentner, D. R.

2017-12-01

Intermediate- and semi-volatile organic compounds (IVOCs and SVOCs) have high secondary organic aerosol (SOA) yields, as well as significant ozone formation potentials. Yet, their emission sources and oxidation pathways remain largely understudied due to limitations in current analytical capabilities. Online mass spectrometers are able to collect real time data but their limited mass resolving power renders molecular level characterization of IVOCs and SVOCs from the unresolved complex mixture unfeasible. With proper sampling techniques and powerful analytical instrumentation, our offline tandem mass spectrometry (i.e. MS×MS) techniques provide molecular-level and structural identification over wide polarity and volatility ranges. We have designed a novel analytical system for offline analysis of gas-phase SOA precursors collected on custom-made multi-bed adsorbent tubes. Samples are desorbed into helium via a gradual temperature ramp and sample flow is split equally for direct-MS×MS analysis and separation via gas chromatography (GC). The effluent from GC separation is split again for analysis via atmospheric pressure chemical ionization quadrupole time-of-flight mass spectrometry (APCI-Q×TOF) and traditional electron ionization mass spectrometry (EI-MS). The compounds for direct-MS×MS analysis are delivered via a transfer line maintained at 70ºC directly to APCI-Q×TOF, thus preserving the molecular integrity of thermally-labile, or other highly-reactive, organic compounds. Both our GC-MS×MS and direct-MS×MS analyses report high accuracy parent ion masses as well as information on molecular structure via MS×MS, which together increase the resolution of unidentified complex mixtures. We demonstrate instrument performance and present preliminary results from urban atmospheric samples collected from New York City with a wide range of compounds including highly-functionalized organic compounds previously understudied in outdoor air. Our work offers new insights into emerging emission sources in urban environments that can have a major impact on public health and also improves understanding of anthropogenic SOA precursor emissions.

Development of a Linear Ion Trap Mass Spectrometer (LITMS) Investigation for Future Planetary Surface Missions

NASA Technical Reports Server (NTRS)

Brinckerhoff, W.; Danell, R.; Van Ameron, F.; Pinnick, V.; Li, X.; Arevalo, R.; Glavin, D.; Getty, S.; Mahaffy, P.; Chu, P.;

Detection of Ketones by a Novel Technology: Dipolar Proton Transfer Reaction Mass Spectrometry (DP-PTR-MS)

NASA Astrophysics Data System (ADS)

Pan, Yue; Zhang, Qiangling; Zhou, Wenzhao; Zou, Xue; Wang, Hongmei; Huang, Chaoqun; Shen, Chengyin; Chu, Yannan

2017-05-01

Proton transfer reaction mass spectrometry (PTR-MS) has played an important role in the field of real-time monitoring of trace volatile organic compounds (VOCs) due to its advantages such as low limit of detection (LOD) and fast time response. Recently, a new technology of proton extraction reaction mass spectrometry (PER-MS) with negative ions OH- as the reagent ions has also been presented, which can be applied to the detection of VOCs and even inorganic compounds. In this work, we combined the functions of PTR-MS and PER-MS in one instrument, thereby developing a novel technology called dipolar proton transfer reaction mass spectrometry (DP-PTR-MS). The selection of PTR-MS mode and PER-MS mode was achieved in DP-PTR-MS using only water vapor in the ion source and switching the polarity. In this experiment, ketones (denoted by M) were selected as analytes. The ketone (molecular weight denoted by m) was ionized as protonated ketone [M + H]+ [mass-to-charge ratio ( m/z) m + 1] in PTR-MS mode and deprotonated ketone [M - H]- ( m/z m - 1) in PER-MS mode. By comparing the m/z value of the product ions in the two modes, the molecular weight of the ketone can be positively identified as m. Results showed that whether it is a single ketone sample or a mixed sample of eight kinds of ketones, the molecular weights can be detected with DP-PTR-MS. The newly developed DP-PTR-MS not only maintains the original advantages of PTR-MS and PER-MS in sensitive and rapid detection of ketones, but also can estimate molecular weight of ketones.

Forensic Mass Spectrometry

NASA Astrophysics Data System (ADS)

Hoffmann, William D.; Jackson, Glen P.

2015-07-01

Developments in forensic mass spectrometry tend to follow, rather than lead, the developments in other disciplines. Examples of techniques having forensic potential born independently of forensic applications include ambient ionization, imaging mass spectrometry, isotope ratio mass spectrometry, portable mass spectrometers, and hyphenated chromatography-mass spectrometry instruments, to name a few. Forensic science has the potential to benefit enormously from developments that are funded by other means, if only the infrastructure and personnel existed to adopt, validate, and implement the new technologies into casework. Perhaps one unique area in which forensic science is at the cutting edge is in the area of chemometrics and the determination of likelihood ratios for the evaluation of the weight of evidence. Such statistical techniques have been developed most extensively for ignitable-liquid residue analyses and isotope ratio analysis. This review attempts to capture the trends, motivating forces, and likely impact of developing areas of forensic mass spectrometry, with the caveat that none of this research is likely to have any real impact in the forensic community unless: (a) The instruments developed are turned into robust black boxes with red and green lights for positives and negatives, respectively, or (b) there are PhD graduates in the workforce who can help adopt these sophisticated techniques.

Mass spectrometry of flavonoid vicenin-2, based sunlight barriers in Lychnophora species.

PubMed

Silva, Denise Brentan; Turatti, Izabel Cristina Casanova; Gouveia, Dayana Rubio; Ernst, Madeleine; Teixeira, Simone Pádua; Lopes, Norberto Peporine

2014-03-07

Lychnophora salicifolia plants collected from four different places in Brazil (three states: Goias, Minas Gerais and Bahia) revealed a conserved accumulation of vicenin-2, a di-C-glycosyl flavonoid. Quantitative studies by UPLC-MS/MS showed high concentration of vicenin-2 in leaves from sixty specimens of six Lychnophora species. So the tissue distributions of vicenin-2 were evaluated in wild Lychnophora leaves (Asteraceae) by laser based imaging mass spectrometry (IMS) to propose its distributions and possible functions for the species analyzed. Mass spectrometric imaging revealed that vicenin-2, unlike other flavonoids, was produced at the top of the leaves. The combination of localization and UV absorption properties of vicenin-2 suggests that it could act as a UV light barrier to protect the plants, since plants are sessile organisms that have to protect themselves from harsh external conditions such as intense sunlight.

Separation and identification of Musa acuminate Colla (banana) leaf proteins by two-dimensional gel electrophoresis and mass spectrometry.

PubMed

Lu, Y; Qi, Y X; Zhang, H; Zhang, H Q; Pu, J J; Xie, Y X

2013-12-19

To establish a proteomic reference map of Musa acuminate Colla (banana) leaf, we separated and identified leaf proteins using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS). Tryptic digests of 44 spots were subjected to peptide mass fingerprinting (PMF) by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS. Three spots that were not identified by MALDI-TOF MS analysis were identified by searching against the NCBInr, SwissProt, and expressed sequence tag (EST) databases. We identified 41 unique proteins. The majority of the identified leaf proteins were found to be involved in energy metabolism. The results indicate that 2D-PAGE is a sensitive and powerful technique for the separation and identification of Musa leaf proteins. A summary of the identified proteins and their putative functions is discussed.

Mass Spectrometry of Flavonoid Vicenin-2, Based Sunlight Barriers in Lychnophora species

PubMed Central

Silva, Denise Brentan; Turatti, Izabel Cristina Casanova; Gouveia, Dayana Rubio; Ernst, Madeleine; Teixeira, Simone Pádua; Lopes, Norberto Peporine

2014-01-01

Lychnophora salicifolia plants collected from four different places in Brazil (three states: Goias, Minas Gerais and Bahia) revealed a conserved accumulation of vicenin-2, a di-C-glycosyl flavonoid. Quantitative studies by UPLC-MS/MS showed high concentration of vicenin-2 in leaves from sixty specimens of six Lychnophora species. So the tissue distributions of vicenin-2 were evaluated in wild Lychnophora leaves (Asteraceae) by laser based imaging mass spectrometry (IMS) to propose its distributions and possible functions for the species analyzed. Mass spectrometric imaging revealed that vicenin-2, unlike other flavonoids, was produced at the top of the leaves. The combination of localization and UV absorption properties of vicenin-2 suggests that it could act as a UV light barrier to protect the plants, since plants are sessile organisms that have to protect themselves from harsh external conditions such as intense sunlight. PMID:24603617

Mass Spectrometry of Flavonoid Vicenin-2, Based Sunlight Barriers in Lychnophora species

NASA Astrophysics Data System (ADS)

Silva, Denise Brentan; Turatti, Izabel Cristina Casanova; Gouveia, Dayana Rubio; Ernst, Madeleine; Teixeira, Simone Pádua; Lopes, Norberto Peporine

2014-03-01

Lychnophora salicifolia plants collected from four different places in Brazil (three states: Goias, Minas Gerais and Bahia) revealed a conserved accumulation of vicenin-2, a di-C-glycosyl flavonoid. Quantitative studies by UPLC-MS/MS showed high concentration of vicenin-2 in leaves from sixty specimens of six Lychnophora species. So the tissue distributions of vicenin-2 were evaluated in wild Lychnophora leaves (Asteraceae) by laser based imaging mass spectrometry (IMS) to propose its distributions and possible functions for the species analyzed. Mass spectrometric imaging revealed that vicenin-2, unlike other flavonoids, was produced at the top of the leaves. The combination of localization and UV absorption properties of vicenin-2 suggests that it could act as a UV light barrier to protect the plants, since plants are sessile organisms that have to protect themselves from harsh external conditions such as intense sunlight.

Application of Fourier-transform ion cyclotron resonance mass spectrometry to metabolic profiling and metabolite identification.

PubMed

Ohta, Daisaku; Kanaya, Shigehiko; Suzuki, Hideyuki

2010-02-01

Metabolomics, as an essential part of genomics studies, intends holistic understanding of metabolic networks through simultaneous analysis of a myriad of both known and unknown metabolites occurring in living organisms. The initial stage of metabolomics was designed for the reproducible analyses of known metabolites based on their comparison to available authentic compounds. Such metabolomics platforms were mostly based on mass spectrometry (MS) technologies enabled by a combination of different ionization methods together with a variety of separation steps including LC, GC, and CE. Among these, Fourier-transform ion cyclotron resonance MS (FT-ICR/MS) is distinguished from other MS technologies by its ultrahigh resolution power in mass to charge ratio (m/z). The potential of FT-ICR/MS as a distinctive metabolomics tool has been demonstrated in nontargeted metabolic profiling and functional characterization of novel genes. Here, we discuss both the advantages and difficulties encountered in the FT-ICR/MS metabolomics studies.

Mass Spectrometry in Studies of Protein Thiol Chemistry and Signaling: Opportunities and Caveats

PubMed Central

Devarie Baez, Nelmi O.; Reisz, Julie A.; Furdui, Cristina M.

2014-01-01

Mass spectrometry (MS) has become a powerful and widely utilized tool in the investigation of protein thiol chemistry, biochemistry, and biology. Very early biochemical studies of metabolic enzymes have brought to light the broad spectrum of reactivity profiles that distinguish cysteine thiols with functions in catalysis and protein stability from other cysteine residues in proteins. The development of MS methods for the analysis of proteins using electrospray ionization (ESI) or matrix-assisted laser desorption/ionization (MALDI) coupled with the emergence of high-resolution mass analyzers have been instrumental in advancing studies of thiol modifications, both in single proteins and within the cellular context. This article reviews MS instrumentation and methods of analysis employed in investigations of thiols and their reactivity toward a range of small biomolecules. A selected number of studies are detailed to highlight the advantages brought about by the MS technologies along with the caveats associated with these analyses. PMID:25261734

Development of quantitative laser ionization mass spectrometry (LIMS). Final report, 1 Aug 87-1 Jan 90

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

Odom, R.W.

1991-06-04

The objective of the research was to develop quantitative microanalysis methods for dielectric thin films using the laser ionization mass spectrometry (LIMS) technique. The research involved preparation of thin (5,000 A) films of SiO2, Al2O3, MgF2, TiO2, Cr2O3, Ta2O5, Si3N4, and ZrO2, and doping these films with ion implant impurities of 11B, 40Ca, 56Fe, 68Zn, 81Br, and 121Sb. Laser ionization mass spectrometry (LIMS), secondary ion mass spectrometry (SIMS) and Rutherford backscattering spectrometry (RBS) were performed on these films. The research demonstrated quantitative LIMS analysis down to detection levels of 10-100 ppm, and led to the development of (1) a compoundmore » thin film standards product line for the performing organization, (2) routine LIMS analytical methods, and (3) the manufacture of high speed preamplifiers for time-of-flight mass spectrometry (TOF-MS) techniques.« less

Mass spectrometry of analytical derivatives. 2. "Ortho" and "Para" effects in electron ionization mass spectra of derivatives of hydroxy, mercapto and amino benzoic acids.

PubMed

Todua, Nino G; Mikaia, Anzor I

2016-01-01

Derivatives requiring either anhydrous or aqueous reaction conditions were prepared for robust and reliable gas chromatography/mass spectrometry (GC/MS) characterization of hydroxyl, mercapto, and amino benzoic acids Methylation and trialkylsilytation are employed for blocking the acidic function. Alkyl, trimethylsilyl, acetyl, perfluoroacyl and alkoxycarbonyl derivatization groups are introduced to hydroxyl, mercapto and amino functions. The electron ionization induced fragmentation characteristics of corresponding derivatives are explained by comparing the MS 1 spectra of unlabeled compounds to their 2 H and 13 C labeled analogs, and analysis of collision-induced dissociation data from MS 2 spectra. Competing fragmentation alternatives are identified and specific decomposition processes are detailed that characterize (a) ortho isomers due to interaction or vicinal functional substituents and (b) para isomers prone to forming para quinoid type structures. Skeletal and hydrogen rearrangements typical for methyl benzoates and the blocking groups are considered when discussing diagnostically important ions. Characteristic ions produced as a result of rearrangements in ortho isomers are classified, and skeletal rearrangements required to produce para quinoid type ions specific for para isomers are noted. Key ions for structure elucidation and differentiation of isomers for derivatives of substituted benzoic acids by GC/MS are suggested.

Mass spectrometry of analytical derivatives. 2. “Ortho” and “Para” effects in electron ionization mass spectra of derivatives of hydroxy, mercapto and amino benzoic acids1

PubMed Central

Todua, Nino G.; Mikaia, Anzor I.

2016-01-01

Derivatives requiring either anhydrous or aqueous reaction conditions were prepared for robust and reliable gas chromatography/mass spectrometry (GC/MS) characterization of hydroxyl, mercapto, and amino benzoic acids Methylation and trialkylsilytation are employed for blocking the acidic function. Alkyl, trimethylsilyl, acetyl, perfluoroacyl and alkoxycarbonyl derivatization groups are introduced to hydroxyl, mercapto and amino functions. The electron ionization induced fragmentation characteristics of corresponding derivatives are explained by comparing the MS1 spectra of unlabeled compounds to their 2H and 13C labeled analogs, and analysis of collision-induced dissociation data from MS2 spectra. Competing fragmentation alternatives are identified and specific decomposition processes are detailed that characterize (a) ortho isomers due to interaction or vicinal functional substituents and (b) para isomers prone to forming para quinoid type structures. Skeletal and hydrogen rearrangements typical for methyl benzoates and the blocking groups are considered when discussing diagnostically important ions. Characteristic ions produced as a result of rearrangements in ortho isomers are classified, and skeletal rearrangements required to produce para quinoid type ions specific for para isomers are noted. Key ions for structure elucidation and differentiation of isomers for derivatives of substituted benzoic acids by GC/MS are suggested. PMID:27891187

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

Carbon Nanotube Fiber Ionization Mass Spectrometry: A Fundamental Study of a Multi-Walled Carbon Nanotube Functionalized Corona Discharge Pin for Polycyclic Aromatic Hydrocarbons Analysis.

PubMed

Nahan, Keaton S; Alvarez, Noe; Shanov, Vesselin; Vonderheide, Anne

2017-11-01

Mass spectrometry continues to tackle many complicated tasks, and ongoing research seeks to simplify its instrumentation as well as sampling. The desorption electrospray ionization (DESI) source was the first ambient ionization source to function without extensive gas requirements and chromatography. Electrospray techniques generally have low efficiency for ionization of nonpolar analytes and some researchers have resorted to methods such as direct analysis in real time (DART) or desorption atmospheric pressure chemical ionization (DAPCI) for their analysis. In this work, a carbon nanotube fiber ionization (nanoCFI) source was developed and was found to be capable of solid phase microextraction (SPME) of nonpolar analytes as well as ionization and sampling similar to that of direct probe atmospheric pressure chemical ionization (DP-APCI). Conductivity and adsorption were maintained by utilizing a corona pin functionalized with a multi-walled carbon nanotube (MWCNT) thread. Quantitative work with the nanoCFI source with a designed corona discharge pin insert demonstrated linearity up to 0.97 (R 2 ) of three target PAHs with phenanthrene internal standard. Graphical Abstract ᅟ.

The speciation of the proteome

PubMed Central

Jungblut, Peter R; Holzhütter, Hermann G; Apweiler, Rolf; Schlüter, Hartmut

2008-01-01

Introduction In proteomics a paradox situation developed in the last years. At one side it is basic knowledge that proteins are post-translationally modified and occur in different isoforms. At the other side the protein expression concept disclaims post-translational modifications by connecting protein names directly with function. Discussion Optimal proteome coverage is today reached by bottom-up liquid chromatography/mass spectrometry. But quantification at the peptide level in shotgun or bottom-up approaches by liquid chromatography and mass spectrometry is completely ignoring that a special peptide may exist in an unmodified form and in several-fold modified forms. The acceptance of the protein species concept is a basic prerequisite for meaningful quantitative analyses in functional proteomics. In discovery approaches only top-down analyses, separating the protein species before digestion, identification and quantification by two-dimensional gel electrophoresis or protein liquid chromatography, allow the correlation between changes of a biological situation and function. Conclusion To obtain biological relevant information kinetics and systems biology have to be performed at the protein species level, which is the major challenge in proteomics today. PMID:18638390

Carbon Nanotube Fiber Ionization Mass Spectrometry: A Fundamental Study of a Multi-Walled Carbon Nanotube Functionalized Corona Discharge Pin for Polycyclic Aromatic Hydrocarbons Analysis

NASA Astrophysics Data System (ADS)

Nahan, Keaton S.; Alvarez, Noe; Shanov, Vesselin; Vonderheide, Anne

2017-09-01

Mass spectrometry continues to tackle many complicated tasks, and ongoing research seeks to simplify its instrumentation as well as sampling. The desorption electrospray ionization (DESI) source was the first ambient ionization source to function without extensive gas requirements and chromatography. Electrospray techniques generally have low efficiency for ionization of nonpolar analytes and some researchers have resorted to methods such as direct analysis in real time (DART) or desorption atmospheric pressure chemical ionization (DAPCI) for their analysis. In this work, a carbon nanotube fiber ionization (nanoCFI) source was developed and was found to be capable of solid phase microextraction (SPME) of nonpolar analytes as well as ionization and sampling similar to that of direct probe atmospheric pressure chemical ionization (DP-APCI). Conductivity and adsorption were maintained by utilizing a corona pin functionalized with a multi-walled carbon nanotube (MWCNT) thread. Quantitative work with the nanoCFI source with a designed corona discharge pin insert demonstrated linearity up to 0.97 (R2) of three target PAHs with phenanthrene internal standard. [Figure not available: see fulltext.

A novel amino acid analysis method using derivatization of multiple functional groups followed by liquid chromatography/tandem mass spectrometry.

PubMed

Sakaguchi, Yohei; Kinumi, Tomoya; Yamazaki, Taichi; Takatsu, Akiko

2015-03-21

We have developed a novel amino acid analysis method using derivatization of multiple functional groups (amino, carboxyl, and phenolic hydroxyl groups). The amino, carboxyl, and phenolic hydroxyl groups of the amino acids were derivatized with 1-bromobutane so that the hydrophobicities and basicities of the amino acids were improved. The derivatized amino acids, including amino group-modified amino acids, could be detected with high sensitivity using liquid chromatography/tandem mass spectrometry (LC-MS/MS). In this study, 17 amino acids obtained by hydrolyzing proteins and 4 amino group-modified amino acids found in the human body (N,N-dimethylglycine, N-formyl-L-methionine, L-pyroglutamic acid, and sarcosine) were selected as target compounds. The 21 derivatized amino acids could be separated using an octadecyl-silylated silica column within 20 min and simultaneously detected. The detection limits for the 21 amino acids were 5.4-91 fmol, and the calibration curves were linear over the range of 10-100 nmol L(-1) (r(2) > 0.9984) with good repeatability. A confirmatory experiment showed that our proposed method could be applied to the determination of a protein certified reference material using the analysis of 12 amino acids combined with isotope dilution mass spectrometry. Furthermore, the proposed method was successfully applied to a stable isotope-coded derivatization method using 1-bromobutane and 1-bromobutane-4,4,4-d3 for comparative analysis of amino acids in human serum.

Development and evaluation of a high-performance liquid chromatography/isotope ratio mass spectrometry methodology for delta13C analyses of amino sugars in soil.

PubMed

Bodé, Samuel; Denef, Karolien; Boeckx, Pascal

2009-08-30

Amino sugars have been used as biomarkers to assess the relative contribution of dead microbial biomass of different functional groups of microorganisms to soil carbon pools. However, little is known about the dynamics of these compounds in soil. The isotopic composition of individual amino sugars can be used as a tool to determine the turnover of these compounds. Methods to determine the delta(13)C of amino sugars using gas chromatography/combustion/isotope ratio mass spectrometry (GC/C/IRMS) have been proposed in literature. However, due to derivatization, the uncertainty on the obtained delta(13)C is too high to be used for natural abundance studies. Therefore, a new high-performance liquid chromatography/isotope ratio mass spectrometry (HPLC/IRMS) methodology, with increased accuracy and precision, has been developed. The repeatability on the obtained delta(13)C values when pure amino sugars were analyzed were not significantly concentration-dependent as long as the injected amount was higher than 1.5 nmol. The delta(13)C value of the same amino sugar spiked to a soil deviated by only 0.3 per thousand from the theoretical value. 2009 John Wiley & Sons, Ltd.

RoboOligo: software for mass spectrometry data to support manual and de novo sequencing of post-transcriptionally modified ribonucleic acids

PubMed Central

Sample, Paul J.; Gaston, Kirk W.; Alfonzo, Juan D.; Limbach, Patrick A.

2015-01-01

Ribosomal ribonucleic acid (RNA), transfer RNA and other biological or synthetic RNA polymers can contain nucleotides that have been modified by the addition of chemical groups. Traditional Sanger sequencing methods cannot establish the chemical nature and sequence of these modified-nucleotide containing oligomers. Mass spectrometry (MS) has become the conventional approach for determining the nucleotide composition, modification status and sequence of modified RNAs. Modified RNAs are analyzed by MS using collision-induced dissociation tandem mass spectrometry (CID MS/MS), which produces a complex dataset of oligomeric fragments that must be interpreted to identify and place modified nucleosides within the RNA sequence. Here we report the development of RoboOligo, an interactive software program for the robust analysis of data generated by CID MS/MS of RNA oligomers. There are three main functions of RoboOligo: (i) automated de novo sequencing via the local search paradigm. (ii) Manual sequencing with real-time spectrum labeling and cumulative intensity scoring. (iii) A hybrid approach, coined ‘variable sequencing’, which combines the user intuition of manual sequencing with the high-throughput sampling of automated de novo sequencing. PMID:25820423

Lipid imaging by mass spectrometry - a review.

PubMed

Gode, David; Volmer, Dietrich A

2013-03-07

Mass spectrometry imaging (MSI) has proven to be extremely useful for applications such as the spatial analysis of peptides and proteins in biological tissue, the performance assessment of drugs in vivo or the measurement of protein or metabolite expression as tissue classifiers or biomarkers from disease versus control tissue comparisons. The most popular MSI technique is MALDI mass spectrometry. First invented by Richard Caprioli in the mid-1990s, it is the highest performing MSI technique in terms of spatial resolution, sensitivity for intact biomolecules and application range today. The unique ability to identify and spatially resolve numerous compounds simultaneously, based on m/z values has inter alia been applied to untargeted and targeted chemical mapping of biological compartments, revealing changes of physiological states, disease pathologies and metabolic faith and distribution of xenobiotics. Many MSI applications focus on lipid species because of the lipids' diverse roles as structural components of cell membranes, their function in the surfactant cycle, and their involvement as second messengers in signalling cascades of tissues and cells. This article gives a comprehensive overview of lipid imaging techniques and applications using established MALDI and SIMS methods but also other promising MSI techniques such as DESI.

Increasing Protein Charge State When Using Laser Electrospray Mass Spectrometry

NASA Astrophysics Data System (ADS)

Karki, Santosh; Flanigan, Paul M.; Perez, Johnny J.; Archer, Jieutonne J.; Levis, Robert J.

2015-05-01

Femtosecond (fs) laser vaporization is used to transfer cytochrome c, myoglobin, lysozyme, and ubiquitin from the condensed phase into an electrospray (ES) plume consisting of a mixture of a supercharging reagent, m-nitrobenzyl alcohol ( m-NBA), and trifluoroacetic acid (TFA), acetic acid (AA), or formic acid (FA). Interaction of acid-sensitive proteins like cytochrome c and myoglobin with the highly charged ES droplets resulted in a shift to higher charge states in comparison with acid-stable proteins like lysozyme and ubiquitin. Laser electrospray mass spectrometry (LEMS) measurements showed an increase in both the average charge states (Zavg) and the charge state with maximum intensity (Zmode) for acid-sensitive proteins compared with conventional electrospray ionization mass spectrometry (ESI-MS) under equivalent solvent conditions. A marked increase in ion abundance of higher charge states was observed for LEMS in comparison with conventional electrospray for cytochrome c (ranging from 19+ to 21+ versus 13+ to 16+) and myoglobin (ranging from 19+ to 26+ versus 18+ to 21+) using an ES solution containing m-NBA and TFA. LEMS measurements as a function of electrospray flow rate yielded increasing charge states with decreasing flow rates for cytochrome c and myoglobin.

Protein Alterations in Infiltrating Ductal Carcinomas of the Breast as Detected by Nonequilibrium pH Gradient Electrophoresis and Mass Spectrometry

PubMed Central

Kabbage, Maria; Chahed, Karim; Hamrita, Bechr; Guillier, Christelle Lemaitre; Trimeche, Mounir; Remadi, Sami; Hoebeke, Johan; Chouchane, Lotfi

2008-01-01

Improvement of breast-cancer detection through the identification of potential cancer biomarkers is considered as a promising strategy for effective assessment of the disease. The current study has used nonequilibrium pH gradient electrophoresis with subsequent analysis by mass spectrometry to identify protein alterations in invasive ductal carcinomas of the breast from Tunisian women. We have identified multiple protein alterations in tumor tissues that were picked, processed, and unambiguously assigned identities by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF). The proteins identified span a wide range of functions and are believed to have potential clinical applications as cancer biomarkers. They include glycolytic enzymes, molecular chaperones, cytoskeletal-related proteins, antioxydant enzymes, and immunologic related proteins. Among these proteins, enolase 1, phosphoglycerate kinase 1, deoxyhemoglobin, Mn-superoxyde dismutase, α-B-crystallin, HSP27, Raf kinase inhibitor protein, heterogeneous nuclear ribonucleoprotein A2/B1, cofilin 1, and peptidylprolyl isomerase A were overexpressed in tumors compared with normal tissues. In contrast, the IGHG1 protein, the complement C3 component C3c, which are two newly identified protein markers, were downregulated in IDCA tissues. PMID:18401453

Simultaneous analysis by Quadrupole-Orbitrap mass spectrometry and UHPLC-MS/MS for the determination of sedative-hypnotics and sleep inducers in adulterated products.

PubMed

Lee, Ji Hyun; Park, Han Na; Choi, Ji Yeon; Kim, Nam Sook; Park, Hyung-Joon; Park, Seong Soo; Baek, Sun Young

2017-12-01

Adulterated products are continuously detected in society and cause problems. In this study, we developed and validated a method for determining synthetic sedative-hypnotics and sleep inducers, including barbital, benzodiazepam, zolpidem, and first-generation antihistamines, in adulterated products using Quadrupole-Orbitrap mass spectrometry and ultrahigh performance liquid chromatography with tandem mass spectrometry. In Quadrupole-Orbitrap mass spectrometry analysis, target compounds were confirmed using a combination of retention time, mass tolerance, mass accuracy, and fragment ions. For quantification, several validation parameters were employed using ultrahigh performance liquid chromatography with tandem mass spectrometry. The limit of detection and limit of quantitation was 0.05-53 and 0.17-177 ng/mL, respectively. The correlation coefficient for linearity was more than 0.995. The intra- and interassay accuracies were 86-110 and 84-111%, respectively. Their precision values were evaluated as within 4.0 (intraday) and 10.7% (interday). Mean recoveries of target compounds in adulterated products ranged from 85 to 116%. The relative standard deviation of stability was less than 10.7% at 4°C for 48 h. The 144 adulterated products obtained over 3 years (2014-2016) from online and in-person vendors were tested using established methods. After rapidly screening with Quadrupole-Orbitrap mass spectrometry, the detected samples were quantified using ultrahigh performance liquid chromatography with tandem mass spectrometry. Two of them were adulterated with phenobarbital. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bile acid profiling and quantification in biofluids using ultra-performance liquid chromatography tandem mass spectrometry.

PubMed

Sarafian, Magali H; Lewis, Matthew R; Pechlivanis, Alexandros; Ralphs, Simon; McPhail, Mark J W; Patel, Vishal C; Dumas, Marc-Emmanuel; Holmes, Elaine; Nicholson, Jeremy K

2015-10-06

Bile acids are important end products of cholesterol metabolism. While they have been identified as key factors in lipid emulsification and absorption due to their detergent properties, bile acids have also been shown to act as signaling molecules and intermediates between the host and the gut microbiota. To further the investigation of bile acid functions in humans, an advanced platform for high throughput analysis is essential. Herein, we describe the development and application of a 15 min UPLC procedure for the separation of bile acid species from human biofluid samples requiring minimal sample preparation. High resolution time-of-flight mass spectrometry was applied for profiling applications, elucidating rich bile acid profiles in both normal and disease state plasma. In parallel, a second mode of detection was developed utilizing tandem mass spectrometry for sensitive and quantitative targeted analysis of 145 bile acid (BA) species including primary, secondary, and tertiary bile acids. The latter system was validated by testing the linearity (lower limit of quantification, LLOQ, 0.25-10 nM and upper limit of quantification, ULOQ, 2.5-5 μM), precision (≈6.5%), and accuracy (81.2-118.9%) on inter- and intraday analysis achieving good recovery of bile acids (serum/plasma 88% and urine 93%). The ultra performance liquid chromatography-mass spectrometry (UPLC-MS)/MS targeted method was successfully applied to plasma, serum, and urine samples in order to compare the bile acid pool compositional difference between preprandial and postprandial states, demonstrating the utility of such analysis on human biofluids.

Analysis of Mammalian Sphingolipids by Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) and Tissue Imaging Mass Spectrometry (TIMS)

PubMed Central

Sullards, M. Cameron; Liu, Ying; Chen, Yanfeng; Merrill, Alfred H.

2011-01-01

Sphingolipids are a highly diverse category of molecules that serve not only as components of biological structures but also as regulators of numerous cell functions. Because so many of the structural features of sphingolipids give rise to their biological activity, there is a need for comprehensive or “sphingolipidomic” methods for identification and quantitation of as many individual subspecies as possible. This review defines sphingolipids as a class, briefly discusses classical methods for their analysis, and focuses primarily on liquid chromatography tandem mass spectrometry (LC-MS/MS) and tissue imaging mass spectrometry (TIMS). Recently, a set of evolving and expanding methods have been developed and rigorously validated for the extraction, identification, separation, and quantitation of sphingolipids by LC-MS/MS. Quantitation of these biomolecules is made possible via the use of an internal standard cocktail. The compounds that can be readily analyzed are free long-chain (sphingoid) bases, sphingoid base 1-phosphates, and more complex species such as ceramides, ceramide 1-phosphates, sphingomyelins, mono- and di-hexosylceramides sulfatides, and novel compounds such as the 1-deoxy- and 1-(deoxymethyl)-sphingoid bases and their N-acyl-derivatives. These methods can be altered slightly to separate and quantitate isomeric species such as glucosyl/galactosylceramide. Because these techniques require the extraction of sphingolipids from their native environment, any information regarding their localization in histological slices is lost. Therefore, this review also describes methods for TIMS. This technique has been shown to be a powerful tool to determine the localization of individual molecular species of sphingolipids directly from tissue slices. PMID:21749933

Synthesis of hydrazide-functionalized hydrophilic polymer hybrid graphene oxide for highly efficient N-glycopeptide enrichment and identification by mass spectrometry.

PubMed

Bai, Haihong; Pan, Yiting; Guo, Cong; Zhao, Xinyuan; Shen, Bingquan; Wang, Xinghe; Liu, Zeyuan; Cheng, Yuanguo; Qin, Weijie; Qian, Xiaohong

2017-08-15

Protein N-glycosylation is one of the most important post-translational modifications, participating in many key biological and pathological processes. Large-scale and precise identification of N-glycosylated proteins and peptides is especially beneficial for understanding their biological functions and for discovery of new clinical biomarkers and therapeutic drug targets. However, protein N-glycosylation is microheterogeneous and low abundant in living organisms, therefore specific enrichment of N-glycosylated proteins/peptides before mass spectrometry analysis is a prerequisite. In this work, we developed a new type of polymer hybrid graphene oxide (GO) by in situ growth of hydrazide-functionalized hydrophilic polymer chains on the GO surface (GO-PAAH) for selective N-glycopeptide enrichment and identification by mass spectrometry. The densely attached and low steric hindrance hydrazide groups as well as the highly hydrophilic nature of GO-PAAH facilitate N-glycopeptide enrichment by the combination of hydrazide capturing and HILIC interaction. Taking advantage of the unique features of GO-PAAH, all of the three N-glycopeptides of bovine fetuin were successfully enriched and identified with significantly enhanced signal intensities from a digest mixture of bovine fetuin and bovine serum albumin at a mass ratio of 1:100, demonstrating the excellent enrichment selectivity of GO-PAAH. Furthermore, a total of 507 N-glycosylation sites and 480 N-glycopeptides in 232 N-glycoproteins were enriched and identified from 10μL of human serum by three replicates using this novel enrichment material, which is nearly two times higher than the commercial hydrazide resin based method (280 N-glycosylation sites, 261 N-glycopeptides and 144 N-glycoproteins in three experiments). Among the identified, 95 N-glycosylation sites were not reported in the Uniprot database, and 106 N-glycoproteins were disease related in the Nextprot database, indicating the potential of this new enrichment material in global mapping of protein N-glycosylation. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

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.

Direct Analysis of Large Living Organism by Megavolt Electrostatic Ionization Mass Spectrometry

NASA Astrophysics Data System (ADS)

Ng, Kwan-Ming; Tang, Ho-Wai; Man, Sin-Heng; Mak, Pui-Yuk; Choi, Yi-Ching; Wong, Melody Yee-Man

2014-09-01

A new ambient ionization method allowing the direct chemical analysis of living human body by mass spectrometry (MS) was developed. This MS method, namely Megavolt Electrostatic Ionization Mass Spectrometry, is based on electrostatic charging of a living individual to megavolt (MV) potential, illicit drugs, and explosives on skin/glove, flammable solvent on cloth/tissue paper, and volatile food substances in breath were readily ionized and detected by a mass spectrometer.

Direct analysis of large living organism by megavolt electrostatic ionization mass spectrometry.

PubMed

Ng, Kwan-Ming; Tang, Ho-Wai; Man, Sin-Heng; Mak, Pui-Yuk; Choi, Yi-Ching; Wong, Melody Yee-Man

2014-09-01

A new ambient ionization method allowing the direct chemical analysis of living human body by mass spectrometry (MS) was developed. This MS method, namely Megavolt Electrostatic Ionization Mass Spectrometry, is based on electrostatic charging of a living individual to megavolt (MV) potential, illicit drugs, and explosives on skin/glove, flammable solvent on cloth/tissue paper, and volatile food substances in breath were readily ionized and detected by a mass spectrometer.

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

Mass Spectrometry Analyses of Multicellular Tumor Spheroids.

PubMed

Acland, Mitchell; Mittal, Parul; Lokman, Noor A; Klingler-Hoffmann, Manuela; Oehler, Martin K; Hoffmann, Peter

2018-05-01

Multicellular tumor spheroids (MCTS) are a powerful biological in vitro model, which closely mimics the 3D structure of primary avascularized tumors. Mass spectrometry (MS) has established itself as a powerful analytical tool, not only to better understand and describe the complex structure of MCTS, but also to monitor their response to cancer therapeutics. The first part of this review focuses on traditional mass spectrometry approaches with an emphasis on elucidating the molecular characteristics of these structures. Then the mass spectrometry imaging (MSI) approaches used to obtain spatially defined information from MCTS is described. Finally the analysis of primary spheroids, such as those present in ovarian cancer, and the great potential that mass spectrometry analysis of these structures has for improved understanding of cancer progression and for personalized in vitro therapeutic testing is discussed. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Laser mass spectrometry for DNA sequencing, disease diagnosis, and fingerprinting

NASA Astrophysics Data System (ADS)

Chen, C. H. Winston; Taranenko, N. I.; Zhu, Y. F.; Chung, C. N.; Allman, S. L.

1997-05-01

Since laser mass spectrometry has the potential for achieving very fast DNA analysis, we recently applied it to DNA sequencing, DNA typing for fingerprinting, and DNA screening for disease diagnosis. Two different approaches for sequencing DNA have been successfully demonstrated. One is to sequence DNA with DNA ladders produced from Sanger's enzymatic method. The other is to do direct sequencing without DNA ladders. The need for quick DNA typing for identification purposes is critical for forensic application. Our preliminary results indicate laser mass spectrometry can possible be used for rapid DNA fingerprinting applications at a much lower cost than gel electrophoresis. Population screening for certain genetic disease can be a very efficient step to reducing medical costs through prevention. Since laser mass spectrometry can provide very fast DNA analysis, we applied laser mass spectrometry to disease diagnosis. Clinical samples with both base deletion and point mutation have been tested with complete success.

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 current role of high-resolution mass spectrometry in food analysis.

PubMed

Kaufmann, Anton

2012-05-01

High-resolution mass spectrometry (HRMS), which is used for residue analysis in food, has gained wider acceptance in the last few years. This development is due to the availability of more rugged, sensitive, and selective instrumentation. The benefits provided by HRMS over classical unit-mass-resolution tandem mass spectrometry are considerable. These benefits include the collection of full-scan spectra, which provides greater insight into the composition of a sample. Consequently, the analyst has the freedom to measure compounds without previous compound-specific tuning, the possibility of retrospective data analysis, and the capability of performing structural elucidations of unknown or suspected compounds. HRMS strongly competes with classical tandem mass spectrometry in the field of quantitative multiresidue methods (e.g., pesticides and veterinary drugs). It is one of the most promising tools when moving towards nontargeted approaches. Certain hardware and software issues still have to be addressed by the instrument manufacturers for it to dislodge tandem mass spectrometry from its position as the standard trace analysis tool.

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.

Enhancing glycan isomer separations with metal ions and positive and negative polarity ion mobility spectrometry-mass spectrometry analyses

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

Zheng, Xueyun; Zhang, Xing; Schocker, Nathaniel S.

Glycomics has become an increasingly important field of research since glycans play critical roles in biology processes ranging from molecular recognition and signaling to cellular communication. Glycans often conjugate with other biomolecules such as proteins and lipids, and alter their properties and functions, so understanding the effect glycans have on cellular systems is essential. However the analysis of glycans is extremely difficult due to their complexity and structural diversity (i.e., the number and identity of monomer units, and configuration of their glycosidic linkages and connectivities). In this work, we coupled ion mobility spectrometry with mass spectrometry (IMS-MS) to characterize glycanmore » standards and biologically important isomers of synthetic αGal-containing O-glycans including glycotopes of the protozoan parasite Trypanosoma cruzi, which is the causative agent of Chagas disease. IMS-MS results showed significant differences for the glycan structural isomers when analyzed in positive and negative polarity and complexed with different metal cations. These results suggest specific metal ions or ion polarities could be used to target and baseline separate glycan isomers of interest with IMS-MS.« less

Review on Ion Mobility Spectrometry. Part 1: Current Instrumentation

PubMed Central

Cumeras, R.; Figueras, E.; Davis, C.E.; Baumbach, J.I.; Gràcia, I.

2014-01-01

Ion Mobility Spectrometry (IMS) is a widely used and ‘well-known’ technique of ion separation in gaseous phase based on the differences of ion mobilities under an electric field. All IMS instruments operate with an electric field that provides space separation, but some IMS instruments also operate with a drift gas flow which provides also a temporal separation. In this review we will summarize the current IMS instrumentation. IMS techniques have received an increased interest as new instrumentation has become available to be coupled with mass spectrometry (MS). For each of the eight types of IMS instruments reviewed it is mentioned whether they can be hyphenated with MS and whether they are commercially available. Finally, out of the described devices, the six most-consolidated ones are compared. The current review article is followed by a companion review article which details the IMS hyphenated techniques (mainly gas chromatography and mass spectrometry) and the factors that make the data from an IMS device change as function of device parameters and sampling conditions. These reviews will provide the reader with an insightful view of the main characteristics and aspects of the IMS technique. PMID:25465076

Fourier Transform Mass Spectrometry.

ERIC Educational Resources Information Center

Gross, Michael L.; Rempel, Don L.

1984-01-01

Discusses the nature of Fourier transform mass spectrometry and its unique combination of high mass resolution, high upper mass limit, and multichannel advantage. Examines its operation, capabilities and limitations, applications (ion storage, ion manipulation, ion chemistry), and future applications and developments. (JN)

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

PubMed

Altuntaş, Esra; Schubert, Ulrich S

2014-01-15

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

Identification of substances migrating from plastic baby bottles using a combination of low-resolution and high-resolution mass spectrometric analysers coupled to gas and liquid chromatography.

PubMed

Onghena, Matthias; Van Hoeck, Els; Van Loco, Joris; Ibáñez, María; Cherta, Laura; Portolés, Tania; Pitarch, Elena; Hernandéz, Félix; Lemière, Filip; Covaci, Adrian

2015-11-01

This work presents a strategy for elucidation of unknown migrants from plastic food contact materials (baby bottles) using a combination of analytical techniques in an untargeted approach. First, gas chromatography (GC) coupled to mass spectrometry (MS) in electron ionisation mode was used to identify migrants through spectral library matching. When no acceptable match was obtained, a second analysis by GC-(electron ionisation) high resolution mass spectrometry time of flight (TOF) was applied to obtain accurate mass fragmentation spectra and isotopic patterns. Databases were then searched to find a possible elemental composition for the unknown compounds. Finally, a GC hybrid quadrupole-TOF-MS with an atmospheric pressure chemical ionisation source was used to obtain the molecular ion or the protonated molecule. Accurate mass data also provided additional information on the fragmentation behaviour as two acquisition functions with different collision energies were available (MS(E) approach). In the low-energy function, limited fragmentation took place, whereas for the high-energy function, fragmentation was enhanced. For less volatile unknowns, ultra-high pressure liquid chromatography-quadrupole-TOF-MS was additionally applied. Using a home-made database containing common migrating compounds and plastic additives, tentative identification was made for several positive findings based on accurate mass of the (de)protonated molecule, product ion fragments and characteristic isotopic ions. Six illustrative examples are shown to demonstrate the modus operandi and the difficulties encountered during identification. The combination of these techniques was proven to be a powerful tool for the elucidation of unknown migrating compounds from plastic baby bottles. Copyright © 2015 John Wiley & Sons, Ltd.

Product study of oleic acid ozonolysis as function of humidity

NASA Astrophysics Data System (ADS)

Vesna, O.; Sax, M.; Kalberer, M.; Gaschen, A.; Ammann, M.

The heterogeneous reaction of ozone with oleic acid (OA) aerosol particles was studied as function of humidity and reaction time in an aerosol flow reactor using an off-line gas chromatography mass spectrometry (GC-MS) technique. We report quantitative yields of the major C9 ozonolysis products in both gas and condensed phases and the effect of relative humidity on the product distribution. The measurements were carried out with OA aerosol particles at room temperature. The results indicate that the product yields are increasing with increasing relative humidity during the reaction. Nonanal (NN) was detected as the major gas-phase product (55.6 ± 2.3%), with 94.5 ± 2.4% of the NN yield in the gas, and 5.5 ± 2.7% in the particulate phase, whereas nonanoic, oxononanoic and azelaic acids were detected exclusively in the particulate phase. Using UV-spectrometry, we observed that peroxides make up the largest fraction of products, about half of the product aerosol mass, and their concentration decreased with increasing humidity.

Separation of Oligosaccharides from Lotus Seeds via Medium-pressure Liquid Chromatography Coupled with ELSD and DAD

NASA Astrophysics Data System (ADS)

Lu, Xu; Zheng, Zhichang; Miao, Song; Li, Huang; Guo, Zebin; Zhang, Yi; Zheng, Yafeng; Zheng, Baodong; Xiao, Jianbo

2017-03-01

Lotus seeds were identified by the Ministry of Public Health of China as both food and medicine. One general function of lotus seeds is to improve intestinal health. However, to date, studies evaluating the relationship between bioactive compounds in lotus seeds and the physiological activity of the intestine are limited. In the present study, by using medium pressure liquid chromatography coupled with evaporative light-scattering detector and diode-array detector, five oligosaccharides were isolated and their structures were further characterized by electrospray ionization-mass spectrometry and gas chromatography-mass spectrometry. In vitro testing determined that LOS3-1 and LOS4 elicited relatively good proliferative effects on Lactobacillus delbrueckii subsp. bulgaricus. These results indicated a structure-function relationship between the physiological activity of oligosaccharides in lotus seeds and the number of probiotics applied, thus providing room for improvement of this particular feature. Intestinal probiotics may potentially become a new effective drug target for the regulation of immunity.

IMS - MS Data Extractor

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

2015-10-20

An automated drift time extraction and computed associated collision cross section software tool for small molecule analysis with ion mobility spectrometry-mass spectrometry (IMS-MS). The software automatically extracts drift times and computes associated collision cross sections for small molecules analyzed using ion mobility spectrometry-mass spectrometry (IMS-MS) based on a target list of expected ions provided by the user.

The expanding universe of mass analyzer configurations for biological analysis.

PubMed

Calvete, Juan J

2014-01-01

Mass spectrometry (MS) is an analytical technique that measures the mass-to-charge ratio of electrically charged gas-phase particles. All mass spectrometers combine ion formation, mass analysis, and ion detection. Although mass analyzers can be regarded as sophisticated devices that manipulate ions in space and time, the rich diversity of possible ways to combine ion separation, focusing, and detection in dynamic mass spectrometers accounts for the large number of instrument designs. A historical perspective of the progress in mass spectrometry that since 1965 until today have contributed to position this technique as an indispensable tool for biological research has been recently addressed by a privileged witness of this golden age of MS (Gelpí J. Mass Spectrom 43:419-435, 2008; Gelpí J. Mass Spectrom 44:1137-1161, 2008). The aim of this chapter is to highlight the view that the operational principles of mass spectrometry can be understood by a simple mathematical language, and that an understanding of the basic concepts of mass spectrometry is necessary to take the most out of this versatile technique.

Identification of the chemical constituents of Chinese medicine Yi-Xin-Shu capsule by molecular feature orientated precursor ion selection and tandem mass spectrometry structure elucidation.

PubMed

Wang, Hong-ping; Chen, Chang; Liu, Yan; Yang, Hong-Jun; Wu, Hong-Wei; Xiao, Hong-Bin

2015-11-01

The incomplete identification of the chemical components of traditional Chinese medicinal formula has been one of the bottlenecks in the modernization of traditional Chinese medicine. Tandem mass spectrometry has been widely used for the identification of chemical substances. Current automatic tandem mass spectrometry acquisition, where precursor ions were selected according to their signal intensity, encounters a drawback in chemical substances identification when samples contain many overlapping signals. Compounds in minor or trace amounts could not be identified because most tandem mass spectrometry information was lost. Herein, a molecular feature orientated precursor ion selection and tandem mass spectrometry structure elucidation method for complex Chinese medicine chemical constituent analysis was developed. The precursor ions were selected according to their two-dimensional characteristics of retention times and mass-to-charge ratio ranges from herbal compounds, so that all precursor ions from herbal compounds were included and more minor chemical constituents in Chinese medicine were identified. Compared to the conventional automatic tandem mass spectrometry setups, the approach is novel and can overcome the drawback for chemical substances identification. As an example, 276 compounds from the Chinese Medicine of Yi-Xin-Shu capsule were identified. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Laser Induced Breakdown Spectroscopy (LIBS)

DTIC Science & Technology

2010-03-31

mass spectrometry and laser induced breakdown spectroscopy, Spe T Trejos, A Flores and JR. Almirall, Micro-spectrochemical analysis of document paper...and gel inks by laser ablation inductively coupled plasma mass spectrometry and laser induced breakdown spectroscopy, Spectrochimica Acta Part B...abstracts): 1. *Schenk, E.R. “Elemental analysis of unprocessed cotton by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) and laser

Proteomic Mass Spectrometry Imaging for Skin Cancer Diagnosis.

PubMed

Lazova, Rossitza; Seeley, Erin H

2017-10-01

Mass spectrometry imaging can be successfully used for skin cancer diagnosis, particularly for the diagnosis of challenging melanocytic lesions. This method analyzes proteins within benign and malignant melanocytic tumor cells and, based on their differences, which constitute a unique molecular signature of 5 to 20 proteins, can render a diagnosis of benign nevus versus malignant melanoma. Mass spectrometry imaging may assist in the differentiation between metastases and nevi as well as between proliferative nodules in nevi and melanoma arising in a nevus. In the difficult area of atypical Spitzoid neoplasms, mass spectrometry diagnosis can predict clinical outcome better than histopathology. Copyright © 2017 Elsevier Inc. All rights reserved.

Silver nanostructures in laser desorption/ionization mass spectrometry and mass spectrometry imaging.

PubMed

Sekuła, Justyna; Nizioł, Joanna; Rode, Wojciech; Ruman, Tomasz

2015-09-21

Silver nanoparticles have been successfully applied as a matrix replacement for the laser desorption/ionization time-of-flight mass spectrometry (LDI-ToF-MS). Nanoparticles, producing spectra with highly reduced chemical background in the low m/z region, are perfectly suited for low-molecular weight compound analysis and imaging. Silver nanoparticles (AgNPs) can efficiently absorb ultraviolet laser radiation, transfer energy to the analyte and promote analyte desorption, but also constitute a source of silver ions suitable for analyte cationisation. This review provides an overview of the literature on silver nanomaterials as non-conventional desorption and ionization promoters in LDI-MS and mass spectrometry imaging.

Comprehensive Urine Drug Screen by Gas Chromatography/Mass Spectrometry (GC/MS).

PubMed

Ramoo, Bheemraj; Funke, Melissa; Frazee, Clint; Garg, Uttam

2016-01-01

Drug screening is an essential component of clinical toxicology laboratory service. Some laboratories use only automated chemistry analyzers for limited screening of drugs of abuse and few other drugs. Other laboratories use a combination of various techniques such as immunoassays, colorimetric tests, and mass spectrometry to provide more detailed comprehensive drug screening. Mass spectrometry, gas or liquid, can screen for hundreds of drugs and is often considered the gold standard for comprehensive drug screening. We describe an efficient and rapid gas chromatography/mass spectrometry (GC/MS) method for comprehensive drug screening in urine which utilizes a liquid-liquid extraction, sample concentration, and analysis by GC/MS.

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 Comparison of Tissue Spray and Lipid Extract Direct Injection Electrospray Ionization Mass Spectrometry for the Differentiation of Eutopic and Ectopic Endometrial Tissues

NASA Astrophysics Data System (ADS)

Chagovets, Vitaliy; Wang, Zhihao; Kononikhin, Alexey; Starodubtseva, Natalia; Borisova, Anna; Salimova, Dinara; Popov, Igor; Kozachenko, Andrey; Chingin, Konstantin; Chen, Huanwen; Frankevich, Vladimir; Adamyan, Leila; Sukhikh, Gennady

2018-02-01

Recent research revealed that tissue spray mass spectrometry enables rapid molecular profiling of biological tissues, which is of great importance for the search of disease biomarkers as well as for online surgery control. However, the payback for the high speed of analysis in tissue spray analysis is the generally lower chemical sensitivity compared with the traditional approach based on the offline chemical extraction and electrospray ionization mass spectrometry detection. In this study, high resolution mass spectrometry analysis of endometrium tissues of different localizations obtained using direct tissue spray mass spectrometry in positive ion mode is compared with the results of electrospray ionization analysis of lipid extracts. Identified features in both cases belong to three lipid classes: phosphatidylcholines, phosphoethanolamines, and sphingomyelins. Lipids coverage is validated by hydrophilic interaction liquid chromatography with mass spectrometry of lipid extracts. Multivariate analysis of data from both methods reveals satisfactory differentiation of eutopic and ectopic endometrium tissues. Overall, our results indicate that the chemical information provided by tissue spray ionization is sufficient to allow differentiation of endometrial tissues by localization with similar reliability but higher speed than in the traditional approach relying on offline extraction.

DETERMINATION OF ELEMENTAL COMPOSITIONS BY HIGH RESOLUTION MASS SPECTROMETRY WITHOUT MASS CALIBRANTS

EPA Science Inventory

Widely applicable mass calibrants, including perfluorokerosene, are available for gas-phase introduction of analytes ionized by electron impact (EI) prior to analysis using high resolution mass spectrometry. Unfortunately, no all-purpose calibrants are available for recently dev...

Mass Spectrometry: A Technique of Many Faces

PubMed Central

Olshina, Maya A.; Sharon, Michal

2016-01-01

Protein complexes form the critical foundation for a wide range of biological process, however understanding the intricate details of their activities is often challenging. In this review we describe how mass spectrometry plays a key role in the analysis of protein assemblies and the cellular pathways which they are involved in. Specifically, we discuss how the versatility of mass spectrometric approaches provides unprecedented information on multiple levels. We demonstrate this on the ubiquitin-proteasome proteolytic pathway, a process that is responsible for protein turnover. We follow the various steps of this degradation route and illustrate the different mass spectrometry workflows that were applied for elucidating molecular information. Overall, this review aims to stimulate the integrated use of multiple mass spectrometry approaches for analyzing complex biological systems. PMID:28100928

Recent developments in atmospheric pressure photoionization-mass spectrometry.

PubMed

Kauppila, Tiina J; Syage, Jack A; Benter, Thorsten

2017-05-01

Recent developments in atmospheric pressure photoionization (APPI), which is one of the three most important ionization techniques in liquid chromatography-mass spectrometry, are reviewed. The emphasis is on the practical aspects of APPI analysis, its combination with different separation techniques, novel instrumental developments - especially in gas chromatography and ambient mass spectrometry - and the applications that have appeared in 2009-2014. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:423-449, 2017. © 2015 Wiley Periodicals, Inc.

Imaging with Mass Spectrometry of Bacteria on the Exoskeleton of Fungus-Growing Ants.

PubMed

Gemperline, Erin; Horn, Heidi A; DeLaney, Kellen; Currie, Cameron R; Li, Lingjun

2017-08-18

Mass spectrometry imaging is a powerful analytical technique for detecting and determining spatial distributions of molecules within a sample. Typically, mass spectrometry imaging is limited to the analysis of thin tissue sections taken from the middle of a sample. In this work, we present a mass spectrometry imaging method for the detection of compounds produced by bacteria on the outside surface of ant exoskeletons in response to pathogen exposure. Fungus-growing ants have a specialized mutualism with Pseudonocardia, a bacterium that lives on the ants' exoskeletons and helps protect their fungal garden food source from harmful pathogens. The developed method allows for visualization of bacterial-derived compounds on the ant exoskeleton. This method demonstrates the capability to detect compounds that are specifically localized to the bacterial patch on ant exoskeletons, shows good reproducibility across individual ants, and achieves accurate mass measurements within 5 ppm error when using a high-resolution, accurate-mass mass spectrometer.

A MASSive Laboratory Tour. An Interactive Mass Spectrometry Outreach Activity for Children

NASA Astrophysics Data System (ADS)

Jungmann, Julia H.; Mascini, Nadine E.; Kiss, Andras; Smith, Donald F.; Klinkert, Ivo; Eijkel, Gert B.; Duursma, Marc C.; Cillero Pastor, Berta; Chughtai, Kamila; Chughtai, Sanaullah; Heeren, Ron M. A.

2013-07-01

It is imperative to fascinate young children at an early stage in their education for the analytical sciences. The exposure of the public to mass spectrometry presently increases rapidly through the common media. Outreach activities can take advantage of this exposure and employ mass spectrometry as an exquisite example of an analytical science in which children can be fascinated. The presented teaching modules introduce children to mass spectrometry and give them the opportunity to experience a modern research laboratory. The modules are highly adaptable and can be applied to young children from the age of 6 to 14 y. In an interactive tour, the students explore three major scientific concepts related to mass spectrometry; the building blocks of matter, charged particle manipulation by electrostatic fields, and analyte identification by mass analysis. Also, the students carry out a mass spectrometry experiment and learn to interpret the resulting mass spectra. The multistage, inquiry-based tour contains flexible methods, which teach the students current-day research techniques and possible applications to real research topics. Besides the scientific concepts, laboratory safety and hygiene are stressed and the students are enthused for the analytical sciences by participating in "hands-on" work. The presented modules have repeatedly been successfully employed during laboratory open days. They are also found to be extremely suitable for (early) high school science classes during laboratory visit-focused field trips.

FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry.

PubMed

Palmer, Andrew; Phapale, Prasad; Chernyavsky, Ilya; Lavigne, Regis; Fay, Dominik; Tarasov, Artem; Kovalev, Vitaly; Fuchser, Jens; Nikolenko, Sergey; Pineau, Charles; Becker, Michael; Alexandrov, Theodore

2017-01-01

High-mass-resolution imaging mass spectrometry promises to localize hundreds of metabolites in tissues, cell cultures, and agar plates with cellular resolution, but it is hampered by the lack of bioinformatics tools for automated metabolite identification. We report pySM, a framework for false discovery rate (FDR)-controlled metabolite annotation at the level of the molecular sum formula, for high-mass-resolution imaging mass spectrometry (https://github.com/alexandrovteam/pySM). We introduce a metabolite-signal match score and a target-decoy FDR estimate for spatial metabolomics.

Mass Spectral Studies of 1-(2-Chloroethoxy)-2-[(2-chloroethyl)thio] Ethane and Related Compounds Using Gas ChromatographyMass Spectrometry and Gas ChromatographyTriple-Quadrupole Mass Spectrometry

DTIC Science & Technology

2016-02-01

NOTES 14. ABSTRACT: The electron impact and collision-induced- dissociation mass spectra of 1-(2-chloroethoxy)-2-[(2-chloroethyl)thio] ethane and 10...Collision-ion dissociation (CID) Triple-quadrupole mass spectrometry (QQQ) 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT...ratio, 10:1), and a 1.0 µL volume of sample was placed on the column. Nitrogen was used as the collision gas for the collision-induced dissociation (CID

Determination of nitroaromatic explosives and their degradation products in unsaturated-zone water samples by high-performance liquid chromatography with photodiode-array, mass spectrometric, and tandem mass spectrometric detection

USGS Publications Warehouse

Gates, Paul M.; Furlong, E.T.; Dorsey, T.F.; Burkhardt, M.R.

1996-01-01

Mass spectrometry and tandem mass spectrometry, coupled by a thermospray interface to a high-performance liguid chromatography system and equipped with a photodiode array detector, were used to determine the presence of nitroaromatic explosives and their degradation products in USA unsaturated-zone water samples. Using this approach, the lower limits of quantitation for explosives determined by mass spectrometry in this study typically ranged from 10 to 100 ng/l.

Real-time measurement of sodium chloride in individual aerosol particles by mass spectrometry

NASA Technical Reports Server (NTRS)

Sinha, M. P.; Friedlander, S. K.

1985-01-01

The method of particle analysis by mass spectrometry has been applied to the quantitative measurement of sodium chloride in individual particles on a real-time basis. Particles of known masses are individually introduced, in the form of a beam, into a miniature Knudsen cell oven (1600 K). The oven is fabricated from rhenium metal sheet (0.018 mm thick) and is situated in the ion source of a quadrupole mass spectrometer. A particle once inside the oven is trapped and completely volatilized; this overcomes the problem of partial volatilization due to particles bouncing from the filament surface. Individual particles are thermally volatilized and ionized inside the rhenium oven, and produce discrete sodium ion pulses whose intensities are measured with the quadrupole mass spectrometer. An ion pulse width of several milliseconds (4-12 ms) is found for particles in the mass range 1.3 x 10 to the -13th to 5.4 x 10 to the -11th g. The sodium ion intensity is found to be proportional to the particle mass to the 0.86-power. The intensity distribution for monodisperse aerosol particles possesses a geometric standard deviation of 1.09, showing that the method can be used for the determination of the mass distribution function with good resolution in a polydisperse aerosol.

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.

Ambient Ionization Mass Spectrometry for Cancer Diagnosis and Surgical Margin Evaluation

PubMed Central

Ifa, Demian R.; Eberlin, Livia S.

2017-01-01

Background There is a clinical need for new technologies that would enable rapid disease diagnosis based on diagnostic molecular signatures. Ambient ionization mass spectrometry has revolutionized the means by which molecular information can be obtained from tissue samples in real time and with minimal sample pretreatment. New developments in ambient ionization techniques applied to clinical research suggest that ambient ionization mass spectrometry will soon become a routine medical tool for tissue diagnosis. Content This review summarizes the main developments in ambient ionization techniques applied to tissue analysis, with focus on desorption electrospray ionization mass spectrometry, probe electrospray ionization, touch spray, and rapid evaporative ionization mass spectrometry. We describe their applications to human cancer research and surgical margin evaluation, highlighting integrated approaches tested for ex vivo and in vivo human cancer tissue analysis. We also discuss the challenges for clinical implementation of these tools and offer perspectives on the future of the field. Summary A variety of studies have showcased the value of ambient ionization mass spectrometry for rapid and accurate cancer diagnosis. Small molecules have been identified as potential diagnostic biomarkers, including metabolites, fatty acids, and glycerophospholipids. Statistical analysis allows tissue discrimination with high accuracy rates (>95%) being common. This young field has challenges to overcome before it is ready to be broadly accepted as a medical tool for cancer diagnosis. Growing research in new, integrated ambient ionization mass spectrometry technologies and the ongoing improvements in the existing tools make this field very promising for future translation into the clinic. PMID:26555455

Quantitative thin-layer chromatography/mass spectrometry analysis of caffeine using a surface sampling probe electrospray ionization tandem mass spectrometry system.

PubMed

Ford, Michael J; Deibel, Michael A; Tomkins, Bruce A; Van Berkel, Gary J

2005-07-15

Quantitative determination of caffeine on reversed-phase C8 thin-layer chromatography plates using a surface sampling electrospray ionization system with tandem mass spectrometry detection is reported. The thin-layer chromatography/electrospray tandem mass spectrometry method employed a deuterium-labeled caffeine internal standard and selected reaction monitoring detection. Up to nine parallel caffeine bands on a single plate were sampled in a single surface scanning experiment requiring 35 min at a surface scan rate of 44 mum/s. A reversed-phase HPLC/UV caffeine assay was developed in parallel to assess the mass spectrometry method performance. Limits of detection for the HPLC/UV and thin-layer chromatography/electrospray tandem mass spectrometry methods determined from the calibration curve statistics were 0.20 ng injected (0.50 muL) and 1.0 ng spotted on the plate, respectively. Spike recoveries with standards and real samples ranged between 97 and 106% for both methods. The caffeine content of three diet soft drinks (Diet Coke, Diet Cherry Coke, Diet Pepsi) and three diet sport drinks (Diet Turbo Tea, Speed Stack Grape, Speed Stack Fruit Punch) was measured. The HPLC/UV and mass spectrometry determinations were in general agreement, and these values were consistent with the quoted values for two of the three diet colas. In the case of Diet Cherry Coke and the diet sports drinks, the determined caffeine amounts using both methods were consistently higher (by approximately 8% or more) than the literature values.

THE APPLICATION OF MASS SPECTROMETRY TO THE STUDY OF MICROORGANISMS

EPA Science Inventory

The purpose of this research project is to use state-of-the-art mass spectrometric techniques, such as electrospray ionization (ESI) and matrix assisted laser desorption ionization (MALDI) mass spectrometry (MS), to provide "protein mass fingerprinting" and protein sequencing i...

Identification of Tyrosine Phosphorylated Proteins by SH2 Domain Affinity Purification and Mass Spectrometry.

PubMed

Buhs, Sophia; Gerull, Helwe; Nollau, Peter

2017-01-01

Phosphotyrosine signaling plays a major role in the control of many important biological functions such as cell proliferation and apoptosis. Deciphering of phosphotyrosine-dependent signaling is therefore of great interest paving the way for the understanding of physiological and pathological processes of signal transduction. On the basis of the specific binding of SH2 domains to phosphotyrosine residues, we here present an experimental workflow for affinity purification and subsequent identification of tyrosine phosphorylated proteins by mass spectrometry. In combination with SH2 profiling, a broadly applicable platform for the characterization of phosphotyrosine profiles in cell extracts, our pull down strategy enables researchers by now to identify proteins in signaling cascades which are differentially phosphorylated and selectively recognized by distinct SH2 domains.

Combining genomic and proteomic approaches for epigenetics research

PubMed Central

Han, Yumiao; Garcia, Benjamin A

2014-01-01

Epigenetics is the study of changes in gene expression or cellular phenotype that do not change the DNA sequence. In this review, current methods, both genomic and proteomic, associated with epigenetics research are discussed. Among them, chromatin immunoprecipitation (ChIP) followed by sequencing and other ChIP-based techniques are powerful techniques for genome-wide profiling of DNA-binding proteins, histone post-translational modifications or nucleosome positions. However, mass spectrometry-based proteomics is increasingly being used in functional biological studies and has proved to be an indispensable tool to characterize histone modifications, as well as DNA–protein and protein–protein interactions. With the development of genomic and proteomic approaches, combination of ChIP and mass spectrometry has the potential to expand our knowledge of epigenetics research to a higher level. PMID:23895656

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.

Static Time-of-Flight Secondary Ion Mass Spectrometry (SIMS) | Materials

Science.gov Websites

-Flight Secondary Ion Mass Spectrometry (SIMS) Image of high mass resolution and mass accuracy provided by TOF SIMS We used the high mass resolution and mass accuracy of TOF SIMS to study surface cleanliness acidic wash resulted in contamination by Fe and other metals. Without high mass accuracy, the CaO signal

Rumen fluid metabolomics analysis associated with feed efficiency on crossbred steers

USDA-ARS?s Scientific Manuscript database

The rumen plays a central role in the efficiency of digestion in ruminants. To identify potential differences in rumen function that lead to differences in feed efficiency, rumen metabolomic analysis by ultra-performance liquid chromatography/ time-of-flight mass spectrometry (MS) and multivariate/u...

Using proteomics to study sexual reproduction in angiosperms

USDA-ARS?s Scientific Manuscript database

While a relative latecomer to the post-genomics era of functional biology, the application of mass spectrometry-based proteomic analysis has increased exponentially over the past 10 years. Some of this increase is the result of transition of chemists physicists, and mathematicians to the study of ...

Activity screening of carrier domains within nonribosomal peptide synthetases using complex substrate mixtures and large molecule mass spectrometry.

PubMed

Dorrestein, Pieter C; Blackhall, Jonathan; Straight, Paul D; Fischbach, Michael A; Garneau-Tsodikova, Sylvie; Edwards, Daniel J; McLaughlin, Shaun; Lin, Myat; Gerwick, William H; Kolter, Roberto; Walsh, Christopher T; Kelleher, Neil L

2006-02-14

For screening a pool of potential substrates that load carrier domains found in nonribosomal peptide synthetases, large molecule mass spectrometry is shown to be a new, unbiased assay. Combining the high resolving power of Fourier transform mass spectrometry with the ability of adenylation domains to select their own substrates, the mass change that takes place upon formation of a covalent intermediate thus identifies the substrate. This assay has an advantage over traditional radiochemical assays in that many substrates, the substrate pool, can be screened simultaneously. Using proteins on the nikkomycin, clorobiocin, coumermycin A1, yersiniabactin, pyochelin, and enterobactin biosynthetic pathways as proof of principle, preferred substrates are readily identified from substrate pools. Furthermore, this assay can be used to provide insight into the timing of tailoring events of biosynthetic pathways as demonstrated using the bromination reaction found on the jamaicamide biosynthetic pathway. Finally, this assay can provide insight into the role and function of orphan gene clusters for which the encoded natural product is unknown. This is demonstrated by identifying the substrates for two NRPS modules from the pksN and pksJ genes that are found on an orphan NRPS/PKS hybrid cluster from Bacillus subtilis. This new assay format is especially timely for activity screening in an era when new types of thiotemplate assembly lines that defy classification are being discovered at an accelerating rate.

The Au(n) cluster probe in secondary ion mass spectrometry: influence of the projectile size and energy on the desorption/ionization rate from biomolecular solids.

PubMed

Novikov, Alexey; Caroff, Martine; Della-Negra, Serge; Depauw, Joël; Fallavier, Mireille; Le Beyec, Yvon; Pautrat, Michèle; Schultz, J Albert; Tempez, Agnès; Woods, Amina S

2005-01-01

A Au-Si liquid metal ion source which produces Au(n) clusters over a large range of sizes was used to study the dependence of both the molecular ion desorption yield and the damage cross-section on the size (n = 1 to 400) and on the kinetic energy (E = 10 to 500 keV) of the clusters used to bombard bioorganic surfaces. Three pure peptides with molecular masses between 750 and 1200 Da were used without matrix. [M+H](+) and [M+cation](+) ion emission yields were enhanced by as much as three orders of magnitude when bombarding with Au(400) (4+) instead of monatomic Au(+), yet very little damage was induced in the samples. A 100-fold increase in the molecular ion yield was observed when the incident energy of Au(9) (+) was varied from 10 to 180 keV. Values of emission yields and damage cross-sections are presented as a function of cluster size and energy. The possibility to adjust both cluster size and energy, depending on the application, makes the analysis of biomolecules by secondary ion mass spectrometry an extremely powerful and flexible technique, particularly when combined with orthogonal time-of-flight mass spectrometry that then allows fast measurements using small primary ion beam currents. Copyright (c) 2005 John Wiley & Sons, Ltd.

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

Peculiarities of data interpretation upon direct tissue analysis by Fourier transform ion cyclotron resonance mass spectrometry.

PubMed

Chagovets, Vtaliy; Kononikhin, Aleksey; Starodubtseva, Nataliia; Kostyukevich, Yury; Popov, Igor; Frankevich, Vladimir; Nikolaev, Eugene

2016-01-01

The importance of high-resolution mass spectrometry for the correct data interpretation of a direct tissue analysis is demonstrated with an example of its clinical application for an endometriosis study. Multivariate analysis of the data discovers lipid species differentially expressed in different tissues under investigation. High-resolution mass spectrometry allows unambiguous separation of peaks with close masses that correspond to proton and sodium adducts of phosphatidylcholines and to phosphatidylcholines differing in double bond number.

Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen.

PubMed

Garg, Neha; Zeng, Yi; Edlund, Anna; Melnik, Alexey V; Sanchez, Laura M; Mohimani, Hosein; Gurevich, Alexey; Miao, Vivian; Schiffler, Stefan; Lim, Yan Wei; Luzzatto-Knaan, Tal; Cai, Shengxin; Rohwer, Forest; Pevzner, Pavel A; Cichewicz, Robert H; Alexandrov, Theodore; Dorrestein, Pieter C

2016-01-01

Microbes are commonly studied as individual species, but they exist as mixed assemblages in nature. At present, we know very little about the spatial organization of the molecules, including natural products that are produced within these microbial networks. Lichens represent a particularly specialized type of symbiotic microbial assemblage in which the component microorganisms exist together. These composite microbial assemblages are typically comprised of several types of microorganisms representing phylogenetically diverse life forms, including fungi, photosymbionts, bacteria, and other microbes. Here, we employed matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) imaging mass spectrometry to characterize the distributions of small molecules within a Peltigera lichen. In order to probe how small molecules are organized and localized within the microbial consortium, analytes were annotated and assigned to their respective producer microorganisms using mass spectrometry-based molecular networking and metagenome sequencing. The spatial analysis of the molecules not only reveals an ordered layering of molecules within the lichen but also supports the compartmentalization of unique functions attributed to various layers. These functions include chemical defense (e.g., antibiotics), light-harvesting functions associated with the cyanobacterial outer layer (e.g., chlorophyll), energy transfer (e.g., sugars) surrounding the sun-exposed cyanobacterial layer, and carbohydrates that may serve a structural or storage function and are observed with higher intensities in the non-sun-exposed areas (e.g., complex carbohydrates). IMPORTANCE Microbial communities have evolved over centuries to live symbiotically. The direct visualization of such communities at the chemical and functional level presents a challenge. Overcoming this challenge may allow one to visualize the spatial distributions of specific molecules involved in symbiosis and to define their functional roles in shaping the community structure. In this study, we examined the diversity of microbial genes and taxa and the presence of biosynthetic gene clusters by metagenomic sequencing and the compartmentalization of organic chemical components within a lichen using mass spectrometry. This approach allowed the identification of chemically distinct sections within this composite organism. Using our multipronged approach, various fungal natural products, not previously reported from lichens, were identified and two different fungal layers were visualized at the chemical level.

Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen

PubMed Central

Garg, Neha; Zeng, Yi; Edlund, Anna; Melnik, Alexey V.; Mohimani, Hosein; Gurevich, Alexey; Miao, Vivian; Schiffler, Stefan; Lim, Yan Wei; Luzzatto-Knaan, Tal; Cai, Shengxin; Rohwer, Forest; Pevzner, Pavel A.; Cichewicz, Robert H.; Alexandrov, Theodore

2016-01-01

ABSTRACT Microbes are commonly studied as individual species, but they exist as mixed assemblages in nature. At present, we know very little about the spatial organization of the molecules, including natural products that are produced within these microbial networks. Lichens represent a particularly specialized type of symbiotic microbial assemblage in which the component microorganisms exist together. These composite microbial assemblages are typically comprised of several types of microorganisms representing phylogenetically diverse life forms, including fungi, photosymbionts, bacteria, and other microbes. Here, we employed matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) imaging mass spectrometry to characterize the distributions of small molecules within a Peltigera lichen. In order to probe how small molecules are organized and localized within the microbial consortium, analytes were annotated and assigned to their respective producer microorganisms using mass spectrometry-based molecular networking and metagenome sequencing. The spatial analysis of the molecules not only reveals an ordered layering of molecules within the lichen but also supports the compartmentalization of unique functions attributed to various layers. These functions include chemical defense (e.g., antibiotics), light-harvesting functions associated with the cyanobacterial outer layer (e.g., chlorophyll), energy transfer (e.g., sugars) surrounding the sun-exposed cyanobacterial layer, and carbohydrates that may serve a structural or storage function and are observed with higher intensities in the non-sun-exposed areas (e.g., complex carbohydrates). IMPORTANCE Microbial communities have evolved over centuries to live symbiotically. The direct visualization of such communities at the chemical and functional level presents a challenge. Overcoming this challenge may allow one to visualize the spatial distributions of specific molecules involved in symbiosis and to define their functional roles in shaping the community structure. In this study, we examined the diversity of microbial genes and taxa and the presence of biosynthetic gene clusters by metagenomic sequencing and the compartmentalization of organic chemical components within a lichen using mass spectrometry. This approach allowed the identification of chemically distinct sections within this composite organism. Using our multipronged approach, various fungal natural products, not previously reported from lichens, were identified and two different fungal layers were visualized at the chemical level. PMID:28028548

FT-ICR mass spectrometric and density functional theory studies of sulfate prenucleation clusters

NASA Astrophysics Data System (ADS)

Lemke, K. H.

2012-12-01

Recent mass spectrometric1 and relaxation spectroscopic studies2 of metal sulfate salts have demonstrated that aqueous clusters play an important role in sulfate prenucleation processes. While such studies provide evidence that that ion clusters are nucleation relevant species, ultra-high resolution mass spectrumetry, in particular, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR/MS) can provide additional valuable information about the molecular composition and stability of individual ion clusters. Prompted by the above studies, our group has begun a systematic survey of metal sulfate clusters using FT-ICR mass spectrometry. Here, I report stoichiometries, structures and thermodynamic properties of calcium sulfate ion clusters, both "dry" and microsolvated, using electrospray ionization FT-ICR mass spectrometry in combination with semi-empirical methods and M062X/aug-cc-PVXZ level density functional theory calculations. In electrosprayed dilute aqueous solutions of CaSO4 (1-20mM), droplet desolvation results in the formation of stable doubly-charged clusters of [Ca(CaSO4)m(H2O)n]+2 (m≤10 & n≤9) as well as larger quadruply-charged ion clusters [Ca2(CaSO4)m(H2O)n]+4 with m≤23 and n≤10, demonstrating considerable sulfate nucleation potential in undersaturated electrolyte solutions. An attempt was also made to assess the extent of ion cluster aggregation in solution prior to electrospray ionization by measuring ion mass spectra at different solution concentrations. In brief, an increase in calcium sulfate concentration from 1-10mM results in a continuous increase in polynuclear ion cluster species, while smaller clusters, for instance, Ca[CaSO4]+2 and corresponding hydrated forms, become increasingly less abundant. Building on semi-empirical methods, M062X calculations have been applied to predict calcium sulfate cluster geometries, both "dry" and microsolvated, as well as the size-dependent evolution of clustering and hydration energies. 1Schoeder et al. (2011) J.Am.Chem.Soc., 133, 2444; 2Chen et al. (2005) J.Sol.Chem., 34, 1045;

A COMPARISON OF PARTICLE MASS SPECTROMETERS DURING THE 1999 ATLANTA SUPERSITES EXPERIMENT

EPA Science Inventory

During the Atlanta SuperSite Experiment, four particle mass spectrometers were operated together for the first time: NOAA's PALMS (Particle Analysis by Laser Mass Spectrometry), U. C. Riverside's ATOFMS (Aerosol Time-of-Flight Mass Spectrometry), U. Delaware's RSMS-II (Rapid Si...

Anatomy and evolution of database search engines-a central component of mass spectrometry based proteomic workflows.

PubMed

Verheggen, Kenneth; Raeder, Helge; Berven, Frode S; Martens, Lennart; Barsnes, Harald; Vaudel, Marc

2017-09-13

Sequence database search engines are bioinformatics algorithms that identify peptides from tandem mass spectra using a reference protein sequence database. Two decades of development, notably driven by advances in mass spectrometry, have provided scientists with more than 30 published search engines, each with its own properties. In this review, we present the common paradigm behind the different implementations, and its limitations for modern mass spectrometry datasets. We also detail how the search engines attempt to alleviate these limitations, and provide an overview of the different software frameworks available to the researcher. Finally, we highlight alternative approaches for the identification of proteomic mass spectrometry datasets, either as a replacement for, or as a complement to, sequence database search engines. © 2017 Wiley Periodicals, Inc.

Imaging mass spectrometry in microbiology

PubMed Central

Watrous, Jeramie D.; Dorrestein, Pieter C.

2013-01-01

Mass spectrometry tools which allow for the 2-D visualization of the distribution of trace metals, metabolites, surface lipids, peptides and proteins directly from biological samples without the need for chemical tagging or antibodies are becoming increasingly useful for microbiology applications. These tools, comprised of different imaging mass spectrometry techniques, are ushering in an exciting new era of discovery by allowing for the generation of chemical hypotheses based on of the spatial mapping of atoms and molecules that can correlate to or transcend observed phenotypes. In this review, we explore the wide range of imaging mass spectrometry techniques available to microbiologists and describe their unique applications to microbiology with respect to the types of microbiology samples to be investigated. PMID:21822293

Symposium on accelerator mass spectrometry

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

None

1981-01-01

The area of accelerator mass spectrometry has expanded considerably over the past few years and established itself as an independent and interdisciplinary research field. Three years have passed since the first meeting was held at Rochester. A Symposium on Accelerator Mass Spectrometry was held at Argonne on May 11-13, 1981. In attendance were 96 scientists of whom 26 were from outside the United States. The present proceedings document the program and excitement of the field. Papers are arranged according to the original program. A few papers not presented at the meeting have been added to complete the information on themore » status of accelerator mass spectrometry. Individual papers were prepared separately for the data base.« 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.

Nanomanipulation-coupled nanospray mass spectrometry as an approach for single cell analysis

NASA Astrophysics Data System (ADS)

Phelps, Mandy; Hamilton, Jason; Verbeck, Guido F.

2014-12-01

Electrospray mass spectrometry is now a widely used technique for observing cell content of various biological tissues. However, electrospray techniques (liquid chromatography and direct infusion) often involve lysing a group of cells and extracting the biomolecules of interest, rather than a sensitive, individual cell method to observe local chemistry. Presented here is an approach of combining a nanomanipulator workstation with nanospray mass spectrometry, which allows for extraction of a single cell, followed by rapid mass analysis that can provide a detailed metabolic profile. Triacylglycerol content was profiled with this tool coupled to mass spectrometry to investigate heterogeneity between healthy and tumorous tissues as well as lipid droplet containing adipocytes in vitro as proof of concept. This selective approach provides cellular resolution and complements existing bioanalytical techniques with minimal invasion to samples. In addition, the coupling of nanomanipulation and mass spectrometry holds the potential to be used in a great number of applications for individual organelles, diseased tissues, and in vitro cell cultures for observing heterogeneity even amongst cells and organelles of the same tissue.

Mass Spectrometry Imaging, an Emerging Technology in Neuropsychopharmacology

PubMed Central

Shariatgorji, Mohammadreza; Svenningsson, Per; Andrén, Per E

2014-01-01

Mass spectrometry imaging is a powerful tool for directly determining the distribution of proteins, peptides, lipids, neurotransmitters, metabolites and drugs in neural tissue sections in situ. Molecule-specific imaging can be achieved using various ionization techniques that are suited to different applications but which all yield data with high mass accuracies and spatial resolutions. The ability to simultaneously obtain images showing the distributions of chemical species ranging from metal ions to macromolecules makes it possible to explore the chemical organization of a sample and to correlate the results obtained with specific anatomical features. The imaging of biomolecules has provided new insights into multiple neurological diseases, including Parkinson's and Alzheimer's disease. Mass spectrometry imaging can also be used in conjunction with other imaging techniques in order to identify correlations between changes in the distribution of important chemical species and other changes in the properties of the tissue. Here we review the applications of mass spectrometry imaging in neuroscience research and discuss its potential. The results presented demonstrate that mass spectrometry imaging is a useful experimental method with diverse applications in neuroscience. PMID:23966069

A Compressive Sensing Approach for Glioma Margin Delineation Using Mass Spectrometry

PubMed Central

Gholami, Behnood; Agar, Nathalie Y. R.; Jolesz, Ferenc A.; Haddad, Wassim M.; Tannenbaum, Allen R.

2013-01-01

Surgery, and specifically, tumor resection, is the primary treatment for most patients suffering from brain tumors. Medical imaging techniques, and in particular, magnetic resonance imaging are currently used in diagnosis as well as image-guided surgery procedures. However, studies show that computed tomography and magnetic resonance imaging fail to accurately identify the full extent of malignant brain tumors and their microscopic infiltration. Mass spectrometry is a well-known analytical technique used to identify molecules in a given sample based on their mass. In a recent study, it is proposed to use mass spectrometry as an intraoperative tool for discriminating tumor and non-tumor tissue. Integration of mass spectrometry with the resection module allows for tumor resection and immediate molecular analysis. In this paper, we propose a framework for tumor margin delineation using compressive sensing. Specifically, we show that the spatial distribution of tumor cell concentration can be efficiently reconstructed and updated using mass spectrometry information from the resected tissue. In addition, our proposed framework is model-free, and hence, requires no prior information of spatial distribution of the tumor cell concentration. PMID:22255629

Mass spectrometry imaging, an emerging technology in neuropsychopharmacology.

PubMed

Shariatgorji, Mohammadreza; Svenningsson, Per; Andrén, Per E

2014-01-01

Mass spectrometry imaging is a powerful tool for directly determining the distribution of proteins, peptides, lipids, neurotransmitters, metabolites and drugs in neural tissue sections in situ. Molecule-specific imaging can be achieved using various ionization techniques that are suited to different applications but which all yield data with high mass accuracies and spatial resolutions. The ability to simultaneously obtain images showing the distributions of chemical species ranging from metal ions to macromolecules makes it possible to explore the chemical organization of a sample and to correlate the results obtained with specific anatomical features. The imaging of biomolecules has provided new insights into multiple neurological diseases, including Parkinson's and Alzheimer's disease. Mass spectrometry imaging can also be used in conjunction with other imaging techniques in order to identify correlations between changes in the distribution of important chemical species and other changes in the properties of the tissue. Here we review the applications of mass spectrometry imaging in neuroscience research and discuss its potential. The results presented demonstrate that mass spectrometry imaging is a useful experimental method with diverse applications in neuroscience.

Environmental applications for the analysis of chlorinated dibenzo-p-dioxins and dibenzofurans using mass spectrometry/mass spectrometry

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

Reiner, E.J.; Schellenberg, D.H.; Taguchi, V.Y.

1991-01-01

A mass spectrometry/mass spectrometry-multiple reaction monitoring (MS/MS-MRM) technique for the analysis of all tetra- through octachlorinated dibenzo-p-dioxins (Cl{sub x}DD, x = 4-8) and dibenzofurans (Cl{sub x}DF, x = 4-8) has been developed at the Ministry of the Environment (MOE) utilizing a triple quadrupole mass spectrometer. Optimization of instrumental parameters using the analyte of interest in a direct insertion probe (DIP) resulted in sensitivities approaching those obtainable by high-resolution mass spectrometric (HRMS) methods. All congeners of dioxins and furans were detected in the femtogram range. Results on selected samples indicated that for some matrices, fewer chemical interferences were observed by MS/MSmore » than by HRMS. The technique used to optimize the instrument for chlorinated dibenzo-p-dioxins (CDDs) and chlorinated dibenzofurans (CDFs) analysis is adaptable to other analytes.« less

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.

The Use of Gas Chromatography and Mass Spectrometry to Introduce General Chemistry Students to Percent Mass and Atomic Mass Calculations

ERIC Educational Resources Information Center

Pfennig, Brian W.; Schaefer, Amy K.

2011-01-01

A general chemistry laboratory experiment is described that introduces students to instrumental analysis using gas chromatography-mass spectrometry (GC-MS), while simultaneously reinforcing the concepts of mass percent and the calculation of atomic mass. Working in small groups, students use the GC to separate and quantify the percent composition…

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.

Peptide Analysis Using Tandem Mass Spectrometry

DTIC Science & Technology

1989-06-01

to give pyroglutamic acid during storage, eliminating ammonia. It is almost absent in the spectrum of a freshly-prepared sample and is not seen in...USING TANDEM MASS SPECTROMETRY INTRODUCTION S The objective of the project was to determine the complete amino acid sequence of the large polypeptide...Ubiquitin by use of fast atom bombardment (FAB) ionization and tandem mass spectrometry. The peptide containing 76 amino acid residues was available

Fractional Analysis of Escherichia coli O157:H7 by Mass Spectrometry-Based Proteomics

DTIC Science & Technology

2012-10-01

column with the Dionex UltiMate 3000 (Thermo Scientific Dionex , Sunnyvale, CA). The resolved peptides were electrosprayed into a linear ion trap MS... chromatography -tandem mass spectrometry, followed by biochemical pathway mapping using the Kyoto Encyclopedia of Genes and Genomes. The fimbriae-specific subset...15. SUBJECT TERMS 3T3 murine fibroblasts Cell toxicity Liquid chromatography Mass spectrometry LC-MS Ricin Ricinus communis

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.

Extraction and Analysis of Sulfur Mustard (HD) from Various Food Matrices by Gas ChromatographyMass Spectrometry

DTIC Science & Technology

2016-01-01

EXTRACTION AND ANALYSIS OF SULFUR MUSTARD (HD) FROM VARIOUS FOOD MATRICES BY GAS CHROMATOGRAPHY–MASS...Sulfur Mustard (HD) from Various Food Matrices by Gas Chromatography–Mass Spectrometry 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT...spectrometry was used to analyze sulfur mustard (HD) in various food matrices. The development of a solid-phase extraction method using a normal

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.

Direct olive oil analysis by mass spectrometry: A comparison of different ambient ionization methods.

PubMed

Lara-Ortega, Felipe J; Beneito-Cambra, Miriam; Robles-Molina, José; García-Reyes, Juan F; Gilbert-López, Bienvenida; Molina-Díaz, Antonio

2018-04-01

Analytical methods based on ambient ionization mass spectrometry (AIMS) combine the classic outstanding performance of mass spectrometry in terms of sensitivity and selectivity along with convenient features related to the lack of sample workup required. In this work, the performance of different mass spectrometry-based methods has been assessed for the direct analyses of virgin olive oil for quality purposes. Two sets of experiments have been setup: (1) direct analysis of untreated olive oil using AIMS methods such as Low-Temperature Plasma Mass Spectrometry (LTP-MS) or paper spray mass spectrometry (PS-MS); or alternatively (2) the use of atmospheric pressure ionization (API) mass spectrometry by direct infusion of a diluted sample through either atmospheric pressure chemical ionization (APCI) or electrospray (ESI) ionization sources. The second strategy involved a minimum sample work-up consisting of a simple olive oil dilution (from 1:10 to 1:1000) with appropriate solvents, which originated critical carry over effects in ESI, making unreliable its use in routine; thus, ESI required the use of a liquid-liquid extraction to shift the measurement towards a specific part of the composition of the edible oil (i.e. polyphenol rich fraction or lipid/fatty acid profile). On the other hand, LTP-MS enabled direct undiluted mass analysis of olive oil. The use of PS-MS provided additional advantages such as an extended ionization coverage/molecular weight range (compared to LTP-MS) and the possibility to increase the ionization efficiency towards nonpolar compounds such as squalene through the formation of Ag + adducts with carbon-carbon double bounds, an attractive feature to discriminate between oils with different degree of unsaturation. Copyright © 2017 Elsevier B.V. All rights reserved.

Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

PubMed

Seng, Piseth; Drancourt, Michel; Gouriet, Frédérique; La Scola, Bernard; Fournier, Pierre-Edouard; Rolain, Jean Marc; Raoult, Didier

2009-08-15

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry accurately identifies both selected bacteria and bacteria in select clinical situations. It has not been evaluated for routine use in the clinic. We prospectively analyzed routine MALDI-TOF mass spectrometry identification in parallel with conventional phenotypic identification of bacteria regardless of phylum or source of isolation. Discrepancies were resolved by 16S ribosomal RNA and rpoB gene sequence-based molecular identification. Colonies (4 spots per isolate directly deposited on the MALDI-TOF plate) were analyzed using an Autoflex II Bruker Daltonik mass spectrometer. Peptidic spectra were compared with the Bruker BioTyper database, version 2.0, and the identification score was noted. Delays and costs of identification were measured. Of 1660 bacterial isolates analyzed, 95.4% were correctly identified by MALDI-TOF mass spectrometry; 84.1% were identified at the species level, and 11.3% were identified at the genus level. In most cases, absence of identification (2.8% of isolates) and erroneous identification (1.7% of isolates) were due to improper database entries. Accurate MALDI-TOF mass spectrometry identification was significantly correlated with having 10 reference spectra in the database (P=.01). The mean time required for MALDI-TOF mass spectrometry identification of 1 isolate was 6 minutes for an estimated 22%-32% cost of current methods of identification. MALDI-TOF mass spectrometry is a cost-effective, accurate method for routine identification of bacterial isolates in <1 h using a database comprising > or =10 reference spectra per bacterial species and a 1.9 identification score (Brucker system). It may replace Gram staining and biochemical identification in the near future.

Characterization of crude oil biomarkers using comprehensive two-dimensional gas chromatography coupled to tandem mass spectrometry.

PubMed

Mogollón, Noroska Gabriela Salazar; Prata, Paloma Santana; Dos Reis, Jadson Zeni; Neto, Eugênio Vaz Dos Santos; Augusto, Fabio

2016-09-01

Oil samples from Recôncavo basin (NE Brazil), previously analyzed by traditional techniques such as gas chromatography coupled to tandem mass spectrometry, were evaluated using comprehensive two-dimensional gas chromatography coupled to quadrupole mass spectrometry and comprehensive two-dimensional gas chromatography coupled to tandem mass spectrometry along with simplified methods of samples preparation to evaluate the differences and advantages of these analytical techniques to better understand the development of the organic matter in this basin without altering the normal distribution of the compounds in the samples. As a result, the geochemical parameters calculated by comprehensive two-dimensional gas chromatography coupled to tandem mass spectrometry described better the origin, maturity, and biodegradation of both samples probably by increased selectivity, resolution, and sensitivity inherent of the multidimensional technique. Additionally, the detection of the compounds such as, the C(14α-) homo-26-nor-17α-hopane series, diamoretanes, nor-spergulanes, C19 -C26 A-nor-steranes and 4α-methylsteranes resolved and detected by comprehensive two-dimensional gas chromatography coupled to tandem mass spectrometry were key to classify and differentiate these lacustrine samples according to their maturity and deposition conditions. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rapid detection of cocaine, benzoylecgonine and methylecgonine in fingerprints using surface mass spectrometry.

PubMed

Bailey, Melanie J; Bradshaw, Robert; Francese, Simona; Salter, Tara L; Costa, Catia; Ismail, Mahado; P Webb, Roger; Bosman, Ingrid; Wolff, Kim; de Puit, Marcel

2015-09-21

Latent fingerprints provide a potential route to the secure, high throughput and non-invasive detection of drugs of abuse. In this study we show for the first time that the excreted metabolites of drugs of abuse can be detected in fingerprints using ambient mass spectrometry. Fingerprints and oral fluid were taken from patients attending a drug and alcohol treatment service. Gas chromatography mass spectrometry (GC-MS) was used to test the oral fluid of patients for the presence of cocaine and benzoylecgonine. The corresponding fingerprints were analysed using Desorption Electrospray Ionization (DESI) which operates under ambient conditions and Ion Mobility Tandem Mass Spectrometry Matrix Assisted Laser Desorption Ionization (MALDI-IMS-MS/MS) and Secondary Ion Mass Spectrometry (SIMS). The detection of cocaine, benzoylecgonine (BZE) and methylecgonine (EME) in latent fingerprints using both DESI and MALDI showed good correlation with oral fluid testing. The sensitivity of SIMS was found to be insufficient for this application. These results provide exciting opportunities for the use of fingerprints as a new sampling medium for secure, non-invasive drug detection. The mass spectrometry techniques used here offer a high level of selectivity and consume only a small area of a single fingerprint, allowing repeat and high throughput analyses of a single sample.

Substrate and Substrate-Mimetic Chaperone Binding Sites in Human α-Galactosidase A Revealed by Affinity-Mass Spectrometry

NASA Astrophysics Data System (ADS)

Moise, Adrian; Maeser, Stefan; Rawer, Stephan; Eggers, Frederike; Murphy, Mary; Bornheim, Jeff; Przybylski, Michael

2016-06-01

Fabry disease (FD) is a rare metabolic disorder of a group of lysosomal storage diseases, caused by deficiency or reduced activity of the enzyme α-galactosidase. Human α-galactosidase A (hαGAL) hydrolyses the terminal α-galactosyl moiety from glycosphingolipids, predominantly globotriaosylceramide (Gb3). Enzyme deficiency leads to incomplete or blocked breakdown and progressive accumulation of Gb3, with detrimental effects on normal organ functions. FD is successfully treated by enzyme replacement therapy (ERT) with purified recombinant hαGAL. An emerging treatment strategy, pharmacologic chaperone therapy (PCT), employs small molecules that can increase and/or reconstitute the activity of lysosomal enzyme trafficking by stabilizing misfolded isoforms. One such chaperone, 1-deoxygalactonojirimycin (DGJ), is a structural galactose analogue currently validated in clinical trials. DGJ is an active-site-chaperone that binds at the same or similar location as galactose; however, the molecular determination of chaperone binding sites in lysosomal enzymes represents a considerable challenge. Here we report the identification of the galactose and DGJ binding sites in recombinant α-galactosidase through a new affinity-mass spectrometry-based approach that employs selective proteolytic digestion of the enzyme-galactose or -inhibitor complex. Binding site peptides identified by mass spectrometry, [39-49], [83-100], and [141-168], contain the essential ligand-contacting amino acids, in agreement with the known X-ray crystal structures. The inhibitory effect of DGJ on galactose recognition was directly characterized through competitive binding experiments and mass spectrometry. The methods successfully employed in this study should have high potential for the characterization of (mutated) enzyme-substrate and -chaperone interactions, and for identifying chaperones without inhibitory effects.

Secondary organic aerosol formation and composition from the photo-oxidation of methyl chavicol (estragole)

NASA Astrophysics Data System (ADS)

Pereira, K. L.; Hamilton, J. F.; Rickard, A. R.; Bloss, W. J.; Alam, M. S.; Camredon, M.; Muñoz, A.; Vásquez, M.; Borrás, E.; Ródenas, M.

2013-12-01

The increasing demand for palm oil for uses in biofuel and food products is leading to rapid expansion of oil palm agriculture. Methyl chavicol (also known as estragole and 1-allyl-4-methoxybenzene) is an oxygenated biogenic volatile organic compound that was recently identified as the main floral emission from an oil palm plantation in Malaysian Borneo. The emissions of methyl chavicol observed may impact regional atmospheric chemistry, but little is known of its ability to form secondary organic aerosol (SOA). The photo-oxidation of methyl chavicol was investigated at the European Photoreactor chamber as a part of the atmospheric chemistry of methyl chavicol (ATMECH) project. Aerosol samples were collected using a particle into liquid sampler (PILS) and analysed offline using an extensive range of instruments including; high performance liquid chromatography mass spectrometry (HPLC-ITMS), high performance liquid chromatography quadrupole time-of-flight mass spectrometry (HPLC-QTOFMS) and Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). The SOA yield was determined as 18-29% depending on initial precursor (VOC : NOx) mixing ratios. In total, 59 SOA compounds were observed and the structures of 10 compounds have been identified using high resolution tandem mass spectrometry. The addition of hydroxyl and/or nitro functional groups to the aromatic ring appears to be an important mechanistic pathway for aerosol formation. This results in the formation of compounds with both low volatility and high O : C ratios, where functionalisation rather than fragmentation is mainly observed as a~result of the stability of the ring. The SOA species observed can be characterized as semi-volatile to low volatile oxygenated organic aerosol (SVOOA and LVOOA) components and therefore may be important in aerosol formation and growth.

An evaluation of coral lophelia pertusa mucus as an analytical matrix for environmental monitoring: A preliminary proteomic study.

PubMed

Provan, Fiona; Nilsen, Mari Mæland; Larssen, Eivind; Uleberg, Kai-Erik; Sydnes, Magne O; Lyng, Emily; Øysæd, Kjell Birger; Baussant, Thierry

2016-01-01

For the environmental monitoring of coral, mucus appears to be an appropriate biological matrix due to its array of functions in coral biology and the non-intrusive manner in which it can be collected. The aim of the present study was to evaluate the feasibility of using mucus of the stony coral Lophelia pertusa (L. pertusa) as an analytical matrix for discovery of biomarkers used for environmental monitoring. More specifically, to assess whether a mass-spectrometry-based proteomic approach can be applied to characterize the protein composition of coral mucus and changes related to petroleum discharges at the seafloor. Surface-enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF MS) screening analyses of orange and white L. pertusa showed that the mucosal protein composition varies significantly with color phenotype, a pattern not reported prior to this study. Hence, to reduce variability from phenotype difference, L. pertusa white individuals only were selected to characterize in more detail the basal protein composition in mucus using liquid chromatography, mass spectrometry, mass spectrometry (LC-MS/MS). In total, 297 proteins were identified in L. pertusa mucus of unexposed coral individuals. Individuals exposed to drill cuttings in the range 2 to 12 mg/L showed modifications in coral mucus protein composition compared to unexposed corals. Although the results were somewhat inconsistent between individuals and require further validation in both the lab and the field, this study demonstrated preliminary encouraging results for discovery of protein markers in coral mucus that might provide more comprehensive insight into potential consequences attributed to anthropogenic stressors and may be used in future monitoring of coral health.

Galaxy-M: a Galaxy workflow for processing and analyzing direct infusion and liquid chromatography mass spectrometry-based metabolomics data.

PubMed

Davidson, Robert L; Weber, Ralf J M; Liu, Haoyu; Sharma-Oates, Archana; Viant, Mark R

2016-01-01

Metabolomics is increasingly recognized as an invaluable tool in the biological, medical and environmental sciences yet lags behind the methodological maturity of other omics fields. To achieve its full potential, including the integration of multiple omics modalities, the accessibility, standardization and reproducibility of computational metabolomics tools must be improved significantly. Here we present our end-to-end mass spectrometry metabolomics workflow in the widely used platform, Galaxy. Named Galaxy-M, our workflow has been developed for both direct infusion mass spectrometry (DIMS) and liquid chromatography mass spectrometry (LC-MS) metabolomics. The range of tools presented spans from processing of raw data, e.g. peak picking and alignment, through data cleansing, e.g. missing value imputation, to preparation for statistical analysis, e.g. normalization and scaling, and principal components analysis (PCA) with associated statistical evaluation. We demonstrate the ease of using these Galaxy workflows via the analysis of DIMS and LC-MS datasets, and provide PCA scores and associated statistics to help other users to ensure that they can accurately repeat the processing and analysis of these two datasets. Galaxy and data are all provided pre-installed in a virtual machine (VM) that can be downloaded from the GigaDB repository. Additionally, source code, executables and installation instructions are available from GitHub. The Galaxy platform has enabled us to produce an easily accessible and reproducible computational metabolomics workflow. More tools could be added by the community to expand its functionality. We recommend that Galaxy-M workflow files are included within the supplementary information of publications, enabling metabolomics studies to achieve greater reproducibility.

Metaproteomics of Microbiota in Naturally Fermented Soybean Paste, Da-jiang.

PubMed

Zhang, Ping; Zhang, Pengfei; Xie, Mengxi; An, Feiyu; Qiu, Boshu; Wu, Rina

2018-05-01

Da-jiang is a typical traditional fermented soybean product in China. At present, the proteins in da-jiang are needed to be explored. The composition and species of microbial proteins in traditional fermented da-jiang were analyzed by metaproteomics based on sodium dodecyl sulfonate-polyacrylamide gel electrophoresis (SDS-PAGE) and liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). The results showed that the number and variety of microbial proteins in the traditional fermented da-jiang from different regions were different. The production site influences the fermentation in da-jiang. Then we analyzed the functions of the microbial proteins identified in da-jiang, and found that they were mainly involved in the process of protein synthesis, glycometabolism and nucleic acid synthesis. In addtion, we compared the proteins composition in different da-jiang. There are 51 common proteins of naturally fermented da-jiang, and 25 common microbial sources. The main commonly microbial sources of fungal proteins are Saccharomyces cerevisiae and Schizosaccharomyces; the main commonly microbial sources of bacterial proteins are Enterococcus faecalis, Leuconostoc mesenteroides, Acinetobacter baumannii, and Bacillus subtilis. These common microbes play the predominant role in da-jiang fermentation. The present results help us to understand the fermentation of da-jiang and improve the quality and safety of final products in the future. The study illustrated metaproteome of microbiota in traditional fermented soybean paste, da-jiang, by sodium dodecyl sulfonate-polyacrylamide gel electrophoresis (SDS-PAGE) and liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). A method of extracting metaproteome from microbiota in da-jiang was attempted. The findings help to understand the fermentation of da-jiang and improve the quality and safety of da-jiang in fermented industry. © 2018 Institute of Food Technologists®.

Quantitation of protein S-glutathionylation by liquid chromatograph-tandem mass spectrometry: Correction for contaminating glutathione and glutathione disulfide

USDA-ARS?s Scientific Manuscript database

Protein S-glutathionylation is a posttranslational modification that links oxidative stimuli to reversible changes in cellular function. Protein-glutathione mixed disulfides (PSSG) are commonly quantified by the reduction of the disulfide and detection of the resultant glutathione species. This met...

Developing a New Interdisciplinary Lab Course for Undergraduate and Graduate Students: Plant Cells and Proteins

ERIC Educational Resources Information Center

Jez, Joseph M.; Schachtman, Daniel P.; Berg, R. Howard; Taylor, Christopher G.; Chen, Sixue; Hicks, Leslie M.; Jaworski, Jan G.; Smith, Thomas J.; Nielsen, Erik; Pikaard, Craig S.

2007-01-01

Studies of protein function increasingly use multifaceted approaches that span disciplines including recombinant DNA technology, cell biology, and analytical biochemistry. These studies rely on sophisticated equipment and methodologies including confocal fluorescence microscopy, mass spectrometry, and X-ray crystallography that are beyond the…

Novel product ions of 2-aminoanilide and benzimidazole Ag(I) complexes using electrospray ionization with multi-stage tandem mass spectrometry.

PubMed

Johnson, Byron S; Burinsky, David J; Burova, Svetlana A; Davis, Roman; Fitzgerald, Russ N; Matsuoka, Richard T

2012-05-15

The 2-aminoaniline scaffold is of significant value to the pharmaceutical industry and is embedded in a number of pharmacophores including 2-aminoanilides and benzimidazoles. A novel application of coordination ion spray mass spectrometry (CIS-MS) for interrogating the silver ion (Ag(+)) complexes of a homologous series of these compounds using multi-stage tandem mass spectrometry is described. Unlike the ubiquitous alkali metal ion complexes, Ag(+) complexes of 2-aminoanilides and benzimidazoles were found to yield [M - H](+) ions in significant abundance via gas-phase elimination of the metal hydride (AgH) resulting in unique product ion cascades. Sample introduction was by liquid chromatography with mass spectrometry analysis performed on a hybrid linear ion trap/orbitrap instrument capable of high-resolution measurements. Rigorous structural characterization by multi-stage tandem mass spectrometry using [M +  H](+), [M - H](-) and [M - H](+) precursor ions derived from ESI and CIS experiments was performed for the homologous series of 2-aminoanilide and benzimidazole compounds. A full tabular comparison of structural information resulting from these product ion cascades was produced. Multi-stage tandem mass spectrometry of [M - H](+) ions resulting from Ag(+) complexes of 2-aminoanilides and benzimidazoles in CIS-MS experiments produced unique product ion cascades that exhibited complementary structural information to that obtained from tandem mass spectrometry of [M  +  H](+) and [M - H](-) ions by electrospray ionization (ESI). These observations may be broadly applicable to other compounds that are observed to form Ag(+) complexes and eliminate AgH. Copyright © 2012 John Wiley & Sons, Ltd.

Quantitative Thin-Layer Chromatography/Mass Spectrometry Analysis of Caffeine Using a Surface Sampling Probe Electrospray Ionization Tandem Mass Spectrometry System

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

Ford, Michael J; Deibel, Michael A.; Tomkins, Bruce A

Quantitative determination of caffeine on reversed-phase C8 thin-layer chromatography plates using a surface sampling electrospray ionization system with tandem mass spectrometry detection is reported. The thin-layer chromatography/electrospray tandem mass spectrometry method employed a deuterium-labeled caffeine internal standard and selected reaction monitoring detection. Up to nine parallel caffeine bands on a single plate were sampled in a single surface scanning experiment requiring 35 min at a surface scan rate of 44 {mu}m/s. A reversed-phase HPLC/UV caffeine assay was developed in parallel to assess the mass spectrometry method performance. Limits of detection for the HPLC/UV and thin-layer chromatography/electrospray tandem mass spectrometry methodsmore » determined from the calibration curve statistics were 0.20 ng injected (0.50 {mu}L) and 1.0 ng spotted on the plate, respectively. Spike recoveries with standards and real samples ranged between 97 and 106% for both methods. The caffeine content of three diet soft drinks (Diet Coke, Diet Cherry Coke, Diet Pepsi) and three diet sport drinks (Diet Turbo Tea, Speed Stack Grape, Speed Stack Fruit Punch) was measured. The HPLC/UV and mass spectrometry determinations were in general agreement, and these values were consistent with the quoted values for two of the three diet colas. In the case of Diet Cherry Coke and the diet sports drinks, the determined caffeine amounts using both methods were consistently higher (by 8% or more) than the literature values.« less

Impact ionisation mass spectrometry of platinum-coated olivine and magnesite-dominated cosmic dust analogues

NASA Astrophysics Data System (ADS)

Hillier, Jon K.; Sternovsky, Z.; Kempf, S.; Trieloff, M.; Guglielmino, M.; Postberg, F.; Price, M. C.

2018-07-01

Impact ionisation mass spectrometry enables the composition of cosmic dust grains to be determined in situ by spacecraft-based instrumentation. The proportion of molecular ions in the impact plasma is a function of the impact velocity, making laboratory calibration vital for the interpretation of the mass spectra, particularly at the low velocities typical of lunar or asteroid encounters. Here we present an analysis of laboratory impact ionisation mass spectra from primarily low (<15 km s-1) velocity impacts of both olivine and magnesite-dominated particles onto the SUrface Dust Mass Analyzer (SUDA) laboratory mass spectrometer. The cation mass spectra show characteristic peaks due to their constituent elements, with Mg, Al, Si, C, Ca, O and Fe frequently present. Contaminant species from the conductive coating process (B, Na, K, C, Pt) also occur, at varying frequencies. Possible saponite or talc inclusions in the magnesite particles are revealed by the presence of Si, Fe, Ca and Al in the magnesite mass spectra. Magnesium is clearly present at the lowest impact velocities (3 km s-1), at which alkali metals were presumed to dominate. Peaks attributed to very minor amounts of water or hydroxyl present in the grains are also seen at low velocities in both cation and anion mass spectra, demonstrating the feasibility of impact ionisation mass spectrometry in identifying hydrated or hydrous minerals, during very low velocity encounters or with very low abundances of water or hydroxy groups, in the impinging grains. Velocity thresholds for the reliable identification of the major elements within the magnesite and olivine cation spectra are presented. Additionally, relative sensitivity factors for Mg (5.1), Fe (1.5) and O (0.6) with respect to Si, in the olivine particles, at impact speeds >19 km s-1, were found to be very similar to those previously determined for orthopyroxene-dominated particles, despite different target and projectile materials. This confirms that quantitative analyses of mineral dust grain composition in space is viable despite initially poorly-constrained mineralogy.

QUANTITATIVE MASS SPECTROMETRIC ANALYSIS OF GLYCOPROTEINS COMBINED WITH ENRICHMENT METHODS

PubMed Central

Ahn, Yeong Hee; Kim, Jin Young; Yoo, Jong Shin

2015-01-01

Mass spectrometry (MS) has been a core technology for high sensitive and high-throughput analysis of the enriched glycoproteome in aspects of quantitative assays as well as qualitative profiling of glycoproteins. Because it has been widely recognized that aberrant glycosylation in a glycoprotein may involve in progression of a certain disease, the development of efficient analysis tool for the aberrant glycoproteins is very important for deep understanding about pathological function of the glycoprotein and new biomarker development. This review first describes the protein glycosylation-targeting enrichment technologies mainly employing solid-phase extraction methods such as hydrizide-capturing, lectin-specific capturing, and affinity separation techniques based on porous graphitized carbon, hydrophilic interaction chromatography, or immobilized boronic acid. Second, MS-based quantitative analysis strategies coupled with the protein glycosylation-targeting enrichment technologies, by using a label-free MS, stable isotope-labeling, or targeted multiple reaction monitoring (MRM) MS, are summarized with recent published studies. © 2014 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc. Rapid Commun. Mass Spec Rev 34:148–165, 2015. PMID:24889823

Organic environments on Saturn's moon, Titan: simulating chemical reactions and analyzing products by FT-ICR and ion-trap mass spectrometry.

PubMed

Somogyi, Arpad; Oh, Chu-Ha; Smith, Mark A; Lunine, Jonathan I

2005-06-01

Laboratory simulations have been carried out to model chemical reactions that possibly take place in the stratosphere of Saturn's moon, Titan. The aerosol products of these reactions (tholin samples) have been systematically analyzed by mass spectrometry using electrospray ionization (ESI) and laser desorption (LD). A wide variety of ions with a general formula C(x)H(y)N(z) detected by ultrahigh resolution and accurate mass measurements in a Fourier transform/ion cyclotron resonance (FT-ICR) cell reflect the complexity of these polymeric products, both in chemical compositions and isomeric distributions. As a common feature, however, tandem mass spectral (MS/MS) data and H/D exchange products in the solution phase support the presence of amino and nitrile functionalities in these (highly unsaturated) "tholin" compounds. The present work demonstrates that ESI-MS coupled with FT-ICR is a suitable and "intact" method to analyze tholin components formed under anaerobic conditions; only species with C(x)H(y)N(z) are detected for freshly prepared and harvested samples. However, when intentionally exposed to water, oxygen-containing compounds are unambiguously detected.

Proteomic Challenges: Sample Preparation Techniques for Microgram-Quantity Protein Analysis from Biological Samples

PubMed Central

Feist, Peter; Hummon, Amanda B.

2015-01-01

Proteins regulate many cellular functions and analyzing the presence and abundance of proteins in biological samples are central focuses in proteomics. The discovery and validation of biomarkers, pathways, and drug targets for various diseases can be accomplished using mass spectrometry-based proteomics. However, with mass-limited samples like tumor biopsies, it can be challenging to obtain sufficient amounts of proteins to generate high-quality mass spectrometric data. Techniques developed for macroscale quantities recover sufficient amounts of protein from milligram quantities of starting material, but sample losses become crippling with these techniques when only microgram amounts of material are available. To combat this challenge, proteomicists have developed micro-scale techniques that are compatible with decreased sample size (100 μg or lower) and still enable excellent proteome coverage. Extraction, contaminant removal, protein quantitation, and sample handling techniques for the microgram protein range are reviewed here, with an emphasis on liquid chromatography and bottom-up mass spectrometry-compatible techniques. Also, a range of biological specimens, including mammalian tissues and model cell culture systems, are discussed. PMID:25664860

Application of Laser Mass Spectrometry to Art and Archaeology

NASA Technical Reports Server (NTRS)

Gulian, Lase Lisa E.; Callahan, Michael P.; Muliadi, Sarah; Owens, Shawn; McGovern, Patrick E.; Schmidt, Catherine M.; Trentelman, Karen A.; deVries, Mattanjah S.

2011-01-01

REMPI laser mass spectrometry is a combination of resonance enhanced multiphoton ionization spectroscopy and time of flight mass spectrometry, This technique enables the collection of mass specific optical spectra as well as of optically selected mass spectra. Analytes are jet-cooled by entrainment in a molecular beam, and this low temperature gas phase analysis has the benefit of excellent vibronic resolution. Utilizing this method, mass spectrometric analysis of historically relevant samples can be simplified and improved; Optical selection of targets eliminates the need for chromatography while knowledge of a target's gas phase spectroscopy allows for facile differentiation of molecules that are in the aqueous phase considered spectroscopically indistinguishable. These two factors allow smaller sample sizes than commercial MS instruments, which in turn will require less damage to objects of antiquity. We have explored methods to optimize REMPI laser mass spectrometry as an analytical tool to archaeology using theobromine and caffeine as molecular markers in Mesoamerican pottery, and are expanding this approach to the field of art to examine laccaic acid in shellacs.

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.

Ion-mobility study of two functionalized pentacene structural isomers using a modified electrospray/triple quadrupole mass spectrometer

NASA Astrophysics Data System (ADS)

Prada, Svitlana V.; Bohme, Diethard K.; Baranov, Vladimir I.

2007-03-01

We report ion-mobility measurements with a modified triple quadrupole mass spectrometer fitted with an ion molecule reactor (IMR) designed to investigate ion molecule reactivity in organic mass spectrometry. Functionalized pentacene ions, which are generally unreactive were chosen for study to decouple drift/diffusion effects from reactivity (including clustering). The IMR is equipped with a variable axial electrostatic drift field (ADF) and is able to trap ions. These capabilities were successfully employed in the measurement of ion mobilities in different modes of IMR operation. Theoretical modeling of the drift dynamics and the special localization of the large ion packet was successfully implemented. The contribution of the quadrupole RF field to the drift dynamics also was taken into consideration.

Stable isotope labeling tandem mass spectrometry (SILT) to quantify protein production and clearance rates

PubMed Central

Bateman, Randall J.; Munsell, Ling Y.; Chen, Xianghong; Holtzman, David M.; Yarasheski, Kevin E.

2007-01-01

In all biological systems, protein amount is a function of the rate of production and clearance. The speed of a response to a disturbance in protein homeostasis is determined by turnover rate. Quantifying alterations in protein synthesis and clearance rates is vital to understanding disease pathogenesis (e.g., aging, inflammation). No methods exist for quantifying production and clearance rates of low abundance (femtomole) proteins in vivo. We describe a novel, mass spectrometry-based method for quantitating low abundance protein synthesis and clearance rates in vitro and in vivo in animals and humans. The utility of this method is demonstrated with amyloid-beta (Aß), an important low abundance protein involved in Alzheimer's disease pathogenesis. We used in vivo stable isotope labeling, immunoprecipitation of Aß from cerebrospinal fluid, and quantitative liquid chromatography electrospray-ionization tandem mass spectrometry (LC-ESI-tandem MS) to quantify human Aß protein production and clearance rates. The method is sensitive and specific for stable isotope labeled amino acid incorporation into CNS (± 1% accuracy). This in vivo method can be used to identify pathophysiologic changes in protein metabolism; and may serve as a biomarker for monitoring disease risk, progression, or response to novel therapeutic agents. The technique is adaptable to other macromolecules, such as carbohydrates or lipids. PMID:17383190

Liquid chromatography with mass spectrometry method based two-step precursor ion scanning for the structural elucidation of flavonoids.

PubMed

Li, Yong; Pang, Tao; Shi, Junli; Lu, Xiuping; Deng, Jianhua; Lin, Qian

2014-11-01

Plant flavonoids are very important secondary metabolites for insect and virus control of their host plant and are potent nutrients for humans. To be able to understand the bioavailability and functions of plant flavonoids, it is necessary to reveal their exact chemical structures. Liquid chromatography with tandem mass spectrometry is a powerful approach for structural elucidation of metabolites. In this report, a two-step precursor ion scanning based liquid chromatography with tandem mass spectrometry method was developed for the structural elucidation of plant flavonoids. The established method consists of the two-step precursor ions scanning for possible flavonoids extraction, MS(2) fragment spectra acquisition and comparison with an online database, liquid chromatography retention rules correction, and commercial standards verification. The developed method was used for the structure elucidation of flavonoids in flowers and leaves of tobacco (Nicotiana tabacum), and 17 flavonoids were identified in the tobacco variety Yunyan 97. Nine of the 17 identified flavonoids were considered to be found in tobacco flowers or/and leaves for the first time based on the available references. This method was proved to be very effective and can be used for the identification of flavonoids in other plants. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantitative Clinical Chemistry Proteomics (qCCP) using mass spectrometry: general characteristics and application.

PubMed

Lehmann, Sylvain; Hoofnagle, Andrew; Hochstrasser, Denis; Brede, Cato; Glueckmann, Matthias; Cocho, José A; Ceglarek, Uta; Lenz, Christof; Vialaret, Jérôme; Scherl, Alexander; Hirtz, Christophe

2013-05-01

Proteomics studies typically aim to exhaustively detect peptides/proteins in a given biological sample. Over the past decade, the number of publications using proteomics methodologies has exploded. This was made possible due to the availability of high-quality genomic data and many technological advances in the fields of microfluidics and mass spectrometry. Proteomics in biomedical research was initially used in 'functional' studies for the identification of proteins involved in pathophysiological processes, complexes and networks. Improved sensitivity of instrumentation facilitated the analysis of even more complex sample types, including human biological fluids. It is at that point the field of clinical proteomics was born, and its fundamental aim was the discovery and (ideally) validation of biomarkers for the diagnosis, prognosis, or therapeutic monitoring of disease. Eventually, it was recognized that the technologies used in clinical proteomics studies [particularly liquid chromatography-tandem mass spectrometry (LC-MS/MS)] could represent an alternative to classical immunochemical assays. Prior to deploying MS in the measurement of peptides/proteins in the clinical laboratory, it seems likely that traditional proteomics workflows and data management systems will need to adapt to the clinical environment and meet in vitro diagnostic (IVD) regulatory constraints. This defines a new field, as reviewed in this article, that we have termed quantitative Clinical Chemistry Proteomics (qCCP).

New Tools & Techniques for the Metallomics Revolution

NASA Astrophysics Data System (ADS)

Koppenaal, D. W.; Hieftje, G. M.

2004-12-01

The metallome has been defined as the complete complement of metals and metal moieties in a biological cell, tissue, or system. This definition is akin to that of the genome (genes), proteome (proteins), and metabolome (metabolites). Metallomics accordingly is the study of metals and metal species, and their interactions, transformations, and functions in biological systems. While traditional bioinorganic chemistry has focused on the role and interactions of a single (or few) metals in a protein or enzyme system, metallomics purports to study global, multi-element interactions and relationships. The metallomics challenges for analytical chemistry and biochemical characterization are significant. This paper will discuss these challenges and the emergent techniques and tools that are being developed to address them. Mass spectrometry will play an important and pivotal role. Two approaches are currently being developed in the authors' laboratories. At Pacific Northwest National Laboratory, an extremely high-resolution approach using Fourier Transform Ion Cyclotron Resonance mass spectrometry (FT-ICRMS) is under development. At Indiana University, a rapid, dual-reflectron Time-of-Flight mass spectrometry (TOFMS) technique is being developed. Both approaches rely on dual inductively coupled plasma (ICP) and electrospray ionization (ESI) sources for elemental and biomolecular ion generation. The initial development of these techniques, and their potential application to systems biology and environmental characterization, will be discussed.

Dual enzyme activities assay by quantitative electrospray ionization quadrupole-time-of-flight mass spectrometry.

PubMed

Cai, Tingting; Zhang, Li; Wang, Haoyang; Zhang, Jing; Wang, Rong; Zhang, Yurong; Guo, Yinlong

2012-01-01

A practical and rapid method based on electrospray ionization quadrupole-time of flight mass spectrometry (ESI-Q-ToF MS) was developed for detecting activities of both acetylcholinesterase IAChEI and glutathione S-transferase (GST). The simultaneous study of these two enzyme activities is significant for studying human bio-functions, especially for those who take in toxic compounds and have a risk of disease. Here, the enzyme activities were represented by the conversion of enzymatic substrates and determined by quantitatively analyzing enzymatic substrates. Different internal standards were used to quantify each enzymatic substrate and the good linearity of calibration curves demonstrated the feasibility of the internal standards. The Michaelis-Menten constants (Km) of both GST and AChE were measured by this method and were consistent with values previously reported. Furthermore, we applied this approach to detect GST and AChE activities of whole bloods from four deceased and healthy people. The variation in enzyme activity was in accord with information from gas chromatography mass spectrometry [GC/MS). The screening of AChE and GST provided reliable results and strong forensic evidence. This method offers an alternative choice for detecting enzyme activities and is anticipated to have wide applications in pharmaceutical research and prevention in toxic compounds.

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.

Biomarkers to Assess Possible Biological Effects on Reproductive Potential, Immune Function, and Energetic Fitness of Bottlenose Dolphins Exposed to Sounds Consistent with Naval Sonars

DTIC Science & Technology

2013-09-30

ion modes. The resulting chromatograms were then processed using XCMS (alignment and peak picking ). The data were processed with in-house...UHPLC liquid chromatography Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry ( MS ). A standard method was developed for rapid analysis...extraction protocols and then implemented LC- MS / MS analyses on our Thermo Fisher Scientific TSQ Vantage triple quadrupole mass spectrometer. This

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.

Mass spectrometry: a revolution in clinical microbiology?

PubMed

Lavigne, Jean-Philippe; Espinal, Paula; Dunyach-Remy, Catherine; Messad, Nourredine; Pantel, Alix; Sotto, Albert

2013-02-01

Recently, different bacteriological laboratory interventions that decrease reporting time have been developed. These promising new broad-based techniques have merit, based on their ability to identify rapidly many bacteria, organisms difficult to grow or newly emerging strains, as well as their capacity to track disease transmission. The benefit of rapid reporting of identification and/or resistance of bacteria can greatly impact patient outcomes, with an improvement in the use of antibiotics, in the reduction of the emergence of multidrug resistant bacteria and in mortality rates. Different techniques revolve around mass spectrometry (MS) technology: matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), PCR combined with electrospray ionization-mass spectrometry (PCR/ESIMS), iPLEX MassArray system and other new evolutions combining different techniques. This report emphasizes the (r)evolution of these technologies in clinical microbiology.

Negative ion electrospray ionization mass spectrometry of nucleoside phosphoramidate monoesters: elucidation of novel rearrangement mechanisms by multistage mass spectrometry incorporating in-source deuterium labelling.

PubMed

Xu, Peng-Xiang; Hu, An-Fu; Hu, Dan; Gao, Xiang; Zhao, Yu-Fen

2008-10-01

Several O-2',3'-isopropylideneuridine-O-5'-phosphoramidate monoesters were synthesized and analyzed by negative ion electrospray ionization tandem mass spectrometry (ESI-MS(n)). Two kinds of novel rearrangement reactions were observed due to the difference in the amino acid in the nucleoside phosphoramidate monoesters, and possible mechanisms were proposed. One involves a five-membered cyclic transition state. The other is formation of a stable five-membered ring intermediate by Michael addition. Results were confirmed by tandem mass spectrometry and isotopically labeled hydrogen atoms. Furthermore, the internal hydrogen exchange between active hydrogen and methyl acrylate in the heated capillary of the mass spectrometer was found. The characteristic fragmentation behavior in ESI-MS may be used to monitor this kind of compounds in the biological metabolism.

Strategies for potential age dating of fingerprints through the diffusion of sebum molecules on a nonporous surface analyzed using time-of-flight secondary ion mass spectrometry.

PubMed

Muramoto, Shin; Sisco, Edward

2015-08-18

Age dating of fingerprints could have a significant impact in forensic science, as it has the potential to facilitate the judicial process by assessing the relevance of a fingerprint found at a crime scene. However, no method currently exists that can reliably predict the age of a latent fingerprint. In this manuscript, time-of-flight secondary ion imaging mass spectrometry (TOF-SIMS) was used to measure the diffusivity of saturated fatty acid molecules from a fingerprint on a silicon wafer. It was found that their diffusion from relatively fresh fingerprints (t ≤ 96 h) could be modeled using an error function, with diffusivities (mm(2)/h) that followed a power function when plotted against molecular weight. The equation x = 0.02t(0.5) was obtained for palmitic acid that could be used to find its position in millimeters (where the concentration is 50% of its initial value or c0/2) as a function of time in hours. The results show that on a clean silicon substrate, the age of a fingerprint (t ≤ 96 h) could reliably be obtained through the extent of diffusion of palmitic acid.

Hydrophilic interaction ultra-performance liquid chromatography coupled with triple-quadrupole tandem mass spectrometry for highly rapid and sensitive analysis of underivatized amino acids in functional foods.

PubMed

Zhou, Guisheng; Pang, Hanqing; Tang, Yuping; Yao, Xin; Mo, Xuan; Zhu, Shaoqing; Guo, Sheng; Qian, Dawei; Qian, Yefei; Su, Shulan; Zhang, Li; Jin, Chun; Qin, Yong; Duan, Jin-ao

2013-05-01

This work presented a new analytical methodology based on hydrophilic interaction ultra-performance liquid chromatography coupled with triple-quadrupole tandem mass spectrometry in multiple-reaction monitoring mode for analysis of 24 underivatized free amino acids (FAAs) in functional foods. The proposed method was first reported and validated by assessing the matrix effects, linearity, limit of detections and limit of quantifications, precision, repeatability, stability and recovery of all target compounds, and it was used to determine the nutritional substances of FAAs in ginkgo seeds and further elucidate the nutritional value of this functional food. The result showed that ginkgo seed turned out to be a good source of FAAs with high levels of several essential FAAs and to have a good nutritional value. Furthermore, the principal component analysis was performed to classify the ginkgo seed samples on the basis of 24 FAAs. As a result, the samples could be mainly clustered into three groups, which were similar to areas classification. Overall, the presented method would be useful for the investigation of amino acids in edible plants and agricultural products.

Mass spectrometry imaging reveals new biological roles for choline esters and Tyrian purple precursors in muricid molluscs

PubMed Central

Rudd, David; Ronci, Maurizio; Johnston, Martin R.; Guinan, Taryn; Voelcker, Nicolas H.; Benkendorff, Kirsten

2015-01-01

Despite significant advances in chemical ecology, the biodistribution, temporal changes and ecological function of most marine secondary metabolites remain unknown. One such example is the association between choline esters and Tyrian purple precursors in muricid molluscs. Mass spectrometry imaging (MSI) on nano-structured surfaces has emerged as a sophisticated platform for spatial analysis of low molecular mass metabolites in heterogeneous tissues, ideal for low abundant secondary metabolites. Here we applied desorption-ionisation on porous silicon (DIOS) to examine in situ changes in biodistribution over the reproductive cycle. DIOS-MSI showed muscle-relaxing choline ester murexine to co-localise with tyrindoxyl sulfate in the biosynthetic hypobranchial glands. But during egg-laying, murexine was transferred to the capsule gland, and then to the egg capsules, where chemical ripening resulted in Tyrian purple formation. Murexine was found to tranquilise the larvae and may relax the reproductive tract. This study shows that DIOS-MSI is a powerful tool that can provide new insights into marine chemo-ecology. PMID:26324173

Technical aspects of gel-based proteomics designed for elucidating an aryl hydrocarbon receptor complex.

PubMed

Wada, Yoshinao; Nakano, Norihiko

2004-01-01

The identification of proteins by mass spectrometry has revolutionalized the basic method of identifying proteins constituting an intracellular unit or network for certain biological functions. The gel-based strategy following immunoprecipitation was applied to elucidating proteins associated with the aryl hydrocarbon receptor (AhR). Two hundred femtomoles of AhR was recovered from approximately 2 x 10(7) HepG2 cells by immunoprecipitation and was sufficient for identification by peptide mass fingerprinting. Possible candidates for the AhR-associated proteins were also identified. Improvements of the current strategy to increase the overall sensitivity tenfold are required to clarify the AhR complex in full detail. For example, a combination of trypsin and Achromobacter protease I for in-gel digestion allows the number of missed cleavage sites to be set at zero for database searching, thereby reducing random matches and facilitating identification. There is also room for improvement in each step of sample preparation prior to mass spectrometry.

Quantitative mass spectrometric analysis of glycoproteins combined with enrichment methods.

PubMed

Ahn, Yeong Hee; Kim, Jin Young; Yoo, Jong Shin

2015-01-01

Mass spectrometry (MS) has been a core technology for high sensitive and high-throughput analysis of the enriched glycoproteome in aspects of quantitative assays as well as qualitative profiling of glycoproteins. Because it has been widely recognized that aberrant glycosylation in a glycoprotein may involve in progression of a certain disease, the development of efficient analysis tool for the aberrant glycoproteins is very important for deep understanding about pathological function of the glycoprotein and new biomarker development. This review first describes the protein glycosylation-targeting enrichment technologies mainly employing solid-phase extraction methods such as hydrizide-capturing, lectin-specific capturing, and affinity separation techniques based on porous graphitized carbon, hydrophilic interaction chromatography, or immobilized boronic acid. Second, MS-based quantitative analysis strategies coupled with the protein glycosylation-targeting enrichment technologies, by using a label-free MS, stable isotope-labeling, or targeted multiple reaction monitoring (MRM) MS, are summarized with recent published studies. © 2014 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc.

Laser mass spectrometry of chemical warfare agents using ultrashort laser pulses

NASA Astrophysics Data System (ADS)

Weickhardt, C.; Grun, C.; Grotemeyer, J.

1998-12-01

Fast relaxation processes in excited molecules such as IC, ISC, and fragmentation are observed in many environmentally and technically relevant substances. They cause severe problems to resonance ionization mass spectrometry because they reduce the ionization yield and lead to mass spectra which do not allow the identification of the compound. By the use of ultrashort laser pulses these problems can be overcome and the advantages of REMPI over conventional ionization techniques in mass spectrometry can be regained. This is demonstrated using soil samples contaminated with a chemical warfare agent.

Structure Identification Using High Resolution Mass ...

EPA Pesticide Factsheets

The iCSS CompTox Dashboard is a publicly accessible dashboard provided by the National Center for Computation Toxicology at the US-EPA. It serves a number of purposes, including providing a chemistry database underpinning many of our public-facing projects (e.g. ToxCast and ExpoCast). The available data and searches provide a valuable path to structure identification using mass spectrometry as the source data. With an underlying database of over 720,000 chemicals, the dashboard has already been used to assist in identifying chemicals present in house dust. This poster reviews the benefits of the EPA’s platform and underlying algorithms used for the purpose of compound identification using high-resolution mass spectrometry data. Standard approaches for both mass and formula lookup are available but the dashboard delivers a novel approach for hit ranking based on functional use of the chemicals. The focus on high-quality data, novel ranking approaches and integration to other resources of value to mass spectrometrists makes the CompTox Dashboard a valuable resource for the identification of environmental chemicals. This abstract does not reflect U.S. EPA policy poster presented at the Eastern Analytical Symposium (EAS) held in Somerset, NJ

Bibliometric mapping: eight decades of analytical chemistry, with special focus on the use of mass spectrometry.

PubMed

Waaijer, Cathelijn J F; Palmblad, Magnus

2015-01-01

In this Feature we use automatic bibliometric mapping tools to visualize the history of analytical chemistry from the 1920s until the present. In particular, we have focused on the application of mass spectrometry in different fields. The analysis shows major shifts in research focus and use of mass spectrometry. We conclude by discussing the application of bibliometric mapping and visualization tools in analytical chemists' research.

Mass spectrometry in life science research.

PubMed

Lehr, Stefan; Markgraf, Daniel

2016-12-01

Investigating complex signatures of biomolecules by mass spectrometry approaches has become indispensable in molecular life science research. Nowadays, various mass spectrometry-based omics technologies are available to monitor qualitative and quantitative changes within hundreds or thousands of biological active components, including proteins/peptides, lipids and metabolites. These comprehensive investigations have the potential to decipher the pathophysiology of disease development at a molecular level and to monitor the individual response of pharmacological treatment or lifestyle intervention.

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

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

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).

Analysis of the Mycoplasma bovis lactate dehydrogenase reveals typical enzymatic activity despite the presence of an atypical catalytic site motif.

PubMed

Masukagami, Yumiko; Tivendale, Kelly Anne; Browning, Glenn Francis; Sansom, Fiona Margaret

2018-02-01

The lactate dehydrogenase (LDH) of Mycoplasma genitalium has been predicted to also act as a malate dehydrogenase (MDH), but there has been no experimental validation of this hypothesized dual function for any mollicute. Our analysis of the metabolite profile of Mycoplasma bovis using gas chromatography/mass spectrometry (GC/MS) and liquid chromatography/mass spectrometry (LC/MS) detected malate, suggesting that there may be MDH activity in M. bovis. To investigate whether the putative l-LDH enzyme of M. bovis has a dual function (MDH and LDH), we performed bioinformatic and functional biochemical analyses. Although the amino acid sequence and predicted structural analysis of M. bovisl-LDH revealed unusual residues within the catalytic site, suggesting that it may have the flexibility to possess a dual function, our biochemical studies using recombinant M. bovis -LDH did not detect any MDH activity. However, we did show that the enzyme has typical LDH activity that could be inhibited by both MDH substrates oxaloacetate (OAA) and malate, suggesting that these substrates may be able to bind to M. bovis LDH. Inhibition of the conversion of pyruvate to lactate by OAA may be one method the mycoplasma cell uses to reduce the potential for accumulation of intracellular lactate.

MULTISPECTRAL IDENTIFICATION OF ALKYL AND CHLOROALKYL PHOSPHATES FROM AN INDUSTRIAL EFFLUENT

EPA Science Inventory

Multispectral techniques (gas chromatography combined with low and high resolution electron-impact mass spectrometry, low and high resolution chemical ionization mass spectrometry, and Fourier transform infrared mass spectroscopy) were used to identify 13 alkyl and chloralkyl pho...

The potential of combining ion trap/MS/MS and TOF/MS for identification of emerging contaminants

USGS Publications Warehouse

Ferrer, I.; Furlong, E.T.; Heine, C.E.; Thurman, E.M.

2002-01-01

The use of a method combining ion trap tandem mass spectrometry (MS/MS) and time of flight mass spectrometry (TOF/MS) for identification of emerging contaminates was discussed. The two tools together complemented each other in sensitivity, fragmentation and accurate mass determination. Liquid chromatography/electrospray ionization/ion-trap tandem mass spectrometry (LC/ESI/MS/MS), in positive ion mode of operation, was used to separate and identify specific compounds. Diagnostic fragment ions were obtained for a polyethyleneglycol(PEG) homolog by ion trap MS/MS, and fragments were measured by TOF/MS. It was observed that the combined method gave an exact mass measurement that differed from the calculated mass.

Myofiber metabolic type determination by mass spectrometry imaging.

PubMed

Centeno, Delphine; Vénien, Annie; Pujos-Guillot, Estelle; Astruc, Thierry; Chambon, Christophe; Théron, Laëtitia

2017-08-01

Matrix assisted laser desorption/ionization (MALDI) mass spectrometry imaging is a powerful tool that opens new research opportunities in the field of biology. In this work, predictive model was developed to discriminate metabolic myofiber types using the MALDI spectral data. Rat skeletal muscles are constituted of type I and type IIA fiber, which have an oxidative metabolism for glycogen degradation, and type IIX and type IIB fiber which have a glycolytic metabolism, present in different proportions according to the muscle function and physiological state. So far, myofiber type is determined by histological methods that are time consuming. Thanks to the predictive model, we were able to predict not only the metabolic fiber type but also their location, on the same muscle section that was used for MALDI imaging. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Automated Interpretation and Extraction of Topographic Information from Time of Flight Secondary Ion Mass Spectrometry Data

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

Ievlev, Anton V.; Belianinov, Alexei; Jesse, Stephen

Time of flight secondary ion mass spectrometry (ToF SIMS) is one of the most powerful characterization tools allowing imaging of the chemical properties of various systems and materials. It allows precise studies of the chemical composition with sub-100-nm lateral and nanometer depth spatial resolution. However, comprehensive interpretation of ToF SIMS results is challengeable, because of the data volume and its multidimensionality. Furthermore, investigation of the samples with pronounced topographical features are complicated by the spectral shift. In this work we developed approach for the comprehensive ToF SIMS data interpretation based on the data analytics and automated extraction of the samplemore » topography based on time of flight shift. We further applied this approach to investigate correlation between biological function and chemical composition in Arabidopsis roots.« less

Automated Interpretation and Extraction of Topographic Information from Time of Flight Secondary Ion Mass Spectrometry Data

DOE PAGES

Ievlev, Anton V.; Belianinov, Alexei; Jesse, Stephen; ...

2017-12-06

Time of flight secondary ion mass spectrometry (ToF SIMS) is one of the most powerful characterization tools allowing imaging of the chemical properties of various systems and materials. It allows precise studies of the chemical composition with sub-100-nm lateral and nanometer depth spatial resolution. However, comprehensive interpretation of ToF SIMS results is challengeable, because of the data volume and its multidimensionality. Furthermore, investigation of the samples with pronounced topographical features are complicated by the spectral shift. In this work we developed approach for the comprehensive ToF SIMS data interpretation based on the data analytics and automated extraction of the samplemore » topography based on time of flight shift. We further applied this approach to investigate correlation between biological function and chemical composition in Arabidopsis roots.« less

Proteome-based bacterial identification using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS): A revolutionary shift in clinical diagnostic microbiology.

PubMed

Nomura, Fumio

2015-06-01

Rapid and accurate identification of microorganisms, a prerequisite for appropriate patient care and infection control, is a critical function of any clinical microbiology laboratory. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is a quick and reliable method for identification of microorganisms, including bacteria, yeast, molds, and mycobacteria. Indeed, there has been a revolutionary shift in clinical diagnostic microbiology. In the present review, the state of the art and advantages of MALDI-TOF MS-based bacterial identification are described. The potential of this innovative technology for use in strain typing and detection of antibiotic resistance is also discussed. This article is part of a Special Issue entitled: Medical Proteomics. Copyright © 2014 Elsevier B.V. All rights reserved.

Fourier transform ion cyclotron resonance mass spectrometry

NASA Astrophysics Data System (ADS)

Marshall, Alan G.

1998-06-01

As for Fourier transform infrared (FT-IR) interferometry and nuclear magnetic resonance (NMR) spectroscopy, the introduction of pulsed Fourier transform techniques revolutionized ion cyclotron resonance mass spectrometry: increased speed (factor of 10,000), increased sensitivity (factor of 100), increased mass resolution (factor of 10,000-an improvement not shared by the introduction of FT techniques to IR or NMR spectroscopy), increased mass range (factor of 500), and automated operation. FT-ICR mass spectrometry is the most versatile technique for unscrambling and quantifying ion-molecule reaction kinetics and equilibria in the absence of solvent (i.e., the gas phase). In addition, FT-ICR MS has the following analytically important features: speed (~1 second per spectrum); ultrahigh mass resolution and ultrahigh mass accuracy for analysis of mixtures and polymers; attomole sensitivity; MSn with one spectrometer, including two-dimensional FT/FT-ICR/MS; positive and/or negative ions; multiple ion sources (especially MALDI and electrospray); biomolecular molecular weight and sequencing; LC/MS; and single-molecule detection up to 108 Dalton. Here, some basic features and recent developments of FT-ICR mass spectrometry are reviewed, with applications ranging from crude oil to molecular biology.

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

PubMed

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

2006-08-01

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

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.

Mass Spectrometry in the Home and Garden

NASA Astrophysics Data System (ADS)

Pulliam, Christopher J.; Bain, Ryan M.; Wiley, Joshua S.; Ouyang, Zheng; Cooks, R. Graham

2015-02-01

Identification of active components in a variety of chemical products used directly by consumers is described at both trace and bulk levels using mass spectrometry. The combination of external ambient ionization with a portable mass spectrometer capable of tandem mass spectrometry provides high chemical specificity and sensitivity as well as allowing on-site monitoring. These experiments were done using a custom-built portable ion trap mass spectrometer in combination with the ambient ionization methods of paper spray, leaf spray, and low temperature plasma ionization. Bactericides, garden chemicals, air fresheners, and other products were examined. Herbicide applied to suburban lawns was detected in situ on single leaves 5 d after application.

Atmospheric Oxidation of Squalene: Molecular Study Using COBRA Modeling and High-Resolution Mass Spectrometry

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

Fooshee, David R.; Aiona, Paige K.; Laskin, Alexander

2015-10-22

Squalene is a major component of skin and plant surface lipids, and is known to be present at high concentrations in indoor dust. Its high reactivity toward ozone makes it an important ozone sink and a natural protectant against atmospheric oxidizing agents. While the volatile products of squalene ozonolysis are known, the condensed-phase products have not been characterized. We present an analysis of condensed-phase products resulting from an extensive oxidation of squalene by ozone probed by electrospray ionization (ESI) high-resolution mass spectrometry (HR-MS). A complex distribution of nearly 1,300 peaks assignable to molecular formulas is observed in direct infusion positivemore » ion mode ESI mass spectra. The distribution of peaks in the mass spectra suggests that there are extensive cross-coupling reactions between hydroxy-carbonyl products of squalene ozonolysis. To get additional insights into the mechanism, we apply a Computational Brewing Application (COBRA) to simulate the oxidation of squalene in the presence of ozone, and compare predicted results with those observed by the HR-MS experiments. The system predicts over one billion molecular structures between 0-1450 Da, which correspond to about 27,000 distinct elemental formulas. Over 83% of the squalene oxidation products inferred from the mass spectrometry data are matched by the simulation. Simulation indicates a prevalence of peroxy groups, with hydroxyl and ether groups being the second-most important O-containing functional groups formed during squalene oxidation. These highly oxidized products of squalene ozonolysis may accumulate on indoor dust and surfaces, and contribute to their redox capacity.« less

Clinical review: improving the measurement of serum thyroglobulin with mass spectrometry.

PubMed

Hoofnagle, Andrew N; Roth, Mara Y

2013-04-01

Serum thyroglobulin (Tg) measurements are central to the management of patients treated for differentiated thyroid carcinoma. For decades, Tg measurements have relied on methods that are subject to interference by commonly found substances in human serum and plasma, such as Tg autoantibodies. As a result, many patients need additional imaging studies to rule out cancer persistence or recurrence that could be avoided with more sensitive and specific testing methods. The aims of this review are to: 1) briefly review the interferences common to Tg immunoassays; 2) introduce readers to liquid chromatography-tandem mass spectrometry as a method for quantifying proteins in human serum/plasma; and 3) discuss the potential benefits and limitations of the method in the quantification of serum Tg. Mass spectrometric methods have traditionally lacked the sensitivity, robustness, and throughput to be useful clinical assays. These methods failed to meet the necessary clinical benchmarks due to the nature of the mass spectrometry workflow and instrumentation. Over the past few years, there have been major advances in reagents, automation, and instrumentation for the quantification of proteins using mass spectrometry. More recently, methods using mass spectrometry to detect and quantify Tg have been developed and are of sufficient quality to be used in the management of patients. Novel serum Tg assays that use mass spectrometry may avoid the issue of autoantibody interference and other problems with currently available immunoassays for Tg. Prospective studies are needed to fully understand the potential benefits of novel Tg assays to patients and care providers.

COMPARATIVE EVALUATION OF GC/MS (GAS CHROMATOGRAPHY/MASS SPECTROMETRY) DATA ANALYSIS PROCESSING

EPA Science Inventory

Mass spectra obtained by fused silica capillary gas chromatography/mass spectrometry/data system (GC/MS/DS) analysis of mixtures of organic chemicals adsorbed on Tenax GC cartridges was subjected to manual and automated interpretative techniques. Synthetic mixtures (85 chemicals ...

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...

ANALYSIS OF POLYCYCLIC AROMATIC HYDROCARBONS BY ION TRAP TANDEM MASS SPECTROMETRY

EPA Science Inventory

An ion-trap mass spectrometer with a wave board and tandem mass spectrometry software was used to analyze gas chromatographically separated polycyclic aromatic hydrocarbons (PAHs) by using collision-induced dissociation (CID). The nonresonant (multiple collision) mode was used to...

NEGATIVE-ION MASS SPECTROMETRY OF SULFONYLUREA HERBICIDES

EPA Science Inventory

Sulfonylurea herbicides have been studied using neg-ion desorption chem.-ionization (DCI) mass spectrometry (MS) and DCI-MS/MS techniques. Both {M-H]- and M.- ions were obsd. in the DCI mass spectra. The collisonally activated dissocn. (CAD) spectra were characteristic of the str...

Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry.

PubMed

Röst, Hannes L; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars

2015-01-01

In mass spectrometry-based proteomics, XML formats such as mzML and mzXML provide an open and standardized way to store and exchange the raw data (spectra and chromatograms) of mass spectrometric experiments. These file formats are being used by a multitude of open-source and cross-platform tools which allow the proteomics community to access algorithms in a vendor-independent fashion and perform transparent and reproducible data analysis. Recent improvements in mass spectrometry instrumentation have increased the data size produced in a single LC-MS/MS measurement and put substantial strain on open-source tools, particularly those that are not equipped to deal with XML data files that reach dozens of gigabytes in size. Here we present a fast and versatile parsing library for mass spectrometric XML formats available in C++ and Python, based on the mature OpenMS software framework. Our library implements an API for obtaining spectra and chromatograms under memory constraints using random access or sequential access functions, allowing users to process datasets that are much larger than system memory. For fast access to the raw data structures, small XML files can also be completely loaded into memory. In addition, we have improved the parsing speed of the core mzML module by over 4-fold (compared to OpenMS 1.11), making our library suitable for a wide variety of algorithms that need fast access to dozens of gigabytes of raw mass spectrometric data. Our C++ and Python implementations are available for the Linux, Mac, and Windows operating systems. All proposed modifications to the OpenMS code have been merged into the OpenMS mainline codebase and are available to the community at https://github.com/OpenMS/OpenMS.

Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry

PubMed Central

Röst, Hannes L.; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars

2015-01-01

Motivation In mass spectrometry-based proteomics, XML formats such as mzML and mzXML provide an open and standardized way to store and exchange the raw data (spectra and chromatograms) of mass spectrometric experiments. These file formats are being used by a multitude of open-source and cross-platform tools which allow the proteomics community to access algorithms in a vendor-independent fashion and perform transparent and reproducible data analysis. Recent improvements in mass spectrometry instrumentation have increased the data size produced in a single LC-MS/MS measurement and put substantial strain on open-source tools, particularly those that are not equipped to deal with XML data files that reach dozens of gigabytes in size. Results Here we present a fast and versatile parsing library for mass spectrometric XML formats available in C++ and Python, based on the mature OpenMS software framework. Our library implements an API for obtaining spectra and chromatograms under memory constraints using random access or sequential access functions, allowing users to process datasets that are much larger than system memory. For fast access to the raw data structures, small XML files can also be completely loaded into memory. In addition, we have improved the parsing speed of the core mzML module by over 4-fold (compared to OpenMS 1.11), making our library suitable for a wide variety of algorithms that need fast access to dozens of gigabytes of raw mass spectrometric data. Availability Our C++ and Python implementations are available for the Linux, Mac, and Windows operating systems. All proposed modifications to the OpenMS code have been merged into the OpenMS mainline codebase and are available to the community at https://github.com/OpenMS/OpenMS. PMID:25927999

Mass spectrometric screening and identification of acidic metabolites in fulvic acid fractions of contaminated groundwater.

PubMed

Jobelius, Carsten; Frimmel, Fritz H; Zwiener, Christian

2014-05-01

The anaerobic microbial degradation of aromatic and heterocyclic compounds is a prevalent process in contaminated groundwater systems. The introduction of functional groups into the contaminant molecules often results in aromatic and heterocyclic and succinic acids. These metabolites can be used as indicators for prevailing degradation processes. Therefore, there is a strong interest in developing analytical methods for screening and identification of these metabolites. In this study, neutral loss scans (NLS) by liquid chromatography-electrospray ionization/tandem mass spectrometry with losses of CO2 (NL ∆m/z = 44) and C2H4(CO2)2 (NL ∆m/z = 116) were applied for the first time successfully to screen selectively for acidic and succinic metabolites of aromatic and heterocyclic contaminants in two fulvic acid fractions from a contaminated site and a downstream region of a tar oil-polluted groundwater. Identification of these preselected signals was performed by high-resolution mass spectrometry with a liquid chromatography-electrospray ionization quadrupole time-of-flight mass spectrometry instrument. High-resolution mass and mass fragmentation data were then compared with a list of known metabolites from a literature search or matched with chemical databases supported with in silico fragmentation. Based on authentic analytical standards, several compounds from NLS were identified (e.g., 4-hydroxy-3-methylbenzoic acid, benzylsuccinic acid, naphthyl-2-methylsuccinic acid, 2-carboxyindane, and 2-carboxybenzothiophene) and tentatively identified (e.g., benzofuranmethylsuccinic acid and dihydrocarboxybenzothiophene) as aromatic, phenolic, heterocyclic, and succinic acids. The acidic metabolites were found exclusively in the contaminated region of the aquifer which indicates active biodegradation processes and no relevant occurrence of acidic metabolites in the downstream region.

Mass spectrometric determination of early and advanced glycation in biology.

PubMed

Rabbani, Naila; Ashour, Amal; Thornalley, Paul J

2016-08-01

Protein glycation in biological systems occurs predominantly on lysine, arginine and N-terminal residues of proteins. Major quantitative glycation adducts are found at mean extents of modification of 1-5 mol percent of proteins. These are glucose-derived fructosamine on lysine and N-terminal residues of proteins, methylglyoxal-derived hydroimidazolone on arginine residues and N(ε)-carboxymethyl-lysine residues mainly formed by the oxidative degradation of fructosamine. Total glycation adducts of different types are quantified by stable isotopic dilution analysis liquid chromatography-tandem mass spectrometry (LC-MS/MS) in multiple reaction monitoring mode. Metabolism of glycated proteins is followed by LC-MS/MS of glycation free adducts as minor components of the amino acid metabolome. Glycated proteins and sites of modification within them - amino acid residues modified by the glycating agent moiety - are identified and quantified by label-free and stable isotope labelling with amino acids in cell culture (SILAC) high resolution mass spectrometry. Sites of glycation by glucose and methylglyoxal in selected proteins are listed. Key issues in applying proteomics techniques to analysis of glycated proteins are: (i) avoiding compromise of analysis by formation, loss and relocation of glycation adducts in pre-analytic processing; (ii) specificity of immunoaffinity enrichment procedures, (iii) maximizing protein sequence coverage in mass spectrometric analysis for detection of glycation sites, and (iv) development of bioinformatics tools for prediction of protein glycation sites. Protein glycation studies have important applications in biology, ageing and translational medicine - particularly on studies of obesity, diabetes, cardiovascular disease, renal failure, neurological disorders and cancer. Mass spectrometric analysis of glycated proteins has yet to find widespread use clinically. Future use in health screening, disease diagnosis and therapeutic monitoring, and drug and functional food development is expected. A protocol for high resolution mass spectrometry proteomics of glycated proteins is given.

Rapid high-throughput characterisation, classification and selection of recombinant mammalian cell line phenotypes using intact cell MALDI-ToF mass spectrometry fingerprinting and PLS-DA modelling.

PubMed

Povey, Jane F; O'Malley, Christopher J; Root, Tracy; Martin, Elaine B; Montague, Gary A; Feary, Marc; Trim, Carol; Lang, Dietmar A; Alldread, Richard; Racher, Andrew J; Smales, C Mark

2014-08-20

Despite many advances in the generation of high producing recombinant mammalian cell lines over the last few decades, cell line selection and development is often slowed by the inability to predict a cell line's phenotypic characteristics (e.g. growth or recombinant protein productivity) at larger scale (large volume bioreactors) using data from early cell line construction at small culture scale. Here we describe the development of an intact cell MALDI-ToF mass spectrometry fingerprinting method for mammalian cells early in the cell line construction process whereby the resulting mass spectrometry data are used to predict the phenotype of mammalian cell lines at larger culture scale using a Partial Least Squares Discriminant Analysis (PLS-DA) model. Using MALDI-ToF mass spectrometry, a library of mass spectrometry fingerprints was generated for individual cell lines at the 96 deep well plate stage of cell line development. The growth and productivity of these cell lines were evaluated in a 10L bioreactor model of Lonza's large-scale (up to 20,000L) fed-batch cell culture processes. Using the mass spectrometry information at the 96 deep well plate stage and phenotype information at the 10L bioreactor scale a PLS-DA model was developed to predict the productivity of unknown cell lines at the 10L scale based upon their MALDI-ToF fingerprint at the 96 deep well plate scale. This approach provides the basis for the very early prediction of cell lines' performance in cGMP manufacturing-scale bioreactors and the foundation for methods and models for predicting other mammalian cell phenotypes from rapid, intact-cell mass spectrometry based measurements. Copyright © 2014 Elsevier B.V. All rights reserved.

Mass Defect from Nuclear Physics to Mass Spectral Analysis.

PubMed

Pourshahian, Soheil

2017-09-01

Mass defect is associated with the binding energy of the nucleus. It is a fundamental property of the nucleus and the principle behind nuclear energy. Mass defect has also entered into the mass spectrometry terminology with the availability of high resolution mass spectrometry and has found application in mass spectral analysis. In this application, isobaric masses are differentiated and identified by their mass defect. What is the relationship between nuclear mass defect and mass defect used in mass spectral analysis, and are they the same? Graphical Abstract ᅟ.

Surface analysis of lipids by mass spectrometry: more than just imaging.

PubMed

Ellis, Shane R; Brown, Simon H; In Het Panhuis, Marc; Blanksby, Stephen J; Mitchell, Todd W

2013-10-01

Mass spectrometry is now an indispensable tool for lipid analysis and is arguably the driving force in the renaissance of lipid research. In its various forms, mass spectrometry is uniquely capable of resolving the extensive compositional and structural diversity of lipids in biological systems. Furthermore, it provides the ability to accurately quantify molecular-level changes in lipid populations associated with changes in metabolism and environment; bringing lipid science to the "omics" age. The recent explosion of mass spectrometry-based surface analysis techniques is fuelling further expansion of the lipidomics field. This is evidenced by the numerous papers published on the subject of mass spectrometric imaging of lipids in recent years. While imaging mass spectrometry provides new and exciting possibilities, it is but one of the many opportunities direct surface analysis offers the lipid researcher. In this review we describe the current state-of-the-art in the direct surface analysis of lipids with a focus on tissue sections, intact cells and thin-layer chromatography substrates. The suitability of these different approaches towards analysis of the major lipid classes along with their current and potential applications in the field of lipid analysis are evaluated. Copyright © 2013 Elsevier Ltd. All rights reserved.

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.

Developments in Plasma-Source Mass Spectrometry

DTIC Science & Technology

1988-07-11

Spectrometry 12 PERSONAL AUTHOR(S) Gary M. Hieftje and George H. Vickers 13a. TYPE OF REPORT b.TMCOEE . TEO POTYerMohay 5.AGCUN Technical FROM TO 11 July...4134006 TECHNICAL REPORT NO. 41 DEVELOPMENTS IN PLASMA-SOURCE MASS SPECTROMETRY by Gary M. Hieftje and George H. Vickers Acessoo i or * NTIS GRMX Prepared...G. M. Hieftje , and A. T. Zander, Spectrochim. Acta 1987, 42B, 29 60 Determination of Lead Isotope Ratios by Inductively Coupled Plasma-Mass

Assessment of Non-traditional Isotopic Ratios by Mass Spectrometry for Analysis of Nuclear Activities. Annual Report 2011

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

Biegalski, Steven R.; Buchholz, Bruce A.

2011-08-24

The objective of this work is to identify isotopic ratios suitable for analysis via mass spectrometry that distinguish between commercial nuclear reactor fuel cycles, fuel cycles for weapons grade plutonium, and products from nuclear weapons explosions. Methods will also be determined to distinguish the above from medical and industrial radionuclide sources. Mass spectrometry systems will be identified that are suitable for field measurement of such isotopes in an expedient manner.

Protein denaturation improves enzymatic digestion efficiency for direct tissue analysis using mass spectrometry

NASA Astrophysics Data System (ADS)

Setou, M.; Hayasaka, T.; Shimma, S.; Sugiura, Y.; Matsumoto, M.

2008-12-01

Molecular identification using high-sensitivity tandem mass spectrometry is essential for protein analysis on the tissue surface. Here we report an improved digestion protocol for protein identification directly on the tissue surface using mass spectrometry. By denaturation process and the use of detergent-supplemented trypsin solution, we could successfully detect and identify many molecules such as tubulin, neurofilament, and synaptosomal-associated 25 kDa protein directly from a mouse cerebellum section.

Subcellular analysis by laser ablation electrospray ionization mass spectrometry

DOEpatents

Vertes, Akos; Stolee, Jessica A; Shrestha, Bindesh

2014-12-02

In various embodiments, a method of laser ablation electrospray ionization mass spectrometry (LAESI-MS) may generally comprise micro-dissecting a cell comprising at least one of a cell wall and a cell membrane to expose at least one subcellular component therein, ablating the at least one subcellular component by an infrared laser pulse to form an ablation plume, intercepting the ablation plume by an electrospray plume to form ions, and detecting the ions by mass spectrometry.

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.

Profiling the metabolic signals involved in chemical communication between microbes using imaging mass spectrometry.

PubMed

Stasulli, Nikolas M; Shank, Elizabeth A

2016-11-01

The ability of microbes to secrete bioactive chemical signals into their environment has been known for over a century. However, it is only in the last decade that imaging mass spectrometry has provided us with the ability to directly visualize the spatial distributions of these microbial metabolites. This technology involves collecting mass spectra from multiple discrete locations across a biological sample, yielding chemical ‘maps’ that simultaneously reveal the distributions of hundreds of metabolites in two dimensions. Advances in microbial imaging mass spectrometry summarized here have included the identification of novel strain- or coculture-specific compounds, the visualization of biotransformation events (where one metabolite is converted into another by a neighboring microbe), and the implementation of a method to reconstruct the 3D subsurface distributions of metabolites, among others. Here we review the recent literature and discuss how imaging mass spectrometry has spurred novel insights regarding the chemical consequences of microbial interactions.

Applications of Mass Spectrometry to Structural Analysis of Marine Oligosaccharides

PubMed Central

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

2014-01-01

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

Two competing ionization processes in ESI-MS analysis of N-(1,3-diphenylallyl)benzenamines: formation of the unusual [M-H]+ ion versus the regular [M+H]+ ion.

PubMed

Fang, Liwen; Dong, Cheng; Guo, Cheng; Xu, Jianxing; Liu, Qiaoling; Qu, Zhirong; Jiang, Kezhi

2018-06-01

A series of N-(1,3-diphenylallyl)benzenamine derivatives (M) were investigated by electrospray ionization mass spectrometry in the positive-ion mode. Both the anomalous [M-H] + and the regular [M+H] + were observed in the ESI mass spectra. The occurrence of [M-H] + has been supported by accurate mass spectrometry, liquid chromatography mass spectrometry, and tandem mass spectrometry analysis. Calculation results indicated that formation of [M-H] + is attributed to the ion-molecule reaction of M with the protonated ESI solvent molecule (e.g. CH 3 OH 2 + ) via hydride abstraction from a tertiary C sp3 -H. The competing ionization processes leading to [M-H] + or [M+H] + were significantly affected by the concentration of formic acid in the electrospray ionization solvent and the proton affinity of the N atom.

Electrospray and MALDI mass spectrometry in the identification of spermicides in criminal investigations.

PubMed

Hollenbeck, T P; Siuzdak, G; Blackledge, R D

1999-07-01

Electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry have been used to examine evidence in a sexual assault investigation. Because condoms are being used increasingly by sexual assailants and some condom brands include the spermicide nonoxynol-9 (nonylphenoxy polyethoxyethanol) in the lubricant formulation, the recovery, and identification of nonoxynol-9 from evidence items may assist in proving corpus delicti. A method was developed for the recovery of nonoxynol-9 from internal vaginal swabs and for its identification by reverse phase liquid chromatography/electrospray ionization mass spectrometry (LC ESI-MS), nanoelectrospray ionization (nanoESI) mass spectrometry, and high resolution MALDI Fourier transform mass spectrometry (MALDI-FTMS). The method was tested on extracts from precoitus, immediate postcoitus, and four-hours postcoitus vaginal swabs provided by a volunteer whose partner does not normally use condoms, but for this trial used a condom having a water-soluble gel-type lubricant that includes 5% nonoxynol-9 in its formulation. Subsequently, LC ESI-MS was used to identify traces of nonoxynol-9 from the internal vaginal swab of a victim of a sexual assault.

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

Recent developments in cyanide detection: A review

PubMed Central

Ma, Jian; Dasgupta, Purnendu K.

2010-01-01

The extreme toxicity of cyanide and environmental concerns from its continued industrial use continue to generate interest in facile and sensitive methods for cyanide detection. In recent years there is also additional recognition of HCN toxicity from smoke inhalation and potential use of cyanide as a weapon of terrorism. This review summarizes the literature since 2005 on cyanide measurement in different matrices ranging from drinking water and wastewater, to cigarette smoke and exhaled breath to biological fluids like blood, urine and saliva. The dramatic increase in the number of publications on cyanide measurement is indicative of the great interest in this field not only from analytical chemists, but also researchers from diverse environmental, medical, forensic and clinical arena. The recent methods cover both established and emerging analytical disciplines and include naked eye visual detection, spectrophotometry/colorimetry, capillary electrophoresis with optical absorbance detection, fluorometry, chemiluminescence, near-infrared cavity ring down spectroscopy, atomic absorption spectrometry, electrochemical methods (potentiometry/amperometry/ion chromatography-pulsed amperometry), mass spectrometry (selected ion flow tube mass spectrometry, electrospray ionization mass spectrometry, gas chromatography-mass spectrometry), gas chromatography (nitrogen phosphorus detector, electron capture detector) and quartz crystal mass monitors. PMID:20599024

[Separation and identification of 5 glycosidic flavor precursors in tobacco by ultra performance liquid chromatography-electrospray ionization tandem mass spectrometry].

PubMed

Wu, Xinhua; Zhu, Ruizhi; Ren, Zhuoying; Wang, Kai; Mou, Dingrong; Wei, Wanzhi; Miao, Mingming

2009-11-01

A qualitative method for the identification of 5 main glycosidic flavor precursors in tobacco was developed by using ultra performance liquid chromatography-electrospray ionization tandem mass spectrometry (UPLC-ESI MS/MS) and gas chromatography-mass spectrometry (GC-MS). The glycosidic flavor precursors in tobacco were extracted with methanol, cleaned up with an XAD-2 column. The aglycones were later released by enzyme-mediated hydrolysis under the condition of pH 5. The 5 volatile aglycone moieties were identified by GC-MS standard spectra library. The precursor ions of glycosides were determined by using electrospray ionization mass spectrometry in negative ion mode, then the 5 glycosidic flavor precursors were identified by using product ion scan (MS2) finally, using UPLC-ESI MS/MS, separation and identification of 5 glycosidic flavor precursors were accomplished on an RP-C,8 column in the multiple reaction monitoring (MRM) mode by using methanol and acetic acid-ammonium acetate aqueous solution as eluent. This work lays a foundation for the analysis of glycosidic flavor precursors without the standards by using liquid chromatography-mass spectrometry.

Electrochemistry coupled online to liquid chromatography-mass spectrometry for fast simulation of biotransformation reactions of the insecticide chlorpyrifos.

PubMed

Mekonnen, Tessema F; Panne, Ulrich; Koch, Matthias

2017-05-01

An automated method is presented for fast simulation of (bio)transformation products (TPs) of the organophosphate insecticide chlorpyrifos (CPF) based on electrochemistry coupled online to liquid chromatography-mass spectrometry (EC-LC-MS). Oxidative TPs were produced by a boron doped diamond (BDD) electrode, separated by reversed phase HPLC and online detected by electrospray ionization-mass spectrometry (ESI-MS). Furthermore, EC oxidative TPs were investigated by HPLC-tandem mass spectrometry (LC-MS/MS) and FT-ICR high resolution mass spectrometry (HRMS) and compared to in vitro assay metabolites (rat and human liver microsomes). Main phase I metabolites of CPF: chlorpyrifos oxon (CPF oxon), trichloropyridinol (TCP), diethylthiophosphate (DETP), diethylphosphate (DEP), desethyl chlorpyrifos (De-CPF), and desethyl chlorpyrifos oxon (De-CPF oxon), were successfully identified by the developed EC-LC-MS method. The EC-LC-MS method showed similar metabolites compared to the in vitro assay with possibilities of determining reactive species. Our results reveal that online EC-(LC)-MS brings an advantage on time of analysis by eliminating sample preparation steps and matrix complexity compared to conventional in vivo or in vitro methods.

Affinity purification mass spectrometry analysis of PD-1 uncovers SAP as a new checkpoint inhibitor.

PubMed

Peled, Michael; Tocheva, Anna S; Sandigursky, Sabina; Nayak, Shruti; Philips, Elliot A; Nichols, Kim E; Strazza, Marianne; Azoulay-Alfaguter, Inbar; Askenazi, Manor; Neel, Benjamin G; Pelzek, Adam J; Ueberheide, Beatrix; Mor, Adam

2018-01-16

Programmed cell death-1 (PD-1) is an essential inhibitory receptor in T cells. Antibodies targeting PD-1 elicit durable clinical responses in patients with multiple tumor indications. Nevertheless, a significant proportion of patients do not respond to anti-PD-1 treatment, and a better understanding of the signaling pathways downstream of PD-1 could provide biomarkers for those whose tumors respond and new therapeutic approaches for those whose tumors do not. We used affinity purification mass spectrometry to uncover multiple proteins associated with PD-1. Among these proteins, signaling lymphocytic activation molecule-associated protein (SAP) was functionally and mechanistically analyzed for its contribution to PD-1 inhibitory responses. Silencing of SAP augmented and overexpression blocked PD-1 function. T cells from patients with X-linked lymphoproliferative disease (XLP), who lack functional SAP, were hyperresponsive to PD-1 signaling, confirming its inhibitory role downstream of PD-1. Strikingly, signaling downstream of PD-1 in purified T cell subsets did not correlate with PD-1 surface expression but was inversely correlated with intracellular SAP levels. Mechanistically, SAP opposed PD-1 function by acting as a molecular shield of key tyrosine residues that are targets for the tyrosine phosphatase SHP2, which mediates PD-1 inhibitory properties. Our results identify SAP as an inhibitor of PD-1 function and SHP2 as a potential therapeutic target in patients with XLP.

Evidence for lysine acetylation in the coat protein of a Polerovirus

USDA-ARS?s Scientific Manuscript database

Virions of the RPV strain of Cereal yellow dwarf virus (CYDV-RPV) were purified from infected oat tissue and analyzed by mass spectrometry. Two conserved residues, K147 and K181, residing in the virus coat protein, were confidently identified to contain epsilon-N-acetyl groups. While no functional ...

Identification and verification of hybridoma-derived monoclonal antibody variable region sequences using recombinant DNA technology and mass spectrometry

USDA-ARS?s Scientific Manuscript database

Antibody engineering requires the identification of antigen binding domains or variable regions (VR) unique to each antibody. It is the VR that define the unique antigen binding properties and proper sequence identification is essential for functional evaluation and performance of recombinant antibo...

Chemical profiling of two congeneric sea mat corals along the Brazilian coast: adaptive and functional patterns.

PubMed

Costa-Lotufo, L V; Carnevale-Neto, F; Trindade-Silva, A E; Silva, R R; Silva, G G Z; Wilke, D V; Pinto, F C L; Sahm, B D B; Jimenez, P C; Mendonça, J N; Lotufo, T M C; Pessoa, O D L; Lopes, N P

2018-02-20

Metabolomic profiles were explored to understand environmental and taxonomic influences on the metabolism of two congeneric zoanthids, Palythoa caribaeorum and P. variabilis, collected across distinct geographical ranges. Integrated mass spectrometry data suggested the major influence of geographical location on chemical divergence when compared to species differentiation.

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

DOE PAGES

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

2016-05-10

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

Preparation, IR spectroscopy, and time-of-flight mass spectrometry of halogenated and methylated Si(111)

NASA Astrophysics Data System (ADS)

Salingue, Nils; Hess, Peter

2011-09-01

The preparation of chlorine-, bromine-, and iodine-terminated silicon surfaces (Si(111):Cl, Br, and I) using atomically flat Si(111)-(1×1):H is described. The halogenated surfaces were obtained by photochemically induced radical substitution reactions with the corresponding dihalogen in a Schlenk tube by conventional inert gas chemistry. The nucleophilic substitution of the Si-Cl functionality with the Grignard reagent (CH3MgCl) resulted in the unreconstructed methylated Si(111)-(1×1):CH3 surface. The halogenated and methylated silicon surfaces were characterized by Fourier transform infrared (FTIR) spectroscopy and laser-induced desorption of monolayers (LIDOM). Calibration of the desorption temperature via analysis of time-of-flight (TOF) distributions as a function of laser fluence allowed the determination of the originally emitted neutral fragments by TOF mass spectrometry using electron-impact ionization. The halogens were desorbed atomically and as SiX n (X = Cl, Br) clusters. The methyl groups mainly desorbed as methyl and ethyl fragments and a small amount of +SiCH3.

Gas chromatography-mass spectrometry of biofluids and extracts.

PubMed

Emwas, Abdul-Hamid M; Al-Talla, Zeyad A; Yang, Yang; Kharbatia, Najeh M

2015-01-01

Gas chromatography-mass spectrometry (GC-MS) has been widely used in metabonomics analyses of biofluid samples. Biofluids provide a wealth of information about the metabolism of the whole body and from multiple regions of the body that can be used to study general health status and organ function. Blood serum and blood plasma, for example, can provide a comprehensive picture of the whole body, while urine can be used to monitor the function of the kidneys, and cerebrospinal fluid (CSF) will provide information about the status of the brain and central nervous system (CNS). Different methods have been developed for the extraction of metabolites from biofluids, these ranging from solvent extracts, acids, heat denaturation, and filtration. These methods vary widely in terms of efficiency of protein removal and in the number of metabolites extracted. Consequently, for all biofluid-based metabonomics studies, it is vital to optimize and standardize all steps of sample preparation, including initial extraction of metabolites. In this chapter, recommendations are made of the optimum experimental conditions for biofluid samples for GC-MS, with a particular focus on blood serum and plasma samples.

Influence of geosmin-producing Streptomyces on the growth and volatile metabolites of yeasts during chinese liquor fermentation.

PubMed

Du, Hai; Lu, Hu; Xu, Yan

2015-01-14

Diverse Streptomyces species act as geosmin producers in the Chinese liquor-making process, causing an earthy, off-odor containment. Through microbiological and metabolite analyses, this paper investigates the influence of several geosmin-producing Streptomyces on the microbial community of a brewing system. The antifungal activity against functional liquor-brewing microbes was assayed by an agar diffusion method. Several Streptomyces, most notably Streptomyces sampsonii QC-2, inhibited the growth of the brewing functional yeasts and molds in pure culture. In a simulated coculture, Streptomyces spp. reduced the flavor compounds (alcohols and esters) contributed by yeasts. Nine components in Streptomyces sampsonii QC-2 broth were detected by ultraperformance liquid chromatography coupled with photo diode array (UPLC–PDA), with characteristic ultraviolet absorptions at 360, 380, and 400 nm. The main products of Streptomyces sampsonii QC-2 were identified by ultraperformance liquid chromatography–quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF–MS/MS), and confirmed by standard mass spectrometry. The antifungal active components were revealed as a series of heptaene macrolide antibiotics.

A proteomics method using immunoaffinity fluorogenic derivatization-liquid chromatography/tandem mass spectrometry (FD-LC-MS/MS) to identify a set of interacting proteins.

PubMed

Nakata, Katsunori; Saitoh, Ryoichi; Ishigai, Masaki; Imai, Kazuhiro

2018-02-01

Biological functions in organisms are usually controlled by a set of interacting proteins, and identifying the proteins that interact is useful for understanding the mechanism of the functions. Immunoprecipitation is a method that utilizes the affinity of an antibody to isolate and identify the proteins that have interacted in a biological sample. In this study, the FD-LC-MS/MS method, which involves fluorogenic derivatization followed by separation and quantification by HPLC and finally identification of proteins by HPLC-tandem mass spectrometry, was used to identify proteins in immunoprecipitated samples, using heat shock protein 90 (HSP90) as a model of an interacting protein in HepaRG cells. As a result, HSC70 protein, which was known to form a complex with HSP90, was isolated, together with three different types of HSP90-beta. The results demonstrated that the proposed immunoaffinity-FD-LC-MS/MS method could be useful for simultaneously detecting and identifying the proteins that interact with a certain protein. Copyright © 2017 John Wiley & Sons, Ltd.

Influence of fermentable carbohydrates or protein on large intestinal and urinary metabolomic profiles in piglets.

PubMed

Pieper, R; Neumann, K; Kröger, S; Richter, J F; Wang, J; Martin, L; Bindelle, J; Htoo, J K; Vahjen, V; Van Kessel, A G; Zentek, J

2012-12-01

It was recently shown that variations in the ratio of dietary fermentable carbohydrates (fCHO) and fermentable protein (fCP) differentially affect large intestinal microbial ecology and the mucosal response. Here we investigated the use of mass spectrometry to profile changes in metabolite composition in colon and urine associated with variation in dietary fCHO and fCP composition and mucosal physiology. Thirty-two weaned piglets were fed 4 diets in a 2 × 2 factorial design with low fCP and low fCHO, low fCP and high fCHO, high fCP and low fCHO, and high fCP and high fCHO. After 21 to 23 d, all pigs were euthanized and colon digesta and urine metabolite profiles were obtained by mass spectrometry. Analysis of mass spectra by partial least squares approach indicated a clustering of both colonic and urinary profiles for each pig by feeding group. Metabolite identification and annotation using the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways revealed increased abundance of metabolites associated with arachidonic acid metabolism in colon of pigs fed a high concentration of fCP irrespective of dietary fCHO. Urinary metabolites did not show as clear patterns. Mass spectrometry can effectively differentiate metabolite profiles in colon contents and urine associated with changes in dietary composition. Whether metabolite profiling is an effective tool to identify specific metabolites (biomarkers) or metabolite profiles associated with gut function and integrity needs further elucidation.

Characterization of Breast Cancer Interstitial Fluids by TmT Labeling, LTQ-Orbitrap Velos Mass Spectrometry and Pathway Analysis

PubMed Central

Cinzia, Raso; Carlo, Cosentino; Marco, Gaspari; Natalia, Malara; Xuemei, Han; Daniel, McClatchy; Kyu, Park Sung; Maria, Renne; Nuria, Vadalà; Ubaldo, Prati; Giovanni, Cuda; Vincenzo, Mollace; Francesco, Amato; Yates, John R.

2012-01-01

Cancer is currently considered as the end point of numerous genomic and epigenomic mutations and as the result of the interaction of transformed cells within the stromal microenvironment. The present work focuses on breast cancer, one of the most common malignancies affecting the female population in industrialized countries. In this study we perform a proteomic analysis of bioptic samples from human breast cancer, namely interstitial fluids and primary cells, normal vs disease tissues, using Tandem mass Tags (TmT) quantitative mass spectrometry combined with the MudPIT technique. To the best of our knowledge this work, with over 1700 proteins identified, represents the most comprehensive characterization of the breast cancer interstitial fluid proteome to date. Network analysis was used to identify functionally active networks in the breast cancer associated samples. From the list of differentially expressed genes we have retrieved the associated functional interaction networks. Many different signaling pathways were found activated, strongly linked to invasion, metastasis development, proliferation and with a significant cross-talking rate. This pilot study presents evidence that the proposed quantitative proteomic approach can be applied to discriminate between normal and tumoral samples and for the discovery of yet unknown carcinogenesis mechanisms and therapeutic strategies. PMID:22563702

A Catalog of Proteins Expressed in the AG Secreted Fluid during the Mature Phase of the Chinese Mitten Crabs (Eriocheir sinensis)

PubMed Central

He, Lin; Li, Qing; Liu, Lihua; Wang, Yuanli; Xie, Jing; Yang, Hongdan; Wang, Qun

2015-01-01

The accessory gland (AG) is an important component of the male reproductive system of arthropods, its secretions enhance fertility, some AG proteins bind to the spermatozoa and affect its function and properties. Here we report the first comprehensive catalog of the AG secreted fluid during the mature phase of the Chinese mitten crab (Eriocheir sinensis). AG proteins were separated by one-dimensional gel electrophoresis and analyzed by reverse phase high-performance liquid chromatography coupled with tandem mass spectrometry (HPLC-MS/MS). Altogether, the mass spectra of 1173 peptides were detected (1067 without decoy and contaminants) which allowed for the identification of 486 different proteins annotated upon the NCBI database (http://www.ncbi.nlm.nih.gov/) and our transcritptome dataset. The mass spectrometry proteomics data have been deposited at the ProteomeXchange with identifier PXD000700. An extensive description of the AG proteome will help provide the basis for a better understanding of a number of reproductive mechanisms, including potentially spermatophore breakdown, dynamic functional and morphological changes in sperm cells and sperm acrosin enzyme vitality. Thus, the comprehensive catalog of proteins presented here can serve as a valuable reference for future studies of sperm maturation and regulatory mechanisms involved in crustacean reproduction. PMID:26305468

Characterization by high-performance liquid chromatography/electrospray ionization quadrupole time-of-flight mass spectrometry of the lipid fraction of Spirulina platensis pressurized ethanol extract.

PubMed

Herrero, Miguel; Vicente, María J; Cifuentes, Alejandro; Ibáñez, Elena

2007-01-01

Microalgae have been suggested as a potential source for new functional ingredients, making possible the development of new functional foods from natural origin. Among the natural ingredients, polyunsaturated fatty acids (PUFAs) have generally been identified as an interesting group of compounds with biological activity, mainly related to their anti-inflammatory properties. In this regard, the use of environmentally friendly extraction procedures (e.g. pressurized liquid extraction, PLE) to obtain such natural ingredients is also becoming necessary. In this work, an exhaustive characterization of the lipid fraction of a pressurized ethanolic extract of the microalga Spirulina platensis is carried out. To achieve this objective high-performance liquid chromatography (HPLC) coupled to quadrupole time-of-flight mass spectrometry (QTOF-MS) is employed. The use of the QTOF analyzer allows the selection and isolation of precursor ions as well as providing the high efficiency, sensitivity and mass accuracy required. By means of this powerful hyphenated technique, it was possible to identify several polar lipids in an extract of S. platensis (some of them, to our knowledge, described for the first time in this work), including four free fatty acids, four monogalactosyl monoacylglycerols, three phosphatidylglycerols and two sulfoquinovosyl diacylglycerols.

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

[Clinical application of mass spectrometry in the pediatric field: current topics].

PubMed

Yamaguchi, Seiji

2013-09-01

Mass spectrometry, including tandem mass spectrometry (MS/MS) and gas chromatography-mass spectrometry (GC/MS), is becoming prominent in the diagnosis of metabolic disorders in the pediatric field. It enables biochemical diagnosis of metabolic disorders from the metabolic profiles obtained by MS/MS and/or GC/MS. In neonatal mass screening for inherited metabolic disease (IMD) using MS/MS, amino acids and acylcarnitines on dried blood spots are analyzed. The target diseases include amino acidemia, urea cycle disorder, organic acidemia, and fatty acid oxidation disorder. In the MS/MS screening, organic acid analysis using GC/MS is required for differential and/or definite diagnosis of the IMDs. GC/MS data processing, however, is difficult, and metabolic diagnosis often requires the necessary skills and expertize. We developed an automated system of GC/MS data processing and autodiagnosis, and the biochemical diagnosis using GC/MS became markedly easier and user-friendly. Mass spectrometric techniques will expand from research laboratories to clinical laboratories in the near future.

Laser Microprobe Mass Spectrometry 1: Basic Principles and Performance Characteristics.

ERIC Educational Resources Information Center

Denoyer, Eric; And Others

1982-01-01

Describes the historical development, performance characteristics (sample requirements, analysis time, ionization characteristics, speciation capabilities, and figures of merit), and applications of laser microprobe mass spectrometry. (JN)

Size, weight and position: ion mobility spectrometry and imaging MS combined.

PubMed

Kiss, András; Heeren, Ron M A

2011-03-01

Size, weight and position are three of the most important parameters that describe a molecule in a biological system. Ion mobility spectrometry is capable of separating molecules on the basis of their size or shape, whereas imaging mass spectrometry is an effective tool to measure the molecular weight and spatial distribution of molecules. Recent developments in both fields enabled the combination of the two technologies. As a result, ion-mobility-based imaging mass spectrometry is gaining more and more popularity as a (bio-)analytical tool enabling the determination of the size, weight and position of several molecules simultaneously on biological surfaces. This paper reviews the evolution of ion-mobility-based imaging mass spectrometry and provides examples of its application in analytical studies of biological surfaces.

Mass Spectrometry in Clinical Laboratory: Applications in Therapeutic Drug Monitoring and Toxicology.

PubMed

Garg, Uttam; Zhang, Yan Victoria

2016-01-01

Mass spectrometry (MS) has been used in research and specialized clinical laboratories for decades as a very powerful technology to identify and quantify compounds. In recent years, application of MS in routine clinical laboratories has increased significantly. This is mainly due to the ability of MS to provide very specific identification, high sensitivity, and simultaneous analysis of multiple analytes (>100). The coupling of tandem mass spectrometry with gas chromatography (GC) or liquid chromatography (LC) has enabled the rapid expansion of this technology. While applications of MS are used in many clinical areas, therapeutic drug monitoring, drugs of abuse, and clinical toxicology are still the primary focuses of the field. It is not uncommon to see mass spectrometry being used in routine clinical practices for those applications.

Capillary electrophoresis electrospray ionization mass spectrometry interface

DOEpatents

Smith, Richard D.; Severs, Joanne C.

1999-01-01

The present invention is an interface between a capillary electrophoresis separation capillary end and an electrospray ionization mass spectrometry emitter capillary end, for transporting an anolyte sample from a capillary electrophoresis separation capillary to a electrospray ionization mass spectrometry emitter capillary. The interface of the present invention has: (a) a charge transfer fitting enclosing both of the capillary electrophoresis capillary end and the electrospray ionization mass spectrometry emitter capillary end; (b) a reservoir containing an electrolyte surrounding the charge transfer fitting; and (c) an electrode immersed into the electrolyte, the electrode closing a capillary electrophoresis circuit and providing charge transfer across the charge transfer fitting while avoiding substantial bulk fluid transfer across the charge transfer fitting. Advantages of the present invention have been demonstrated as effective in providing high sensitivity and efficient analyses.

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

Ozone Modulation/Membrane Introduction Mass Spectrometry for Analysis of Hydrocarbon Pollutants in Air

NASA Astrophysics Data System (ADS)

Atkinson, D. B.

2001-12-01

Modulation of volatile hydrocarbons in two-component mixtures is demonstrated using an ozonolysis pretreatment with membrane introduction mass spectrometry (MIMS). The MIMS technique allows selective introduction of volatile and semivolatile analytes into a mass spectrometer via processes known collectively as pervaporation [Kotiaho and Cooks, 1992]. A semipermeable polymer membrane acts as an interface between the sample (vapor or solution) and the vacuum of the mass spectrometer. This technique has been demonstrated to allow for sensitive analysis of hydrocarbons and other non-polar volatile organic compounds (VOC`s) in air samples[Cisper et al., 1995] . The methodology has the advantages of no sample pretreatment and short analysis time, which are promising for online monitoring applications but the chief disadvantage of lack of a separation step for the different analytes in a mixture. Several approaches have been investigated to overcome this problem including use of selective chemical ionization [Bier and Cooks, 1987] and multivariate calibration techniques[Ketola et al., 1999] . A new approach is reported for the quantitative measurement of VOCs in complex matrices. The method seeks to reduce the complexity of mass spectra observed in hydrocarbon mixture analysis by selective pretreatment of the analyte mixture. In the current investigation, the rapid reaction of ozone with alkenes is used, producing oxygenated compounds which are suppressed by the MIMS system. This has the effect of removing signals due to unsaturated analytes from the compound mass spectra, and comparison of the spectra before and after the ozone treatment reveals the nature of the parent compounds. In preliminary investigations, ozone reacted completely with cyclohexene from a mixture of cylohexene and cyclohexane, and with β -pinene from a mixture of toluene and β -pinene, suppressing the ion signals from the olefins. A slight attenuation of the cyclohexane and toluene in those mixtures was also observed. Despite this problem, the hydrocarbon signal response can be calibrated and the method can be used for quantitative analysis of volatile hydrocarbon compounds in air samples. This methodology should augment the efficiency of the MIMS approach in online and onsite monitoring of VOC emissions. Bier, M.R., and R.G. Cooks, Membrane Interface for Selective Introduction of Volatile Compounds Directly into The Ionization Chamber of a Mass Spectrometer, Anal. Chem., 59 (4), 597, 1987. Cisper, M.E., C.G. Gill, L.E. Townsend, and P.H. Hemberger, On-Line Detection of Volatile Organic Compounds in Air at Parts-per-Trillion Levels by Membrane Introduction Mass Spectrometry, Anal. Chem., 67 (8), 1413-1417, 1995. Ketola, R.A., M. Ojala, and J. Heikkonen, A Non-linear Asymmetric Error Function-based Least Mean Square Approach for the Analysis of Multicomponent Mass Spectra Measured by Membrane Inlet Mass Spectrometry, Rapid Commun. Mass Spectrom., 13 (8), 654, 1999. Kotiaho, T., and R.G. Cooks, Membrane Introduction Mass Spectrometry in Environmental Analysis, in: J.J. Breen, M. J. Dellarco, (Eds), Pollution in Industrial processes, 126 pp., ACS Symp. Ser., Washington, D.C. 508, 1992.

Study of Simvastatin Self-Association Using Electrospray-Ionization Mass Spectrometry

NASA Astrophysics Data System (ADS)

Vetrova, E. V.; Lekar, A. V.; Filonova, O. V.; Borisenko, S. N.; Maksimenko, E. V.; Borisenko, N. I.

2015-07-01

Self-association of simvastatin, which is widely used to treat coronary heart disease, was investigated using electrospray-ionization mass spectrometry. Formation of simvastatin self-associates in various solvents was demonstrated using mass spectrometry. Solvation effects were shown to play a special role in the formation of the self-associates. Self-associates containing from two to fi ve simvastatin molecules were detected in mass spectra of an aqueous MeOH (20%) solution of simvastatin. The formation of simvastatin self-associates could compete with the complexation of supramolecular structures during the synthesis of new generation drugs.

Nuclear Forensics: Measurements of Uranium Oxides Using Time-of-Flight Secondary Ion Mass Spectrometry (TOF-SIMS)

DTIC Science & Technology

2010-03-01

Isotope Ratio Analysis of Actinides , Fission Products, and Geolocators by High- efficiency Multi-collector Thermal Ionization Mass Spectrometry...Information, 1999. Hou, Xiaolin, and Per Roos. “ Critical Comparison of radiometric and Mass Spectrometric Methods for the Determination of...NUCLEAR FORENSICS: MEASUREMENTS OF URANIUM OXIDES USING TIME-OF-FLIGHT SECONDARY ION MASS

Linear electric field mass spectrometry

DOEpatents

McComas, David J.; Nordholt, Jane E.

1992-01-01

A mass spectrometer and methods for mass spectrometry. The apparatus is compact and of low weight and has a low power requirement, making it suitable for use on a space satellite and as a portable detector for the presence of substances. High mass resolution measurements are made by timing ions moving through a gridless cylindrically symmetric linear electric field.

Application of Solid Phase Microextraction Coupled with Gas Chromatography/Mass Spectrometry as a Rapid Method for Field Sampling and Analysis of Chemical Warfare Agents and Toxic Industrial Chemicals

DTIC Science & Technology

2003-01-01

PHASE MICROEXTRACTION COUPLED WITH GAS CHROMATOGRAPHY/MASS SPECTROMETRY AS A RAPID METHOD FOR FIELD SAMPLING AND ANALYSIS OF CHEMICAL WARFARE AGENTS...SAMPLING AND ANALYSIS OF CHEMICAL WARFARE AGENTS AND TOXIC INDUSTRIAL CHEMICALS 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6...GAS CHROMATOGRAPHY/MASS SPECTROMETRY AS A RAPID METHOD FOR FIELD SAMPLING AND ANALYSIS OF CHEMICAL WARFARE AGENTS AND TOXIC INDUSTRIAL CHEMICALS

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.

Analysis of chirality by femtosecond laser ionization mass spectrometry.

PubMed

Horsch, Philipp; Urbasch, Gunter; Weitzel, Karl-Michael

2012-09-01

Recent progress in the field of chirality analysis employing laser ionization mass spectrometry is reviewed. Emphasis is given to femtosecond (fs) laser ionization work from the author's group. We begin by reviewing fundamental aspects of determining circular dichroism (CD) in fs-laser ionization mass spectrometry (fs-LIMS) discussing an example from the literature (resonant fs-LIMS of 3-methylcyclopentanone). Second, we present new data indicating CD in non-resonant fs-LIMS of propylene oxide. Copyright © 2012 Wiley Periodicals, Inc., A Wiley Company.

Evaporation Rates of Chemical Warfare Agents Using 5-CM Wind Tunnels I. CASARM Sulfur Mustard (HD) from Glass

DTIC Science & Technology

2008-10-01

Blank CONTENTS 1. INTRODUCTION 9 2. EXPERIMENTAL PROCEDURES 9 2.1 Wind Tunnel 9 2.2 Agent 10 2.3 Gas Chromatography /Mass Spectrometry Detection 10...protective equipment. 2.3 Gas Chromatography /Mass Spectrometry Detection (GC/MSD) The GC/MSD analysis of the thermal desorption tubes was performed on a...coupled to thermal desorption tubes that were analyzed using gas chromatography /mass spectrometry detection (GC/MSD). Differences between the tunnels

Iron-Isotopic Fractionation Studies Using Multiple Collector Inductively Coupled Plasma Mass Spectrometry

NASA Technical Reports Server (NTRS)

Anbar, A. D.; Zhang, C.; Barling, J.; Roe, J. E.; Nealson, K. H.

1999-01-01

The importance of Fe biogeochemistry has stimulated interest in Fe isotope fractionation. Recent studies using thermal ionization mass spectrometry (TIMS) and a "double spike" demonstrate the existence of biogenic Fe isotope effects. Here, we assess the utility of multiple-collector inductively-coupled plasma mass spectrometry(MC-ICP-MS) with a desolvating sample introduction system for Fe isotope studies, and present data on Fe biominerals produced by a thermophilic bacterium. Additional information is contained in the original extended abstract.

A new scoring function for top-down spectral deconvolution

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

Kou, Qiang; Wu, Si; Liu, Xiaowen

2014-12-18

Background: Top-down mass spectrometry plays an important role in intact protein identification and characterization. Top-down mass spectra are more complex than bottom-up mass spectra because they often contain many isotopomer envelopes from highly charged ions, which may overlap with one another. As a result, spectral deconvolution, which converts a complex top-down mass spectrum into a monoisotopic mass list, is a key step in top-down spectral interpretation. Results: In this paper, we propose a new scoring function, L-score, for evaluating isotopomer envelopes. By combining L-score with MS-Deconv, a new software tool, MS-Deconv+, was developed for top-down spectral deconvolution. Experimental results showedmore » that MS-Deconv+ outperformed existing software tools in top-down spectral deconvolution. Conclusions: L-score shows high discriminative ability in identification of isotopomer envelopes. Using L-score, MS-Deconv+ reports many correct monoisotopic masses missed by other software tools, which are valuable for proteoform identification and characterization.« less

A mass spectrometry-based multiplex SNP genotyping by utilizing allele-specific ligation and strand displacement amplification.

PubMed

Park, Jung Hun; Jang, Hyowon; Jung, Yun Kyung; Jung, Ye Lim; Shin, Inkyung; Cho, Dae-Yeon; Park, Hyun Gyu

2017-05-15

We herein describe a new mass spectrometry-based method for multiplex SNP genotyping by utilizing allele-specific ligation and strand displacement amplification (SDA) reaction. In this method, allele-specific ligation is first performed to discriminate base sequence variations at the SNP site within the PCR-amplified target DNA. The primary ligation probe is extended by a universal primer annealing site while the secondary ligation probe has base sequences as an overhang with a nicking enzyme recognition site and complementary mass marker sequence. The ligation probe pairs are ligated by DNA ligase only at specific allele in the target DNA and the resulting ligated product serves as a template to promote the SDA reaction using a universal primer. This process isothermally amplifies short DNA fragments, called mass markers, to be analyzed by mass spectrometry. By varying the sizes of the mass markers, we successfully demonstrated the multiplex SNP genotyping capability of this method by reliably identifying several BRCA mutations in a multiplex manner with mass spectrometry. Copyright © 2016 Elsevier B.V. All rights reserved.

Comprehensive evaluation of direct injection mass spectrometry for the quantitative profiling of volatiles in food samples

PubMed Central

2016-01-01

Although qualitative strategies based on direct injection mass spectrometry (DIMS) have recently emerged as an alternative for the rapid classification of food samples, the potential of these approaches in quantitative tasks has scarcely been addressed to date. In this paper, the applicability of different multivariate regression procedures to data collected by DIMS from simulated mixtures has been evaluated. The most relevant factors affecting quantitation, such as random noise, the number of calibration samples, type of validation, mixture complexity and similarity of mass spectra, were also considered and comprehensively discussed. Based on the conclusions drawn from simulated data, and as an example of application, experimental mass spectral fingerprints collected by direct thermal desorption coupled to mass spectrometry were used for the quantitation of major volatiles in Thymus zygis subsp. zygis chemotypes. The results obtained, validated with the direct thermal desorption coupled to gas chromatography–mass spectrometry method here used as a reference, show the potential of DIMS approaches for the fast and precise quantitative profiling of volatiles in foods. This article is part of the themed issue ‘Quantitative mass spectrometry’. PMID:27644978

IDENTIFICATION OF POLLUTANTS IN A MUNICIPAL WELL USING HIGH RESOLUTION MASS SPECTROMETRY

EPA Science Inventory

An elevated incidence of childhood cancer was observed near a contaminated site. Trace amounts of several isomeric compounds were detected by gas chromatography/mass spectrometry (GC/MS) in a concentrated extract of municipal well water. No matching library mass spectra were foun...

Speciation and preservation of CrVI and CrIII in finished drinking water matrices using collision cell ion chromatography-inductively coupled plasma-mass spectrometry

EPA Science Inventory

The polyatomic background at the major isotope of Cr was evaluated as a function of collision cell gas flow rate using three different mobile phases. The stability of CrVI was evaluated as a function of solution pH using an enriched 53CrVI. The recovery was ≥ 95% at pH 7.8 but...

Mechanism for odd-electron anion generation of dihydroxybenzoic acid isomers in matrix-assisted laser desorption/ionization mass spectrometry with density functional theory calculations.

PubMed

Yamagaki, Tohru; Takeuchi, Michika; Watanabe, Takehiro; Sugahara, Kohtaro; Takeuchi, Takae

2016-12-30

Proton and radical are transferred between matrices and matrix and analyte in matrix-assisted laser desorption/ionization (MALDI) and these transfers drive ionization of analytes. The odd-electron anion [M-2H] •- was generated in dihydroxybenzoic acids (DHBs) and the ion abundance of the 2,5-DHB was the highest among six DHB isomers. We were interested in the mechanism of the ion generation of the odd-electron anion. The observed [M-2H] •- and [M-3H] - ions, which were generated with the hydrogen radical removed from the phenolic hydroxyl groups (OH) in DHB isomers, were analyzed using negative-ion MALDI-MS. The enthalpy for ion generation and their stable structures were calculated using the density functional theory (DFT) calculation program Gaussian 09 with the B3LYP functional and the 6-31+G(d) basis set. The number of observed [M-2H] •- and [M-3H] - ions of the DHB isomers was dependent on the positions of the phenolic OH groups in the DHB isomers because the carboxy group interacts with the ortho OH group due to neighboring group participation, as confirmed from the stable structures of the [M-2H] •- anions calculated with the Gaussian 09 program. The DHB isomers were placed into three categories according to the number of the ions. Odd-electron anions ([M-2H] •- ) and [M-2H • -H] - ([M-3H] - ) ions were generated from DHB isomers due to removal of the hydrogen radical from the phenolic groups. The enthalpy for ion generation revealed that ion formation proceeds via a two-step pathway through the [M-M] - ion as an intermediate. © 2016 The Authors. Rapid Communications in Mass Spectrometry Published by John Wiley & Sons Ltd. © 2016 The Authors. Rapid Communications in Mass Spectrometry Published by John Wiley & Sons Ltd.

Towards a Proteomic Catalogue and Differential Annotation of Salivary Gland Proteins in Blood Fed Malaria Vector Anopheles culicifacies by Mass Spectrometry.

PubMed

Rawal, Ritu; Vijay, Sonam; Kadian, Kavita; Singh, Jagbir; Pande, Veena; Sharma, Arun

2016-01-01

In order to understand the importance of functional proteins in mosquito behavior, following blood meal, a baseline proteomic dataset is essential for providing insights into the physiology of blood feeding. Therefore, in this study as first step, in solution and 1-D electrophoresis digestion approach combined with tandem mass spectrometry (nano LC-MS/MS) and computational bioinformatics for data mining was used to prepare a baseline proteomic catalogue of salivary gland proteins of sugar fed An. culicifacies mosquitoes. A total of 106 proteins were identified and analyzed by SEQUEST algorithm against mosquito protein database from Uniprot/NCBI. Importantly, D7r1, D7r2, D7r4, salivary apyrase, anti-platelet protein, calreticulin, antigen 5 family proteins were identified and grouped on the basis of biological and functional roles. Secondly, differential protein expression and annotations between salivary glands of sugar fed vs blood fed mosquitoes was analyzed using 2-Delectrophoresis combined with MALDI-TOF mass spectrometry. The alterations in the differential expression of total 38 proteins was observed out of which 29 proteins like beclin-1, phosphorylating proteins, heme oxygenase 1, ferritin, apoptotic proteins, coagulation and immunity like, serine proteases, serpins, c-type lectin and protein in regulation of blood feeding behavior were found to be up regulated while 9 proteins related to blood feeding, juvenile hormone epoxide hydrolase ii, odorant binding proteins and energy metabolic enzymes were found to be down regulated. To our knowledge, this study provides a first time baseline proteomic dataset and functional annotations of An. culicifacies salivary gland proteins that may be involved during the blood feeding. Identification of differential salivary proteins between sugar fed and blood fed mosquitoes and their plausible role may provide insights into the physiological processes associated with feeding behavior and sporozoite transmission during the process of blood feeding.

Towards a Proteomic Catalogue and Differential Annotation of Salivary Gland Proteins in Blood Fed Malaria Vector Anopheles culicifacies by Mass Spectrometry

PubMed Central

Rawal, Ritu; Vijay, Sonam; Kadian, Kavita; Singh, Jagbir; Pande, Veena; Sharma, Arun

2016-01-01

In order to understand the importance of functional proteins in mosquito behavior, following blood meal, a baseline proteomic dataset is essential for providing insights into the physiology of blood feeding. Therefore, in this study as first step, in solution and 1-D electrophoresis digestion approach combined with tandem mass spectrometry (nano LC-MS/MS) and computational bioinformatics for data mining was used to prepare a baseline proteomic catalogue of salivary gland proteins of sugar fed An. culicifacies mosquitoes. A total of 106 proteins were identified and analyzed by SEQUEST algorithm against mosquito protein database from Uniprot/NCBI. Importantly, D7r1, D7r2, D7r4, salivary apyrase, anti-platelet protein, calreticulin, antigen 5 family proteins were identified and grouped on the basis of biological and functional roles. Secondly, differential protein expression and annotations between salivary glands of sugar fed vs blood fed mosquitoes was analyzed using 2-Delectrophoresis combined with MALDI-TOF mass spectrometry. The alterations in the differential expression of total 38 proteins was observed out of which 29 proteins like beclin-1, phosphorylating proteins, heme oxygenase 1, ferritin, apoptotic proteins, coagulation and immunity like, serine proteases, serpins, c-type lectin and protein in regulation of blood feeding behavior were found to be up regulated while 9 proteins related to blood feeding, juvenile hormone epoxide hydrolase ii, odorant binding proteins and energy metabolic enzymes were found to be down regulated. To our knowledge, this study provides a first time baseline proteomic dataset and functional annotations of An. culicifacies salivary gland proteins that may be involved during the blood feeding. Identification of differential salivary proteins between sugar fed and blood fed mosquitoes and their plausible role may provide insights into the physiological processes associated with feeding behavior and sporozoite transmission during the process of blood feeding. PMID:27602567

Comparative Proteomics Reveals a Significant Bias Toward Alternative Protein Isoforms with Conserved Structure and Function

PubMed Central

Ezkurdia, Iakes; del Pozo, Angela; Frankish, Adam; Rodriguez, Jose Manuel; Harrow, Jennifer; Ashman, Keith; Valencia, Alfonso; Tress, Michael L.

2012-01-01

Advances in high-throughput mass spectrometry are making proteomics an increasingly important tool in genome annotation projects. Peptides detected in mass spectrometry experiments can be used to validate gene models and verify the translation of putative coding sequences (CDSs). Here, we have identified peptides that cover 35% of the genes annotated by the GENCODE consortium for the human genome as part of a comprehensive analysis of experimental spectra from two large publicly available mass spectrometry databases. We detected the translation to protein of “novel” and “putative” protein-coding transcripts as well as transcripts annotated as pseudogenes and nonsense-mediated decay targets. We provide a detailed overview of the population of alternatively spliced protein isoforms that are detectable by peptide identification methods. We found that 150 genes expressed multiple alternative protein isoforms. This constitutes the largest set of reliably confirmed alternatively spliced proteins yet discovered. Three groups of genes were highly overrepresented. We detected alternative isoforms for 10 of the 25 possible heterogeneous nuclear ribonucleoproteins, proteins with a key role in the splicing process. Alternative isoforms generated from interchangeable homologous exons and from short indels were also significantly enriched, both in human experiments and in parallel analyses of mouse and Drosophila proteomics experiments. Our results show that a surprisingly high proportion (almost 25%) of the detected alternative isoforms are only subtly different from their constitutive counterparts. Many of the alternative splicing events that give rise to these alternative isoforms are conserved in mouse. It was striking that very few of these conserved splicing events broke Pfam functional domains or would damage globular protein structures. This evidence of a strong bias toward subtle differences in CDS and likely conserved cellular function and structure is remarkable and strongly suggests that the translation of alternative transcripts may be subject to selective constraints. PMID:22446687

Capture compound mass spectrometry sheds light on the molecular mechanisms of liver toxicity of two Parkinson drugs.

PubMed

Fischer, Jenny J; Michaelis, Simon; Schrey, Anna K; Graebner, Olivia Graebner nee; Glinski, Mirko; Dreger, Mathias; Kroll, Friedrich; Koester, Hubert

2010-01-01

Capture compound mass spectrometry (CCMS) is a novel technology that helps understand the molecular mechanism of the mode of action of small molecules. The Capture Compounds are trifunctional probes: A selectivity function (the drug) interacts with the proteins in a biological sample, a reactivity function (phenylazide) irreversibly forms a covalent bond, and a sorting function (biotin) allows the captured protein(s) to be isolated for mass spectrometric analysis. Tolcapone and entacapone are potent inhibitors of catechol-O-methyltransferase (COMT) for the treatment of Parkinson's disease. We aimed to understand the molecular basis of the difference of both drugs with respect to side effects. Using Capture Compounds with these drugs as selectivity functions, we were able to unambiguously and reproducibly isolate and identify their known target COMT. Tolcapone Capture Compounds captured five times more proteins than entacapone Capture Compounds. Moreover, tolcapone Capture Compounds isolated mitochondrial and peroxisomal proteins. The major tolcapone-protein interactions occurred with components of the respiratory chain and of the fatty acid beta-oxidation. Previously reported symptoms in tolcapone-treated rats suggested that tolcapone might act as decoupling reagent of the respiratory chain (Haasio et al., 2002b). Our results demonstrate that CCMS is an effective tool for the identification of a drug's potential off targets. It fills a gap in currently used in vitro screens for drug profiling that do not contain all the toxicologically relevant proteins. Thereby, CCMS has the potential to fill a technological need in drug safety assessment and helps reengineer or to reject drugs at an early preclinical stage.

Lower circulating insulin-like growth factor-I is associated with better cognition in females with exceptional longevity without compromise to muscle mass and function.

PubMed

Perice, Leland; Barzilai, Nir; Verghese, Joe; Weiss, Erica F; Holtzer, Roee; Cohen, Pinchas; Milman, Sofiya

2016-10-14

Mutations that reduce somatotropic signaling result in improved lifespan and health-span in model organisms and humans. However, whether reduced circulating insulin-like growth factor-I (IGF-I) level is detrimental to cognitive and muscle function in older adults remains understudied. A cross-sectional analysis was performed in Ashkenazi Jews with exceptional longevity (age ≥95 years). Cognition was assessed using the Mini-Mental State Examination and muscle function with the chair rise test, grip-strength, and gait speed. Muscle mass was estimated using the skeletal muscle index. Serum IGF-I was measured with liquid chromatography mass spectrometry. In gender stratified age-adjusted logistic regression analysis, females with IGF-I levels in the first tertile had lower odds of being cognitively impaired compared to females with IGF-I levels within the upper two tertiles, OR (95% CI) 0.39 (0.19-0.82). The result remained significant after adjustment for multiple parameters. No significant association was identified in males between IGF-I and cognition. No relationship was found between IGF-I tertiles and muscle function and muscle mass in females or males. Lower circulating IGF-I is associated with better cognitive function in females with exceptional longevity, with no detriment to skeletal muscle mass and function.

Characterizing the Chemical Stability of High Temperature Materials for Application in Extreme Environments

NASA Technical Reports Server (NTRS)

Opila, Elizabeth

2005-01-01

The chemical stability of high temperature materials must be known for use in the extreme environments of combustion applications. The characterization techniques available at NASA Glenn Research Center vary from fundamental thermodynamic property determination to material durability testing in actual engine environments. In this paper some of the unique techniques and facilities available at NASA Glenn will be reviewed. Multiple cell Knudsen effusion mass spectrometry is used to determine thermodynamic data by sampling gas species formed by reaction or equilibration in a Knudsen cell held in a vacuum. The transpiration technique can also be used to determine thermodynamic data of volatile species but at atmospheric pressures. Thermodynamic data in the Si-O-H(g) system were determined with this technique. Free Jet Sampling Mass Spectrometry can be used to study gas-solid interactions at a pressure of one atmosphere. Volatile Si(OH)4(g) was identified by this mass spectrometry technique. A High Pressure Burner Rig is used to expose high temperature materials in hydrocarbon-fueled combustion environments. Silicon carbide (SiC) volatility rates were measured in the burner rig as a function of total pressure, gas velocity and temperature. Finally, the Research Combustion Lab Rocket Test Cell is used to expose high temperature materials in hydrogen/oxygen rocket engine environments to assess material durability. SiC recession due to rocket engine exposures was measured as a function of oxidant/fuel ratio, temperature, and total pressure. The emphasis of the discussion for all techniques will be placed on experimental factors that must be controlled for accurate acquisition of results and reliable prediction of high temperature material chemical stability.

Spatially resolved chemical analysis of cicada wings using laser-ablation electrospray ionization (LAESI) imaging mass spectrometry (IMS).

PubMed

Román, Jessica K; Walsh, Callee M; Oh, Junho; Dana, Catherine E; Hong, Sungmin; Jo, Kyoo D; Alleyne, Marianne; Miljkovic, Nenad; Cropek, Donald M

2018-03-01

Laser-ablation electrospray ionization (LAESI) imaging mass spectrometry (IMS) is an emerging bioanalytical tool for direct imaging and analysis of biological tissues. Performing ionization in an ambient environment, this technique requires little sample preparation and no additional matrix, and can be performed on natural, uneven surfaces. When combined with optical microscopy, the investigation of biological samples by LAESI allows for spatially resolved compositional analysis. We demonstrate here the applicability of LAESI-IMS for the chemical analysis of thin, desiccated biological samples, specifically Neotibicen pruinosus cicada wings. Positive-ion LAESI-IMS accurate ion-map data was acquired from several wing cells and superimposed onto optical images allowing for compositional comparisons across areas of the wing. Various putative chemical identifications were made indicating the presence of hydrocarbons, lipids/esters, amines/amides, and sulfonated/phosphorylated compounds. With the spatial resolution capability, surprising chemical distribution patterns were observed across the cicada wing, which may assist in correlating trends in surface properties with chemical distribution. Observed ions were either (1) equally dispersed across the wing, (2) more concentrated closer to the body of the insect (proximal end), or (3) more concentrated toward the tip of the wing (distal end). These findings demonstrate LAESI-IMS as a tool for the acquisition of spatially resolved chemical information from fragile, dried insect wings. This LAESI-IMS technique has important implications for the study of functional biomaterials, where understanding the correlation between chemical composition, physical structure, and biological function is critical. Graphical abstract Positive-ion laser-ablation electrospray ionization mass spectrometry coupled with optical imaging provides a powerful tool for the spatially resolved chemical analysis of cicada wings.

Identification of polychlorinated styrene compounds in heron tissues by gas-liquid chromatography-mass spectrometry

USGS Publications Warehouse

Reichel, W.L.; Prouty, R.M.; Gay, M.L.

1977-01-01

Unknown compounds detected in Ardea herodias tissues are identified by gas-liquid chromatography-mass spectrometry as residues of octachlorostyrene. Heptachlorostyrene and hexachlorostyrene were tentatively identified.

Mass Spectrometry Approaches for Identification and Quantitation of Therapeutic Monoclonal Antibodies in the Clinical Laboratory.

PubMed

Ladwig, Paula M; Barnidge, David R; Willrich, Maria A V

2017-05-01

Therapeutic monoclonal antibodies (MAbs) are an important class of drugs used to treat diseases ranging from autoimmune disorders to B cell lymphomas to other rare conditions thought to be untreatable in the past. Many advances have been made in the characterization of immunoglobulins as a result of pharmaceutical companies investing in technologies that allow them to better understand MAbs during the development phase. Mass spectrometry is one of the new advancements utilized extensively by pharma to analyze MAbs and is now beginning to be applied in the clinical laboratory setting. The rise in the use of therapeutic MAbs has opened up new challenges for the development of assays for monitoring this class of drugs. MAbs are larger and more complex than typical small-molecule therapeutic drugs routinely analyzed by mass spectrometry. In addition, they must be quantified in samples that contain endogenous immunoglobulins with nearly identical structures. In contrast to an enzyme-linked immunosorbent assay (ELISA) for quantifying MAbs, mass spectrometry-based assays do not rely on MAb-specific reagents such as recombinant antigens and/or anti-idiotypic antibodies, and time for development is usually shorter. Furthermore, using molecular mass as a measurement tool provides increased specificity since it is a first-order principle unique to each MAb. This enables rapid quantification of MAbs and multiplexing. This review describes how mass spectrometry can become an important tool for clinical chemists and especially immunologists, who are starting to develop assays for MAbs in the clinical laboratory and are considering mass spectrometry as a versatile platform for the task. Copyright © 2017 Ladwig et al.

Atmospheric pressure ionization-tandem mass spectrometry of the phenicol drug family.

PubMed

Alechaga, Élida; Moyano, Encarnación; Galceran, M Teresa

2013-11-01

In this work, the mass spectrometry behaviour of the veterinary drug family of phenicols, including chloramphenicol (CAP) and its related compounds thiamphenicol (TAP), florfenicol (FF) and FF amine (FFA), was studied. Several atmospheric pressure ionization sources, electrospray (ESI), atmospheric pressure chemical ionization and atmospheric pressure photoionization were compared. In all atmospheric pressure ionization sources, CAP, TAP and FF were ionized in both positive and negative modes; while for the metabolite FFA, only positive ionization was possible. In general, in positive mode, [M + H](+) dominated the mass spectrum for FFA, while the other compounds, CAP, TAP and FF, with lower proton affinity showed intense adducts with species present in the mobile phase. In negative mode, ESI and atmospheric pressure photoionization showed the deprotonated molecule [M-H](-), while atmospheric pressure chemical ionization provided the radical molecular ion by electron capture. All these ions were characterized by tandem mass spectrometry using the combined information obtained by multistage mass spectrometry and high-resolution mass spectrometry in a quadrupole-Orbitrap instrument. In general, the fragmentation occurred via cyclization and losses or fragmentation of the N-(alkyl)acetamide group, and common fragmentation pathways were established for this family of compounds. A new chemical structure for the product ion at m/z 257 for CAP, on the basis of the MS(3) and MS(4) spectra is proposed. Thermally assisted ESI and selected reaction monitoring are proposed for the determination of these compounds by ultra high-performance liquid chromatography coupled to tandem mass spectrometry, achieving instrumental detection limits down to 0.1 pg. Copyright © 2013 John Wiley & Sons, Ltd.

40 CFR 63.2354 - What performance tests, design evaluations, and performance evaluations must I conduct?

Code of Federal Regulations, 2011 CFR

2011-07-01

... of Gaseous Organic Compounds by Direct Interface Gas Chromatography-Mass Spectrometry (incorporated... Method for Determination of Gaseous Organic Compounds by Direct Interface Gas Chromatography-Mass... Interface Gas Chromatography-Mass Spectrometry (incorporated by reference, see § 63.14),; or (B) For target...

Introduction of Mass Spectrometry in an First-Semester General Chemistry Laboratory Course: Quantification of Mtbe or Dmso in Water

ERIC Educational Resources Information Center

Solow, Mike

2004-01-01

Quantification of a contaminant in water provides the first-year general chemistry students with a tangible application of mass spectrometry. The relevance of chemistry to assessing and solving environmental problems is highlighted for students when they perform mass spectroscopy experiments.

Mass Spectrometry for the Masses

ERIC Educational Resources Information Center

Persinger, Jared D.; Hoops, Geoffrey, C.; Samide, Michael J.

2004-01-01

A simple, qualitative experiment is developed for implementation, where the gas chromatography-mass spectrometry (GC-MS) plays an important role, into the laboratory curriculum of a chemistry course designed for nonscience majors. This laboratory experiment is well suited for the students as it helps them to determine the validity of their…

Affinity purification and mass spectrometry: an attractive choice to investigate protein-protein interactions in plant immunity

USDA-ARS?s Scientific Manuscript database

Affinity purification of protein complexes from biological tissues, followed by liquid chromatography- tandem mass spectrometry (AP-MS/MS), has ballooned in recent years due to sizeable increases in nucleic acid sequence data essential for interpreting mass spectra, improvements in affinity purifica...

The simulacrum system as a construct for mass spectrometry of triacylglycerols and others

USDA-ARS?s Scientific Manuscript database

A construct called a simulacrum is defined that provides all possible solutions to a sum of two mass spectral abundances, based on values (abundances) or ratios of those values. The defined construct is applied to atmospheric pressure chemical ionization (APCI) mass spectrometry (MS) of triacylglyce...

Attachment of chloride anion to sugars: mechanistic investigation and discovery of a new dopant for efficient sugar ionization/detection in mass spectrometers.

PubMed

Boutegrabet, Lemia; Kanawati, Basem; Gebefügi, Istvan; Peyron, Dominique; Cayot, Philippe; Gougeon, Régis D; Schmitt-Kopplin, Philippe

2012-10-08

A new method for efficient ionization of sugars in the negative-ion mode of electrospray mass spectrometry is presented. Instead of using strongly hydrophobic dopants such as dichloromethane or chloroform, efficient ionization of sugars has been achieved by using aqueous HCl solution for the first time. This methodology makes it possible to use hydrophilic dopants, which are more appropriate for chromatographic separation techniques with efficient sugar ionization and detection in mass spectrometry. The interaction between chloride anions and monosaccharides (glucose and galactose) was studied by DFT in the gas phase and by implementing the polarizable continuum model (PCM) for calculations in solution at the high B3LYP/6-31+G(d,p)//B3LYP/6-311+G(2d,p) level of theory. In all optimized geometries of identified [M+Cl](-) anions, a non-covalent interaction exists. Differences were revealed between monodentate and bidentate complex anions, with the latter having noticeably higher binding energies. The calculated affinity of glucose and galactose toward the chloride anion in the gas phase and their chloride anion binding energies in solution are in excellent agreement with glucose and galactose [M+Cl](-) experimental intensity profiles that are represented as a function of the chloride ion concentration. Density functional calculations of gas-phase affinities toward chloride anion were also performed for the studied disaccharides sucrose and gentiobiose. All calculations are in excellent agreement with the experimental data. An example is introduced wherein HCl was used to effectively ionize sugars and form chlorinated adduct anions to detect sugars and glycosylated metabolites (anthocyanins) in real biological systems (Vitis vinifera grape extracts and wines), whereas they would not have been easily detectable under standard infusion electrospray mass spectrometry conditions as deprotonated species. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Linear electric field mass spectrometry

DOEpatents

McComas, D.J.; Nordholt, J.E.

1992-12-01

A mass spectrometer and methods for mass spectrometry are described. The apparatus is compact and of low weight and has a low power requirement, making it suitable for use on a space satellite and as a portable detector for the presence of substances. High mass resolution measurements are made by timing ions moving through a gridless cylindrically symmetric linear electric field. 8 figs.

Analysis of psilocybin and psilocin in Psilocybe subcubensis Guzmán by ion mobility spectrometry and gas chromatography-mass spectrometry.

PubMed

Keller, T; Schneider, A; Regenscheit, P; Dirnhofer, R; Rücker, T; Jaspers, J; Kisser, W

1999-01-11

A new method has been developed for the rapid analysis of psilocybin and/or psilocin in fungus material using ion mobility spectrometry. Quantitative analysis was performed by gas chromatography-mass spectrometry after a simple one-step extraction involving homogenization of the dried fruit bodies of fungi in chloroform and derivatization with MSTFA. The proposed methods resulted in rapid procedures useful in analyzing psychotropic fungi for psilocybin and psilocin.

High-accuracy mass spectrometry for fundamental studies.

PubMed

Kluge, H-Jürgen

2010-01-01

Mass spectrometry for fundamental studies in metrology and atomic, nuclear and particle physics requires extreme sensitivity and efficiency as well as ultimate resolving power and accuracy. An overview will be given on the global status of high-accuracy mass spectrometry for fundamental physics and metrology. Three quite different examples of modern mass spectrometric experiments in physics are presented: (i) the retardation spectrometer KATRIN at the Forschungszentrum Karlsruhe, employing electrostatic filtering in combination with magnetic-adiabatic collimation-the biggest mass spectrometer for determining the smallest mass, i.e. the mass of the electron anti-neutrino, (ii) the Experimental Cooler-Storage Ring at GSI-a mass spectrometer of medium size, relative to other accelerators, for determining medium-heavy masses and (iii) the Penning trap facility, SHIPTRAP, at GSI-the smallest mass spectrometer for determining the heaviest masses, those of super-heavy elements. Finally, a short view into the future will address the GSI project HITRAP at GSI for fundamental studies with highly-charged ions.

Recent applications of mass spectrometry in forensic toxicology

NASA Astrophysics Data System (ADS)

Foltz, Rodger L.

1992-09-01

This review encompasses applications of mass spectrometry reported during the years 1989, 1990 and 1991 for the analysis of cannabinoids, cocaine, opiates, amphetamines, lysergic acid diethylamide (LSD), and their metabolites in physiological specimens.

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

Applications of Fourier Transform Ion Cyclotron Resonance (FT-ICR) and Orbitrap Based High Resolution Mass Spectrometry in Metabolomics and Lipidomics.

PubMed

Ghaste, Manoj; Mistrik, Robert; Shulaev, Vladimir

2016-05-25

Metabolomics, along with other "omics" approaches, is rapidly becoming one of the major approaches aimed at understanding the organization and dynamics of metabolic networks. Mass spectrometry is often a technique of choice for metabolomics studies due to its high sensitivity, reproducibility and wide dynamic range. High resolution mass spectrometry (HRMS) is a widely practiced technique in analytical and bioanalytical sciences. It offers exceptionally high resolution and the highest degree of structural confirmation. Many metabolomics studies have been conducted using HRMS over the past decade. In this review, we will explore the latest developments in Fourier transform mass spectrometry (FTMS) and Orbitrap based metabolomics technology, its advantages and drawbacks for using in metabolomics and lipidomics studies, and development of novel approaches for processing HRMS data.

Applications of Fourier Transform Ion Cyclotron Resonance (FT-ICR) and Orbitrap Based High Resolution Mass Spectrometry in Metabolomics and Lipidomics

PubMed Central

Ghaste, Manoj; Mistrik, Robert; Shulaev, Vladimir

2016-01-01

Metabolomics, along with other “omics” approaches, is rapidly becoming one of the major approaches aimed at understanding the organization and dynamics of metabolic networks. Mass spectrometry is often a technique of choice for metabolomics studies due to its high sensitivity, reproducibility and wide dynamic range. High resolution mass spectrometry (HRMS) is a widely practiced technique in analytical and bioanalytical sciences. It offers exceptionally high resolution and the highest degree of structural confirmation. Many metabolomics studies have been conducted using HRMS over the past decade. In this review, we will explore the latest developments in Fourier transform mass spectrometry (FTMS) and Orbitrap based metabolomics technology, its advantages and drawbacks for using in metabolomics and lipidomics studies, and development of novel approaches for processing HRMS data. PMID:27231903

Acrylamide: formation, occurrence in food products, detection methods, and legislation.

PubMed

Arvanitoyannis, Ioannis S; Dionisopoulou, Niki

2014-01-01

This review aims at summarizing the most recent updates in the field of acrylamide (AA) formation (mechanism, conditions) and the determination of AA in a number of foods (fried or baked potatoes, chips, coffee, bread, etc). The methods applied for AA detection [Capillary Electrophoresis-Mass Spectrometry (CE-MS), Liquid Chromatography-Mass Spectrometry (LC-MS), Non-Aqueous Capillary Electrophoresis (NACE), High Performance Liquid Chromatography-Mass Spectrometry (HPLC-MS), Pressurized Fluid Extraction (PFE), Matrix Solid-Phase Dispersion (MSPD), Gas Chromatography-Mass Spectrometry (GC-MS), Solid-Phase MicroExtraction-Gas Chromatography (SPME-GC), Enzyme Linked Immunosorbent Assay (ELISA), and MicroEmulsion ElectroKinetic Chromatography (MEEKC) are presented and commented. Several informative figures and tables are included to show the effect of conditions (temperature, time) on the AA formation. A section is also included related to AA legislation in EU and US.