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Sample records for mass spectrometry workflow

  1. Proteomic Workflows for Biomarker Identification Using Mass Spectrometry — Technical and Statistical Considerations during Initial Discovery

    PubMed Central

    Orton, Dennis J.; Doucette, Alan A.

    2013-01-01

    Identification of biomarkers capable of differentiating between pathophysiological states of an individual is a laudable goal in the field of proteomics. Protein biomarker discovery generally employs high throughput sample characterization by mass spectrometry (MS), being capable of identifying and quantifying thousands of proteins per sample. While MS-based technologies have rapidly matured, the identification of truly informative biomarkers remains elusive, with only a handful of clinically applicable tests stemming from proteomic workflows. This underlying lack of progress is attributed in large part to erroneous experimental design, biased sample handling, as well as improper statistical analysis of the resulting data. This review will discuss in detail the importance of experimental design and provide some insight into the overall workflow required for biomarker identification experiments. Proper balance between the degree of biological vs. technical replication is required for confident biomarker identification. PMID:28250400

  2. Selecting Sample Preparation Workflows for Mass Spectrometry-Based Proteomic and Phosphoproteomic Analysis of Patient Samples with Acute Myeloid Leukemia

    PubMed Central

    Hernandez-Valladares, Maria; Aasebø, Elise; Selheim, Frode; Berven, Frode S.; Bruserud, Øystein

    2016-01-01

    Global mass spectrometry (MS)-based proteomic and phosphoproteomic studies of acute myeloid leukemia (AML) biomarkers represent a powerful strategy to identify and confirm proteins and their phosphorylated modifications that could be applied in diagnosis and prognosis, as a support for individual treatment regimens and selection of patients for bone marrow transplant. MS-based studies require optimal and reproducible workflows that allow a satisfactory coverage of the proteome and its modifications. Preparation of samples for global MS analysis is a crucial step and it usually requires method testing, tuning and optimization. Different proteomic workflows that have been used to prepare AML patient samples for global MS analysis usually include a standard protein in-solution digestion procedure with a urea-based lysis buffer. The enrichment of phosphopeptides from AML patient samples has previously been carried out either with immobilized metal affinity chromatography (IMAC) or metal oxide affinity chromatography (MOAC). We have recently tested several methods of sample preparation for MS analysis of the AML proteome and phosphoproteome and introduced filter-aided sample preparation (FASP) as a superior methodology for the sensitive and reproducible generation of peptides from patient samples. FASP-prepared peptides can be further fractionated or IMAC-enriched for proteome or phosphoproteome analyses. Herein, we will review both in-solution and FASP-based sample preparation workflows and encourage the use of the latter for the highest protein and phosphorylation coverage and reproducibility. PMID:28248234

  3. An evolving computational platform for biological mass spectrometry: workflows, statistics and data mining with MASSyPup64.

    PubMed

    Winkler, Robert

    2015-01-01

    In biological mass spectrometry, crude instrumental data need to be converted into meaningful theoretical models. Several data processing and data evaluation steps are required to come to the final results. These operations are often difficult to reproduce, because of too specific computing platforms. This effect, known as 'workflow decay', can be diminished by using a standardized informatic infrastructure. Thus, we compiled an integrated platform, which contains ready-to-use tools and workflows for mass spectrometry data analysis. Apart from general unit operations, such as peak picking and identification of proteins and metabolites, we put a strong emphasis on the statistical validation of results and Data Mining. MASSyPup64 includes e.g., the OpenMS/TOPPAS framework, the Trans-Proteomic-Pipeline programs, the ProteoWizard tools, X!Tandem, Comet and SpiderMass. The statistical computing language R is installed with packages for MS data analyses, such as XCMS/metaXCMS and MetabR. The R package Rattle provides a user-friendly access to multiple Data Mining methods. Further, we added the non-conventional spreadsheet program teapot for editing large data sets and a command line tool for transposing large matrices. Individual programs, console commands and modules can be integrated using the Workflow Management System (WMS) taverna. We explain the useful combination of the tools by practical examples: (1) A workflow for protein identification and validation, with subsequent Association Analysis of peptides, (2) Cluster analysis and Data Mining in targeted Metabolomics, and (3) Raw data processing, Data Mining and identification of metabolites in untargeted Metabolomics. Association Analyses reveal relationships between variables across different sample sets. We present its application for finding co-occurring peptides, which can be used for target proteomics, the discovery of alternative biomarkers and protein-protein interactions. Data Mining derived models

  4. An evolving computational platform for biological mass spectrometry: workflows, statistics and data mining with MASSyPup64

    PubMed Central

    2015-01-01

    In biological mass spectrometry, crude instrumental data need to be converted into meaningful theoretical models. Several data processing and data evaluation steps are required to come to the final results. These operations are often difficult to reproduce, because of too specific computing platforms. This effect, known as ‘workflow decay’, can be diminished by using a standardized informatic infrastructure. Thus, we compiled an integrated platform, which contains ready-to-use tools and workflows for mass spectrometry data analysis. Apart from general unit operations, such as peak picking and identification of proteins and metabolites, we put a strong emphasis on the statistical validation of results and Data Mining. MASSyPup64 includes e.g., the OpenMS/TOPPAS framework, the Trans-Proteomic-Pipeline programs, the ProteoWizard tools, X!Tandem, Comet and SpiderMass. The statistical computing language R is installed with packages for MS data analyses, such as XCMS/metaXCMS and MetabR. The R package Rattle provides a user-friendly access to multiple Data Mining methods. Further, we added the non-conventional spreadsheet program teapot for editing large data sets and a command line tool for transposing large matrices. Individual programs, console commands and modules can be integrated using the Workflow Management System (WMS) taverna. We explain the useful combination of the tools by practical examples: (1) A workflow for protein identification and validation, with subsequent Association Analysis of peptides, (2) Cluster analysis and Data Mining in targeted Metabolomics, and (3) Raw data processing, Data Mining and identification of metabolites in untargeted Metabolomics. Association Analyses reveal relationships between variables across different sample sets. We present its application for finding co-occurring peptides, which can be used for target proteomics, the discovery of alternative biomarkers and protein–protein interactions. Data Mining derived models

  5. A Quantitative Proteomic Workflow for Characterization of Frozen Clinical Biopsies: Laser Capture Microdissection Coupled with Label-Free Mass Spectrometry

    PubMed Central

    Shapiro, John P.; Biswas, Sabyasachi; Merchant, Anand S.; Satoskar, Anjali; Taslim, Cenny; Lin, Shili; Rovin, Brad H.; Sen, Chandan K.; Roy, Sashwati; Freitas, Michael A.

    2013-01-01

    This paper describes a simple, highly efficient and robust proteomic workflow for routine liquid-chromatography tandem mass spectrometry analysis of Laser Microdissection Pressure Catapulting (LMPC) isolates. Highly efficient protein recovery was achieved by optimization of a “one-pot” protein extraction and digestion allowing for reproducible proteomic analysis on as few as 500 LMPC isolated cells. The method was combined with label-free spectral count quantitation to characterize proteomic differences from 3,000–10,000 LMPC isolated cells. Significance analysis of spectral count data was accomplished using the edgeR tag-count R package combined with hierarchical cluster analysis. To illustrate the capability of this robust workflow, two examples are presented: 1) analysis of keratinocytes from human punch biopsies of normal skin and a chronic diabetic wound and 2) comparison of glomeruli from needle biopsies of patients with kidney disease. Differentially expressed proteins were validated by use of immunohistochemistry. These examples illustrate that tissue proteomics carried out on limited clinical material can obtain informative proteomic signatures for disease pathogenesis and demonstrate the suitability of this approach for biomarker discovery. PMID:23022584

  6. A quantitative proteomic workflow for characterization of frozen clinical biopsies: laser capture microdissection coupled with label-free mass spectrometry.

    PubMed

    Shapiro, John P; Biswas, Sabyasachi; Merchant, Anand S; Satoskar, Anjali; Taslim, Cenny; Lin, Shili; Rovin, Brad H; Sen, Chandan K; Roy, Sashwati; Freitas, Michael A

    2012-12-21

    This paper describes a simple, highly efficient and robust proteomic workflow for routine liquid-chromatography tandem mass spectrometry analysis of Laser Microdissection Pressure Catapulting (LMPC) isolates. Highly efficient protein recovery was achieved by optimization of a "one-pot" protein extraction and digestion allowing for reproducible proteomic analysis on as few as 500 LMPC isolated cells. The method was combined with label-free spectral count quantitation to characterize proteomic differences from 3000-10,000 LMPC isolated cells. Significance analysis of spectral count data was accomplished using the edgeR tag-count R package combined with hierarchical cluster analysis. To illustrate the capability of this robust workflow, two examples are presented: 1) analysis of keratinocytes from human punch biopsies of normal skin and a chronic diabetic wound and 2) comparison of glomeruli from needle biopsies of patients with kidney disease. Differentially expressed proteins were validated by use of immunohistochemistry. These examples illustrate that tissue proteomics carried out on limited clinical material can obtain informative proteomic signatures for disease pathogenesis and demonstrate the suitability of this approach for biomarker discovery.

  7. DeMix Workflow for Efficient Identification of Cofragmented Peptides in High Resolution Data-dependent Tandem Mass Spectrometry*

    PubMed Central

    Zhang, Bo; Pirmoradian, Mohammad; Chernobrovkin, Alexey; Zubarev, Roman A.

    2014-01-01

    Based on conventional data-dependent acquisition strategy of shotgun proteomics, we present a new workflow DeMix, which significantly increases the efficiency of peptide identification for in-depth shotgun analysis of complex proteomes. Capitalizing on the high resolution and mass accuracy of Orbitrap-based tandem mass spectrometry, we developed a simple deconvolution method of “cloning” chimeric tandem spectra for cofragmented peptides. Additional to a database search, a simple rescoring scheme utilizes mass accuracy and converts the unwanted cofragmenting events into a surprising advantage of multiplexing. With the combination of cloning and rescoring, we obtained on average nine peptide-spectrum matches per second on a Q-Exactive workbench, whereas the actual MS/MS acquisition rate was close to seven spectra per second. This efficiency boost to 1.24 identified peptides per MS/MS spectrum enabled analysis of over 5000 human proteins in single-dimensional LC-MS/MS shotgun experiments with an only two-hour gradient. These findings suggest a change in the dominant “one MS/MS spectrum - one peptide” paradigm for data acquisition and analysis in shotgun data-dependent proteomics. DeMix also demonstrated higher robustness than conventional approaches in terms of lower variation among the results of consecutive LC-MS/MS runs. PMID:25100859

  8. A Comprehensive Workflow of Mass Spectrometry-Based Untargeted Metabolomics in Cancer Metabolic Biomarker Discovery Using Human Plasma and Urine

    PubMed Central

    Zou, Wei; She, Jianwen; Tolstikov, Vladimir V.

    2013-01-01

    Current available biomarkers lack sensitivity and/or specificity for early detection of cancer. To address this challenge, a robust and complete workflow for metabolic profiling and data mining is described in details. Three independent and complementary analytical techniques for metabolic profiling are applied: hydrophilic interaction liquid chromatography (HILIC–LC), reversed-phase liquid chromatography (RP–LC), and gas chromatography (GC). All three techniques are coupled to a mass spectrometer (MS) in the full scan acquisition mode, and both unsupervised and supervised methods are used for data mining. The univariate and multivariate feature selection are used to determine subsets of potentially discriminative predictors. These predictors are further identified by obtaining accurate masses and isotopic ratios using selected ion monitoring (SIM) and data-dependent MS/MS and/or accurate mass MSn ion tree scans utilizing high resolution MS. A list combining all of the identified potential biomarkers generated from different platforms and algorithms is used for pathway analysis. Such a workflow combining comprehensive metabolic profiling and advanced data mining techniques may provide a powerful approach for metabolic pathway analysis and biomarker discovery in cancer research. Two case studies with previous published data are adapted and included in the context to elucidate the application of the workflow. PMID:24958150

  9. A comprehensive workflow of mass spectrometry-based untargeted metabolomics in cancer metabolic biomarker discovery using human plasma and urine.

    PubMed

    Zou, Wei; She, Jianwen; Tolstikov, Vladimir V

    2013-09-11

    Current available biomarkers lack sensitivity and/or specificity for early detection of cancer. To address this challenge, a robust and complete workflow for metabolic profiling and data mining is described in details. Three independent and complementary analytical techniques for metabolic profiling are applied: hydrophilic interaction liquid chromatography (HILIC-LC), reversed-phase liquid chromatography (RP-LC), and gas chromatography (GC). All three techniques are coupled to a mass spectrometer (MS) in the full scan acquisition mode, and both unsupervised and supervised methods are used for data mining. The univariate and multivariate feature selection are used to determine subsets of potentially discriminative predictors. These predictors are further identified by obtaining accurate masses and isotopic ratios using selected ion monitoring (SIM) and data-dependent MS/MS and/or accurate mass MSn ion tree scans utilizing high resolution MS. A list combining all of the identified potential biomarkers generated from different platforms and algorithms is used for pathway analysis. Such a workflow combining comprehensive metabolic profiling and advanced data mining techniques may provide a powerful approach for metabolic pathway analysis and biomarker discovery in cancer research. Two case studies with previous published data are adapted and included in the context to elucidate the application of the workflow.

  10. Successful adaption of a forensic toxicological screening workflow employing nontargeted liquid chromatography-tandem mass spectrometry to water analysis.

    PubMed

    Steger, Julia; Arnhard, Kathrin; Haslacher, Sandra; Geiger, Klemens; Singer, Klaus; Schlapp, Michael; Pitterl, Florian; Oberacher, Herbert

    2016-04-01

    Forensic toxicology and environmental water analysis share the common interest and responsibility in ensuring comprehensive and reliable confirmation of drugs and pharmaceutical compounds in samples analyzed. Dealing with similar analytes, detection and identification techniques should be exchangeable between scientific disciplines. Herein, we demonstrate the successful adaption of a forensic toxicological screening workflow employing nontargeted LC/MS/MS under data-dependent acquisition control and subsequent database search to water analysis. The main modification involved processing of an increased sample volume with SPE (500 mL vs. 1-10 mL) to reach LODs in the low ng/L range. Tandem mass spectra acquired with a qTOF instrument were submitted to database search. The targeted data mining strategy was found to be sensitive and specific; automated search produced hardly any false results. To demonstrate the applicability of the adapted workflow to complex samples, 14 wastewater effluent samples collected on seven consecutive days at the local wastewater-treatment plant were analyzed. Of the 88,970 fragment ion mass spectra produced, 8.8% of spectra were successfully assigned to one of the 1040 reference compounds included in the database, and this enabled the identification of 51 compounds representing important illegal drugs, members of various pharmaceutical compound classes, and metabolites thereof.

  11. Mathematical Modeling and Analysis of Mass Spectrometry Data in Workflows for the Discovery of Biomarkets in Breast Cancer

    DTIC Science & Technology

    2008-07-01

    improve the statistical power and clinical interpretation of the results, the protein identifications were mapped to high quality publicly available...data with metabolomic analysis, and will provide additional data from protein microarrays. 15. SUBJECT TERMS Mass-spectrometry proteomics, plasma ...proteomics, LC-MS/MS, cancer proteins . 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT 18 . NUMBER OF PAGES 19a. NAME OF

  12. Conformational analysis of large and highly disulfide-stabilized proteins by integrating online electrochemical reduction into an optimized H/D exchange mass spectrometry workflow.

    PubMed

    Trabjerg, Esben; Jakobsen, Rasmus U; Mysling, Simon; Christensen, Søren; Jørgensen, Thomas J D; Rand, Kasper D

    2015-09-01

    Analysis of disulfide-bonded proteins by hydrogen/deuterium exchange mass spectrometry (HDX-MS) requires effective and rapid reduction of disulfide bonds before enzymatic digestion in order to increase sequence coverage. In a conventional HDX-MS workflow, disulfide bonds are reduced chemically by addition of a reducing agent to the quench solution (e.g., tris(2-carboxyethyl)phosphine (TCEP)). The chemical reduction, however, is severely limited under quenched conditions due to a narrow time window as well as low pH and temperature. Here, we demonstrate the real-world applicability of integrating electrochemical reduction into an online HDX-MS workflow. We have optimized the electrochemical reduction efficiency during HDX-MS analysis of two particularly challenging disulfide stabilized proteins: a therapeutic IgG1-antibody and nerve growth factor-β (NGF). Several different parameters (flow rate and applied square wave potential, as well as the type of labeling and quench buffer) were investigated, and the optimized workflow increased the sequence coverage of NGF from 46% with chemical reduction to 99%, when electrochemical reduction was applied. Additionally, the optimized workflow also enabled a similar high sequence coverage of 96% and 87% for the heavy and light chain of the IgG1-antibody, respectively. The presented results demonstrate the successful electrochemical reduction during HDX-MS analysis of both a small exceptional tightly disulfide-bonded protein (NGF) as well as the largest protein attempted to date (IgG1-antibody). We envision that online electrochemical reduction is poised to decrease the complexity of sample handling and increase the versatility of the HDX-MS technique.

  13. 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.

  14. Middle-down hybrid chromatography/tandem mass spectrometry workflow for characterization of combinatorial post-translational modifications in histones.

    PubMed

    Sidoli, Simone; Schwämmle, Veit; Ruminowicz, Chrystian; Hansen, Thomas A; Wu, Xudong; Helin, Kristian; Jensen, Ole N

    2014-10-01

    We present an integrated middle-down proteomics platform for sensitive mapping and quantification of coexisting PTMs in large polypeptides (5-7 kDa). We combined an RP trap column with subsequent weak cation exchange-hydrophilic interaction LC interfaced directly to high mass accuracy ESI MS/MS using electron transfer dissociation. This enabled automated and efficient separation and sequencing of hypermodified histone N-terminal tails for unambiguous localization of combinatorial PTMs. We present Histone Coder and IsoScale software to extract, filter, and analyze MS/MS data, including quantification of cofragmenting isobaric polypeptide species. We characterized histone tails derived from murine embryonic stem cells knockout in suppressor of zeste12 (Suz12(-/-) ) and quantified 256 combinatorial histone marks in histones H3, H4, and H2A. Furthermore, a total of 713 different combinatorial histone marks were identified in purified histone H3. We measured a seven-fold reduction of H3K27me2/me3 (where me2 and me3 are dimethylation and trimethylation, respectively) in Suz12(-) (/) (-) cells and detected significant changes of the relative abundance of 16 other single PTMs of histone H3 and other combinatorial marks. We conclude that the inactivation of Suz12 is associated with changes in the abundance of not only H3K27 methylation but also multiple other PTMs in histone H3 tails.

  15. Mass spectrometry

    SciTech Connect

    Burlingame, A.L.; Baillie, T.A.; Derrick, P.J.

    1986-04-01

    It is the intention of the review to bring together in one source the direction of major developments in mass spectrometry and to illustrate these by citing key contributions from both fundamental and applied research. The Review is intended to provide the reader with a sense of the main currents, their breadth and depth, and probable future directions. It is also intended to provide the reader with a glimpse of the diverse discoveries and results that underpin the eventual development of new methods and instruments - the keys to obtaining new insights in all the physical, chemical, and biological sciences which depend on mass spectrometry at various levels of sophistication. Focal points for future interdisciplinary synergism might be selective quantitative derivatization of large peptides, which would convey properties that direct fragmentation providing specific sequence information, or optimization of LCMS for biooligomer sequencing and mixture analysis, or the perfect way to control or enhance the internal energy of ions of any size, or many others. 1669 references.

  16. A workflow for multiclass determination of 256 pesticides in essential oils by liquid chromatography tandem mass spectrometry using evaporation and dilution approaches: Application to lavandin, lemon and cypress essential oils.

    PubMed

    Fillatre, Yoann; Rondeau, David; Daguin, Antoine; Communal, Pierre-Yves

    2016-01-01

    This paper describes the determination of 256 multiclass pesticides in cypress and lemon essential oils (EOs) by the way of liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI/MS/MS) analysis using the scheduled selected reaction monitoring mode (sSRM) available on a hybrid quadrupole linear ion trap (QLIT) mass spectrometer. The performance of a sample preparation of lemon and cypress EOs based on dilution or evaporation under nitrogen assisted by a controlled heating were assessed. The best limits of quantification (LOQs) were achieved with the evaporation under nitrogen method giving LOQs≤10µgL(-1) for 91% of the pesticides. In addition the very satisfactory results obtained for recovery, repeatability and linearity showed that for EOs of relatively low evaporation temperature, a sample preparation based on evaporation under nitrogen is well adapted and preferable to dilution. By compiling these results with those previously published by some of us on lavandin EO, we proposed a workflow dedicated to multiresidue determination of pesticides in various EOs by LC-ESI/sSRM. Among the steps involved in this workflow, the protocol related to mass spectrometry proposes an alternative confirmation method to the classical SRM ratio criteria based on a sSRM survey scan followed by an information-dependent acquisition using the sensitive enhanced product ion (EPI) scan to generate MS/MS spectra then compared to a reference. The submitted workflow was applied to the case of lemon EOs samples highlighting for the first time the simultaneous detection of 20 multiclass pesticides in one EO. Some pesticides showed very high concentration levels with amounts greatly exceeding the mgL(-1).

  17. MASS SPECTROMETRY

    DOEpatents

    Nier, A.O.C.

    1959-08-25

    A voltage switching apparatus is described for use with a mass spectrometer in the concentratron analysis of several components of a gas mixture. The system automatically varies the voltage on the accelerating electrode of the mass spectrometer through a program of voltages which corresponds to the particular gas components under analysis. Automatic operation may be discontinued at any time to permit the operator to manually select any desired predetermined accelerating voltage. Further, the system may be manually adjusted to vary the accelerating voltage over a wide range.

  18. MASS SPECTROMETRY

    DOEpatents

    Friedman, L.

    1962-01-01

    method is described for operating a mass spectrometer to improve its resolution qualities and to extend its period of use substantially between cleanings. In this method, a small amount of a beta emitting gas such as hydrogen titride or carbon-14 methane is added to the sample being supplied to the spectrometer for investigation. The additive establishes leakage paths on the surface of the non-conducting film accumulating within the vacuum chamber of the spectrometer, thereby reducing the effect of an accumulated static charge on the electrostatic and magnetic fields established within the instrument. (AEC)

  19. A liquid chromatography–mass spectrometry-based workflow for measurement of branched Fatty Acid esters of Hydroxy Fatty Acids (FAHFAs)

    PubMed Central

    Zhang, Tejia; Chen, Shili; Syed, Ismail; Ståhlman, Marcus; Kolar, Matthew J.; Homan, Edwin A.; Chu, Qian; Smith, Ulf; Borén, Jan; Kahn, Barbara B.; Saghatelian, Alan

    2016-01-01

    Branched Fatty Acid esters of Hydroxy Fatty Acids (FAHFAs) are a recently discovered class of endogenous mammalian lipids with anti-diabetic and anti-inflammatory effects. We identified 16 different FAHFA families, such as branched Palmitic Acid esters of Hydroxy Stearic Acids (PAHSA), and each family consists of multiple isomers where the branched ester is at different positions (e.g. 5- and 9-PAHSA). We anticipate increased need for PAHSA measurements as markers of metabolic and inflammatory diseases. In this protocol, we provide a detailed description of the extraction and subsequent liquid chromatography–mass spectrometry (LC–MS) of FAHFAs from human or mouse tissues. For a sample size of 6–12 the time frame is 2–3 days. PMID:26985573

  20. Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis

    PubMed Central

    Sidoli, Simone; Bhanu, Natarajan V.; Karch, Kelly R.; Wang, Xiaoshi; Garcia, Benjamin A.

    2016-01-01

    Nucleosomes are the smallest structural unit of chromatin, composed of 147 base pairs of DNA wrapped around an octamer of histone proteins. Histone function is mediated by extensive post-translational modification by a myriad of nuclear proteins. These modifications are critical for nuclear integrity as they regulate chromatin structure and recruit enzymes involved in gene regulation, DNA repair and chromosome condensation. Even though a large part of the scientific community adopts antibody-based techniques to characterize histone PTM abundance, these approaches are low throughput and biased against hypermodified proteins, as the epitope might be obstructed by nearby modifications. This protocol describes the use of nano liquid chromatography (nLC) and mass spectrometry (MS) for accurate quantification of histone modifications. This method is designed to characterize a large variety of histone PTMs and the relative abundance of several histone variants within single analyses. In this protocol, histones are derivatized with propionic anhydride followed by digestion with trypsin to generate peptides of 5 - 20 aa in length. After digestion, the newly exposed N-termini of the histone peptides are derivatized to improve chromatographic retention during nLC-MS. This method allows for the relative quantification of histone PTMs spanning four orders of magnitude. PMID:27286567

  1. A workflow for large-scale empirical identification of cell wall N-linked glycoproteins of tomato (Solanum lycopersicum) fruit by tandem mass spectrometry

    PubMed Central

    Thannhauser, Theodore W.; Shen, Miaoqing; Sherwood, Robert; Howe, Kevin; Fish, Tara; Yang, Yong; Chen, Wei; Zhang, Sheng

    2013-01-01

    Glycosylation is a common post-translational modification of plant proteins that impacts a large number of important biological processes. Nevertheless, the impacts of differential site occupancy and the nature of specific glycoforms are obscure. Historically, characterization of glycoproteins has been difficult due to the distinct physicochemical properties of the peptidyl and glycan moieties, the variable and dynamic nature of the glycosylation process, their heterogeneous nature, and the low relative abundance of each glycoform. In this study, we explore a new pipeline developed for large-scale empirical identification of N-linked glycoproteins of tomato fruit as part of our ongoing efforts to characterize the tomato secretome. The workflow presented involves a combination of lectin affinity, tryptic digestion, ion-pairing HILIC and precursor ion-driven data dependent MS/MS analysis with a script to facilitate the identification and characterization of occupied N-linked glycosylation sites. A total of 212 glycoproteins were identified in this study, in which 26 glycopeptides from 24 glycoproteins were successfully characterized in just one HILIC fraction. Further precursor ion discovery (PID)-based MS/MS and deglycosylation followed by high accuracy and resolution MS analysis were used to confirm the glycosylation sites and determine site occupancy rates. The workflow reported is robust and capable of producing large amounts of empirical data involving N-linked glycosylation sites and their associated glycoforms. PMID:23580464

  2. Metabolite identification of bentysrepinine (Y101), a novel anti-HBV agent in rats using a five-step strategy based on a combined workflow with two different platforms of liquid chromatography-tandem mass spectrometry.

    PubMed

    Fan, Huirong; Hu, Zhanxing; Li, Ruixing; Dong, Shiqi; Gu, Yuan; Liu, Ting; Si, Duanyun; Liang, Guangyi; Liu, Changxiao

    2017-01-01

    Bentysrepinine (Y101), a derivative of repensine (a compound isolated from Dichondrarepens Forst), is a novel phenyalanine dipeptide inhibiting DNA-HBV and cccDNA activities and is currently under development for the treatment of hepatitis B virus (HBV)-infected hepatitis. Our previous study implied that there might be an existence of extensive metabolism of Y101 in rats. Therefore, it is necessary to perform metabolic profiling study to further evaluate its safety and drug-like properties. In this study, the metabolism of Y101 in rats was investigated by a convincible five-step strategy to characterize metabolites in plasma and that excreted into urine, bile and feces. The five-step strategy was realized by using an combined workflow on two different MS platforms, including various scan modes of liquid chromatography with hybrid quadruple-linear ion trap mass spectrometry (LC-QTRAP-MS/MS) and various post-acquiring data mining tools of liquid chromatography-quadrupole time-of-flight tandem mass spectrometry (LC-QTOF-MS/MS). QTOF MS/MS was employed as a powerful complementary tool to enable high confidence of metabolites identification using its functions of accurate MS and MS/MS fragmentation. As a result, a total of 30 metabolites were detected, including 25 phase I and 5 phase II metabolites. Among them, four primary metabolites (M6-M9) were further identified by comparing with the authentic standards chemically synthesized. The possible metabolic pathways of Y101 in rats were proposed to be amide hydrolysis, monohydroxylation, dihydroxylation, N-oxidation, demethylation, methylation, glucosidation and glucuronidation. This is the first study of the metabolism of Y101 in rats. The five-step strategy was successfully used to systematically characterize metabolites of Y101 in rats, and it would be generally applied for metabolite identification of new drug candidate.

  3. 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)

  4. 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…

  5. 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.

  6. Forensic Mass Spectrometry.

    PubMed

    Hoffmann, William D; Jackson, Glen P

    2015-01-01

    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.

  7. 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

  8. Ambient ionization mass spectrometry

    NASA Astrophysics Data System (ADS)

    Lebedev, A. T.

    2015-07-01

    Ambient ionization mass spectrometry emerged as a new scientific discipline only about ten years ago. A considerable body of information has been reported since that time. Keeping the sensitivity, performance and informativity of classical mass spectrometry methods, the new approach made it possible to eliminate laborious sample preparation procedures and triggered the development of miniaturized instruments to work directly in the field. The review concerns the theoretical foundations and design of ambient ionization methods. Their advantages and drawbacks, as well as prospects for application in chemistry, biology, medicine, environmetal analysis, etc., are discussed. The bibliography includes 194 references.

  9. Analytical mass spectrometry

    SciTech Connect

    Not Available

    1990-01-01

    This 43rd Annual Summer Symposium on Analytical Chemistry was held July 24--27, 1990 at Oak Ridge, TN and contained sessions on the following topics: Fundamentals of Analytical Mass Spectrometry (MS), MS in the National Laboratories, Lasers and Fourier Transform Methods, Future of MS, New Ionization and LC/MS Methods, and an extra session. (WET)

  10. Analytical mass spectrometry. Abstracts

    SciTech Connect

    Not Available

    1990-12-31

    This 43rd Annual Summer Symposium on Analytical Chemistry was held July 24--27, 1990 at Oak Ridge, TN and contained sessions on the following topics: Fundamentals of Analytical Mass Spectrometry (MS), MS in the National Laboratories, Lasers and Fourier Transform Methods, Future of MS, New Ionization and LC/MS Methods, and an extra session. (WET)

  11. Mass spectrometry with accelerators.

    PubMed

    Litherland, A E; Zhao, X-L; Kieser, W E

    2011-01-01

    As one in a series of articles on Canadian contributions to mass spectrometry, this review begins with an outline of the history of accelerator mass spectrometry (AMS), noting roles played by researchers at three Canadian AMS laboratories. After a description of the unique features of AMS, three examples, (14)C, (10)Be, and (129)I are given to illustrate the methods. The capabilities of mass spectrometry have been extended by the addition of atomic isobar selection, molecular isobar attenuation, further ion acceleration, followed by ion detection and ion identification at essentially zero dark current or ion flux. This has been accomplished by exploiting the techniques and accelerators of atomic and nuclear physics. In 1939, the first principles of AMS were established using a cyclotron. In 1977 the selection of isobars in the ion source was established when it was shown that the (14)N(-) ion was very unstable, or extremely difficult to create, making a tandem electrostatic accelerator highly suitable for assisting the mass spectrometric measurement of the rare long-lived radioactive isotope (14)C in the environment. This observation, together with the large attenuation of the molecular isobars (13)CH(-) and (12)CH 2(-) during tandem acceleration and the observed very low background contamination from the ion source, was found to facilitate the mass spectrometry of (14)C to at least a level of (14)C/C ~ 6 × 10(-16), the equivalent of a radiocarbon age of 60,000 years. Tandem Accelerator Mass Spectrometry, or AMS, has now made possible the accurate radiocarbon dating of milligram-sized carbon samples by ion counting as well as dating and tracing with many other long-lived radioactive isotopes such as (10)Be, (26)Al, (36)Cl, and (129)I. The difficulty of obtaining large anion currents with low electron affinities and the difficulties of isobar separation, especially for the heavier mass ions, has prompted the use of molecular anions and the search for alternative

  12. 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...

  13. Desorption in Mass Spectrometry.

    PubMed

    Usmanov, Dilshadbek Tursunbayevich; Ninomiya, Satoshi; Chen, Lee Chuin; Saha, Subhrakanti; Mandal, Mridul Kanti; Sakai, Yuji; Takaishi, Rio; Habib, Ahsan; Hiraoka, Kenzo; Yoshimura, Kentaro; Takeda, Sen; Wada, Hiroshi; Nonami, Hiroshi

    2017-01-01

    In mass spectrometry, analytes must be released in the gas phase. There are two representative methods for the gasification of the condensed samples, i.e., ablation and desorption. While ablation is based on the explosion induced by the energy accumulated in the condensed matrix, desorption is a single molecular process taking place on the surface. In this paper, desorption methods for mass spectrometry developed in our laboratory: flash heating/rapid cooling, Leidenfrost phenomenon-assisted thermal desorption (LPTD), solid/solid friction, liquid/solid friction, electrospray droplet impact (EDI) ionization/desorption, and probe electrospray ionization (PESI), will be described. All the methods are concerned with the surface and interface phenomena. The concept of how to desorb less-volatility compounds from the surface will be discussed.

  14. Desorption in Mass Spectrometry

    PubMed Central

    Usmanov, Dilshadbek Tursunbayevich; Ninomiya, Satoshi; Chen, Lee Chuin; Saha, Subhrakanti; Mandal, Mridul Kanti; Sakai, Yuji; Takaishi, Rio; Habib, Ahsan; Hiraoka, Kenzo; Yoshimura, Kentaro; Takeda, Sen; Wada, Hiroshi; Nonami, Hiroshi

    2017-01-01

    In mass spectrometry, analytes must be released in the gas phase. There are two representative methods for the gasification of the condensed samples, i.e., ablation and desorption. While ablation is based on the explosion induced by the energy accumulated in the condensed matrix, desorption is a single molecular process taking place on the surface. In this paper, desorption methods for mass spectrometry developed in our laboratory: flash heating/rapid cooling, Leidenfrost phenomenon-assisted thermal desorption (LPTD), solid/solid friction, liquid/solid friction, electrospray droplet impact (EDI) ionization/desorption, and probe electrospray ionization (PESI), will be described. All the methods are concerned with the surface and interface phenomena. The concept of how to desorb less-volatility compounds from the surface will be discussed. PMID:28337398

  15. Hybrid instruments for mass spectrometry/mass spectrometry

    SciTech Connect

    Glish, G.L.; McLuckey, S.A.

    1986-01-01

    In order to refine further the technique of mass spectrometry/mass spectrometry efforts are being made to combine the desirable features of sector based tandem instruments with those of triple quadrupole mass spectrometers. This has resulted in the construction of tandem mass spectrometers which incorporate both sector type analyzers and quadrupole mass filters. These so-called hybrid instruments, designed specifically for mass spectrometry/mass spectrometry applications, are appearing in a variety of geometries each with unique features. This review describes the hybrid instruments reported to data and discusses general considerations for evaluating hybrid instruments with regard to application. 100 references.

  16. "Magic" Ionization Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Trimpin, Sarah

    2016-01-01

    The systematic study of the temperature and pressure dependence of matrix-assisted ionization (MAI) led us to the discovery of the seemingly impossible, initially explained by some reviewers as either sleight of hand or the misinterpretation by an overzealous young scientist of results reported many years before and having little utility. The "magic" that we were attempting to report was that with matrix assistance, molecules, at least as large as bovine serum albumin (66 kDa), are lifted into the gas phase as multiply charged ions simply by exposure of the matrix:analyte sample to the vacuum of a mass spectrometer. Applied heat, a laser, or voltages are not necessary to achieve charge states and ion abundances only previously observed with electrospray ionization (ESI). The fundamentals of how solid phase volatile or nonvolatile compounds are converted to gas-phase ions without added energy currently involves speculation providing a great opportunity to rethink mechanistic understanding of ionization processes used in mass spectrometry. Improved understanding of the mechanism(s) of these processes and their connection to ESI and matrix-assisted laser desorption/ionization may provide opportunities to further develop new ionization strategies for traditional and yet unforeseen applications of mass spectrometry. This Critical Insights article covers developments leading to the discovery of a seemingly magic ionization process that is simple to use, fast, sensitive, robust, and can be directly applied to surface characterization using portable or high performance mass spectrometers.

  17. "Magic" Ionization Mass Spectrometry.

    PubMed

    Trimpin, Sarah

    2016-01-01

    The systematic study of the temperature and pressure dependence of matrix-assisted ionization (MAI) led us to the discovery of the seemingly impossible, initially explained by some reviewers as either sleight of hand or the misinterpretation by an overzealous young scientist of results reported many years before and having little utility. The “magic” that we were attempting to report was that with matrix assistance, molecules, at least as large as bovine serum albumin (66 kDa), are lifted into the gas phase as multiply charged ions simply by exposure of the matrix:analyte sample to the vacuum of a mass spectrometer. Applied heat, a laser, or voltages are not necessary to achieve charge states and ion abundances only previously observed with electrospray ionization (ESI). The fundamentals of how solid phase volatile or nonvolatile compounds are converted to gas-phase ions without added energy currently involves speculation providing a great opportunity to rethink mechanistic understanding of ionization processes used in mass spectrometry. Improved understanding of the mechanism(s) of these processes and their connection to ESI and matrix-assisted laser desorption/ionization may provide opportunities to further develop new ionization strategies for traditional and yet unforeseen applications of mass spectrometry. This Critical Insights article covers developments leading to the discovery of a seemingly magic ionization process that is simple to use, fast, sensitive, robust, and can be directly applied to surface characterization using portable or high performance mass spectrometers.

  18. Single event mass spectrometry

    DOEpatents

    Conzemius, Robert J.

    1990-01-16

    A means and method for single event time of flight mass spectrometry for analysis of specimen materials. The method of the invention includes pulsing an ion source imposing at least one pulsed ion onto the specimen to produce a corresponding emission of at least one electrically charged particle. The emitted particle is then dissociated into a charged ion component and an uncharged neutral component. The ion and neutral components are then detected. The time of flight of the components are recorded and can be used to analyze the predecessor of the components, and therefore the specimen material. When more than one ion particle is emitted from the specimen per single ion impact, the single event time of flight mass spectrometer described here furnis This invention was made with Government support under Contract No. W-7405-ENG82 awarded by the Department of Energy. The Government has certain rights in the invention.

  19. Absorption mode FTICR mass spectrometry imaging.

    PubMed

    Smith, Donald F; Kilgour, David P A; Konijnenburg, Marco; O'Connor, Peter B; Heeren, Ron M A

    2013-12-03

    Fourier transform ion cyclotron resonance mass spectrometry offers the highest mass resolving power for molecular imaging experiments. This high mass resolving power ensures that closely spaced peaks at the same nominal mass are resolved for proper image generation. Typically higher magnetic fields are used to increase mass resolving power. However, a gain in mass resolving power can also be realized by phase correction of the data for absorption mode display. In addition to mass resolving power, absorption mode offers higher mass accuracy and signal-to-noise ratio over the conventional magnitude mode. Here, we present the first use of absorption mode for Fourier transform ion cyclotron resonance mass spectrometry imaging. The Autophaser algorithm is used to phase correct each spectrum (pixel) in the image, and then, these parameters are used by the Chameleon work-flow based data processing software to generate absorption mode "Datacubes" for image and spectral viewing. Absorption mode reveals new mass and spatial features that are not resolved in magnitude mode and results in improved selected ion image contrast.

  20. Biomedical accelerator mass spectrometry

    NASA Astrophysics Data System (ADS)

    Freeman, Stewart P. H. T.; Vogel, John S.

    1995-05-01

    Ultrasensitive SIMS with accelerator based spectrometers has recently begun to be applied to biomedical problems. Certain very long-lived radioisotopes of very low natural abundances can be used to trace metabolism at environmental dose levels ( [greater-or-equal, slanted] z mol in mg samples). 14C in particular can be employed to label a myriad of compounds. Competing technologies typically require super environmental doses that can perturb the system under investigation, followed by uncertain extrapolation to the low dose regime. 41Ca and 26Al are also used as elemental tracers. Given the sensitivity of the accelerator method, care must be taken to avoid contamination of the mass spectrometer and the apparatus employed in prior sample handling including chemical separation. This infant field comprises the efforts of a dozen accelerator laboratories. The Center for Accelerator Mass Spectrometry has been particularly active. In addition to collaborating with groups further afield, we are researching the kinematics and binding of genotoxins in-house, and we support innovative uses of our capability in the disciplines of chemistry, pharmacology, nutrition and physiology within the University of California. The field can be expected to grow further given the numerous potential applications and the efforts of several groups and companies to integrate more the accelerator technology into biomedical research programs; the development of miniaturized accelerator systems and ion sources capable of interfacing to conventional HPLC and GMC, etc. apparatus for complementary chemical analysis is anticipated for biomedical laboratories.

  1. Accelerator mass spectrometry.

    PubMed

    Hellborg, Ragnar; Skog, Göran

    2008-01-01

    In this overview the technique of accelerator mass spectrometry (AMS) and its use are described. AMS is a highly sensitive method of counting atoms. It is used to detect very low concentrations of natural isotopic abundances (typically in the range between 10(-12) and 10(-16)) of both radionuclides and stable nuclides. The main advantages of AMS compared to conventional radiometric methods are the use of smaller samples (mg and even sub-mg size) and shorter measuring times (less than 1 hr). The equipment used for AMS is almost exclusively based on the electrostatic tandem accelerator, although some of the newest systems are based on a slightly different principle. Dedicated accelerators as well as older "nuclear physics machines" can be found in the 80 or so AMS laboratories in existence today. The most widely used isotope studied with AMS is 14C. Besides radiocarbon dating this isotope is used in climate studies, biomedicine applications and many other fields. More than 100,000 14C samples are measured per year. Other isotopes studied include 10Be, 26Al, 36Cl, 41Ca, 59Ni, 129I, U, and Pu. Although these measurements are important, the number of samples of these other isotopes measured each year is estimated to be less than 10% of the number of 14C samples.

  2. Assessment of current mass spectrometric workflows for the quantification of low abundant proteins and phosphorylation sites

    PubMed Central

    Bauer, Manuel; Ahrné, Erik; Baron, Anna P.; Glatter, Timo; Fava, Luca L.; Santamaria, Anna; Nigg, Erich A.; Schmidt, Alexander

    2015-01-01

    The data described here provide a systematic performance evaluation of popular data-dependent (DDA) and independent (DIA) mass spectrometric (MS) workflows currently used in quantitative proteomics. We assessed the limits of identification, quantification and detection for each method by analyzing a dilution series of 20 unmodified and 10 phosphorylated synthetic heavy labeled reference peptides, respectively, covering six orders of magnitude in peptide concentration with and without a complex human cell digest background. We found that all methods performed very similarly in the absence of background proteins, however, when analyzing whole cell lysates, targeted methods were at least 5–10 times more sensitive than directed or DDA methods. In particular, higher stage fragmentation (MS3) of the neutral loss peak using a linear ion trap increased dynamic quantification range of some phosphopeptides up to 100-fold. We illustrate the power of this targeted MS3 approach for phosphopeptide monitoring by successfully quantifying 9 phosphorylation sites of the kinetochore and spindle assembly checkpoint component Mad1 over different cell cycle states from non-enriched pull-down samples. The data are associated to the research article ‘Evaluation of data-dependent and data-independent mass spectrometric workflows for sensitive quantification of proteins and phosphorylation sites׳ (Bauer et al., 2014) [1]. The mass spectrometry and the analysis dataset have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD000964. PMID:26550600

  3. Mass spectrometry in environmental toxicology.

    PubMed

    Groh, Ksenia J; Suter, Marc J-F

    2014-01-01

    In environmental toxicology, mass spectrometry can be applied to evaluate both exposure to chemicals as well as their effects in organisms. Various ultra-trace techniques are employed today to measure pollutants in different environmental compartments. Increasingly, effect-directed analysis is being applied to focus chemical monitoring on sites of ecotoxicological concern. Mass spectrometry is also very instrumental for studying the interactions of chemicals with organisms on the molecular and cellular level, providing new insights into mechanisms of toxicity. In the future, diverse mass spectrometry-based techniques are expected to become even more widely used in this field, contributing to the refinement of currently used environmental risk assessment strategies.

  4. Ion mobility-mass spectrometry.

    PubMed

    Kanu, Abu B; Dwivedi, Prabha; Tam, Maggie; Matz, Laura; Hill, Herbert H

    2008-01-01

    This review article compares and contrasts various types of ion mobility-mass spectrometers available today and describes their advantages for application to a wide range of analytes. Ion mobility spectrometry (IMS), when coupled with mass spectrometry, offers value-added data not possible from mass spectra alone. Separation of isomers, isobars, and conformers; reduction of chemical noise; and measurement of ion size are possible with the addition of ion mobility cells to mass spectrometers. In addition, structurally similar ions and ions of the same charge state can be separated into families of ions which appear along a unique mass-mobility correlation line. This review describes the four methods of ion mobility separation currently used with mass spectrometry. They are (1) drift-time ion mobility spectrometry (DTIMS), (2) aspiration ion mobility spectrometry (AIMS), (3) differential-mobility spectrometry (DMS) which is also called field-asymmetric waveform ion mobility spectrometry (FAIMS) and (4) traveling-wave ion mobility spectrometry (TWIMS). DTIMS provides the highest IMS resolving power and is the only IMS method which can directly measure collision cross-sections. AIMS is a low resolution mobility separation method but can monitor ions in a continuous manner. DMS and FAIMS offer continuous-ion monitoring capability as well as orthogonal ion mobility separation in which high-separation selectivity can be achieved. TWIMS is a novel method of IMS with a low resolving power but has good sensitivity and is well intergrated into a commercial mass spectrometer. One hundred and sixty references on ion mobility-mass spectrometry (IMMS) are provided.

  5. 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.

  6. 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.

  7. 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.

  8. Instrumentation for mass spectrometry: 1997

    SciTech Connect

    McLuckey, S.A.

    1997-08-01

    All mass spectrometry experiments involve the manipulation of material, an interface with the mass spectrometer, ionization, ion manipulation/analysis, detection and data collection/reduction. Each of these elements involve instrumentation. The wide range of species now amenable to mass spectrometry and the diverse areas of physical science in which it plays a role have led to a seemingly unlimited array of instrumental combinations. However, only a limited number of mass analyzers, and their combinations, dominate. The dominant analyzers include time-of-flight, Fourier transform ion cyclotron resonance, the Paul trap, the mass filter, and the sector mass spectrometer. Why there are so few (or so many, depending upon one`s point of view) can be understood upon consideration of a set of mass analyzer figures of merit. These include mass resolution, mass accuracy, mass range, dynamic range, abundance sensitivity, precision, efficiency, speed, MS{sup n} capability, compatibility with the ionizer, cost, and size. The most appropriate form of mass spectrometry is determined by the priorities of the particular measurement placed on the various mass analyzer characteristics and the relative strengths of the analyzers in meeting the requirements. Each of the analyzer types has a unique set of figures of merit that makes it optimally suited for particular applications. This paper discusses these figures of merit, provides data illustrating recent developments for each analyzer type, and gives the figures of merit of each type of analyzer as they stand in 1997. 101 refs., 24 figs.

  9. Mass spectrometry guided structural biology.

    PubMed

    Liko, Idlir; Allison, Timothy M; Hopper, Jonathan Ts; Robinson, Carol V

    2016-10-01

    With the convergence of breakthroughs in structural biology, specifically breaking the resolution barriers in cryo-electron microscopy and with continuing developments in crystallography, novel interfaces with other biophysical methods are emerging. Here we consider how mass spectrometry can inform these techniques by providing unambiguous definition of subunit stoichiometry. Moreover recent developments that increase mass spectral resolution enable molecular details to be ascribed to unassigned density within high-resolution maps of membrane and soluble protein complexes. Importantly we also show how developments in mass spectrometry can define optimal solution conditions to guide downstream structure determination, particularly of challenging biomolecules that refuse to crystallise.

  10. Improvement of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identification of difficult-to-identify bacteria and its impact in the workflow of a clinical microbiology laboratory.

    PubMed

    Rodríguez-Sánchez, Belén; Marín, Mercedes; Sánchez-Carrillo, Carlos; Cercenado, Emilia; Ruiz, Adrián; Rodríguez-Créixems, Marta; Bouza, Emilio

    2014-05-01

    This study evaluates matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) capability for the identification of difficult-to-identify microorganisms. A total of 150 bacterial isolates inconclusively identified with conventional phenotypic tests were further assessed by 16S rRNA sequencing and by MALDI-TOF MS following 2 methods: a) a simplified formic acid-based, on-plate extraction and b) performing a tube-based extraction step. Using the simplified method, 29 isolates could not be identified. For the remaining 121 isolates (80.7%), we obtained a reliable identification by MALDI-TOF: in 103 isolates, the identification by 16S rRNA sequencing and MALDI TOF coincided at the species level (68.7% from the total 150 analyzed isolates and 85.1% from the samples with MALDI-TOF result), and in 18 isolates, the identification by both methods coincided at the genus level (12% from the total and 14.9% from the samples with MALDI-TOF results). No discordant results were observed. The performance of the tube-based extraction step allowed the identification at the species level of 6 of the 29 unidentified isolates by the simplified method. In summary, MALDI-TOF can be used for the rapid identification of many bacterial isolates inconclusively identified by conventional methods.

  11. 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

  12. Symposium on accelerator mass spectrometry

    SciTech Connect

    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 the status of accelerator mass spectrometry. Individual papers were prepared separately for the data base.

  13. Ion Mobility Spectrometry (IMS) and Mass Spectrometry

    SciTech Connect

    Shvartsburg, Alexandre A.

    2010-04-20

    In a media of finite viscosity, the Coulomb force of external electric field moves ions with some terminal speed. This dynamics is controlled by “mobility” - a property of the interaction potential between ions and media molecules. This fact has been used to separate and characterize gas-phase ions in various modes of ion mobility spectrometry (IMS) developed since 1970. Commercial IMS devices were introduced in 1980-s for field detection of volatile traces such as explosives and chemical warfare agents. Coupling to soft-ionization sources, mass spectrometry (MS), and chromatographic methods in 1990-s had allowed IMS to handle complex samples, enabling new applications in biological and environmental analyses, nanoscience, and other areas. Since 2003, the introduction of commercial systems by major instrument vendors started bringing the IMS/MS capability to broad user community. The other major development of last decade has been the differential IMS or “field asymmetric waveform IMS” (FAIMS) that employs asymmetric time-dependent electric field to sort ions not by mobility itself, but by the difference between its values in strong and weak electric fields. Coupling of FAIMS to conventional IMS and stacking of conventional IMS stages have enabled two-dimensional separations that dramatically expand the power of ion mobility methods.

  14. "EMERGING" POLLUTANTS, MASS SPECTROMETRY, AND ...

    EPA Pesticide Factsheets

    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 definitive data that environmental scientists rely upon for identifying the molecular compositions (and ultimately the structures) of chemicals. This is not to ignore the complementary, critical roles played by the adjunct practices of sample enrichment (via any of various means of selective extraction) and analyte separation (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 undergirdidng our existing knowledge about environmental processes and pollution, what recognition it does enjoy is usually relegated to that of a tool. It is ususally the relevance of ssignificance of the knowledge acquired from the application of the tool that has ultimate meaning to the public and science at large - not how the knowledge was acquired. The research focused on in the subtasks is the development and application of state-of the-art technologies to meet the needs of the public, Office of Water, and ORD in

  15. Electrospray Ionization Mass Spectrometry

    SciTech Connect

    Kelly, Ryan T.; Marginean, Ioan; Tang, Keqi

    2014-06-13

    Electrospray Ionization (ESI) is a process whereby gas phase ions are created from molecules in solution. As a solution exits a narrow tube in the presence of a strong electric field, an aerosol of charged droplets are is formed that produces gas phase ions as they it desolvates. ESI-MS comprises the creation of ions by ESI and the determination of their mass to charge ratio (m/z) by MS.

  16. MASS SPECTROMETRY-BASED METABOLOMICS

    PubMed Central

    Dettmer, Katja; Aronov, Pavel A.; Hammock, Bruce D.

    2007-01-01

    This review presents an overview of the dynamically developing field of mass spectrometry-based metabolomics. Metabolomics aims at the comprehensive and quantitative analysis of wide arrays of metabolites in biological samples. These numerous analytes have very diverse physico-chemical properties and occur at different abundance levels. Consequently, comprehensive metabolomics investigations are primarily a challenge for analytical chemistry and specifically mass spectrometry has vast potential as a tool for this type of investigation. Metabolomics require special approaches for sample preparation, separation, and mass spectrometric analysis. Current examples of those approaches are described in this review. It primarily focuses on metabolic fingerprinting, a technique that analyzes all detectable analytes in a given sample with subsequent classification of samples and identification of differentially expressed metabolites, which define the sample classes. To perform this complex task, data analysis tools, metabolite libraries, and databases are required. Therefore, recent advances in metabolomics bioinformatics are also discussed. PMID:16921475

  17. Mass spectrometry of aerospace materials

    NASA Technical Reports Server (NTRS)

    Colony, J. A.

    1976-01-01

    Mass spectrometry is used for chemical analysis of aerospace materials and contaminants. Years of analytical aerospace experience have resulted in the development of specialized techniques of sampling and analysis which are required in order to optimize results. This work has resulted in the evolution of a hybrid method of indexing mass spectra which include both the largest peaks and the structurally significant peaks in a concise format. With this system, a library of mass spectra of aerospace materials was assembled, including the materials responsible for 80 to 90 percent of the contamination problems at Goddard Space Flight Center during the past several years.

  18. Mass spectrometry and tandem mass spectrometry of citrus limonoids.

    PubMed

    Tian, Qingguo; Schwartz, Steven J

    2003-10-15

    Methods for atmospheric pressure chemical ionization tandem mass spectrometry (APCI-MS/MS) of citrus limonoid aglycones and electrospray ionization tandem mass spectrometry (ESI-MS/MS) of limonoid glucosides are reported. The fragmentation patterns of four citrus limonoid aglycones (limonin, nomilin, obacunone, and deacetylnomilin) and six limonoid glucosides, that is, limonin 17-beta-D-glucopyranoside (LG), nomilin 17-beta-D-glucopyranoside (NG), nomilinic acid 17-beta-D-glucopyranoside (NAG), deacetyl nomilinic acid 17-beta-D-glucopyranoside (DNAG), obacunone 17-beta-D-glucopyranoside (OG), and obacunoic acid 17-beta-D-glucopyranoside (OAG) were investigated using a quadruple mass spectrometer in low-energy collisionally activated dissociation (CAD). The four limonoid aglycones and four limonoid glucosides (LG, OG, NAG, and DNAG) were purified from citrus seeds; the other two limonoid glucosides (NG and OAG) were tentatively identified in the crude extract of grapefruit seeds by ESI mass spectrometry in both positive and negative ion analysis. Ammonium hydroxide or acetic acid was added to the mobile phase to facilitate ionization. During positive ion APCI analysis of limonoid aglycones, protonated molecular ion, [M + H]+, or adduct ion, [M + NH3 + H]-, was formed as base peaks when ammonium hydroxide was added to the mobile phase. Molecular anions or adduct ions with acetic acid ([M + HOAc - H] and [M + HOAc]-) or a deprotonated molecular ion were produced during negative ion APCI analysis of limonoid aglycones, depending on the mobile-phase modifier used. Positive ion ESI-MS of limonoid glucosides produced adduct ions of [M + H + NH3]+, [M + Na]+, and [M + K]+ when ammonium hydroxide was added to the mobile phase. After collisionally activated dissociation (CAD) of the limonoid aglycone molecular ions in negative ion APCI analysis, fragment ions indicated structural information of the precursor ions, showing the presence of methyl, carboxyl, and oxygenated ring

  19. EMERGING POLLUTANTS, MASS SPECTROMETRY, AND ...

    EPA Pesticide Factsheets

    Historically fundamental to amassing our understanding of environmental processes and chemical pollution is the realm of mass spectrometry (MS) - the mainstay of analytical chemistry - the workhorse that supplies definitive data that environmental scientists and engineers reply upon for identifying molecular compositions (and ultimately structures) of chemicals. While the power of MS has long been visible to the practicing environmental chemist, it borders on obscurity to the lay public and many scientists. While MS has played a long, historic (and largely invisible) role in establishing our knowledge of environmental processes and pollution, what recognition it does enjoy is usually relegated to that of a tool. It is usually the relevance or significance of the knowledge acquired from the application of the tool that has ultimate meaning to the public and science at large - not how the data were acquired. Methods (736/800): Mass Spectrometry and the

  20. Imaging Mass Spectrometry in Neuroscience

    PubMed Central

    2013-01-01

    Imaging mass spectrometry is an emerging technique of great potential for investigating the chemical architecture in biological matrices. Although the potential for studying neurobiological systems is evident, the relevance of the technique for application in neuroscience is still in its infancy. In the present Review, a principal overview of the different approaches, including matrix assisted laser desorption ionization and secondary ion mass spectrometry, is provided with particular focus on their strengths and limitations for studying different neurochemical species in situ and in vitro. The potential of the various approaches is discussed based on both fundamental and biomedical neuroscience research. This Review aims to serve as a general guide to familiarize the neuroscience community and other biomedical researchers with the technique, highlighting its great potential and suitability for comprehensive and specific chemical imaging. PMID:23530951

  1. Mass spectrometry. [review of techniques

    NASA Technical Reports Server (NTRS)

    Burlingame, A. L.; Kimble, B. J.; Derrick, P. J.

    1976-01-01

    Advances in mass spectrometry (MS) and its applications over the past decade are reviewed in depth, with annotated literature references. New instrumentation and techniques surveyed include: modulated-beam MS, chromatographic MS on-line computer techniques, digital computer-compatible quadrupole MS, selected ion monitoring (mass fragmentography), and computer-aided management of MS data and interpretation. Areas of application surveyed include: organic MS and electron impact MS, field ionization kinetics, appearance potentials, translational energy release, studies of metastable species, photoionization, calculations of molecular orbitals, chemical kinetics, field desorption MS, high pressure MS, ion cyclotron resonance, biochemistry, medical/clinical chemistry, pharmacology, and environmental chemistry and pollution studies.

  2. Glycosaminoglycan Glycomics Using Mass Spectrometry*

    PubMed Central

    Zaia, Joseph

    2013-01-01

    The fact that sulfated glycosaminoglycans (GAGs) are necessary for the functioning of all animal physiological systems drives the need to understand their biology. This understanding is limited, however, by the heterogeneous nature of GAG chains and their dynamic spatial and temporal expression patterns. GAGs have a regulated structure overlaid by heterogeneity but lack the detail necessary to build structure/function relationships. In order to provide this information, we need glycomics platforms that are sensitive, robust, high throughput, and information rich. This review summarizes progress on mass-spectrometry-based GAG glycomics methods. The areas covered include disaccharide analysis, oligosaccharide profiling, and tandem mass spectrometric sequencing. PMID:23325770

  3. A mass spectrometry primer for mass spectrometry imaging

    PubMed Central

    Rubakhin, Stanislav S.; Sweedler, Jonathan V.

    2011-01-01

    Mass spectrometry imaging (MSI), a rapidly growing subfield of chemical imaging, employs mass spectrometry (MS) technologies to create single- and multi-dimensional localization maps for a variety of atoms and molecules. Complimentary to other imaging approaches, MSI provides high chemical specificity and broad analyte coverage. This powerful analytical toolset is capable of measuring the distribution of many classes of inorganics, metabolites, proteins and pharmaceuticals in chemically and structurally complex biological specimens in vivo, in vitro, and in situ. The MSI approaches highlighted in this Methods in Molecular Biology volume provide flexibility of detection, characterization, and identification of multiple known and unknown analytes. The goal of this chapter is to introduce investigators who may be unfamiliar with MS to the basic principles of the mass spectrometric approaches as used in MSI. In addition to guidelines for choosing the most suitable MSI method for specific investigations, cross-references are provided to the chapters in this volume that describe the appropriate experimental protocols. PMID:20680583

  4. Quantitative mass spectrometry: an overview

    NASA Astrophysics Data System (ADS)

    Urban, Pawel L.

    2016-10-01

    Mass spectrometry (MS) is a mainstream chemical analysis technique in the twenty-first century. It has contributed to numerous discoveries in chemistry, physics and biochemistry. Hundreds of research laboratories scattered all over the world use MS every day to investigate fundamental phenomena on the molecular level. MS is also widely used by industry-especially in drug discovery, quality control and food safety protocols. In some cases, mass spectrometers are indispensable and irreplaceable by any other metrological tools. The uniqueness of MS is due to the fact that it enables direct identification of molecules based on the mass-to-charge ratios as well as fragmentation patterns. Thus, for several decades now, MS has been used in qualitative chemical analysis. To address the pressing need for quantitative molecular measurements, a number of laboratories focused on technological and methodological improvements that could render MS a fully quantitative metrological platform. In this theme issue, the experts working for some of those laboratories share their knowledge and enthusiasm about quantitative MS. I hope this theme issue will benefit readers, and foster fundamental and applied research based on quantitative MS measurements. This article is part of the themed issue 'Quantitative mass spectrometry'.

  5. Affinity membrane introduction mass spectrometry

    SciTech Connect

    Xu, C.; Patrick, J.S.; Cooks, R.G. )

    1995-02-15

    A new technique, affinity membrane introduction mass spectrometry, is described. In this method, a chemically modified membrane is used to selectively adsorb analytes bearing a particular functional group and concentrate them from solution. Release of the bound analyte results in its transfer across the membrane and allows it to be monitored mass spectrometrically, using, in the present case, a benchtop ion trap instrument. Alkylamine-modified cellulose membranes are used to bind substituted benzaldehydes through imine formation at high pH. Release of the bound aldehyde is achieved by acid hydrolysis of the surface-bound imine. Benzaldehyde is detected with excellent specificity at 10 ppm in a complex mixture using this method. Using the enrichment capability of the membrane, a full mass spectrum of benzaldehyde can be measured at a concentration of 10 ppb. The behavior of a variety of other aldehydes is also discussed to illustrate the capabilities of the method. 21 refs., 5 figs., 2 tabs.

  6. Electrophoresis-mass spectrometry probe

    DOEpatents

    Andresen, Brian D.; Fought, Eric R.

    1987-01-01

    The invention involves a new technique for the separation of complex mixtures of chemicals, which utilizes a unique interface probe for conventional mass spectrometers which allows the electrophoretically separated compounds to be analyzed in real-time by a mass spectrometer. This new chemical analysis interface, which couples electrophoresis with mass spectrometry, allows complex mixtures to be analyzed very rapidly, with much greater specificity, and with greater sensitivity. The interface or probe provides a means whereby large and/or polar molecules in complex mixtures to be completely characterized. The preferred embodiment of the probe utilizes a double capillary tip which allows the probe tip to be continually wetted by the buffer, which provides for increased heat dissipation, and results in a continually operating interface which is more durable and electronically stable than the illustrated single capillary tip probe interface.

  7. Electrophoresis-mass spectrometry probe

    DOEpatents

    Andresen, B.D.; Fought, E.R.

    1987-11-10

    The invention involves a new technique for the separation of complex mixtures of chemicals, which utilizes a unique interface probe for conventional mass spectrometers which allows the electrophoretically separated compounds to be analyzed in real-time by a mass spectrometer. This new chemical analysis interface, which couples electrophoresis with mass spectrometry, allows complex mixtures to be analyzed very rapidly, with much greater specificity, and with greater sensitivity. The interface or probe provides a means whereby large and/or polar molecules in complex mixtures to be completely characterized. The preferred embodiment of the probe utilizes a double capillary tip which allows the probe tip to be continually wetted by the buffer, which provides for increased heat dissipation, and results in a continually operating interface which is more durable and electronically stable than the illustrated single capillary tip probe interface. 8 figs.

  8. File Formats Commonly Used in Mass Spectrometry Proteomics*

    PubMed Central

    Deutsch, Eric W.

    2012-01-01

    The application of mass spectrometry (MS) to the analysis of proteomes has enabled the high-throughput identification and abundance measurement of hundreds to thousands of proteins per experiment. However, the formidable informatics challenge associated with analyzing MS data has required a wide variety of data file formats to encode the complex data types associated with MS workflows. These formats encompass the encoding of input instruction for instruments, output products of the instruments, and several levels of information and results used by and produced by the informatics analysis tools. A brief overview of the most common file formats in use today is presented here, along with a discussion of related topics. PMID:22956731

  9. File formats commonly used in mass spectrometry proteomics.

    PubMed

    Deutsch, Eric W

    2012-12-01

    The application of mass spectrometry (MS) to the analysis of proteomes has enabled the high-throughput identification and abundance measurement of hundreds to thousands of proteins per experiment. However, the formidable informatics challenge associated with analyzing MS data has required a wide variety of data file formats to encode the complex data types associated with MS workflows. These formats encompass the encoding of input instruction for instruments, output products of the instruments, and several levels of information and results used by and produced by the informatics analysis tools. A brief overview of the most common file formats in use today is presented here, along with a discussion of related topics.

  10. High Technology Mass Spectrometry Laboratory

    DTIC Science & Technology

    2010-08-01

    GSH, hemoglobin beta-Cys93 ( Hb -C93-AN) were monitored. The second order rate constants in M-ls-1 were: disappe 0.0806; appearance of GS-AN in whole...blood, 0.0776, appearance of Hb -C9 appearance of AbC34-AN in plasma, 0.224. The data indicate that the mos blood is Cys34 of albumin. This site...than Hb -C93 15. SUBJECT TERMS acrylonitrile, adduct, mass spectrometry, biomarker, toxic industrial chemicals 16. SECURITY CLASSIFICATION OF: a

  11. Neuroscience and Accelerator Mass Spectrometry

    SciTech Connect

    Palmblad, M N; Buchholz, B A; Hillegonds, D J; Vogel, J S

    2004-08-02

    Accelerator mass spectrometry (AMS) is a mass spectrometric method for quantifying rare isotopes. It has had great impact in geochronology and archaeology and is now being applied in biomedicine. AMS measures radioisotopes such as {sup 3}H, {sup 14}C, {sup 26}Al, {sup 36}Cl and {sup 41}Ca, with zepto- or attomole sensitivity and high precision and throughput, enabling safe human pharmacokinetic studies involving: microgram doses, agents having low bioavailability, or toxicology studies where administered doses must be kept low (<1 {micro}g/kg). It is used to study long-term pharmacokinetics, to identify biomolecular interactions, to determine chronic and low-dose effects or molecular targets of neurotoxic substances, to quantify transport across the blood-brain barrier and to resolve molecular turnover rates in the human brain on the timescale of decades. We will here review how AMS is applied in neurotoxicology and neuroscience.

  12. Neuroscience and accelerator mass spectrometry.

    PubMed

    Palmblad, Magnus; Buchholz, Bruce A; Hillegonds, Darren J; Vogel, John S

    2005-02-01

    Accelerator mass spectrometry (AMS) is a mass spectrometric method for quantifying rare isotopes. It has had a great impact in geochronology and archaeology and is now being applied in biomedicine. AMS measures radioisotopes such as 3H, 14C, 26Al, 36Cl and 41Ca, with zepto- or attomole sensitivity and high precision and throughput, allowing safe human pharmacokinetic studies involving microgram doses, agents having low bioavailability or toxicology studies where administered doses must be kept low (<1 microg kg(-1)). It is used to study long-term pharmacokinetics, to identify biomolecular interactions, to determine chronic and low-dose effects or molecular targets of neurotoxic substances, to quantify transport across the blood-brain barrier and to resolve molecular turnover rates in the human brain on the time-scale of decades. We review here how AMS is applied in neurotoxicology and neuroscience.

  13. Mass spectrometry in combinatorial chemistry.

    PubMed

    Enjalbal, C; Martinez, J; Aubagnac, J L

    2000-01-01

    In the fast expanding field of combinatorial chemistry, profiling libraries has always been a matter of concern--as illustrated by the buoyant literature over the past seven years. Spectroscopic methods, including especially mass spectrometry and to a lesser extent IR and NMR, have been applied at different levels of combinatorial library synthesis: in the rehearsal phase to optimize the chemistry prior to library generation, to confirm library composition, and to characterize after screening each structure that exhibits positive response. Most of the efforts have been concentrated on library composition assessment. The difficulties of such analyses have evolved from the infancy of the combinatorial concept, where large mixtures were prepared, to the recent parallel syntheses of collections of discrete compounds. Whereas the complexity of the analyses has diminished, an increased degree of automation was simultaneously required to achieve efficient library component identification and quantification. In this respect, mass spectrometry has been found to be the method of choice, providing rapid, sensitive, and informative analyses, especially when coupled to chromatographic separation. Fully automated workstations able to cope with several hundreds of compounds per day have been designed. After a brief introduction to describe the combinatorial approach, library characterization will be discussed in detail, considering first the solution-based methodologies and secondly the support-bound material analyses.

  14. Mass Spectrometry Applications for Toxicology

    PubMed Central

    Mbughuni, Michael M.; Jannetto, Paul J.

    2016-01-01

    Toxicology is a multidisciplinary study of poisons, aimed to correlate the quantitative and qualitative relationships between poisons and their physiological and behavioural effects in living systems. Other key aspects of toxicology focus on elucidation of the mechanisms of action of poisons and development of remedies and treatment plans for associated toxic effects. In these endeavours, Mass spectrometry (MS) has become a powerful analytical technique with a wide range of application used in the Toxicological analysis of drugs, poisons, and metabolites of both. To date, MS applications have permeated all fields of toxicology which include; environmental, clinical, and forensic toxicology. While many different analytical applications are used in these fields, MS and its hyphenated applications such as; gas chromatography MS (GC-MS), liquid chromatography MS (LC-MS), inductively coupled plasma ionization MS (ICP-MS), tandem mass spectrometry (MS/MS and MSn) have emerged as powerful tools used in toxicology laboratories. This review will focus on these hyphenated MS technologies and their applications for toxicology. PMID:28149262

  15. Mass Spectrometry Applications for Toxicology.

    PubMed

    Mbughuni, Michael M; Jannetto, Paul J; Langman, Loralie J

    2016-12-01

    Toxicology is a multidisciplinary study of poisons, aimed to correlate the quantitative and qualitative relationships between poisons and their physiological and behavioural effects in living systems. Other key aspects of toxicology focus on elucidation of the mechanisms of action of poisons and development of remedies and treatment plans for associated toxic effects. In these endeavours, Mass spectrometry (MS) has become a powerful analytical technique with a wide range of application used in the Toxicological analysis of drugs, poisons, and metabolites of both. To date, MS applications have permeated all fields of toxicology which include; environmental, clinical, and forensic toxicology. While many different analytical applications are used in these fields, MS and its hyphenated applications such as; gas chromatography MS (GC-MS), liquid chromatography MS (LC-MS), inductively coupled plasma ionization MS (ICP-MS), tandem mass spectrometry (MS/MS and MS(n)) have emerged as powerful tools used in toxicology laboratories. This review will focus on these hyphenated MS technologies and their applications for toxicology.

  16. Absorption Mode FT-ICR Mass Spectrometry Imaging

    SciTech Connect

    Smith, Donald F.; Kilgour, David P.; Konijnenburg, Marco; O'Connor, Peter B.; Heeren, Ronald M.

    2013-12-03

    Fourier transform ion cyclotron resonance mass spectrometry offers the highest mass resolving power for molecular imaging experiments. This high mass resolving power ensures that closely spaced peaks at the same nominal mass are resolved for proper image generation. Typically higher magnetic fields are used to increase mass resolving power. However, a gain in mass resolving power can also be realized by phase correction of the data for absorption mode display. In addition to mass resolving power, absorption mode offers higher mass accuracy and signal-to-noise ratio over the conventional magnitude mode. Here we present the first use of absorption mode for Fourier transform ion cyclotron resonance mass spectrometry imaging. The Autophaser algorithm is used to phase correct each spectrum (pixel) in the image and then these parameters are used by the Chameleon work-flow based data processing software to generate absorption mode ?Datacubes? for image and spectral viewing. Absorption mode reveals new mass and spatial features that are not resolved in magnitude mode and results in improved selected ion image contrast.

  17. Quantitative mass spectrometry: an overview

    PubMed Central

    2016-01-01

    Mass spectrometry (MS) is a mainstream chemical analysis technique in the twenty-first century. It has contributed to numerous discoveries in chemistry, physics and biochemistry. Hundreds of research laboratories scattered all over the world use MS every day to investigate fundamental phenomena on the molecular level. MS is also widely used by industry—especially in drug discovery, quality control and food safety protocols. In some cases, mass spectrometers are indispensable and irreplaceable by any other metrological tools. The uniqueness of MS is due to the fact that it enables direct identification of molecules based on the mass-to-charge ratios as well as fragmentation patterns. Thus, for several decades now, MS has been used in qualitative chemical analysis. To address the pressing need for quantitative molecular measurements, a number of laboratories focused on technological and methodological improvements that could render MS a fully quantitative metrological platform. In this theme issue, the experts working for some of those laboratories share their knowledge and enthusiasm about quantitative MS. I hope this theme issue will benefit readers, and foster fundamental and applied research based on quantitative MS measurements. This article is part of the themed issue ‘Quantitative mass spectrometry’. PMID:27644965

  18. 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

  19. 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

  20. Characterization of microbial siderophores by mass spectrometry.

    PubMed

    Pluháček, Tomáš; Lemr, Karel; Ghosh, Dipankar; Milde, David; Novák, Jiří; Havlíček, Vladimír

    2016-01-01

    Siderophores play important roles in microbial iron piracy, and are applied as infectious disease biomarkers and novel pharmaceutical drugs. Inductively coupled plasma and molecular mass spectrometry (ICP-MS) combined with high resolution separations allow characterization of siderophores in complex samples taking advantages of mass defect data filtering, tandem mass spectrometry, and iron-containing compound quantitation. The enrichment approaches used in siderophore analysis and current ICP-MS technologies are reviewed. The recent tools for fast dereplication of secondary metabolites and their databases are reported. This review on siderophores is concluded with their recent medical, biochemical, geochemical, and agricultural applications in mass spectrometry context.

  1. Cloud parallel processing of tandem mass spectrometry based proteomics data.

    PubMed

    Mohammed, Yassene; Mostovenko, Ekaterina; Henneman, Alex A; Marissen, Rob J; Deelder, André M; Palmblad, Magnus

    2012-10-05

    Data analysis in mass spectrometry based proteomics struggles to keep pace with the advances in instrumentation and the increasing rate of data acquisition. Analyzing this data involves multiple steps requiring diverse software, using different algorithms and data formats. Speed and performance of the mass spectral search engines are continuously improving, although not necessarily as needed to face the challenges of acquired big data. Improving and parallelizing the search algorithms is one possibility; data decomposition presents another, simpler strategy for introducing parallelism. We describe a general method for parallelizing identification of tandem mass spectra using data decomposition that keeps the search engine intact and wraps the parallelization around it. We introduce two algorithms for decomposing mzXML files and recomposing resulting pepXML files. This makes the approach applicable to different search engines, including those relying on sequence databases and those searching spectral libraries. We use cloud computing to deliver the computational power and scientific workflow engines to interface and automate the different processing steps. We show how to leverage these technologies to achieve faster data analysis in proteomics and present three scientific workflows for parallel database as well as spectral library search using our data decomposition programs, X!Tandem and SpectraST.

  2. Broadband Analysis of Bioagents by Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Fenselau, Catherine; Wynne, Colin; Edwards, Nathan

    Mass spectrometry was first reported to provide analysis of intact metabolite biomarkers from whole cells in 1975.1 Since then advances in ionization techniques have extended our capabilities to polar lipids and, eventually, to proteins.2, 3 Mass spectrometry provides a broadband detection system, which, however, has great specificity. Bioinformatics plays an important role in providing flexible and rapid characterization of species, based on protein and peptide mass spectra collected in the field.

  3. Application of mass spectrometry in proteomics.

    PubMed

    Guerrera, Ida Chiara; Kleiner, Oliver

    2005-01-01

    Mass spectrometry has arguably become the core technology in proteomics. The application of mass spectrometry based techniques for the qualitative and quantitative analysis of global proteome samples derived from complex mixtures has had a big impact in the understanding of cellular function. Here, we give a brief introduction to principles of mass spectrometry and instrumentation currently used in proteomics experiments. In addition, recent developments in the application of mass spectrometry in proteomics are summarised. Strategies allowing high-throughput identification of proteins from highly complex mixtures include accurate mass measurement of peptides derived from total proteome digests and multidimensional peptide separations coupled with mass spectrometry. Mass spectrometric analysis of intact proteins permits the characterisation of protein isoforms. Recent developments in stable isotope labelling techniques and chemical tagging allow the mass spectrometry based differential display and quantitation of proteins, and newly established affinity procedures enable the targeted characterisation of post-translationally modified proteins. Finally, advances in mass spectrometric imaging allow the gathering of specific information on the local molecular composition, relative abundance and spatial distribution of peptides and proteins in thin tissue sections.

  4. Methods for recalibration of mass spectrometry data

    DOEpatents

    Tolmachev, Aleksey V.; Smith, Richard D.

    2009-03-03

    Disclosed are methods for recalibrating mass spectrometry data that provide improvement in both mass accuracy and precision by adjusting for experimental variance in parameters that have a substantial impact on mass measurement accuracy. Optimal coefficients are determined using correlated pairs of mass values compiled by matching sets of measured and putative mass values that minimize overall effective mass error and mass error spread. Coefficients are subsequently used to correct mass values for peaks detected in the measured dataset, providing recalibration thereof. Sub-ppm mass measurement accuracy has been demonstrated on a complex fungal proteome after recalibration, providing improved confidence for peptide identifications.

  5. Plasma Desorption Mass Spectrometry: Coming of Age.

    ERIC Educational Resources Information Center

    Cotter, Robert J.

    1988-01-01

    Discusses the history and development of Plasma Desorption Mass Spectrometry to determine molecular weights and structures of proteins and polymers. Outlines theory, instrumentation, and sample preparation commonly used. Gives several examples of resulting spectra. (ML)

  6. Mass Spectrometry Imaging of Complex Microbial Communities

    PubMed Central

    2016-01-01

    Conspectus In the two decades since mass spectrometry imaging (MSI) was first applied to visualize the distribution of peptides across biological tissues and cells, the technique has become increasingly effective and reliable. MSI excels at providing complementary information to existing methods for molecular analysis—such as genomics, transcriptomics, and metabolomics—and stands apart from other chemical imaging modalities through its capability to generate information that is simultaneously multiplexed and chemically specific. Today a diverse family of MSI approaches are applied throughout the scientific community to study the distribution of proteins, peptides, and small-molecule metabolites across many biological models. The inherent strengths of MSI make the technique valuable for studying microbial systems. Many microbes reside in surface-attached multicellular and multispecies communities, such as biofilms and motile colonies, where they work together to harness surrounding nutrients, fend off hostile organisms, and shield one another from adverse environmental conditions. These processes, as well as many others essential for microbial survival, are mediated through the production and utilization of a diverse assortment of chemicals. Although bacterial cells are generally only a few microns in diameter, the ecologies they influence can encompass entire ecosystems, and the chemical changes that they bring about can occur over time scales ranging from milliseconds to decades. Because of their incredible complexity, our understanding of and influence over microbial systems requires detailed scientific evaluations that yield both chemical and spatial information. MSI is well-positioned to fulfill these requirements. With small adaptations to existing methods, the technique can be applied to study a wide variety of chemical interactions, including those that occur inside single-species microbial communities, between cohabitating microbes, and between microbes

  7. Mass spectrometry in the home and garden.

    PubMed

    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.

  8. 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.

  9. 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.

  10. Analytical aspects of hydrogen exchange mass spectrometry

    PubMed Central

    Engen, John R.; Wales, Thomas E.

    2016-01-01

    The analytical aspects of measuring hydrogen exchange by mass spectrometry are reviewed. The nature of analytical selectivity in hydrogen exchange is described followed by review of the analytical tools required to accomplish fragmentation, separation, and the mass spectrometry measurements under restrictive exchange quench conditions. In contrast to analytical quantitation that relies on measurements of peak intensity or area, quantitation in hydrogen exchange mass spectrometry depends on measuring a mass change with respect to an undeuterated or deuterated control, resulting in a value between zero and the maximum amount of deuterium that could be incorporated. Reliable quantitation is a function of experimental fidelity and to achieve high measurement reproducibility, a large number of experimental variables must be controlled during sample preparation and analysis. The method also reports on important qualitative aspects of the sample, including conformational heterogeneity and population dynamics. PMID:26048552

  11. Soft-landing preparative mass spectrometry.

    PubMed

    Verbeck, Guido; Hoffmann, William; Walton, Barbara

    2012-10-07

    Preparative mass spectrometry has become a diverse field that covers the spectrum of kinetic energy deposition. Of these methods, soft-landing mass spectrometry has many fundamental properties, which make it an advantageous technique for ion isolation and deposition. Its definition implies the preservation of ionic structural integrity after landing, which ensures the structure-function relationship of a molecule remains intact. Here the focus is on the instruments and applications of studying ion-surface landing in the hyperthermal and thermal kinetic energy regimes. Soft-landing preparative mass spectrometry covers the breadth of mass spectrometric ionization sources, instrumental configurations, and molecular families. Due to the diverse nature of soft landing, and to maximize readability, this review has been organized according to instrumental considerations and molecular families, with a discussion of theoretical work at the end.

  12. Mass spectrometry and the environmental sciences

    NASA Astrophysics Data System (ADS)

    Hites, Ronald A.

    1992-09-01

    Research in environmental mass spectrometry focuses on two broad areas: development of new methods for a wide range of pollutants; and using existing methods to understand the fate of pollutants in nature. This paper will present examples of both types of research. In some environmental settings it is important to have rapid analytical turnaround, which suggests that samples should be analyzed in the field rather than in a remote laboratory. Thus, there has been considerable interest in "fieldable" mass spectrometers. Volatile and water soluble analytes can be introduced into a mass spectrometer by passing the water sample over a semi-permeable membrane. The analytes of interest pass through the membrane, but the water does not. This method may be useful in situations that require a continuous readout of concentration. Like mass spectrometrists everywhere, environmental scientists have explored the many facets of liquid chromatographic mass spectrometry. Work in our laboratory has centered on continuous flow fast atom bombardment (CF-FAB) as the LCMS interface. In addition, flow injection analysis is possible using CF-FAB. By avoiding chromatographic separation, the throughput of the analytical system is increased. Frequently, tandem mass spectrometry is necessary to unscramble the chemical signals produced by this technique. Electron capture negative ionization mass spectrometry can achieve sensitivities of a few attomoles for selected compounds; furthermore, the technique can be remarkably specific. These features make it ideal for the analysis of highly chlorinated environmental contaminants such as chlorinated dioxins. Such an application will be presented in detail.

  13. Scientific Workflow Management in Proteomics

    PubMed Central

    de Bruin, Jeroen S.; Deelder, André M.; Palmblad, Magnus

    2012-01-01

    Data processing in proteomics can be a challenging endeavor, requiring extensive knowledge of many different software packages, all with different algorithms, data format requirements, and user interfaces. In this article we describe the integration of a number of existing programs and tools in Taverna Workbench, a scientific workflow manager currently being developed in the bioinformatics community. We demonstrate how a workflow manager provides a single, visually clear and intuitive interface to complex data analysis tasks in proteomics, from raw mass spectrometry data to protein identifications and beyond. PMID:22411703

  14. 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.

  15. MSM, an Efficient Workflow for Metabolite Identification Using Hybrid Linear Ion Trap Orbitrap Mass Spectrometer

    NASA Astrophysics Data System (ADS)

    Cho, Robert; Huang, Yingying; Schwartz, Jae C.; Chen, Yan; Carlson, Timothy J.; Ma, Ji

    2012-05-01

    Identification of drug metabolites can often yield important information regarding clearance mechanism, pharmacologic activity, or toxicity for drug candidate molecules. Additionally, the identification of metabolites can provide beneficial structure-activity insight to help guide lead optimization efforts towards molecules with optimal metabolic profiles. There are challenges associated with detecting and identifying metabolites in the presence of complex biological matrices, and new LC-MS technologies have been developed to meet these challenges. In this report, we describe the development of an experimental approach that applies unique features of the hybrid linear ion trap Orbitrap mass spectrometer to streamline in vitro and in vivo metabolite identification experiments. The approach, referred to as MSM, utilizes multiple collision cells, dissociation methods, mass analyzers, and detectors. With multiple scan types and different dissociation modes built into one experimental method, along with flexible post-acquisition analysis options, the MSM workflow offers an attractive option to fast and reliable identification of metabolites in different kinds of in vitro and in vivo samples. The MSM workflow was successfully applied to metabolite identification analysis of verapamil in both in vitro rat hepatocyte incubations and in vivo rat bile samples.

  16. Fast Atom Bombardment Mass Spectrometry.

    ERIC Educational Resources Information Center

    Rinehart, Kenneth L., Jr.

    1982-01-01

    Discusses reactions and characteristics of fast atom bombardment (FAB) mass spectroscopy in which samples are ionized in a condensed state by bombardment with xenon or argon atoms, yielding positive/negative secondary ions. Includes applications of FAB to structural problems and considers future developments using the technique. (Author/JN)

  17. Targeted Quantitation of Proteins by Mass Spectrometry

    PubMed Central

    2013-01-01

    Quantitative measurement of proteins is one of the most fundamental analytical tasks in a biochemistry laboratory, but widely used immunochemical methods often have limited specificity and high measurement variation. In this review, we discuss applications of multiple-reaction monitoring (MRM) mass spectrometry, which allows sensitive, precise quantitative analyses of peptides and the proteins from which they are derived. Systematic development of MRM assays is permitted by databases of peptide mass spectra and sequences, software tools for analysis design and data analysis, and rapid evolution of tandem mass spectrometer technology. Key advantages of MRM assays are the ability to target specific peptide sequences, including variants and modified forms, and the capacity for multiplexing that allows analysis of dozens to hundreds of peptides. Different quantitative standardization methods provide options that balance precision, sensitivity, and assay cost. Targeted protein quantitation by MRM and related mass spectrometry methods can advance biochemistry by transforming approaches to protein measurement. PMID:23517332

  18. Pyrolysis Mass Spectrometry of Complex Organic Materials.

    ERIC Educational Resources Information Center

    Meuzelaar, Henk L. C.; And Others

    1984-01-01

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

  19. Nanostructure-initiator mass spectrometry biometrics

    DOEpatents

    Leclerc, Marion; Bowen, Benjamin; Northen, Trent

    2015-09-08

    Several embodiments described herein are drawn to methods of identifying an analyte on a subject's skin, methods of generating a fingerprint, methods of determining a physiological change in a subject, methods of diagnosing health status of a subject, and assay systems for detecting an analyte and generating a fingerprint, by nanostructure-initiator mass spectrometry (NIMS).

  20. Laser desorption mass spectrometry for molecular diagnosis

    NASA Astrophysics Data System (ADS)

    Chen, C. H. Winston; Taranenko, N. I.; Zhu, Y. F.; Allman, S. L.; Tang, K.; Matteson, K. J.; Chang, L. Y.; Chung, C. N.; Martin, Steve; Haff, Lawrence

    1996-04-01

    Laser desorption mass spectrometry has been used for molecular diagnosis of cystic fibrosis. Both 3-base deletion and single-base point mutation have been successfully detected by clinical samples. This new detection method can possibly speed up the diagnosis by one order of magnitude in the future. It may become a new biotechnology technique for population screening of genetic disease.

  1. Analysis of protein complexes using mass spectrometry.

    PubMed

    Gingras, Anne-Claude; Gstaiger, Matthias; Raught, Brian; Aebersold, Ruedi

    2007-08-01

    The versatile combination of affinity purification and mass spectrometry (AP-MS) has recently been applied to the detailed characterization of many protein complexes and large protein-interaction networks. The combination of AP-MS with other techniques, such as biochemical fractionation, intact mass measurement and chemical crosslinking, can help to decipher the supramolecular organization of protein complexes. AP-MS can also be combined with quantitative proteomics approaches to better understand the dynamics of protein-complex assembly.

  2. Optimization Of A Mass Spectrometry Process

    SciTech Connect

    Lopes, Jose; Alegria, F. Correa; Redondo, Luis; Barradas, N. P.; Alves, E.; Rocha, Jorge

    2011-06-01

    In this paper we present and discuss a system developed in order to optimize the mass spectrometry process of an ion implanter. The system uses a PC to control and display the mass spectrum. The operator interacts with the I/O board, that interfaces with the computer and the ion implanter by a LabVIEW code. Experimental results are shown and the capabilities of the system are discussed.

  3. Application of mass spectrometry for metabolite identification.

    PubMed

    Ma, Shuguang; Chowdhury, Swapan K; Alton, Kevin B

    2006-06-01

    Metabolism studies play a pivotal role in drug discovery and development. Characterization of metabolic "hot-spots" as well as reactive and pharmacologically active metabolites is critical to designing new drug candidates with improved metabolic stability, toxicological profile and efficacy. Metabolite identification in the preclinical species used for safety evaluation is required in order to determine whether human metabolites have been adequately tested during non-clinical safety assessment. From an instrumental standpoint, high performance liquid chromatography (HPLC) coupled with mass spectrometry (MS) dominates all analytical tools used for metabolite identification. The general strategies employed for metabolite identification in both drug discovery and drug development settings together with sample preparation techniques are reviewed herein. These include a discussion of the various ionization methods, mass analyzers, and tandem mass spectrometry (MS/MS) techniques that are used for structural characterization in a modern drug metabolism laboratory. Mass spectrometry-based techniques, such as stable isotope labeling, on-line H/D exchange, accurate mass measurement to enhance metabolite identification and recent improvements in data acquisition and processing for accelerating metabolite identification are also described. Rounding out this review, we offer additional thoughts about the potential of alternative and less frequently used techniques such as LC-NMR/MS, CRIMS and ICPMS.

  4. Isotope ratio measurements by secondary ion mass spectrometry (SIMS) and glow discharge mass spectrometry (GDMS)

    NASA Astrophysics Data System (ADS)

    Betti, Maria

    2005-04-01

    The basic principles of secondary ion mass spectrometry and glow discharge mass spectrometry have been shortly revisited. The applications of both techniques as exploited for the isotope ratio measurements in several matrices have been reviewed. Emphasis has been given to research fields in expansions such as solar system studies, medicine, biology, environment and nuclear forensic. The characteristics of the two techniques are discussed in terms of sensitivity and methodology of quantification. Considerations on the different detection possibilities in SIMS are also presented.

  5. Space Applications of Mass Spectrometry. Chapter 31

    NASA Technical Reports Server (NTRS)

    Hoffman, John H.; Griffin, Timothy P.; Limero, Thomas; Arkin, C. Richard

    2010-01-01

    Mass spectrometers have been involved in essentially all aspects of space exploration. This chapter outlines some of these many uses. Mass spectrometers have not only helped to expand our knowledge and understanding of the world and solar system around us, they have helped to put man safely in space and expand our frontier. Mass spectrometry continues to prove to be a very reliable, robust, and flexible analytical instrument, ensuring that its use will continue to help aid our investigation of the universe and this small planet that we call home.

  6. Initial results of positron ionization mass spectrometry

    NASA Technical Reports Server (NTRS)

    Donohue, D. L.; Hulett, L. D., Jr.; Mcluckey, S. A.; Glish, G. L.; Eckenrode, B. A.

    1990-01-01

    The use of monoenergetic positrons for the ionization of organic molecules in the gas phase is described. The ionic products are analyzed with a time-of-flight mass spectrometer and detected to produce a mass spectrum. The ionization mechanisms which can be studied in this way include positron impact at energies above the ionization limit of the target molecules, positronium formation in the Ore gap energy range, and positron attachment at energies less than 1eV. The technique of positron ionization mass spectrometry (PIMS) may have analytical utility in that chemical selectivity is observed for one or more of these processes.

  7. Nuclear applications of inorganic mass spectrometry.

    PubMed

    De Laeter, John

    2010-01-01

    There are several basic characteristics of mass spectrometry that are not always fully appreciated by the science community. These characteristics include the distinction between relative and absolute isotope abundances, and the influence of isotope fractionation on the accuracy of isotopic measurements. These characteristics can be illustrated in the field of nuclear physics with reference to the measurement of nuclear parameters, which involve the use of enriched isotopes, and to test models of s-, r-, and p-process nucleosynthesis. The power of isotope-dilution mass spectrometry (IDMS) to measure trace elements in primitive meteorites to produce accurate Solar System abundances has been essential to the development of nuclear astrophysics. The variety of mass spectrometric instrumentation used to measure the isotopic composition of elements has sometimes been accompanied by a lack of implementation of basic mass spectrometric protocols which are applicable to all instruments. These metrological protocols are especially important in atomic weight determinations, but must also be carefully observed in cases where the anomalies might be very small, such as in studies of the daughter products of extinct radionuclides to decipher events in the early history of the Solar System. There are occasions in which misleading conclusions have been drawn from isotopic data derived from mass spectrometers where such protocols have been ignored. It is important to choose the mass spectrometer instrument most appropriate to the proposed experiment. The importance of the integrative nature of mass spectrometric measurements has been demonstrated by experiments in which long, double beta decay and geochronological decay half-lives have been measured as an alternative to costly radioactive-counting experiments. This characteristic is also illustrated in the measurement of spontaneous fission yields, which have accumulated over long periods of time. Mass spectrometry is also a

  8. Linking Mass Spectrometry with Toxicology for Emerging Water Contaminants

    EPA Science Inventory

    This overview presentation will discuss the benefits of combining mass spectrometry with toxicology. These benefits will be described for 3 main areas: (1) Toxicity assays used to test new environmental contaminants previously identified using mass spectrometry, such that furth...

  9. 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

  10. Ultrahigh-Mass Mass Spectrometry of Single Biomolecules and Bioparticles

    NASA Astrophysics Data System (ADS)

    Chang, Huan-Cheng

    2009-07-01

    Since the advent of soft ionization methods, mass spectrometry (MS) has found widespread application in the life sciences. Mass is now known to be a critical parameter for characterization of biomolecules and their complexes; it is also a useful parameter to characterize bioparticles such as viruses and cells. However, because of the genetic diversity of these entities, it is necessary to measure their masses individually and to obtain the corresponding mean masses and mass distributions. Here, I review recent technological developments that enable mass measurement of ultrahigh-mass biomolecules and bioparticles at the single-ion level. Some representative examples include cryodetection time-of-flight MS of single-megadalton protein ions, Millikan-type mass measurements of single viruses in a cylindrical ion trap, and charge-detection quadrupole ion trap MS of single whole cells. I also discuss the promises and challenges of these new technologies in real-world applications.

  11. Biological particle analysis by mass spectrometry

    NASA Technical Reports Server (NTRS)

    Vilker, V. L.; Platz, R. M.

    1983-01-01

    An instrument that analyzes the chemical composition of biological particles in aerosol or hydrosol form was developed. Efforts were directed toward the acquisition of mass spectra from aerosols of biomolecules and bacteria. The filament ion source was installed on the particle analysis by mass spectrometry system. Modifications of the vacuum system improved the sensitivity of the mass spectrometer. After the modifications were incorporated, detailed mass spectra of simple compounds from the three major classes of biomolecules, proteins, nucleic acids, and carbohydrates were obtained. A method of generating bacterial aerosols was developed. The aerosols generated were collected and examined in the scanning electron microscope to insure that the bacteria delivered to the mass spectrometer were intact and free from debris.

  12. Identification of carotenoids using mass spectrometry.

    PubMed

    Rivera, Sol M; Christou, Paul; Canela-Garayoa, Ramon

    2014-01-01

    The present review compiles positive MS fragmentation data of selected carotenoids obtained using various ionization techniques and matrices. In addition, new experimental data from the analysis of carotenoids in transgenic maize and rice callus are provided. Several carotenes and oxygen-functionalized carotenoids containing epoxy, hydroxyl, and ketone groups were ionized by atmospheric pressure chemical ionization (APCI)-tandem mass spectrometry (MS/MS) in positive ion mode. Thus, on the basis of the information obtained from the literature and our own experiments, we identified characteristic carotenoid ions that can be associated to functional groups in the structures of these compounds. In addition, pigments with a very similar structure were differentiated through comparison of the intensities of their fragments. The data provide a basis for the structural elucidation of carotenoids by mass spectrometry (MS).

  13. Impact of automation on mass spectrometry.

    PubMed

    Zhang, Yan Victoria; Rockwood, Alan

    2015-10-23

    Mass spectrometry coupled to liquid chromatography (LC-MS and LC-MS/MS) is an analytical technique that has rapidly grown in popularity in clinical practice. In contrast to traditional technology, mass spectrometry is superior in many respects including resolution, specificity, multiplex capability and has the ability to measure analytes in various matrices. Despite these advantages, LC-MS/MS remains high cost, labor intensive and has limited throughput. This specialized technology requires highly trained personnel and therefore has largely been limited to large institutions, academic organizations and reference laboratories. Advances in automation will be paramount to break through this bottleneck and increase its appeal for routine use. This article reviews these challenges, shares perspectives on essential features for LC-MS/MS total automation and proposes a step-wise and incremental approach to achieve total automation through reducing human intervention, increasing throughput and eventually integrating the LC-MS/MS system into the automated clinical laboratory operations.

  14. Quantitative interaction proteomics using mass spectrometry.

    PubMed

    Wepf, Alexander; Glatter, Timo; Schmidt, Alexander; Aebersold, Ruedi; Gstaiger, Matthias

    2009-03-01

    We present a mass spectrometry-based strategy for the absolute quantification of protein complex components isolated through affinity purification. We quantified bait proteins via isotope-labeled reference peptides corresponding to an affinity tag sequence and prey proteins by label-free correlational quantification using the precursor ion signal intensities of proteotypic peptides generated in reciprocal purifications. We used this method to quantitatively analyze interaction stoichiometries in the human protein phosphatase 2A network.

  15. Radiation Biomarker Research Using Mass Spectrometry

    DTIC Science & Technology

    2007-07-01

    The data was of insufficient quality to obtain definitive biomarkers. Trips were also made to AFRL/HEDR at Brooks City Base to assist with their...sample analysis using the Finnigan LTQ located there. Mr. Mullens and Ms. Nagore assisted with training personnel at AFRL/HEDR and when necessary...techniques with saliva samples and matrix- assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS), we have been able to

  16. Monolithic multinozzle emitters for nanoelectrospray mass spectrometry

    DOEpatents

    Wang, Daojing; Yang, Peidong; Kim, Woong; Fan, Rong

    2011-09-20

    Novel and significantly simplified procedures for fabrication of fully integrated nanoelectrospray emitters have been described. For nanofabricated monolithic multinozzle emitters (NM.sup.2 emitters), a bottom up approach using silicon nanowires on a silicon sliver is used. For microfabricated monolithic multinozzle emitters (M.sup.3 emitters), a top down approach using MEMS techniques on silicon wafers is used. The emitters have performance comparable to that of commercially-available silica capillary emitters for nanoelectrospray mass spectrometry.

  17. Accelerator mass spectrometry - from DNA to astrophysics

    NASA Astrophysics Data System (ADS)

    Kutschera, Walter

    2013-12-01

    A brief review of accelerator mass spectrometry (AMS) is presented. The present work touches on a few technical aspects and recent developments of AMS, and describes two specific applications of AMS, the dating of human DNA with the 14C bomb peak and the search for superheavy elements in nature. Since two extended general reviews on technical developments in AMS [1] and applications of AMS [2] will appear in 2013, frequent reference to these reviews is made.

  18. Toward Single-Molecule Nanomechanical Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Roukes, Michael

    2009-03-01

    Mass spectrometry (MS) has become a preeminent methodology of proteomics since it provides rapid and quantitative identification of protein species with relatively low sample consumption. Yet with the trend toward biological analysis at increasingly smaller scales, ultimately down to the volume of an individual cell, MS with few-to-single molecule resolution will be required. We report the first realization of MS based on single-biological-molecule detection with nanoelectromechanical systems (NEMS). NEMS provide unparalleled mass resolution, now sufficient for detection of individual molecular species in real time. However, high sensitivity is only one of several components required for MS. We demonstrate a first complete prototype NEMS-MS system for single-molecule mass spectrometry providing proof-of-principle for this new technique. Nanoparticles and protein species are introduced by electrospray injection from the fluid phase in ambient conditions into vacuum and subsequently delivered to the NEMS detector by hexapole ion optics . Mass measurements are then recorded in real-time as analytes adsorb, one-by-one, onto a phase-locked, ultrahigh frequency (UHF) NEMS resonator. These first NEMS-MS spectra, obtained with modest resolution from only several hundred mass adsorption events, presage the future capabilities of this methodology. We outline the substantial improvements feasible in near term, through recent advances and technological avenues that are unique to NEMS-MS.

  19. Mass Spectrometry of Proteins in Liquids

    NASA Astrophysics Data System (ADS)

    Baltz-Knorr, Michelle; Papantonakis, Michael; Ermer Haglund, David, Jr.

    1999-11-01

    Infrared matrix assisted laser desorption/ionization mass spectrometry (IR-MALDI) is an effective technique for mass identification and structural analysis of biomolecules. We are using liquid glycerol/water matrices in a reflectron time-of-flight mass spectrometer equipped with a liquid nitrogen cooled sample stage to provide a more natural environment for biomolecules. An Er:YAG laser (2.94 μm) and also a tunable free electron laser (2-9 μm) are used to induce desorption and ionization by exciting the O-H and CH2 stretching vibrations in the glycerol. This vibrationally enhanced ionization makes IR-MALDI very efficient, as observed in the mass spectra of small peptides. This work is a first step toward using mass spectrometry to study noncovalently bound protein complexes in vitro and to study proteins in their cellular environment. Supported by the Medical Free Electron Laser Program of the Office of Naval Research and the Vanderbilt Molecular Biophysics Training Grant of the National Institutes of Health

  20. Mass spectrometry with direct supercritical fluid injection

    SciTech Connect

    Smith, R.D.; Udseth, H.R.

    1983-12-01

    Direct fluid injection mass spectrometry utilizes supercritical fluids for solvation and transfer of materials to a mass spectrometer chemical ionization (CI) source. Available data suggest that any material soluble in a supercritical fluid is transferred efficiently to the ionization region. Mass spectra are presented for mycotoxins of the trichothecene group obtained by use of supercritical carbon dioxide with isobutane as the CI reagent gas. Direct fluid injection MS/MS is also illustrated for major ions in the isobutane chemical ionization of T-2 toxin. The effect of pressure and temperature upon solubility in supercritical fluids is described and illustrated for diacetoxycirpenol. A potential method is also demonstrated for on-line fraction during MS analysis using pressure to control supercritical fluid solubility. Mass spectra are also presented for polar compounds, using supercritical ammonia, and the extension to complex mixtures is described. The fundamental basis and experimental requirements of the direct fluid injection process are discussed. 34 references, 11 figures, 1 table.

  1. Mass spectrometry with direct supercritical fluid injection

    SciTech Connect

    Smith, R.D.; Udseth, H.R.

    1983-12-01

    Direct fluid injection mass spectrometry utilizes supercritical fluids for solvation and transfer of materials to a mass spectrometer chemical ionization (CI) source. Available data suggest that any material soluble in a supercritical fluid is transferred efficiently to the ionization region. Mass spectra are presented for mycotoxins of the trichothecene group obtained by use of supercritical carbon dioxide with isobutane as the CI reagent gas. Direct fluid injection MS/MS is also illustrated for major ions in the isobutane chemical ionization of T-2 toxin. The effect of pressure and temperature upon solubility in supercritical fluids is described and illustrated for diacetoxyscirpenol. A potential method is also demonstrated for ''on-line fractionation'' during MS analysis using pressure to control supercritical fluid solubility. Mass spectra are also presented for polar compounds, using supercritical ammonia, and the extension to complex mixtures is described. The fundamental basis and experimental requirements of the direct fluid injection process are discussed. 1 figure, 11 tables.

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

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  3. Analysis of the Human Adult Urinary Metabolome Variations with Age, Body Mass Index, and Gender by Implementing a Comprehensive Workflow for Univariate and OPLS Statistical Analyses.

    PubMed

    Thévenot, Etienne A; Roux, Aurélie; Xu, Ying; Ezan, Eric; Junot, Christophe

    2015-08-07

    Urine metabolomics is widely used for biomarker research in the fields of medicine and toxicology. As a consequence, characterization of the variations of the urine metabolome under basal conditions becomes critical in order to avoid confounding effects in cohort studies. Such physiological information is however very scarce in the literature and in metabolomics databases so far. Here we studied the influence of age, body mass index (BMI), and gender on metabolite concentrations in a large cohort of 183 adults by using liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS). We implemented a comprehensive statistical workflow for univariate hypothesis testing and modeling by orthogonal partial least-squares (OPLS), which we made available to the metabolomics community within the online Workflow4Metabolomics.org resource. We found 108 urine metabolites displaying concentration variations with either age, BMI, or gender, by integrating the results from univariate p-values and multivariate variable importance in projection (VIP). Several metabolite clusters were further evidenced by correlation analysis, and they allowed stratification of the cohort. In conclusion, our study highlights the impact of gender and age on the urinary metabolome, and thus it indicates that these factors should be taken into account for the design of metabolomics studies.

  4. Computational mass spectrometry for small molecules

    PubMed Central

    2013-01-01

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

  5. Current challenges in software solutions for mass spectrometry-based quantitative proteomics.

    PubMed

    Cappadona, Salvatore; Baker, Peter R; Cutillas, Pedro R; Heck, Albert J R; van Breukelen, Bas

    2012-09-01

    Mass spectrometry-based proteomics has evolved as a high-throughput research field over the past decade. Significant advances in instrumentation, and the ability to produce huge volumes of data, have emphasized the need for adequate data analysis tools, which are nowadays often considered the main bottleneck for proteomics development. This review highlights important issues that directly impact the effectiveness of proteomic quantitation and educates software developers and end-users on available computational solutions to correct for the occurrence of these factors. Potential sources of errors specific for stable isotope-based methods or label-free approaches are explicitly outlined. The overall aim focuses on a generic proteomic workflow.

  6. Identifying Kinase Substrates via a Heavy ATP Kinase Assay and Quantitative Mass Spectrometry

    PubMed Central

    Müller, André C.; Giambruno, Roberto; Weißer, Juliane; Májek, Peter; Hofer, Alexandre; Bigenzahn, Johannes W.; Superti-Furga, Giulio; Jessen, Henning J.; Bennett, Keiryn L.

    2016-01-01

    Mass spectrometry-based in vitro kinase screens play an essential role in the discovery of kinase substrates, however, many suffer from biological and technical noise or necessitate genetically-altered enzyme-cofactor systems. We describe a method that combines stable γ-[18O2]-ATP with classical in vitro kinase assays within a contemporary quantitative proteomic workflow. Our approach improved detection of known substrates of the non-receptor tyrosine kinase ABL1; and identified potential, new in vitro substrates. PMID:27346722

  7. Improving gene annotation using peptide mass spectrometry

    PubMed Central

    Tanner, Stephen; Shen, Zhouxin; Ng, Julio; Florea, Liliana; Guigó, Roderic; Briggs, Steven P.; Bafna, Vineet

    2007-01-01

    Annotation of protein-coding genes is a key goal of genome sequencing projects. In spite of tremendous recent advances in computational gene finding, comprehensive annotation remains a challenge. Peptide mass spectrometry is a powerful tool for researching the dynamic proteome and suggests an attractive approach to discover and validate protein-coding genes. We present algorithms to construct and efficiently search spectra against a genomic database, with no prior knowledge of encoded proteins. By searching a corpus of 18.5 million tandem mass spectra (MS/MS) from human proteomic samples, we validate 39,000 exons and 11,000 introns at the level of translation. We present translation-level evidence for novel or extended exons in 16 genes, confirm translation of 224 hypothetical proteins, and discover or confirm over 40 alternative splicing events. Polymorphisms are efficiently encoded in our database, allowing us to observe variant alleles for 308 coding SNPs. Finally, we demonstrate the use of mass spectrometry to improve automated gene prediction, adding 800 correct exons to our predictions using a simple rescoring strategy. Our results demonstrate that proteomic profiling should play a role in any genome sequencing project. PMID:17189379

  8. Isotopic trace analysis by atomic mass spectrometry

    SciTech Connect

    Stoffels, J.J.

    1993-12-01

    All the production facilities at Hanford are now shut down. However, the legacy from half a century of plutonium production includes 177 underground storage tanks of up to one million gallons each containing the largest accumulation of high-level radioactive waste in what used to be called ``the free world.`` Hanford`s new mission, in addition to a spectrum of ongoing research and development, is radioactive waste management and environmental restoration. Isotope-ratio mass spectrometry will continue to be an essential tool in monitoring the progress of that mission.

  9. [Application of mass spectrometry in mycology].

    PubMed

    Quiles Melero, Inmaculada; Peláez, Teresa; Rezusta López, Antonio; Garcia-Rodríguez, Julio

    2016-06-01

    MALDI-TOF (matrix-assisted laser desorption ionization time-of-flight) mass spectrometry (MS) is becoming an essential tool in most microbiology laboratories. At present, by using a characteristic fungal profile obtained from whole cells or through simple extraction protocols, MALDI-TOF MS allows the identification of pathogenic fungi with a high performance potential. This methodology decreases the laboratory turnaround time, optimizing the detection of mycoses. This article describes the state-of-the-art of the use of MALDI-TOF MS for the detection of human clinical fungal pathogens in the laboratory and discusses the future applications of this technology, which will further improve routine mycological diagnosis.

  10. Biological accelerator mass spectrometry at Uppsala University.

    PubMed

    Salehpour, Mehran; Possnert, Göran; Bryhni, Helge; Palminger-Hallén, Ira; Ståhle, Lars

    2009-03-01

    A new research programme for the biological applications of accelerator mass spectrometry has been initiated at Uppsala University and the first results are presented. A (14)C-labelled pharmaceutical substance has been dissolved in human blood, plasma and urine and diluted over 3 orders of magnitude. The measured drug concentrations were found to be in good agreement with the predicted values. Furthermore, the effect of the sample preparation background contribution has been studied as the sample amount was varied down to sub-microl sizes.

  11. Accelerator mass spectrometry of the planetary elements

    NASA Astrophysics Data System (ADS)

    Fifield, L. K.; Clacher, A. P.; Morris, K.; King, S. J.; Cresswell, R. G.; Day, J. P.; Livens, F. R.

    1997-03-01

    Accelerator mass spectrometry has been applied for the first time to the detection of 237Np. Sensitivity approaches 105 atoms. A first measurement of the mobility of 237Np in a marine environment is reported, and lends support to the prediction that neptunium should be substantially more mobile than plutonium. Measurements of backgrounds and transmissions for plutonium and neptunium in different charge states are also reported. In addition, the relative negative ion formation probabilities for the monoxide ions of Th, U, Np and Pu have been measured.

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  13. Proteomic analysis of formalin-fixed paraffin embedded tissue by MALDI imaging mass spectrometry

    PubMed Central

    Casadonte, Rita; Caprioli, Richard M

    2012-01-01

    Archived formalin-fixed paraffin-embedded (FFPE) tissue collections represent a valuable informational resource for proteomic studies. Multiple FFPE core biopsies can be assembled in a single block to form tissue microarrays (TMAs). We describe a protocol for analyzing protein in FFPE -TMAs using matrix-assisted laser desorption/ionization (MAL DI) imaging mass spectrometry (IMS). The workflow incorporates an antigen retrieval step following deparaffinization, in situ trypsin digestion, matrix application and then mass spectrometry signal acquisition. The direct analysis of FFPE -TMA tissue using IMS allows direct analysis of multiple tissue samples in a single experiment without extraction and purification of proteins. The advantages of high speed and throughput, easy sample handling and excellent reproducibility make this technology a favorable approach for the proteomic analysis of clinical research cohorts with large sample numbers. For example, TMA analysis of 300 FFPE cores would typically require 6 h of total time through data acquisition, not including data analysis. PMID:22011652

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

    PubMed

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

    2016-06-12

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

  15. Pathology interface for the molecular analysis of tissue by mass spectrometry

    PubMed Central

    Norris, Jeremy L.; Tsui, Tina; Gutierrez, Danielle B.; Caprioli, Richard M.

    2016-01-01

    Background: Imaging mass spectrometry (IMS) generates molecular images directly from tissue sections to provide better diagnostic insights and expand the capabilities of clinical anatomic pathology. Although IMS technology has matured over recent years, the link between microscopy imaging currently used by pathologists and MS-based molecular imaging has not been established. Methods: We adapted the Vanderbilt University Tissue Core workflow for IMS into a web-based system that facilitates remote collaboration. The platform was designed to perform within acceptable web response times for viewing, annotating, and processing high resolution microscopy images. Results: We describe a microscopy-driven approach to tissue analysis by IMS. Conclusion: The Pathology Interface for Mass Spectrometry is designed to provide clinical access to IMS technology and deliver enhanced diagnostic value. PMID:27141319

  16. FAPA mass spectrometry of designer drugs.

    PubMed

    Smoluch, Marek; Gierczyk, Blazej; Reszke, Edward; Babij, Michal; Gotszalk, Teodor; Schroeder, Grzegorz; Silberring, Jerzy

    2016-01-01

    Application of a flowing atmospheric-pressure afterglow ion source for mass spectrometry (FAPA-MS) for the analysis of designer drugs is described. In this paper, we present application of FAPA MS for identification of exemplary psychotropic drugs: JWH-122, 4BMC, Pentedrone, 3,4-DNNC and ETH-CAT. We have utilized two approaches for introducing samples into the plasma stream; first in the form of a methanolic aerosol from the nebulizer, and the second based on a release of vapors from the electrically heated crucible by thermal desorption. The analytes were ionized by FAPA and identified in the mass analyzer. The order of release of the compounds depends on their volatility. These methods offer fast and reliable structural information, without pre-separation, and can be an alternative to the Electron Impact, GC/MS, and ESI for fast analysis of designer-, and other psychoactive drugs.

  17. Study of odor recorder using Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Miura, Tomohiro; Nakamoto, Takamichi; Moriizumi, Toyosaka

    It is necessary to determine the recipe of a target odor with sufficient accuracy to realize an odor recorder for recording and reproducing it. We studied the recipe measurement method of a target odor using a mass spectrometry. It was confirmed that the linear superposition was valid when the binary mixture of the apple-flavor components such as isobutyric acid and ethyl valerate was measured. The superposition of a mass spectrum pattern may enable the recipe determination of a multi-component odor easily. In this research, we succeeded in the recipe determinations of orange flavor made up of 14 component odors when its typical recipe, the equalized, the citral-enhanced and the citronellol-enhanced ones were measured.

  18. Mass Spectrometry for Rapid Characterization of Microorganisms

    NASA Astrophysics Data System (ADS)

    Demirev, Plamen A.; Fenselau, Catherine

    2008-07-01

    Advances in instrumentation, proteomics, and bioinformatics have contributed to the successful applications of mass spectrometry (MS) for detection, identification, and classification of microorganisms. These MS applications are based on the detection of organism-specific biomarker molecules, which allow differentiation between organisms to be made. Intact proteins, their proteolytic peptides, and nonribosomal peptides have been successfully utilized as biomarkers. Sequence-specific fragments for biomarkers are generated by tandem MS of intact proteins or proteolytic peptides, obtained after, for instance, microwave-assisted acid hydrolysis. In combination with proteome database searching, individual biomarker proteins are unambiguously identified from their tandem mass spectra, and from there the source microorganism is also identified. Such top-down or bottom-up proteomics approaches permit rapid, sensitive, and confident characterization of individual microorganisms in mixtures and are reviewed here. Examples of MS-based functional assays for detection of targeted microorganisms, e.g., Bacillus anthracis, in environmental or clinically relevant backgrounds are also reviewed.

  19. Radiocarbon positive-ion mass spectrometry

    NASA Astrophysics Data System (ADS)

    Freeman, Stewart P. H. T.; Shanks, Richard P.; Donzel, Xavier; Gaubert, Gabriel

    2015-10-01

    Proof-of-principle of a new mass spectrometric technique for radiocarbon measurement is demonstrated. Interfering nitrogen and hydrocarbon molecules are largely eliminated in a charge-exchange cell operating on non-metallic gas. The positive-to-negative ion conversion is the reverse of that conventionally used in accelerator mass spectrometry (AMS) and is compatible with plasma ion sources that may be significantly more efficient and capable of greater output than are AMS sputter ion sources. The Nanogan electron cyclotron resonance (ECR) ion source employed exhibited no sample memory and the >50 kyrs age range of AMS was reproduced. A bespoke prototype new instrument is now required to optimise the plasma and cell physics and to realise hypothetical performance gains over AMS.

  20. Protein Sequencing with Tandem Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Ziady, Assem G.; Kinter, Michael

    The recent introduction of electrospray ionization techniques that are suitable for peptides and whole proteins has allowed for the design of mass spectrometric protocols that provide accurate sequence information for proteins. The advantages gained by these approaches over traditional Edman Degradation sequencing include faster analysis and femtomole, sometimes attomole, sensitivity. The ability to efficiently identify proteins has allowed investigators to conduct studies on their differential expression or modification in response to various treatments or disease states. In this chapter, we discuss the use of electrospray tandem mass spectrometry, a technique whereby protein-derived peptides are subjected to fragmentation in the gas phase, revealing sequence information for the protein. This powerful technique has been instrumental for the study of proteins and markers associated with various disorders, including heart disease, cancer, and cystic fibrosis. We use the study of protein expression in cystic fibrosis as an example.

  1. Secondary Ion Mass Spectrometry of Environmental Aerosols

    SciTech Connect

    Gaspar, Daniel J.; Cliff, John B.

    2010-08-01

    Atmospheric particles influence many aspects of climate, air quality and human health. Understanding the composition, chemistry and behavior of atmospheric aerosols is a key remaining challenge in improving climate models. Furthermore, particles may be traced back to a particular source based on composition, stable isotope ratios, or the presence of particular surface chemistries. Finally, the characterization of atmospheric particles in the workplace plays an important role in understanding the potential for exposure and environmental and human health effects to engineered and natural nanoscale particles. Secondary ion mass spectrometry (SIMS) is a useful tool in determining any of several aspects of the structure, composition and chemistry of these particles. Often used in conjunction with other surface analysis and electron microscopy methods, SIMS has been used to determine or confirm reactions on and in particles, the presence of particular organic species on the surface of atmospheric aerosols and several other interesting and relevant findings. Various versions of SIMS instruments – dynamic SIMS, time of flight secondary ion mass spectrometry or TOF-SIMS, nanoSIMS – have been used to determine specific aspects of aerosol structure and chemistry. This article describes the strengths of each type of SIMS instrument in the characterization of aerosols, along with guidance on sample preparation, specific characterization specific to the particular information sought in the analysis. Examples and guidance are given for each type of SIMS analysis.

  2. [Mass spectrometry in the clinical microbiology laboratory].

    PubMed

    Jordana-Lluch, Elena; Martró Català, Elisa; Ausina Ruiz, Vicente

    2012-12-01

    Infectious diseases are still a cause of high mortality and morbidity rates. Current microbiological diagnostic methods are based on culture and phenotypic identification of isolated microorganisms, which can be obtained in about 24-48 h. Given that the microbiological identification is of major importance for patient management, new diagnostic methods are needed in order to detect and identify microorganisms in a timely and accurate manner. Over the last few years, several molecular techniques based on the amplification of microbial nucleic acids have been developed with the aim of reducing the time needed for the identification of the microorganisms involved in different infectious processes. On the other hand, mass spectrometry has emerged as a rapid and consistent alternative to conventional methods for microorganism identification. This review describes the most widely used mass spectrometry technologies -matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and electrospray ionization time-of-flight (ESI-TOF)-, both for protein and nucleic acid analysis, as well as the commercial platforms available. Related publications of most interest in clinical microbiology are also reviewed.

  3. 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.

  4. Mass Spectrometry on Future Mars Landers

    NASA Technical Reports Server (NTRS)

    Brinckerhoff, W. B.; Mahaffy, P. R.

    2011-01-01

    Mass spectrometry investigations on the 2011 Mars Science Laboratory (MSL) and the 2018 ExoMars missions will address core science objectives related to the potential habitability of their landing site environments and more generally the near-surface organic inventory of Mars. The analysis of complex solid samples by mass spectrometry is a well-known approach that can provide a broad and sensitive survey of organic and inorganic compounds as well as supportive data for mineralogical analysis. The science value of such compositional information is maximized when one appreciates the particular opportunities and limitations of in situ analysis with resource-constrained instrumentation in the context of a complete science payload and applied to materials found in a particular environment. The Sample Analysis at Mars (SAM) investigation on MSL and the Mars Organic Molecule Analyzer (MOMA) investigation on ExoMars will thus benefit from and inform broad-based analog field site work linked to the Mars environments where such analysis will occur.

  5. Research Using Accelerator Mass Spectrometry at Arizona

    NASA Astrophysics Data System (ADS)

    Jull, A.; Donahue, D. J.; Burr, G. S.; Beck, W.; Hatheway, A. L.; Biddulph, D. L.; McHargue, L. R.

    2002-12-01

    An Accelerator Mass Spectrometry (AMS) facility has been operated at the University of Arizona since 1982. This is an excellent example of a facility which has benefitted from the NSF Earth Sciences Instrumentation and Facilities Program. AMS has many applications to the fields of geochronology, geoarchaeology, paleoclimatology. A wide range of climatic, geologic and archeological records can be characterized by measuring their 14C and 10Be concentrations, using accelerator mass spectrometry (AMS). These records are found not only in the traditional sampling sites such as lake sediments and ice cores, but also in diverse natural accumulates and biogeochemical products such as: loess/paleosol deposits, corals, speleothems, and forest-fire horizons. The in-situ production of cosmogenic radionuclides in terrestrial and extraterrestrial materials provides several possibilities of determining their chronology. Thes studies are important for understanding cosmic-ray production of radionuclides in rock surfaces, by which we can draw conclusions about exposure time and erosion. Studies on extraterrestrial materials such as lunar samples allow us to determine the solar and galactic cosmic-ray fluxes in the past, and the cosmogenic 14C and 10Be in meteorites can be used to determine terrestrial ages. In this paper, we will highlight some selected applications of AMS, including dating of some interesting art works and artifacts, to show some of the great range of studies which can be undertaken.

  6. Preliminary Investigation into Pyrotechnic Chemical Products via Mass Spectrometry Techniques

    DTIC Science & Technology

    2015-03-11

    predicted by theory. 15. SUBJECT TERMS mass spectrometry, gas chromatography , pyrolysis, combustion products, pyrotechnics 16. SECURITY CLASSIFICATION OF...Eric Miklaszewski Dr. Douglas Papenmeier Matthew Neiswinger Christina Yamamoto Approach: Pyrolysis / Gas Chromatography / Mass Spectrometry (Py/GC...Oven GC Column Sample Inlet 0 Mass Spectrometer Gas Chromatography GC Transfer Line Thermo Finnigan PolarisQ Ion Trap with Trace GC/MSn with a

  7. OpenMS: a flexible open-source software platform for mass spectrometry data analysis.

    PubMed

    Röst, Hannes L; Sachsenberg, Timo; Aiche, Stephan; Bielow, Chris; Weisser, Hendrik; Aicheler, Fabian; Andreotti, Sandro; Ehrlich, Hans-Christian; Gutenbrunner, Petra; Kenar, Erhan; Liang, Xiao; Nahnsen, Sven; Nilse, Lars; Pfeuffer, Julianus; Rosenberger, George; Rurik, Marc; Schmitt, Uwe; Veit, Johannes; Walzer, Mathias; Wojnar, David; Wolski, Witold E; Schilling, Oliver; Choudhary, Jyoti S; Malmström, Lars; Aebersold, Ruedi; Reinert, Knut; Kohlbacher, Oliver

    2016-08-30

    High-resolution mass spectrometry (MS) has become an important tool in the life sciences, contributing to the diagnosis and understanding of human diseases, elucidating biomolecular structural information and characterizing cellular signaling networks. However, the rapid growth in the volume and complexity of MS data makes transparent, accurate and reproducible analysis difficult. We present OpenMS 2.0 (http://www.openms.de), a robust, open-source, cross-platform software specifically designed for the flexible and reproducible analysis of high-throughput MS data. The extensible OpenMS software implements common mass spectrometric data processing tasks through a well-defined application programming interface in C++ and Python and through standardized open data formats. OpenMS additionally provides a set of 185 tools and ready-made workflows for common mass spectrometric data processing tasks, which enable users to perform complex quantitative mass spectrometric analyses with ease.

  8. Multinozzle Emitter Arrays for Nanoelectrospray Mass Spectrometry

    SciTech Connect

    Mao, Pan; Wang, Hung-Ta; Yang, Peidong; Wang, Daojing

    2011-06-16

    Mass spectrometry (MS) is the enabling technology for proteomics and metabolomics. However, dramatic improvements in both sensitivity and throughput are still required to achieve routine MS-based single cell proteomics and metabolomics. Here, we report the silicon-based monolithic multinozzle emitter array (MEA), and demonstrate its proof-of-principle applications in high-sensitivity and high-throughput nanoelectrospray mass spectrometry. Our MEA consists of 96 identical 10-nozzle emitters in a circular array on a 3-inch silicon chip. The geometry and configuration of the emitters, the dimension and number of the nozzles, and the micropillar arrays embedded in the main channel, can be systematically and precisely controlled during the microfabrication process. Combining electrostatic simulation and experimental testing, we demonstrated that sharpened-end geometry at the stem of the individual multinozzle emitter significantly enhanced the electric fields at its protruding nozzle tips, enabling sequential nanoelectrospray for the high-density emitter array. We showed that electrospray current of the multinozzle emitter at a given total flow rate was approximately proportional to the square root of the number of its spraying-nozzles, suggesting the capability of high MS sensitivity for multinozzle emitters. Using a conventional Z-spray mass spectrometer, we demonstrated reproducible MS detection of peptides and proteins for serial MEA emitters, achieving sensitivity and stability comparable to the commercial capillary emitters. Our robust silicon-based MEA chip opens up the possibility of a fully-integrated microfluidic system for ultrahigh-sensitivity and ultrahigh-throughput proteomics and metabolomics.

  9. Multinozzle Emitter Arrays for Nanoelectrospray Mass Spectrometry

    PubMed Central

    Mao, Pan; Wang, Hung-Ta; Yang, Peidong; Wang, Daojing

    2011-01-01

    Mass spectrometry (MS) is the enabling technology for proteomics and metabolomics. However, dramatic improvements in both sensitivity and throughput are still required to achieve routine MS-based single cell proteomics and metabolomics. Here, we report the silicon-based monolithic multinozzle emitter array (MEA), and demonstrate its proof-of-principle applications in high-sensitivity and high-throughput nanoelectrospray mass spectrometry. Our MEA consists of 96 identical 10-nozzle emitters in a circular array on a 3-inch silicon chip. The geometry and configuration of the emitters, the dimension and number of the nozzles, and the micropillar arrays embedded in the main channel, can be systematically and precisely controlled during the microfabrication process. Combining electrostatic simulation and experimental testing, we demonstrated that sharpened-end geometry at the stem of the individual multinozzle emitter significantly enhanced the electric fields at its protruding nozzle tips, enabling sequential nanoelectrospray for the high-density emitter array. We showed that electrospray current of the multinozzle emitter at a given total flow rate was approximately proportional to the square root of the number of its spraying-nozzles, suggesting the capability of high MS sensitivity for multinozzle emitters. Using a conventional Z-spray mass spectrometer, we demonstrated reproducible MS detection of peptides and proteins for serial MEA emitters, achieving sensitivity and stability comparable to the commercial capillary emitters. Our robust silicon-based MEA chip opens up the possibility of a fully-integrated microfluidic system for ultrahigh-sensitivity and ultrahigh-throughput proteomics and metabolomics. PMID:21728281

  10. 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)

  11. Emerging capabilities of mass spectrometry for natural products.

    PubMed

    Jarmusch, Alan K; Cooks, R Graham

    2014-06-01

    Covering up to the end of 2013 A brief history of mass spectrometry in natural products research serves to identify themes which have driven progress in this area of application and in mass spectrometry itself. This account covers six decades of ionization methods, starting with traditional electron ionization and progressing through today's ambient ionization methods. Corresponding developments in mass analyzers are indicated, ranging from sector magnetic fields, through hybrid quadrupole mass filters to miniature ion traps. Current capabilities of mass spectrometry in natural products studies include direct in situ analysis, mass spectrometry imaging, and the study of biosynthetic pathways using metabolomic information. The survey concludes with a discussion of new experiments and capabilities including ion soft landing, preparative mass spectrometry, and accelerated ionic reactions in confined volumes.

  12. Characterisation of DEFB107 by mass spectrometry

    NASA Astrophysics Data System (ADS)

    McCullough, Bryan J.; Eastwood, Hayden; Clark, Dave J.; Polfer, Nick C.; Campopiano, Dominic J.; Dorin, Julia A.; Maxwell, Alison; Langley, Ross J.; Govan, John R. W.; Bernstein, Summer L.; Bowers, Michael T.; Barran, Perdita E.

    2006-05-01

    Mammalian defensins are small endogenous cationic proteins which form a class of antimicrobial peptides that is part of the innate immune response of all mammalian species [R. Lehrer, Nat. Rev. Microbiol. 2 (9) (2004) 727; T. Ganz, R.I. Lehrer, Curr. Opin. Immunol. 6 (4) (1994) 584] [1] and [2]. We have developed mass spectrometry based strategies for characterising the structure-activity relationship of defensins [D.J. Campopiano, D.J. Clarke, N.C. Polfer, P.E. Barran, R.J. Langley, J.R.W. Govan, A. Maxwell, J.R. Dorin, J. Biol. Chem. 279 (47) (2004) 48671; P.E. Barran, N.C. Polfer, D.J. Campopiano, D.J. Clarke, P.R.R. Langridge-Smith, R.J. Langley, J.R.W. Govan, A. Maxwell, J.R. Dorin, R.P. Millar, M.T. Bowers, Int. J. Mass Spectrom. 240 (2005) 273] [3] and [4], and here we present data obtained from a five cysteine containing [beta]-defensin, DEFB107. The synthetic product of this human defensin exists with a glutathione capping group, its oxidation state and disulphide connectivity have been determined via accurate mass measurements and peptide mass mapping respectively, and despite possessing three disulphide bridges, it does not fit the [beta]-defensin canonical motif. With the use of molecular modelling, we have generated candidate geometries to discern the influence of disulphide bridging on the overall tertiary structure of DEFB107. These are compared with experimental results from ion mobility measurements. Defensins display activity against a wide variety of pathogens including both gram-negative and gram-positive bacteria. Their mechanism of mode of action is unknown, but is believed to involve defensin aggregation at cell surfaces, followed by cell permeabilisation and hence deathE To probe this mechanism, the localisation of DEFB107 in synthetic vesicles was studied using H/D exchange and mass spectrometry. The results obtained are used to analyse the antimicrobial activity of DEFB107.

  13. Interfacing membrane mimetics with mass spectrometry

    PubMed Central

    Marty, Michael T.; Hoi, Kin Kuan; Robinson, Carol V.

    2017-01-01

    Conspectus Membrane proteins play critical physiological roles and make up the majority of drug targets. Due to their generally low expression levels and amphipathic nature, membrane proteins represent challenging molecular entities for biophysical study. Mass spectrometry offers several sensitive approaches to study the biophysics of membrane proteins. By preserving noncovalent interactions in the gas phase and using collisional activation to remove solubilization agents inside the mass spectrometer, native mass spectrometry (MS) is capable of studying isolated assemblies that would be insoluble in aqueous solution, such as membrane protein oligomers and protein-lipid complexes. Conventional methods use detergent to solubilize the protein prior to electrospray ionization. Gas-phase activation inside the mass spectrometer removes the detergent to yield the isolated proteins with bound ligands. This approach has proven highly successful for ionizing membrane proteins. With the appropriate choice of detergents, membrane proteins with bound lipid species can be observed, which allows characterization of protein-lipid interactions. However, detergents have several limitations. They do not necessarily replicate the native lipid bilayer environment, and only a small number of protein-lipid interactions can be resolved. In this Account, we summarize the development of different membrane mimetics as cassettes for MS analysis of membrane proteins. Examples include amphipols, bicelles, and picodiscs with a special emphasis on lipoprotein Nanodiscs. Polydispersity and heterogeneity of the membrane mimetic cassette is a critical issue for study by MS. Ever more complex datasets consisting of overlapping protein charge states and multiple lipid-bound entities have required development of new computational, theoretical, and experimental approaches to interpret both mass and ion mobility spectra. We will present the rationale and limitations of these approaches. Starting with the

  14. Characterization of Microorganisms by MALDI Mass Spectrometry

    SciTech Connect

    Petersen, Catherine E.; Valentine, Nancy B.; Wahl, Karen L.

    2008-10-02

    Matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) for characterization and analysis of microorganisms, specifically bacteria, is described here as a rapid screening tool. The objective of this technique is not comprehensive protein analysis of a microorganism but rather a rapid screening of the organism and the accessible protein pattern for characterization and distinction. This method is based on the ionization of the readily accessible and easily ionizable portion of the protein profile of an organism that is often characteristic of different bacterial species. The utility of this screening approach is yet to reach its full potential but could be applied to food safety, disease outbreak monitoring in hospitals, culture stock integrity and verification, microbial forensics or homeland security applications.

  15. [Future applications of mass spectrometry in microbiology].

    PubMed

    Vila, Jordi; Zboromyrska, Yuliya; Burillo, Almudena; Bouza, Emilio

    2016-06-01

    MALDI-TOF (matrix-assisted laser desorption ionization time-of-flight) mass spectrometry (MS) has been vigorously introduced in many clinical microbiology laboratories for the rapid and accurate identification of bacteria and fungi. In fact, the implementation of this methodology can be considered a revolution in these laboratories. In addition to microbial identification, MALDI-TOF MS is being used for the detection of some mechanisms of antibiotic resistance and for the molecular typing of bacteria. A number of current and future applications that increase the versatility of this methodology may also be mentioned. Among these are its direct application on clinical samples, the detection of toxins or specific microbial antigens, and its application in the fields of virology and parasitology.

  16. Recent trends in inorganic mass spectrometry

    SciTech Connect

    Smith, D.H.; Barshick, C.M.; Duckworth, D.C.; Riciputi, L.R.

    1996-10-01

    The field of inorganic mass spectrometry has seen substantial change in the author`s professional lifetime (over 30 years). Techniques in their infancy 30 years ago have matured; some have almost disappeared. New and previously unthought of techniques have come into being; some of these, such as ICP-MS, are reasonably mature now, while others have some distance to go before they can be so considered. Most of these new areas provide fertile fields for researchers, both in the development of new analytical techniques and by allowing fundamental studies to be undertaken that were previously difficult, impossible, or completely unforeseen. As full coverage of the field is manifestly impossible within the framework of this paper, only those areas with which the author has personal contact will be discussed. Most of the work originated in his own laboratory, but that of other laboratories is covered where it seemed appropriate.

  17. 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

  18. Accelerator mass spectrometry (AMS) in plutonium analysis.

    PubMed

    Strumińska-Parulska, Dagmara I

    The paper summarizes the results of the (240)Pu/(239)Pu atomic ratio studies in atmospheric fallout samples collected in 1986 over Gdynia (Poland) as well as three Baltic fish species collected in 1997 using the accelerator mass spectrometry. A new generation of AMS has been developed during last years and this method is an efficient and good technique to measure long-lived radioisotopes in the environment and provides the most accurate determination of the atomic ratios between (240)Pu and (239)Pu. The nuclide compositions of plutonium in filter samples correspond to their means of production. AMS measurements of atmospheric fallout collected in April showed sufficient increase of the (240)Pu/(239)Pu atomic ratio from 0.28 from March to 0.47. Also such high increase of (240)Pu/(239)Pu atomic ratio, close to reactor core (240)Pu/(239)Pu atomic ratio, was observed in September and equaled 0.47.

  19. Detection of gunshot residues using mass spectrometry.

    PubMed

    Taudte, Regina Verena; Beavis, Alison; Blanes, Lucas; Cole, Nerida; Doble, Philip; Roux, Claude

    2014-01-01

    In recent years, forensic scientists have become increasingly interested in the detection and interpretation of organic gunshot residues (OGSR) due to the increasing use of lead- and heavy metal-free ammunition. This has also been prompted by the identification of gunshot residue- (GSR-) like particles in environmental and occupational samples. Various techniques have been investigated for their ability to detect OGSR. Mass spectrometry (MS) coupled to a chromatographic system is a powerful tool due to its high selectivity and sensitivity. Further, modern MS instruments can detect and identify a number of explosives and additives which may require different ionization techniques. Finally, MS has been applied to the analysis of both OGSR and inorganic gunshot residue (IGSR), although the "gold standard" for analysis is scanning electron microscopy with energy dispersive X-ray microscopy (SEM-EDX). This review presents an overview of the technical attributes of currently available MS and ionization techniques and their reported applications to GSR analysis.

  20. Mass spectrometry and Web 2.0.

    PubMed

    Murray, Kermit K

    2007-10-01

    The term Web 2.0 is a convenient shorthand for a new era in the Internet in which users themselves are both generating and modifying existing web content. Several types of tools can be used. With social bookmarking, users assign a keyword to a web resource and the collection of the keyword 'tags' from multiple users form the classification of these resources. Blogs are a form of diary or news report published on the web in reverse chronological order and are a popular form of information sharing. A wiki is a website that can be edited using a web browser and can be used for collaborative creation of information on the site. This article is a tutorial that describes how these new ways of creating, modifying, and sharing information on the Web are being used for on-line mass spectrometry resources.

  1. Dating silk by capillary electrophoresis mass spectrometry.

    PubMed

    Moini, Mehdi; Klauenberg, Kathryn; Ballard, Mary

    2011-10-01

    A new capillary electrophoresis mass spectrometry (CE-MS) technique is introduced for age estimation of silk textiles based on amino acid racemization rates. With an L to D conversion half-life of ~2500 years for silk (B. mori) aspartic acid, the technique is capable of dating silk textiles ranging in age from several decades to a few-thousand-years-old. Analysis required only ~100 μg or less of silk fiber. Except for a 2 h acid hydrolysis at 110 °C, no other sample preparation is required. The CE-MS analysis takes ~20 min, consumes only nanoliters of the amino acid mixture, and provides both amino acid composition profiles and D/L ratios for ~11 amino acids.

  2. In situ secondary ion mass spectrometry analysis

    SciTech Connect

    Groenewold, G.S.; Applehans, A.D.; Ingram, J.C.; Delmore, J.E.; Dahl, D.A.

    1993-01-01

    The direct detection of tributyl phosphate (TBP) on rocks using molecular beam surface analysis [MBSA or in situ secondary ion mass spectrometry (SIMS)] is demonstrated. Quantities as low as 250 ng were detected on basalt and sandstone with little or no sample preparation. Detection of TBP on soil has proven to be more problematic and requires further study. Ethylenediaminetetraacetic acid (EDTA) is more difficult to detect because it is very reactive with surfaces of interest. Nevertheless, it is possible to detect EDTA if the acidity of the surface is controlled. The detection of EDTA-metal complexes is currently an open question, but evidence is presented for the detection of ions arising from a EDTA-lead complex. Carboxylic acids (i.e., citric, ascorbic, malic, succinic, malonic, and oxalic) give characteristic SIM spectra, but their detection on sample surfaces awaits evaluation.

  3. Forensic applications of ambient ionization mass spectrometry.

    PubMed

    Ifa, Demian R; Jackson, Ayanna U; Paglia, Giuseppe; Cooks, R Graham

    2009-08-01

    This review highlights and critically assesses forensic applications in the developing field of ambient ionization mass spectrometry. Ambient ionization methods permit the ionization of samples outside the mass spectrometer in the ordinary atmosphere, with minimal sample preparation. Several ambient ionization methods have been created since 2004 and they utilize different mechanisms to create ions for mass-spectrometric analysis. Forensic applications of these techniques--to the analysis of toxic industrial compounds, chemical warfare agents, illicit drugs and formulations, explosives, foodstuff, inks, fingerprints, and skin--are reviewed. The minimal sample pretreatment needed is illustrated with examples of analysis from complex matrices (e.g., food) on various substrates (e.g., paper). The low limits of detection achieved by most of the ambient ionization methods for compounds of forensic interest readily offer qualitative confirmation of chemical identity; in some cases quantitative data are also available. The forensic applications of ambient ionization methods are a growing research field and there are still many types of applications which remain to be explored, particularly those involving on-site analysis. Aspects of ambient ionization currently undergoing rapid development include molecular imaging and increased detection specificity through simultaneous chemical reaction and ionization by addition of appropriate chemical reagents.

  4. Atmospheric-pressure Penning ionization mass spectrometry.

    PubMed

    Hiraoka, Kenzo; Fujimaki, Susumu; Kambara, Shizuka; Furuya, Hiroko; Okazaki, Shigemitsu

    2004-01-01

    A preliminary study on the atmospheric-pressure Penning ionization (APP(e)I) of gaseous organic compounds with Ar* has been made. The metastable argon atoms (Ar*: 11.55 eV for (3)P(2) and 11.72 eV for (3)P(0)) were generated by the negative-mode corona discharge of atmospheric-pressure argon gas. By applying a high positive voltage (+500 to +1000 V) to the stainless steel capillary for the sample introduction (0.1 mm i.d., 0.3 mm o.d.), strong ion signals could be obtained. The ions formed were sampled through an orifice into the vacuum and mass-analyzed by an orthogonal time-of-flight mass spectrometer. The major ions formed by APP(e)I are found to be molecular-related ions for alkanes, aromatics, and oxygen-containing compounds. Because only the molecules with ionization energies less than the internal energy of Ar* are ionized, the present method will be a selective and highly sensitive interface for gas chromatography/mass spectrometry.

  5. Rapid Detection of Necrosis in Breast Cancer with Desorption Electrospray Ionization Mass Spectrometry

    PubMed Central

    Tata, Alessandra; Woolman, Michael; Ventura, Manuela; Bernards, Nicholas; Ganguly, Milan; Gribble, Adam; Shrestha, Bindesh; Bluemke, Emma; Ginsberg, Howard J.; Vitkin, Alex; Zheng, Jinzi; Zarrine-Afsar, Arash

    2016-01-01

    Identification of necrosis in tumors is of prognostic value in treatment planning, as necrosis is associated with aggressive forms of cancer and unfavourable outcomes. To facilitate rapid detection of necrosis with Mass Spectrometry (MS), we report the lipid MS profile of necrotic breast cancer with Desorption Electrospray Ionization Mass Spectrometry (DESI-MS) imaging validated with statistical analysis and correlating pathology. This MS profile is characterized by (1) the presence of the ion of m/z 572.48 [Cer(d34:1) + Cl]− which is a ceramide absent from the viable cancer subregions; (2) the absence of the ion of m/z 391.25 which is present in small abundance only in viable cancer subregions; and (3) a slight increase in the relative intensity of known breast cancer biomarker ions of m/z 281.25 [FA(18:1)-H]− and 303.23 [FA(20:4)-H]−. Necrosis is accompanied by alterations in the tissue optical depolarization rate, allowing tissue polarimetry to guide DESI-MS analysis for rapid MS profiling or targeted MS imaging. This workflow, in combination with the MS profile of necrosis, may permit rapid characterization of necrotic tumors from tissue slices. Further, necrosis-specific biomarker ions are detected in seconds with single MS scans of necrotic tumor tissue smears, which further accelerates the identification workflow by avoiding tissue sectioning and slide preparation. PMID:27734938

  6. Enantioselectivity of mass spectrometry: challenges and promises.

    PubMed

    Awad, Hanan; El-Aneed, Anas

    2013-01-01

    With the fast growing market of pure enantiomer drugs and bioactive molecules, new chiral-selective analytical tools have been instigated including the use of mass spectrometry (MS). Even though MS is one of the best analytical tools that has efficiently been used in several pharmaceutical and biological applications, traditionally MS is considered as a "chiral-blind" technique. This limitation is due to the MS inability to differentiate between two enantiomers of a chiral molecule based merely on their masses. Several approaches have been explored to assess the potential role of MS in chiral analysis. The first approach depends on the use of MS-hyphenated techniques utilizing fast and sensitive chiral separation tools such as liquid chromatography (LC), gas chromatography (GC), and capillary electrophoresis (CE) coupled to MS detector. More recently, several alternative separation techniques have been evaluated such as supercritical fluid chromatography (SFC) and capillary electrochromatography (CEC); the latter being a hybrid technique that combines the efficiency of CE with the selectivity of LC. The second approach is based on using the MS instrument solely for the chiral recognition. This method depends on the behavioral differences between enantiomers towards a foreign molecule and the ability of MS to monitor such differences. These behavioral differences can be divided into three types: (i) differences in the enantiomeric affinity for association with the chiral selector, (ii) differences of the enantiomeric exchange rate with a foreign reagent, and (iii) differences in the complex MS dissociation behaviors of the enantiomers. Most recently, ion mobility spectrometry was introduced to qualitatively and quantitatively evaluate chiral compounds. This article provides an overview of MS role in chiral analysis by discussing MS based methodologies and presenting the challenges and promises associated with each approach.

  7. Nanospray ion mobility mass spectrometry of selected high mass species.

    PubMed

    Campuzano, Iain; Giles, Kevin

    2011-01-01

    The introduction of electrospray ionization (ESI) and in particular nano-electrospray (nESI) has enabled the routine mass spectrometric (MS) analysis of large protein complexes in native aqueous buffers. Time-of-flight (ToF) mass spectrometers, in particular the hybrid quadrupole time-of-flight (Q-ToF) instruments, are well suited to the analysis of large protein complexes. When ionized under native-MS conditions, protein complexes routinely exhibit multiple charge states in excess of m/z 6,000, well above the standard mass range of many quadrupole or ion cyclotron-based instruments. The research area of native MS has expanded considerably in the last decade and has shown particular relevance in the area of protein structure determination. Researchers are now able to routinely measure intact MS spectra of protein complexes above 1 MDa in mass. The advent of ion mobility mass spectrometry (IM-MS), in combination with molecular dynamics (MD) studies, is now allowing researchers to infer the shape of the protein complex being analyzed. Herein, we describe how to acquire IM-MS data that ranges from inorganic salt clusters of caesium iodide (CsI) to large biomolecular complexes such as the chaperone protein GroEL.

  8. Advantageous Uses of Mass Spectrometry for the Quantification of Proteins

    PubMed Central

    Hale, John E.

    2013-01-01

    Quantitative protein measurements by mass spectrometry have gained wide acceptance in research settings. However, clinical uptake of mass spectrometric protein assays has not followed suit. In part, this is due to the long-standing acceptance by regulatory agencies of immunological assays such as ELISA assays. In most cases, ELISAs provide highly accurate, sensitive, relatively inexpensive, and simple assays for many analytes. The barrier to acceptance of mass spectrometry in these situations will remain high. However, mass spectrometry provides solutions to certain protein measurements that are difficult, if not impossible, to accomplish by immunological methods. Cases where mass spectrometry can provide solutions to difficult assay development include distinguishing between very closely related protein species and monitoring biological and analytical variability due to sample handling and very high multiplexing capacity. This paper will highlight several examples where mass spectrometry has made certain protein measurements possible where immunological techniques have had a great difficulty. PMID:23365751

  9. 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

  10. Advances in imaging secondary ion mass spectrometry for biological samples

    SciTech Connect

    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 has 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.

  11. Direct infusion mass spectrometry metabolomics dataset: a benchmark for data processing and quality control.

    PubMed

    Kirwan, Jennifer A; Weber, Ralf J M; Broadhurst, David I; Viant, Mark R

    2014-01-01

    Direct-infusion mass spectrometry (DIMS) metabolomics is an important approach for characterising molecular responses of organisms to disease, drugs and the environment. Increasingly large-scale metabolomics studies are being conducted, necessitating improvements in both bioanalytical and computational workflows to maintain data quality. This dataset represents a systematic evaluation of the reproducibility of a multi-batch DIMS metabolomics study of cardiac tissue extracts. It comprises of twenty biological samples (cow vs. sheep) that were analysed repeatedly, in 8 batches across 7 days, together with a concurrent set of quality control (QC) samples. Data are presented from each step of the workflow and are available in MetaboLights. The strength of the dataset is that intra- and inter-batch variation can be corrected using QC spectra and the quality of this correction assessed independently using the repeatedly-measured biological samples. Originally designed to test the efficacy of a batch-correction algorithm, it will enable others to evaluate novel data processing algorithms. Furthermore, this dataset serves as a benchmark for DIMS metabolomics, derived using best-practice workflows and rigorous quality assessment.

  12. Multidimensional Interactive Radiology Report and Analysis: standardization of workflow and reporting for renal mass tracking and quantification

    NASA Astrophysics Data System (ADS)

    Hwang, Darryl H.; Ma, Kevin; Yepes, Fernando; Nadamuni, Mridula; Nayyar, Megha; Liu, Brent; Duddalwar, Vinay; Lepore, Natasha

    2015-12-01

    A conventional radiology report primarily consists of a large amount of unstructured text, and lacks clear, concise, consistent and content-rich information. Hence, an area of unmet clinical need consists of developing better ways to communicate radiology findings and information specific to each patient. Here, we design a new workflow and reporting system that combines and integrates advances in engineering technology with those from the medical sciences, the Multidimensional Interactive Radiology Report and Analysis (MIRRA). Until recently, clinical standards have primarily relied on 2D images for the purpose of measurement, but with the advent of 3D processing, many of the manually measured metrics can be automated, leading to better reproducibility and less subjective measurement placement. Hence, we make use this newly available 3D processing in our workflow. Our pipeline is used here to standardize the labeling, tracking, and quantifying of metrics for renal masses.

  13. Mass Spectrometry of Acoustically Levitated Droplets

    PubMed Central

    Westphall, Michael S.; Jorabchi, Kaveh; Smith, Lloyd M.

    2008-01-01

    Containerless sample handling techniques such as acoustic levitation offer potential advantages for mass spectrometry, by eliminating surfaces where undesired adsorption/desorption processes can occur. In addition, they provide a unique opportunity to study fundamental aspects of the ionization process as well as phenomena occurring at the air–droplet interface. Realizing these advantages is contingent, however, upon being able to effectively interface levitated droplets with a mass spectrometer, a challenging task that is addressed in this report. We have employed a newly developed charge and matrix-assisted laser desorption/ionization (CALDI) technique to obtain mass spectra from a 5-μL acoustically levitated droplet containing peptides and an ionic matrix. A four-ring electrostatic lens is used in conjunction with a corona needle to produce bursts of corona ions and to direct those ions toward the droplet, resulting in droplet charging. Analyte ions are produced from the droplet by a 337-nm laser pulse and detected by an atmospheric sampling mass spectrometer. The ion generation and extraction cycle is repeated at 20 Hz, the maximum operating frequency of the laser employed. It is shown in delayed ion extraction experiments that both positive and negative ions are produced, behavior similar to that observed for atmospheric pressure matrix-assisted laser absorption/ionization. No ion signal is observed in the absence of droplet charging. It is likely, although not yet proven, that the role of the droplet charging is to increase the strength of the electric field at the surface of the droplet, reducing chargere combination after ion desorption. PMID:18582090

  14. Laser ablation/Fourier transform mass spectrometry of polymers

    NASA Astrophysics Data System (ADS)

    Creasy, William R.; Brenna, J. T.

    1989-10-01

    Laser ablation/ionization followed by Fourier transform mass spectrometry is used to identify and characterize polymers. The mass spectra of several polymers are discussed, including polyimide, polyamic acid, Dupont Tefzel, and polyphenylene sulfide.

  15. 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

  16. Reliability of veterinary drug residue confirmation: high resolution mass spectrometry versus tandem mass spectrometry.

    PubMed

    Kaufmann, A; Butcher, P; Maden, K; Walker, S; Widmer, M

    2015-01-26

    Confirmation of suspected residues has been a long time domain of tandem triple quadrupole mass spectrometry (QqQ). The currently most widely used confirmation strategy relies on the use of two selected reaction monitoring signals (SRM). The details of this confirmation procedure are described in detail in the Commission Decision 93/256/EC (CD). On the other hand, high resolution mass spectrometry (HRMS) is nowadays increasingly used for trace analysis. Yet its utility for confirmatory purposes has not been well explored and utilized, since established confirmation strategies like the CD do not yet include rules for modern HRMS technologies. It is the focus of this paper to evaluate the likelihood of false positive and false negative confirmation results, when using a variety of HRMS based measurement modes as compared to conventional QqQ mass spectrometry. The experimental strategy relies on the chromatographic separation of a complex blank sample (bovine liver extract) and the subsequent monitoring of a number of dummy transitions respectively dummy accurate masses. The term "dummy" refers to precursor and derived product ions (based on a realistic neutral loss) whose elemental compositions (CxHyNzOdCle) were produced by a random number generator. Monitoring a large number of such hypothetical SRM's, or accurate masses inevitably produces a number of mass traces containing chromatographic peaks (false detects) which are caused by eluting matrix compounds. The number and intensity of these peaks were recorded and standardized to permit a comparison among the two employed MS technologies. QqQ performance (compounds which happen to produce a response in two SRM traces at identical retention time) was compared with a number of different HRMS(1) and HRMS(2) detection based modes. A HRMS confirmation criterion based on two full scans (an unfragmented and an all ion fragmented) was proposed. Compared to the CD criteria, a significantly lower probability of false

  17. Multifunctional Carbon Fiber Ionization Mass Spectrometry.

    PubMed

    Wu, Meng-Xi; Wang, Hao-Yang; Zhang, Jun-Ting; Guo, Yin-Long

    2016-10-04

    A carbon fiber ionization (CFI) technique was developed for the mass spectrometric analysis of various organic compounds with different polarities. The design of the CFI technique was based on the good compatibility and dispersion of samples and solutions in different solvents on carbon fiber. As a fast, convenient, and versatile ionization method, CFI-MS is especially efficient for analyzing many low/nonpolar organic compounds, such as polycyclic aromatic hydrocarbons, long-chain aliphatic aldehydes, sensitive steroids, terpenoids, and organometallic compounds. Some of these compounds may not be well-analyzed by electrospray ionization or electron ionization mass spectrometry. On the basis of our experimental results, the major ion formation mechanism of CFI-MS was suggested to involve desorption in a steam-distillation-like process, and then, ionization occurred mainly via corona discharge under high voltage. CFI-MS could not only work alone but also be coupled with separation techniques. It works well when coupled with supercritical fluid chromatography (SFC) as well as in the analysis of exhaled human air. The high flexibility and versatility of CFI-MS has extended its applications in many areas, such as fast chemical screening, clinical testing, and forensic analysis.

  18. Clinical Mass Spectrometry: Achieving Prominence in Laboratory Medicine

    SciTech Connect

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

    2016-01-04

    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 on Mass Spectrometry. The Q&A Transcript is attached

  19. Applications of Mass Spectrometry to Lipids and Membranes

    PubMed Central

    Harkewicz, Richard; Dennis, Edward A.

    2012-01-01

    Lipidomics, a major part of metabolomics, constitutes the detailed analysis and global characterization, both spatial and temporal, of the structure and function of lipids (the lipidome) within a living system. As with proteomics, mass spectrometry has earned a central analytical role in lipidomics, and this role will continue to grow with technological developments. Currently, there exist two mass spectrometry-based lipidomics approaches, one based on a division of lipids into categories and classes prior to analysis, the “comprehensive lipidomics analysis by separation simplification” (CLASS), and the other in which all lipid species are analyzed together without prior separation, shotgun. In exploring the lipidome of various living systems, novel lipids are being discovered, and mass spectrometry is helping characterize their chemical structure. Deuterium exchange mass spectrometry (DXMS) is being used to investigate the association of lipids and membranes with proteins and enzymes, and imaging mass spectrometry (IMS) is being applied to the in situ analysis of lipids in tissues. PMID:21469951

  20. 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.

  1. Molecular typing of Meningiomas by Desorption Electrospray Ionization Mass Spectrometry Imaging for Surgical Decision-Making

    PubMed Central

    Calligaris, David; Feldman, Daniel R.; Norton, Isaiah; Brastianos, Priscilla K.; Dunn, Ian F.; Santagata, Sandro; Agar, Nathalie Y. R.

    2014-01-01

    Meningiomas are the most frequent intracranial tumors. The majority is benign slow-growing tumors but they can be difficult to treat depending on their location and size. While meningiomas are well delineated on magnetic resonance imaging by their uptake of contrast, surgical limitations still present themselves from not knowing the extent of invasion of the dura matter by meningioma cells. The development of tools to characterize tumor tissue in real or near real time could prevent recurrence after tumor resection by allowing for more precise surgery, i.e. removal of tumor with preservation of healthy tissue. The development of ambient ionization mass spectrometry for molecular characterization of tissue and its implementation in the surgical decision-making workflow carry the potential to fulfill this need. Here, we present the characterization of meningioma and dura mater by desorption electrospray ionization mass spectrometry to validate the technique for the molecular assessment of surgical margins and diagnosis of meningioma from surgical tissue in real-time. Nine stereotactically resected surgical samples and three autopsy samples were analyzed by standard histopathology and mass spectrometry imaging. All samples indicated a strong correlation between results from both techniques. We then highlight the value of desorption electrospray ionization mass spectrometry for the molecular subtyping/subgrouping of meningiomas from a series of forty genetically characterized specimens. The minimal sample preparation required for desorption electrospray ionization mass spectrometry offers a distinct advantage for applications relying on real-time information such as surgical decision-making. The technology here was tested to distinguish meningioma from dura mater as an approach to precisely define surgical margins. In addition we classify meningiomas into fibroblastic and meningothelial subtypes and more notably recognize meningiomas with NF2 genetic aberrations. PMID

  2. Differential mobility spectrometry/mass spectrometry history, theory, design optimization, simulations, and applications.

    PubMed

    Schneider, Bradley B; Nazarov, Erkinjon G; Londry, Frank; Vouros, Paul; Covey, Thomas R

    2016-10-01

    This review of differential mobility spectrometry focuses primarily on mass spectrometry coupling, starting with the history of the development of this technique in the Soviet Union. Fundamental principles of the separation process are covered, in addition to efforts related to design optimization and advancements in computer simulations. The flexibility of differential mobility spectrometry design features is explored in detail, particularly with regards to separation capability, speed, and ion transmission. 2015 Wiley Periodicals, Inc. Mass Spec Rev 35:687-737, 2016.

  3. Mass spectrometry innovations in drug discovery and development.

    PubMed

    Papac, D I; Shahrokh, Z

    2001-02-01

    This review highlights the many roles mass spectrometry plays in the discovery and development of new therapeutics by both the pharmaceutical and the biotechnology industries. Innovations in mass spectrometer source design, improvements to mass accuracy, and implementation of computer-controlled automation have accelerated the purification and characterization of compounds derived from combinatorial libraries, as well as the throughput of pharmacokinetics studies. The use of accelerator mass spectrometry, chemical reaction interface-mass spectrometry and continuous flow-isotope ratio mass spectrometry are promising alternatives for conducting mass balance studies in man. To meet the technical challenges of proteomics, discovery groups in biotechnology companies have led the way to development of instruments with greater sensitivity and mass accuracy (e.g., MALDI-TOF, ESI-Q-TOF, Ion Trap), the miniaturization of separation techniques and ion sources (e.g., capillary HPLC and nanospray), and the utilization of bioinformatics. Affinity-based methods coupled to mass spectrometry are allowing rapid and selective identification of both synthetic and biological molecules. With decreasing instrument cost and size and increasing reliability, mass spectrometers are penetrating both the manufacturing and the quality control arenas. The next generation of technologies to simplify the investigation of the complex fate of novel pharmaceutical entities in vitro and in vivo will be chip-based approaches coupled with mass spectrometry.

  4. 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…

  5. Mass Spectrometry Imaging: facts and perspectives from a non-mass spectrometrist point of view.

    PubMed

    Cameron, L C

    2012-08-01

    Mass Spectrometry Imaging (MSI, also called Imaging Mass Spectrometry) can be used to map molecules according to their chemical abundance and spatial distribution. This technique is not widely used in mass spectrometry circles and is barely known by other scientists. In this review, a brief overview of the mass spectrometer hardware used in MSI and some of the possible applications of this powerful technique are discussed. I intend to call attention to MSI uses from cell biology to histopathology for biological scientists who have little background in mass spectrometry. MSI facts and perspectives are presented from a non-mass spectrometrist point of view.

  6. 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.

  7. [Application of mass spectrometry to bacterial identification].

    PubMed

    Hernández, Álvaro Pascual; Ballestero-Téllez, Mónica; Galán-Sánchez, Fátima; Iglesias, Manuel Rodríguez

    2016-06-01

    Correct and rapid identification of bacteria is essential for the correct diagnosis and treatment of infected patients. Until a few years ago, biochemical, colorimetric or even antibiotic sensitivity tests were used to identify genera and species. The main limitations of these methods were the time needed for their performance and the difficulty of distinguishing between microorganisms that were little reactive, highly similar, or difficult to culture. Many of these problems have been solved by the introduction of mass spectrometry (MS) in the laboratory with the use of MALDI-TOF (matrix-assisted laser desorption ionization time-of-flight). Knowledge of the strengths and weaknesses of this technology is essential to be able to take maximum advantage of this technique. Not all microorganisms can be identified with the same ease and reliability by MALDI-TOF and microbiologists need to know how to interpret the results obtained with this technique and the available alternatives in order to identify the microorganisms causing the most problems. This article aims to summarise the available information on the correct identification of the main human pathogenic bacteria through the use of MALDI-TOF MS, focusing on Gram-negative, Grampositive and anaerobic microorganisms. The main factors that must be taken into account for the reliable identification of any bacterium are the conditions for culture, sample preparation with the ideal extraction method and especially the use of a correct and updated database.

  8. Signatures for Mass Spectrometry Data Quality

    PubMed Central

    2014-01-01

    Ensuring data quality and proper instrument functionality is a prerequisite for scientific investigation. Manual quality assurance is time-consuming and subjective. Metrics for describing liquid chromatography mass spectrometry (LC–MS) data have been developed; however, the wide variety of LC–MS instruments and configurations precludes applying a simple cutoff. Using 1150 manually classified quality control (QC) data sets, we trained logistic regression classification models to predict whether a data set is in or out of control. Model parameters were optimized by minimizing a loss function that accounts for the trade-off between false positive and false negative errors. The classifier models detected bad data sets with high sensitivity while maintaining high specificity. Moreover, the composite classifier was dramatically more specific than single metrics. Finally, we evaluated the performance of the classifier on a separate validation set where it performed comparably to the results for the testing/training data sets. By presenting the methods and software used to create the classifier, other groups can create a classifier for their specific QC regimen, which is highly variable lab-to-lab. In total, this manuscript presents 3400 LC–MS data sets for the same QC sample (whole cell lysate of Shewanella oneidensis), deposited to the ProteomeXchange with identifiers PXD000320–PXD000324. PMID:24611607

  9. Proton Dynamics in Protein Mass Spectrometry.

    PubMed

    Li, Jinyu; Lyu, Wenping; Rossetti, Giulia; Konijnenberg, Albert; Natalello, Antonino; Ippoliti, Emiliano; Orozco, Modesto; Sobott, Frank; Grandori, Rita; Carloni, Paolo

    2017-03-16

    Native electrospray ionization/ion mobility-mass spectrometry (ESI/IM-MS) allows an accurate determination of low-resolution structural features of proteins. Yet, the presence of proton dynamics, observed already by us for DNA in the gas phase, and its impact on protein structural determinants, have not been investigated so far. Here, we address this issue by a multistep simulation strategy on a pharmacologically relevant peptide, the N-terminal residues of amyloid-β peptide (Aβ(1-16)). Our calculations reproduce the experimental maximum charge state from ESI-MS and are also in fair agreement with collision cross section (CCS) data measured here by ESI/IM-MS. Although the main structural features are preserved, subtle conformational changes do take place in the first ∼0.1 ms of dynamics. In addition, intramolecular proton dynamics processes occur on the picosecond-time scale in the gas phase as emerging from quantum mechanics/molecular mechanics (QM/MM) simulations at the B3LYP level of theory. We conclude that proton transfer phenomena do occur frequently during fly time in ESI-MS experiments (typically on the millisecond time scale). However, the structural changes associated with the process do not significantly affect the structural determinants.

  10. Accelerator mass spectrometry of small biological samples.

    PubMed

    Salehpour, Mehran; Forsgard, Niklas; Possnert, Göran

    2008-12-01

    Accelerator mass spectrometry (AMS) is an ultra-sensitive technique for isotopic ratio measurements. In the biomedical field, AMS can be used to measure femtomolar concentrations of labeled drugs in body fluids, with direct applications in early drug development such as Microdosing. Likewise, the regenerative properties of cells which are of fundamental significance in stem-cell research can be determined with an accuracy of a few years by AMS analysis of human DNA. However, AMS nominally requires about 1 mg of carbon per sample which is not always available when dealing with specific body substances such as localized, organ-specific DNA samples. Consequently, it is of analytical interest to develop methods for the routine analysis of small samples in the range of a few tens of microg. We have used a 5 MV Pelletron tandem accelerator to study small biological samples using AMS. Different methods are presented and compared. A (12)C-carrier sample preparation method is described which is potentially more sensitive and less susceptible to contamination than the standard procedures.

  11. Accelerator Mass Spectrometry in Laboratory Nuclear Astrophysics

    NASA Astrophysics Data System (ADS)

    Nusair, O.; Bauder, W.; Gyürky, G.; Paul, M.; Collon, P.; Fülöp, Zs; Greene, J.; Kinoshita, N.; Palchan, T.; Pardo, R.; Rehm, K. E.; Scott, R.; Vondrasek, R.

    2016-01-01

    The extreme sensitivity and discrimination power of accelerator mass spectrometry (AMS) allows for the search and the detection of rare nuclides either in natural samples or produced in the laboratory. At Argonne National Laboratory, we are developing an AMS setup aimed in particular at the detection of medium and heavy nuclides, relying on the high ion energy achievable with the ATLAS superconducting linear accelerator and on gas-filled magnet isobaric separation. The setup was recently used for the detection of the 146Sm p-process nuclide and for a new determination of the 146Sm half-life (68.7 My). AMS plays an important role in the measurement of stellar nuclear reaction cross sections by the activation method, extending thus the technique to the study of production of long-lived radionuclides. Preliminary measurements of the 147Sm(γ,n)146Sm are described. A measurement of the 142Nd(α,γ)146Sm and 142Nd(α,n)145Sm reactions is in preparation. A new laser-ablation method for the feeding of the Electron Cyclotron Resonance (ECR) ion source is described.

  12. 1912: a Titanic year for mass spectrometry.

    PubMed

    Downard, Kevin M

    2012-08-01

    The 1912 sinking of the Titanic continues to capture the imagination and fascination of the general public. The year coincides with the birth of mass spectrometry that began with the cathode ray experiments performed by Joseph John (J. J.) Thomson in Cambridge. Modifications made to Thomson's cathode ray apparatus by Francis William Aston, resulted in an increase in the brightness of the positive rays that aided their detection. This led to the discovery of heavy isotopes for many of the chemical elements in the ensuing decades. As the discovery of (22) Ne was reported in 1913, another of Thomson's students was taking part in an expedition to help save future ocean liners from the fate of the Titanic. Geoffrey Ingram Taylor took part in the first ice patrol of the North Atlantic in 1913 aboard the SS Scotia to investigate the formation and position of icebergs. This article, 100 years on, describes Taylor's work and its impact on safe ocean passage across the Atlantic.

  13. Detection of Gunshot Residues Using Mass Spectrometry

    PubMed Central

    Blanes, Lucas; Cole, Nerida; Doble, Philip; Roux, Claude

    2014-01-01

    In recent years, forensic scientists have become increasingly interested in the detection and interpretation of organic gunshot residues (OGSR) due to the increasing use of lead- and heavy metal-free ammunition. This has also been prompted by the identification of gunshot residue- (GSR-) like particles in environmental and occupational samples. Various techniques have been investigated for their ability to detect OGSR. Mass spectrometry (MS) coupled to a chromatographic system is a powerful tool due to its high selectivity and sensitivity. Further, modern MS instruments can detect and identify a number of explosives and additives which may require different ionization techniques. Finally, MS has been applied to the analysis of both OGSR and inorganic gunshot residue (IGSR), although the “gold standard” for analysis is scanning electron microscopy with energy dispersive X-ray microscopy (SEM-EDX). This review presents an overview of the technical attributes of currently available MS and ionization techniques and their reported applications to GSR analysis. PMID:24977168

  14. Secondary Ion Mass Spectrometry SIMS XI

    NASA Astrophysics Data System (ADS)

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

    2003-05-01

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

  15. Charging of Proteins in Native Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Susa, Anna C.; Xia, Zijie; Tang, Henry Y. H.; Tainer, John A.; Williams, Evan R.

    2017-02-01

    Factors that influence the charging of protein ions formed by electrospray ionization from aqueous solutions in which proteins have native structures and function were investigated. Protein ions ranging in molecular weight from 12.3 to 79.7 kDa and pI values from 5.4 to 9.6 were formed from different solutions and reacted with volatile bases of gas-phase basicities higher than that of ammonia in the cell of a Fourier-transform ion cyclotron resonance mass spectrometer. The charge-state distribution of cytochrome c ions formed from aqueous ammonium or potassium acetate is the same. Moreover, ions formed from these two solutions do not undergo proton transfer to 2-fluoropyridine, which is 8 kcal/mol more basic than ammonia. These results provide compelling evidence that proton transfer between ammonia and protein ions does not limit protein ion charge in native electrospray ionization. Both circular dichroism and ion mobility measurements indicate that there are differences in conformations of proteins in pure water and aqueous ammonium acetate, and these differences can account for the difference in the extent of charging and proton-transfer reactivities of protein ions formed from these solutions. The extent of proton transfer of the protein ions with higher gas-phase basicity bases trends with how closely the protein ions are charged to the value predicted by the Rayleigh limit for spherical water droplets approximately the same size as the proteins. These results indicate that droplet charge limits protein ion charge in native mass spectrometry and are consistent with these ions being formed by the charged residue mechanism.

  16. Hydroponic isotope labeling of entire plants and high-performance mass spectrometry for quantitative plant proteomics.

    PubMed

    Bindschedler, Laurence V; Mills, Davinia J S; Cramer, Rainer

    2012-01-01

    Hydroponic isotope labeling of entire plants (HILEP) combines hydroponic plant cultivation and metabolic labeling with stable isotopes using (15)N-containing inorganic salts to label whole and mature plants. Employing (15)N salts as the sole nitrogen source for HILEP leads to the production of healthy-looking plants which contain (15)N proteins labeled to nearly 100%. Therefore, HILEP is suitable for quantitative plant proteomic analysis, where plants are grown in either (14)N- or (15)N-hydroponic media and pooled when the biological samples are collected for relative proteome quantitation. The pooled (14)N-/(15)N-protein extracts can be fractionated in any suitable way and digested with a protease for shotgun proteomics, using typically reverse phase liquid chromatography nanoelectrospray ionization tandem mass spectrometry (RPLC-nESI-MS/MS). Best results were obtained with a hybrid ion trap/FT-MS mass spectrometer, combining high mass accuracy and sensitivity for the MS data acquisition with speed and high-throughput MS/MS data acquisition, increasing the number of proteins identified and quantified and improving protein quantitation. Peak processing and picking from raw MS data files, protein identification, and quantitation were performed in a highly automated way using integrated MS data analysis software with minimum manual intervention, thus easing the analytical workflow. In this methodology paper, we describe how to grow Arabidopsis plants hydroponically for isotope labeling using (15)N salts and how to quantitate the resulting proteomes using a convenient workflow that does not require extensive bioinformatics skills.

  17. Mass spectrometry of Natural Products: Current, Emerging and Future Technologies

    PubMed Central

    Bouslimani, Amina; Sanchez, Laura M; Garg, Neha; Dorrestein, Pieter C

    2014-01-01

    Although mass spectrometry is a century old technology, we are entering into an exciting time for the analysis of molecular information directly from complex biological systems. In this viewpoint article, we highlight emerging mass spectrometric methods and tools used by the natural product community and give a perspective of future directions where the mass spectrometry field is migrating towards over the next decade. PMID:24801551

  18. 3D Imaging by Mass Spectrometry: A New Frontier

    PubMed Central

    Seeley, Erin H.; Caprioli, Richard M.

    2012-01-01

    Summary Imaging mass spectrometry can generate three-dimensional volumes showing molecular distributions in an entire organ or animal through registration and stacking of serial tissue sections. Here we review the current state of 3D imaging mass spectrometry as well as provide insights and perspectives on the process of generating 3D mass spectral data along with a discussion of the process necessary to generate a 3D image volume. PMID:22276611

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

    PubMed Central

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

    2016-01-01

    Mass spectrometry–based proteomics has emerged as the leading method for detection, quantification, and characterization of proteins. Nearly all proteomic workflows rely on proteomic databases to identify peptides and proteins, but these databases typically contain a generic set of proteins that lack variations unique to a given sample, precluding their detection. Fortunately, proteogenomics enables the detection of such proteomic variations and can be defined, broadly, as the use of nucleotide sequences to generate candidate protein sequences for mass spectrometry database searching. Proteogenomics is experiencing heightened significance due to two developments: (a) advances in DNA sequencing technologies that have made complete sequencing of human genomes and transcriptomes routine, and (b) the unveiling of the tremendous complexity of the human proteome as expressed at the levels of genes, cells, tissues, individuals, and populations. We review here the field of human proteogenomics, with an emphasis on its history, current implementations, the types of proteomic variations it reveals, and several important applications. PMID:27049631

  20. Characterization of Membrane Protein-Lipid Interactions by Mass Spectrometry Ion Mobility Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Liu, Yang; Cong, Xiao; Liu, Wen; Laganowsky, Arthur

    2016-12-01

    Lipids in the biological membrane can modulate the structure and function of integral and peripheral membrane proteins. Distinguishing individual lipids that bind selectively to membrane protein complexes from an ensemble of lipid-bound species remains a daunting task. Recently, ion mobility mass spectrometry (IM-MS) has proven to be invaluable for interrogating the interactions between protein and individual lipids, where the complex undergoes collision induced unfolding followed by quantification of the unfolding pathway to assess the effect of these interactions. However, gas-phase unfolding experiments for membrane proteins are typically performed on the entire ensemble (apo and lipid bound species), raising uncertainty to the contribution of individual lipids and the species that are ejected in the unfolding process. Here, we describe the application of mass spectrometry ion mobility mass spectrometry (MS-IM-MS) for isolating ions corresponding to lipid-bound states of a model integral membrane protein, ammonia channel (AmtB) from Escherichia coli. Free of ensemble effects, MS-IM-MS reveals that bound lipids are ejected as neutral species; however, no correlation was found between the lipid-induced stabilization of complex and their equilibrium binding constants. In comparison to data obtained by IM-MS, there are surprisingly limited differences in stability measurements from IM-MS and MS-IM-MS. The approach described here to isolate ions of membrane protein complexes will be useful for other MS methods, such as surface induced dissociation or collision induced dissociation to determine the stoichiometry of hetero-oligomeric membrane protein complexes.

  1. Metabolomics by Gas Chromatography-Mass Spectrometry: Combined Targeted and Untargeted Profiling.

    PubMed

    Fiehn, Oliver

    2016-04-01

    Gas chromatography-mass spectrometry (GC-MS)-based metabolomics is ideal for identifying and quantitating small-molecule metabolites (<650 Da), including small acids, alcohols, hydroxyl acids, amino acids, sugars, fatty acids, sterols, catecholamines, drugs, and toxins, often using chemical derivatization to make these compounds sufficiently volatile for gas chromatography. This unit shows how GC-MS-based metabolomics allows integration of targeted assays for absolute quantification of specific metabolites with untargeted metabolomics to discover novel compounds. Complemented by database annotations using large spectral libraries and validated standard operating procedures, GC-MS can identify and semiquantify over 200 compounds from human body fluids (e.g., plasma, urine, or stool) per study. Deconvolution software enables detection of more than 300 additional unidentified signals that can be annotated through accurate mass instruments with appropriate data processing workflows, similar to untargeted profiling using liquid chromatography-mass spectrometry. GC-MS is a mature technology that uses not only classic detectors (quadrupole) but also target mass spectrometers (triple quadrupole) and accurate mass instruments (quadrupole-time of flight). This unit covers sample preparation from mammalian samples, data acquisition, quality control, and data processing.

  2. 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.

  3. Integrated microscale analysis system for targeted liquid chromatography mass spectrometry proteomics on limited amounts of enriched cell populations.

    PubMed

    Martin, Jeffrey G; Rejtar, Tomas; Martin, Stephen A

    2013-11-19

    Limited samples, such as those that are in vivo sourced via biopsy, are closely representative of biological systems and contain valuable information for drug discovery. However, these precious samples are often heterogeneous and require cellular prefractionation prior to proteomic analysis to isolate specific subpopulations of interest. Enriched cells from in vivo samples are often very limited (<10(4) cells) and pose a significant challenge to proteomic nanoliquid chromatography mass spectrometry (nanoLCMS) sample preparation. To enable the streamlined analysis of these limited samples, we have developed an online cell enrichment, microscale sample preparation, nanoLCMS proteomics workflow by integrating fluorescence activated cell sorting (FACS), focused ultrasonication, microfluidics, immobilized trypsin digestion, and nanoLCMS. To assess the performance of the online FACS-Chip-LCMS workflow, 5000 fluorescent labeled cells were enriched from a 5% heterogeneous cell population and processed for LCMS proteomics in less than 2 h. Within these 5000 enriched cells, 30 peptides corresponding to 17 proteins spanning more than 4 orders of magnitude of cellular abundance were quantified using a QExactive MS. The results from the online FACS-Chip-LCMS workflow starting from 5000 enriched cells were directly compared to results from a traditional macroscale sample preparation workflow starting from 2.0 × 10(6) cells. The microscale FACS-Chip-LCMS workflow demonstrated high cellular enrichment efficiency and high peptide recovery across the wide dynamic range of targeted peptides. Overall the microscale FACS-Chip-LCMS workflow has shown effectiveness in efficiently preparing limited amounts of FACS enriched cells in an online manner for proteomic LCMS.

  4. Application of Lithium Attachment Mass Spectrometry for Knudsen Evaporation and Chemical Ionisation Mass Spectrometry (KEMS, CIMS)

    NASA Astrophysics Data System (ADS)

    Bannan, T.; Booth, M.; Benyezzar, M.; Bacak, A.; Alfarra, M. R. R.; Topping, D. O.; Percival, C.

    2015-12-01

    Lithium ion attachment mass spectrometry provides a non-specific, non-fragmenting and sensitive method for detection of volatile species in the gas phase. The design, manufacture, and results from lithium ion attachment ionisation sources for two mass spectrometry systems are presented. Trace gas analysis is investigated using a modified Chemical Ionization Mass Spectrometer (CIMS) and vapour pressure (VP) measurements using a modified Knudsen Effusion Mass Spectrometer (KEMS) are presented. The Li+ modified CIMS provided limits of detection of 4 ppt for acetone, 0.2 ppt for formic acid, 15 ppt for nitric acid and 120 ppt from ammonia. Despite improvements, the problem of burnout remained persistent. The Li+ CIMS would unlikely be suitable for field or aircraft work, but could be appropriate for certain lab applications. The KEMS currently utilizes an electron impact (EI) ionisation source which provides a highly sensitive source, with the drawback of fragmentation of ionized molecules (Booth et al., 2009). Using Li+ KEMS the VP of samples can be measured without fragmentation and can therefore be used to identify VPs of individual components in mixtures. The validity of using Li+ for determining the VP of mixtures was tested by making single component VP measurements, which showed good agreement with EI measurements of Poly ethylene glycol (PEG) 3 and PEG 4, both when individually measured and when mixed. The Li+ KEMS was then used to investigate a system of atmospheric relevance, α-pinene secondary organic aerosol, generated in a reaction chamber (Alfarra et al., 2012). The VPs of the individual components from this generated sample are within the range we expect for compounds capable of partitioning between the particle and gas phase of an aerosol (0.1-10-5 Pa). Li+ source has a calculated sensitivity approximately 75 times less than that of EI, but the lack of fragmentation using the Li+ source is a significant advantage.

  5. Application of Lithium Attachment Mass Spectrometry for Knudsen Evaporation and Chemical Ionisation Mass Spectrometry (KEMS, CIMS)

    NASA Astrophysics Data System (ADS)

    Bannan, Thomas; Booth, A. Murray; Alfarra, Rami; Bacak, Asan; Pericval, Carl

    2016-04-01

    Lithium ion attachment mass spectrometry provides a non-specific, non-fragmenting and sensitive method for detection of volatile species in the gas phase. The design, manufacture, and results from lithium ion attachment ionisation sources for two mass spectrometry systems are presented. Trace gas analysis is investigated using a modified Chemical Ionization Mass Spectrometer (CIMS) and vapour pressure (VP) measurements using a modified Knudsen Effusion Mass Spectrometer (KEMS) are presented. The Li+ modified CIMS provided limits of detection of 4 ppt for acetone, 0.2 ppt for formic acid, 15 ppt for nitric acid and 120 ppt from ammonia. Despite improvements, the problem of burnout remained persistent. The Li+ CIMS would unlikely be suitable for field or aircraft work, but could be appropriate for certain lab applications. The KEMS currently utilizes an electron impact (EI) ionisation source which provides a highly sensitive source, with the drawback of fragmentation of ionized molecules (Booth et al., 2009). Using Li+ KEMS the VP of samples can be measured without fragmentation and can therefore be used to identify VPs of individual components in mixtures. The validity of using Li+ for determining the VP of mixtures was tested by making single component VP measurements, which showed good agreement with EI measurements of Poly ethylene glycol (PEG) 3 and PEG 4, both when individually measured and when mixed. The Li+ KEMS was then used to investigate a system of atmospheric relevance, α-pinene secondary organic aerosol, generated in a reaction chamber (Alfarra et al., 2012). The VPs of the individual components from this generated sample are within the range we expect for compounds capable of partitioning between the particle and gas phase of an aerosol (0.1-10-5 Pa). Li+ source has a calculated sensitivity approximately 75 times less than that of EI, but the lack of fragmentation using the Li+ source is a significant advantage.

  6. imzML: Imaging Mass Spectrometry Markup Language: A common data format for mass spectrometry imaging.

    PubMed

    Römpp, Andreas; Schramm, Thorsten; Hester, Alfons; Klinkert, Ivo; Both, Jean-Pierre; Heeren, Ron M A; Stöckli, Markus; Spengler, Bernhard

    2011-01-01

    Imaging mass spectrometry is the method of scanning a sample of interest and generating an "image" of the intensity distribution of a specific analyte. The data sets consist of a large number of mass spectra which are usually acquired with identical settings. Existing data formats are not sufficient to describe an MS imaging experiment completely. The data format imzML was developed to allow the flexible and efficient exchange of MS imaging data between different instruments and data analysis software.For this purpose, the MS imaging data is divided in two separate files. The mass spectral data is stored in a binary file to ensure efficient storage. All metadata (e.g., instrumental parameters, sample details) are stored in an XML file which is based on the standard data format mzML developed by HUPO-PSI. The original mzML controlled vocabulary was extended to include specific parameters of imaging mass spectrometry (such as x/y position and spatial resolution). The two files (XML and binary) are connected by offset values in the XML file and are unambiguously linked by a universally unique identifier. The resulting datasets are comparable in size to the raw data and the separate metadata file allows flexible handling of large datasets.Several imaging MS software tools already support imzML. This allows choosing from a (growing) number of processing tools. One is no longer limited to proprietary software, but is able to use the processing software which is best suited for a specific question or application. On the other hand, measurements from different instruments can be compared within one software application using identical settings for data processing. All necessary information for evaluating and implementing imzML can be found at http://www.imzML.org .

  7. Mass spectrometry of membrane proteins: a focus on aquaporins.

    PubMed

    Schey, Kevin L; Grey, Angus C; Nicklay, Joshua J

    2013-06-04

    Membrane proteins are abundant, critically important biomolecules that conduct essential functions in all cells and are the targets of a significant number of therapeutic drugs. However, the analysis of their expression, modification, protein-protein interactions, and structure by mass spectrometry has lagged behind similar studies of soluble proteins. Here we review the limitations to analysis of integral membrane and membrane-associated proteins and highlight advances in sample preparation and mass spectrometry methods that have led to the successful analysis of this protein class. Advances in the analysis of membrane protein posttranslational modification, protein-protein interaction, protein structure, and tissue distributions by imaging mass spectrometry are discussed. Furthermore, we focus our discussion on the application of mass spectrometry for the analysis of aquaporins as a prototypical integral membrane protein and how advances in analytical methods have revealed new biological insights into the structure and function of this family of proteins.

  8. 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.

  9. Molecular Beam Mass Spectrometry (MBMS) (Revised) (Fact Sheet)

    SciTech Connect

    Not Available

    2011-07-01

    This fact sheet provides information about Molecular Beam Mass Spectrometry (MBMS) capabilities and applications at NREL's National Bioenergy Center. NREL has six MBMS systems that researchers and industry partners can use to understand thermochemical biomass conversion and biomass composition recalcitrance.

  10. Mass Spectrometry of Membrane Proteins: A Focus on Aquaporins

    PubMed Central

    Schey, Kevin L.; Grey, Angus C.; Nicklay, Joshua J.

    2015-01-01

    Membrane proteins are abundant, critically important biomolecules that conduct essential functions in all cells and are the targets of a significant number of therapeutic drugs. However, the analysis of their expression, modification, protein–protein interactions, and structure by mass spectrometry has lagged behind similar studies of soluble proteins. Here we review the limitations to analysis of integral membrane and membrane-associated proteins and highlight advances in sample preparation and mass spectrometry methods that have led to the successful analysis of this protein class. Advances in the analysis of membrane protein posttranslational modification, protein–protein interaction, protein structure, and tissue distributions by imaging mass spectrometry are discussed. Furthermore, we focus our discussion on the application of mass spectrometry for the analysis of aquaporins as a prototypical integral membrane protein and how advances in analytical methods have revealed new biological insights into the structure and function of this family of proteins. PMID:23394619

  11. Challenges and developments in tandem mass spectrometry based clinical metabolomics.

    PubMed

    Ceglarek, Uta; Leichtle, Alexander; Brügel, Mathias; Kortz, Linda; Brauer, Romy; Bresler, Kristin; Thiery, Joachim; Fiedler, Georg Martin

    2009-03-25

    'Clinical metabolomics' aims at evaluating and predicting health and disease risk in an individual by investigating metabolic signatures in body fluids or tissues, which are influenced by genetics, epigenetics, environmental exposures, diet, and behaviour. Powerful analytical techniques like liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) offers a rapid, effective and economical way to analyze metabolic alterations of pre-defined target metabolites in biological samples. Novel hyphenated technical approaches like the combination of tandem mass spectrometry combined with linear ion trap (QTrap mass spectrometry) combines both identification and quantification of known and unknown metabolic targets. We describe new concepts and developments of mass spectrometry based multi-target metabolome profiling in the field of clinical diagnostics and research. Particularly, the experiences from newborn screening provided important insights about the diagnostic potential of metabolite profiling arrays and directs to the clinical aim of predictive, preventive and personalized medicine by metabolomics.

  12. Environmental Mass Spectrometry: Emerging Contaminants and Current Issues, 2008 Review

    EPA Science Inventory

    This biennial review covers developments in Environmental Mass Spectrometry for Emerging Environmental Contaminants over the period of 2006-2007. A few significant references that appeared between January and February 2008 are also included. Analytical Chemistry’s current polic...

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

    SciTech Connect

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

    1997-03-01

    Since laser mass spectrometry has the potential for achieving very fast DNA analysis, the authors 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 Snager`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. The preliminary results indicate laser mass spectrometry can possibly 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, the authors applied laser mass spectrometry to disease diagnosis. Clinical samples with both base deletion and point mutation have been tested with complete success.

  14. Protein Quantitation of the Developing Cochlea Using Mass Spectrometry.

    PubMed

    Darville, Lancia N F; Sokolowski, Bernd H A

    2016-01-01

    Mass spectrometry-based proteomics allows for the measurement of hundreds to thousands of proteins in a biological system. Additionally, mass spectrometry can also be used to quantify proteins and peptides. However, observing quantitative differences between biological systems using mass spectrometry-based proteomics can be challenging because it is critical to have a method that is fast, reproducible, and accurate. Therefore, to study differential protein expression in biological samples labeling or label-free quantitative methods can be used. Labeling methods have been widely used in quantitative proteomics, however label-free methods have become equally as popular and more preferred because they produce faster, cleaner, and simpler results. Here, we describe the methods by which proteins are isolated and identified from cochlear sensory epithelia tissues at different ages and quantitatively differentiated using label-free mass spectrometry.

  15. Environmental Mass Spectrometry: Emerging Contaminants and Current Issues (2010 Review)

    EPA Science Inventory

    This biennial review covers developments in environmental mass spectrometry for emerging environmental contaminants over the period of 2008-2009. A few significant references that appeared between January and February 2010 are also included. Analytical Chemistry’s current polic...

  16. Photodissociation mass spectrometry: New tools for characterization of biological molecules

    PubMed Central

    Brodbelt, Jennifer S.

    2014-01-01

    Photodissociation mass spectrometry combines the ability to activate and fragment ions using photons with the sensitive detection of the resulting product ions by mass spectrometry. The resulting combination affords a versatile tool for characterization of biological molecules. The scope and breadth of photodissociation mass spectrometry have increased substantially over the past decade as new research groups have entered the field and developed a number of innovative applications that illustrate the ability of photodissociation to produce rich fragmentation patterns, to cleave bonds selectively, and to target specific molecules based on incorporation of chromophores. This review focuses on many of the key developments in photodissociation mass spectrometry over the past decade with a particular emphasis on its applications to biological molecules. PMID:24481009

  17. 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.

  18. 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...

  19. 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.

  20. 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.

  1. Determination of nitrofuran and chloramphenicol residues by high resolution mass spectrometry versus tandem quadrupole mass spectrometry.

    PubMed

    Kaufmann, A; Butcher, P; Maden, K; Walker, S; Widmer, M

    2015-03-03

    An ultra-high performance liquid chromatography based method, coupled to high resolution mass spectrometry (UHPLC-HRMS), was developed to permit the detection and quantification of various nitrofuran and chloramphenicol residues in a number of animal based food products. This method is based on the hydrolysis of covalently bound metabolites and derivatization with 2-nitrobenzaldehyde. Clean-up is achieved by a liquid/liquid and a reversed phase/solid phase extraction. Not only are the four conventional nitrofurans (nitrofurantoin, furazolidone, nitrofurazone and furaltadone) detected, but also nifursol, nitrovin and nifuroxazide. Furthermore, an underivatizable nitrofuran (nifurpirinol) and another banned drug (chloramphenicol) can be quantified as well. The compounds are detected in the form of their precursor ions, [M+H](+) and [M-H](-), respectively. The mass resolving power of 70,000 FWHM, and the applied mass window ensure sufficient selectivity and sensitivity. Confirmation is obtained by monitoring the HRMS resolved product ions which were derived from the unit-mass resolved precursor ions. The multiplexing capability of the utilized Orbitrap instrument provides not only highly selective, but also sensitive confirmatory signals. This method has been validated according to the CD 2002/657/EC for the following matrices: muscle, liver, kidney, fish, honey, eggs and milk.

  2. Calculating Measurement Uncertainties for Mass Spectrometry Data

    NASA Astrophysics Data System (ADS)

    Essex, R. M.; Goldberg, S. A.

    2006-12-01

    A complete and transparent characterization of measurement uncertainty is fundamentally important to the interpretation of analytical results. We have observed that the calculation and reporting of uncertainty estimates for isotopic measurement from a variety of analytical facilities are inconsistent, making it difficult to compare and evaluate data. Therefore, we recommend an approach to uncertainty estimation that has been adopted by both US national metrology facilities and is becoming widely accepted within the analytical community. This approach is outlined in the ISO "Guide to the Expression of Uncertainty in Measurement" (GUM). The GUM approach to uncertainty estimation includes four major steps: 1) Specify the measurand; 2) Identify uncertainty sources; 3) Quantify components by determining the standard uncertainty (u) for each component; and 4) Calculate combined standard uncertainty (u_c) by using established propagation laws to combine the various components. To obtain a desired confidence level, the combined standard uncertainty is multiplied by a coverage factor (k) to yield an expanded uncertainty (U). To be consistent with the GUM principles, it is also necessary create an uncertainty budget, which is a listing of all the components comprising the uncertainty and their relative contribution to the combined standard uncertainty. In mass spectrometry, Step 1 is normally the determination of an isotopic ratio for a particular element. Step 2 requires the identification of the many potential sources of measurement variability and bias including: gain, baseline, cup efficiency, Schottky noise, counting statistics, CRM uncertainties, yield calibrations, linearity calibrations, run conditions, and filament geometry. Then an equation expressing the relationship of all of the components to the measurement value must be written. To complete Step 3, these potential sources of uncertainty must be characterized (Type A or Type B) and quantified. This information

  3. Enhanced Acylcarnitine Annotation in High-Resolution Mass Spectrometry Data: Fragmentation Analysis for the Classification and Annotation of Acylcarnitines

    PubMed Central

    van der Hooft, Justin J. J.; Ridder, Lars; Barrett, Michael P.; Burgess, Karl E. V.

    2015-01-01

    Metabolite annotation and identification are primary challenges in untargeted metabolomics experiments. Rigorous workflows for reliable annotation of mass features with chemical structures or compound classes are needed to enhance the power of untargeted mass spectrometry. High-resolution mass spectrometry considerably improves the confidence in assigning elemental formulas to mass features in comparison to nominal mass spectrometry, and embedding of fragmentation methods enables more reliable metabolite annotations and facilitates metabolite classification. However, the analysis of mass fragmentation spectra can be a time-consuming step and requires expert knowledge. This study demonstrates how characteristic fragmentations, specific to compound classes, can be used to systematically analyze their presence in complex biological extracts like urine that have undergone untargeted mass spectrometry combined with data dependent or targeted fragmentation. Human urine extracts were analyzed using normal phase liquid chromatography (hydrophilic interaction chromatography) coupled to an Ion Trap-Orbitrap hybrid instrument. Subsequently, mass chromatograms and collision-induced dissociation and higher-energy collisional dissociation (HCD) fragments were annotated using the freely available MAGMa software1. Acylcarnitines play a central role in energy metabolism by transporting fatty acids into the mitochondrial matrix. By filtering on a combination of a mass fragment and neutral loss designed based on the MAGMa fragment annotations, we were able to classify and annotate 50 acylcarnitines in human urine extracts, based on high-resolution mass spectrometry HCD fragmentation spectra at different energies for all of them. Of these annotated acylcarnitines, 31 are not described in HMDB yet and for only 4 annotated acylcarnitines the fragmentation spectra could be matched to reference spectra. Therefore, we conclude that the use of mass fragmentation filters within the context

  4. Mass Spectrometry Based Molecular 3D-Cartography of Plant Metabolites

    PubMed Central

    Floros, Dimitrios J.; Petras, Daniel; Kapono, Clifford A.; Melnik, Alexey V.; Ling, Tie-Jun; Knight, Rob; Dorrestein, Pieter C.

    2017-01-01

    Plants play an essential part in global carbon fixing through photosynthesis and are the primary food and energy source for humans. Understanding them thoroughly is therefore of highest interest for humanity. Advances in DNA and RNA sequencing and in protein and metabolite analysis allow the systematic description of plant composition at the molecular level. With imaging mass spectrometry, we can now add a spatial level, typically in the micrometer-to-centimeter range, to their compositions, essential for a detailed molecular understanding. Here we present an LC-MS based approach for 3D plant imaging, which is scalable and allows the analysis of entire plants. We applied this approach in a case study to pepper and tomato plants. Together with MS/MS spectra library matching and spectral networking, this non-targeted workflow provides the highest sensitivity and selectivity for the molecular annotations and imaging of plants, laying the foundation for studies of plant metabolism and plant-environment interactions.

  5. Current Applications of Liquid Chromatography/Mass Spectrometry in Pharmaceutical Discovery After a Decade of Innovation

    NASA Astrophysics Data System (ADS)

    Ackermann, Bradley L.; Berna, Michael J.; Eckstein, James A.; Ott, Lee W.; Chaudhary, Ajai K.

    2008-07-01

    Current drug discovery involves a highly iterative process pertaining to three core disciplines: biology, chemistry, and drug disposition. For most pharmaceutical companies the path to a drug candidate comprises similar stages: target identification, biological screening, lead generation, lead optimization, and candidate selection. Over the past decade, the overall efficiency of drug discovery has been greatly improved by a single instrumental technique, liquid chromatography/mass spectrometry (LC/MS). Transformed by the commercial introduction of the atmospheric pressure ionization interface in the mid-1990s, LC/MS has expanded into almost every area of drug discovery. In many cases, drug discovery workflow has been changed owing to vastly improved efficiency. This review examines recent trends for these three core disciplines and presents seminal examples where LC/MS has altered the current approach to drug discovery.

  6. Secondary Ion Mass Spectrometry Imaging of Dictyostelium discoideum Aggregation Streams

    SciTech Connect

    Debord, J. Daniel; Smith, Donald F.; Anderton, Christopher R.; Heeren, Ronald M.; Pasa-Tolic, Ljiljana; Gomer, Richard H.; Fernandez-Lima, Francisco A.

    2014-06-09

    High resolution imaging mass spectrometry could become a valuable tool for cell and developmental biology, but both, high spatial and mass spectral resolution are needed to enable this. In this report, we employed Bi3 bombardment time-of-flight (Bi3 ToF-SIMS) and C60 bombardment Fourier transform ion cyclotron resonance secondary ion mass spectrometry (C60 FTICR-SIMS) to image Dictyostelium discoideum aggregation streams. Nearly 300 lipid species were identified from the aggregation streams. High resolution mass spectrometry imaging (FTICR-SIMS) enabled the generation of multiple molecular ion maps at the nominal mass level and provided good coverage for fatty acyls, prenol lipids, and sterol lipids. The comparison of Bi3 ToF-SIMS and C60 FTICR-SIMS suggested that while the first provides fast, high spatial resolution molecular ion images, the chemical complexity of biological samples warrants the use of high resolution analyzers for accurate ion identification.

  7. NCBI Peptidome: a new repository for mass spectrometry proteomics data.

    PubMed

    Ji, Li; Barrett, Tanya; Ayanbule, Oluwabukunmi; Troup, Dennis B; Rudnev, Dmitry; Muertter, Rolf N; Tomashevsky, Maxim; Soboleva, Alexandra; Slotta, Douglas J

    2010-01-01

    Peptidome is a public repository that archives and freely distributes tandem mass spectrometry peptide and protein identification data generated by the scientific community. Data from all stages of a mass spectrometry experiment are captured, including original mass spectra files, experimental metadata and conclusion-level results. The submission process is facilitated through acceptance of data in commonly used open formats, and all submissions undergo syntactic validation and curation in an effort to uphold data integrity and quality. Peptidome is not restricted to specific organisms, instruments or experiment types; data from any tandem mass spectrometry experiment from any species are accepted. In addition to data storage, web-based interfaces are available to help users query, browse and explore individual peptides, proteins or entire Samples and Studies. Results are integrated and linked with other NCBI resources to ensure dissemination of the information beyond the mass spectroscopy proteomics community. Peptidome is freely accessible at http://www.ncbi.nlm.nih.gov/peptidome.

  8. Mass spectrometry imaging and profiling of single cells

    PubMed Central

    Lanni, Eric J.; Rubakhin, Stanislav S.; Sweedler, Jonathan V.

    2012-01-01

    Mass spectrometry imaging and profiling of individual cells and subcellular structures provide unique analytical capabilities for biological and biomedical research, including determination of the biochemical heterogeneity of cellular populations and intracellular localization of pharmaceuticals. Two mass spectrometry technologies—secondary ion mass spectrometry (SIMS) and matrix assisted laser desorption ionization mass spectrometry (MALDI MS)—are most often used in micro-bioanalytical investigations. Recent advances in ion probe technologies have increased the dynamic range and sensitivity of analyte detection by SIMS, allowing two- and three-dimensional localization of analytes in a variety of cells. SIMS operating in the mass spectrometry imaging (MSI) mode can routinely reach spatial resolutions at the submicron level; therefore, it is frequently used in studies of the chemical composition of subcellular structures. MALDI MS offers a large mass range and high sensitivity of analyte detection. It has been successfully applied in a variety of single-cell and organelle profiling studies. Innovative instrumentation such as scanning microprobe MALDI and mass microscope spectrometers enable new subcellular MSI measurements. Other approaches for MS-based chemical imaging and profiling include those based on near-field laser ablation and inductively-coupled plasma MS analysis, which offer complementary capabilities for subcellular chemical imaging and profiling. PMID:22498881

  9. Recommendations for the generation, quantification, storage and handling of peptides used for mass spectrometry-based assays

    SciTech Connect

    Hoofnagle, Andrew N.; Whiteaker, Jeffrey R.; Carr, Steven A.; Kuhn, Eric; Liu, Tao; Massoni, Sam A.; Thomas, Stefani N.; Townsend, Reid; Zimmerman, Lisa J.; Boja, Emily; Chen, Jing; Crimmins, Daniel L.; Davies, Sherri; Gao, Yuqian; Hiltke, Tara R.; Ketchum, Karen; Kinsinger, Christopher; Mesri, Mehdi; Meyer, Matthew R.; Qian, Weijun; Schoenherr, Regine M.; Scott, Mitchell; Shi, Tujin; Whiteley, Gordon; Wrobel, John; Wu, Chaochao; Ackermann, Bradley L.; Aebersold, Ruedi; Barnidge, David R.; Bunk, David M.; Clarke, Nigel; Fishman, Jordan B.; Grant, Russ P.; Kusebauch, Ulrike; Kushnir, Mark M.; Lowenthal, Mark S.; Moritz, Robert; Neubert, Hendrik; Patterson, Scott D.; Rockwood, Alan L.; Rogers, John; Singh, Ravinder J.; Van Eyk, Jennifer; Wong, Steven H.; Zhang, Shucha; Chan, Daniel W.; Chen, Xian; Ellis, Matthew J.; Liebler, Daniel; Rodland, Karin D.; Rodriguez, Henry; Smith, Richard D.; Zhang, Zhen; Zhang, Hui; Paulovich, Amanda G.

    2015-12-30

    The Clinical Proteomic Tumor Analysis Consortium (1) (CPTAC) of the National Cancer Institute (NCI) is a comprehensive and coordinated effort to accelerate the understanding of the molecular basis of cancer through the application of robust technologies and workflows for the quantitative measurements of proteins. The Assay Development Working Group of the CPTAC Program aims to foster broad uptake of targeted mass spectrometry-based assays employing isotopically labeled peptides for confident assignment and quantification, including multiple reaction monitoring (MRM; also referred to as Selected Reaction Monitoring), parallel reaction monitoring (PRM), and other targeted methods.

  10. OpenMS – An open-source software framework for mass spectrometry

    PubMed Central

    Sturm, Marc; Bertsch, Andreas; Gröpl, Clemens; Hildebrandt, Andreas; Hussong, Rene; Lange, Eva; Pfeifer, Nico; Schulz-Trieglaff, Ole; Zerck, Alexandra; Reinert, Knut; Kohlbacher, Oliver

    2008-01-01

    Background Mass spectrometry is an essential analytical technique for high-throughput analysis in proteomics and metabolomics. The development of new separation techniques, precise mass analyzers and experimental protocols is a very active field of research. This leads to more complex experimental setups yielding ever increasing amounts of data. Consequently, analysis of the data is currently often the bottleneck for experimental studies. Although software tools for many data analysis tasks are available today, they are often hard to combine with each other or not flexible enough to allow for rapid prototyping of a new analysis workflow. Results We present OpenMS, a software framework for rapid application development in mass spectrometry. OpenMS has been designed to be portable, easy-to-use and robust while offering a rich functionality ranging from basic data structures to sophisticated algorithms for data analysis. This has already been demonstrated in several studies. Conclusion OpenMS is available under the Lesser GNU Public License (LGPL) from the project website at . PMID:18366760

  11. High resolution mass spectrometry imaging of plant tissues: towards a plant metabolite atlas.

    PubMed

    Bhandari, Dhaka Ram; Wang, Qing; Friedt, Wolfgang; Spengler, Bernhard; Gottwald, Sven; Römpp, Andreas

    2015-11-21

    Mass spectrometry (MS) imaging provides spatial and molecular information for a wide range of compounds. This tool can be used to investigate metabolic changes in plant physiology and environmental interactions. A major challenge in our study was to prepare tissue sections that were compatible with high spatial resolution analysis and therefore dedicated sample preparation protocols were established and optimized for the physicochemical properties of all major plant organs. We combined high spatial resolution (5 μm), in order to detect cellular features, and high mass accuracy (<2 ppm root mean square error), for molecular specificity. Mass spectrometry imaging experiments were performed in positive and negative ion mode. Changes in metabolite patterns during plant development were investigated for germination of oilseed rape. The detailed localization of more than 90 compounds allowed assignment to metabolic processes and indicated possible functions in plant tissues. The 'untargeted' nature of MS imaging allows the detection of marker compounds for the physiological status, as demonstrated for plant-pathogen interactions. Our images show excellent correlation with optical/histological examination. In contrast to previous MS imaging studies of plants, we present a complete workflow that covers multiple species, such as oilseed rape, wheat seed and rice. In addition, different major plant organs and a wide variety of compound classes were analyzed. Thus, our method could be used to develop a plant metabolite atlas as a reference to investigate systemic and local effects of pathogen infection or environmental stress.

  12. Liquid chromatography-bioassay-mass spectrometry for profiling of physiologically active food.

    PubMed

    Morlock, Gertrud E; Klingelhöfer, Ines

    2014-08-19

    Complex samples like food contain thousands of single compounds. In the past, only known target compounds were looked for; however, most bioactive compounds in food are unknown. On the contrary, nontarget analyses face the challenge of determining the thousand peaks' identities, but it remains largely unclear which peaks are bioactive. Here, we show a novel effect-directed food profiling, as food and food supplements can be unknowingly physiologically active. By the combination of planar chromatography, using water-wettable reversed phase high-performance thin-layer chromatography (HPTLC RP18 W) plates, with detection by specific microorganisms, endocrine compounds in food were quantitatively detected as sharp-bounded zones and further characterized by mass spectrometry. This analytical workflow allowed frequent food intakes to be identified as risky with regard to estrogen-effective compounds, in discussion for their potential involvement in foodborne pathogenesis and for use in personalized health care. Using this accelerated workflow with its comprehensive detection potential, unknown endocrine compounds can be discovered. Exemplarily, the discovery of up to six endocrine disrupting compounds was shown in seven propolis samples and in four spices. For example, microorganisms quantitatively detected an estrogen-effective compound in the range of 0.07-0.24% in seven propolis samples, which was assigned to be caffeic acid phenethyl ester by mass spectrometry. This streamlined nontarget analysis detected modes of action, followed by targeted characterization of newly discovered effective compounds. Also, drug discovery or analysis of traditional medicines may profit from this effect-directed profiling of complex samples.

  13. Noncovalent Shiga-like toxin assemblies: characterization by means of mass spectrometry and tandem mass spectrometry.

    PubMed

    Williams, Jonathan P; Green, Brian N; Smith, Daniel C; Jennings, Keith R; Moore, Katherine A H; Slade, Susan E; Roberts, Lynne M; Scrivens, James H

    2005-06-14

    Shiga-like toxin 1 (SLTx), produced by enterohemorrhagic strains of Escherichia coli (EHEC), belongs to a family of structurally and functionally related AB(5) protein toxins that are associated with human disease. EHEC infection often gives rise to hemolytic colitis, while toxin-induced kidney damage is one of the major causes of hemolytic uremic syndrome (HUS) and acute renal failure in children. As such, an understanding and analysis of the noncovalent interactions that maintain the quaternary structure of this toxin are fundamentally important since such interactions have significant biochemical and medical implications. This paper reports on the analysis of the noncovalent homopentameric complex of Shiga-like toxin B chain (SLTx-B(5)) using electrospray ionization (ESI) triple-quadrupole (QqQ) mass spectrometry (MS) and tandem mass spectrometry (MS/MS) and the analysis of the noncovalent hexameric holotoxin (SLTx-AB(5)) using ESI time-of-flight (TOF) MS. The triple-quadrupole analysis revealed highly charged monomer ions dissociate from the multiprotein complex to form dimer, trimer, and tetramer product ions, which were also seen to further dissociate. The ESI-TOFMS analysis of SLTx-AB(5) revealed the complex remained intact and was observed in the gas phase over a range of pHs. Theses findings demonstrate that the gas-phase structure observed for both the holotoxin and the isoloated B chains correlates well with the structures reported to exist in the solution phase for these proteins. Such analysis provides a rapid screening technique for assessing the noncovalent structure of this family of proteins and other structurally related toxins.

  14. 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...

  15. 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…

  16. Advances in mass spectrometry based strategies to study receptor tyrosine kinases.

    PubMed

    Vyse, Simon; Desmond, Howard; Huang, Paul H

    2017-03-01

    Receptor tyrosine kinases (RTKs) are key transmembrane environmental sensors that are capable of transmitting extracellular information into phenotypic responses, including cell proliferation, survival and metabolism. Advances in mass spectrometry (MS)-based phosphoproteomics have been instrumental in providing the foundations of much of our current understanding of RTK signalling networks and activation dynamics. Furthermore, new insights relating to the deregulation of RTKs in disease, for instance receptor co-activation and kinome reprogramming, have largely been identified using phosphoproteomic-based strategies. This review outlines the current approaches employed in phosphoproteomic workflows, including phosphopeptide enrichment and MS data-acquisition methods. Here, recent advances in the application of MS-based phosphoproteomics to bridge critical gaps in our knowledge of RTK signalling are focused on. The current limitations of the technology are discussed and emerging areas such as computational modelling, high-throughput phospho-proteomic workflows and next-generation single-cell approaches to further our understanding in new areas of RTK biology are highlighted.

  17. Quantitative cross-linking/mass spectrometry reveals subtle protein conformational changes

    PubMed Central

    2016-01-01

    Quantitative cross-linking/mass spectrometry (QCLMS) probes protein structural dynamics in solution by quantitatively comparing the yields of cross-links between different conformational statuses. We have used QCLMS to understand the final maturation step of the proteasome lid and also to elucidate the structure of complement C3(H2O). Here we benchmark our workflow using a structurally well-described reference system, the human complement protein C3 and its activated cleavage product C3b. We found that small local conformational changes affect the yields of cross-linking residues that are near in space while larger conformational changes affect the detectability of cross-links. Distinguishing between minor and major changes required robust analysis based on replica analysis and a label-swapping procedure. By providing workflow, code of practice and a framework for semi-automated data processing, we lay the foundation for QCLMS as a tool to monitor the domain choreography that drives binary switching in many protein-protein interaction networks. PMID:27976756

  18. Advances in mass spectrometry based strategies to study receptor tyrosine kinases

    PubMed Central

    Vyse, Simon; Desmond, Howard; Huang, Paul H.

    2017-01-01

    Receptor tyrosine kinases (RTKs) are key transmembrane environmental sensors that are capable of transmitting extracellular information into phenotypic responses, including cell proliferation, survival and metabolism. Advances in mass spectrometry (MS)-based phosphoproteomics have been instrumental in providing the foundations of much of our current understanding of RTK signalling networks and activation dynamics. Furthermore, new insights relating to the deregulation of RTKs in disease, for instance receptor co-activation and kinome reprogramming, have largely been identified using phosphoproteomic-based strategies. This review outlines the current approaches employed in phosphoproteomic workflows, including phosphopeptide enrichment and MS data-acquisition methods. Here, recent advances in the application of MS-based phosphoproteomics to bridge critical gaps in our knowledge of RTK signalling are focused on. The current limitations of the technology are discussed and emerging areas such as computational modelling, high-throughput phospho­proteomic workflows and next-generation single-cell approaches to further our understanding in new areas of RTK biology are highlighted. PMID:28250950

  19. The importance of matrix-assisted laser desorption ionization-time of flight mass spectrometry for correct identification of Clostridium difficile isolated from chromID C. difficile chromogenic agar.

    PubMed

    Chen, Jonathan H K; Cheng, Vincent C C; Wong, Oi-Ying; Wong, Sally C Y; So, Simon Y C; Yam, Wing-Cheong; Yuen, Kwok-Yung

    2016-01-11

    The clinical workflow of using chromogenic agar and matrix-assisted laser desorption ionization time-of-fight mass spectrometry (MALDI-TOF MS) for Clostridium difficile identification was evaluated. The addition of MALDI-TOF MS identification after the chromID C. difficile chromogenic agar culture could significantly improve the diagnostic accuracy of C. difficile.

  20. mzML—a Community Standard for Mass Spectrometry Data*

    PubMed Central

    Martens, Lennart; Chambers, Matthew; Sturm, Marc; Kessner, Darren; Levander, Fredrik; Shofstahl, Jim; Tang, Wilfred H.; Römpp, Andreas; Neumann, Steffen; Pizarro, Angel D.; Montecchi-Palazzi, Luisa; Tasman, Natalie; Coleman, Mike; Reisinger, Florian; Souda, Puneet; Hermjakob, Henning; Binz, Pierre-Alain; Deutsch, Eric W.

    2011-01-01

    Mass spectrometry is a fundamental tool for discovery and analysis in the life sciences. With the rapid advances in mass spectrometry technology and methods, it has become imperative to provide a standard output format for mass spectrometry data that will facilitate data sharing and analysis. Initially, the efforts to develop a standard format for mass spectrometry data resulted in multiple formats, each designed with a different underlying philosophy. To resolve the issues associated with having multiple formats, vendors, researchers, and software developers convened under the banner of the HUPO PSI to develop a single standard. The new data format incorporated many of the desirable technical attributes from the previous data formats, while adding a number of improvements, including features such as a controlled vocabulary with validation tools to ensure consistent usage of the format, improved support for selected reaction monitoring data, and immediately available implementations to facilitate rapid adoption by the community. The resulting standard data format, mzML, is a well tested open-source format for mass spectrometer output files that can be readily utilized by the community and easily adapted for incremental advances in mass spectrometry technology. PMID:20716697

  1. Basics of mass spectrometry based metabolomics.

    PubMed

    Courant, Frédérique; Antignac, Jean-Philippe; Dervilly-Pinel, Gaud; Le Bizec, Bruno

    2014-11-01

    The emerging field of metabolomics, aiming to characterize small molecule metabolites present in biological systems, promises immense potential for different areas such as medicine, environmental sciences, agronomy, etc. The purpose of this article is to guide the reader through the history of the field, then through the main steps of the metabolomics workflow, from study design to structure elucidation, and help the reader to understand the key phases of a metabolomics investigation and the rationale underlying the protocols and techniques used. This article is not intended to give standard operating procedures as several papers related to this topic were already provided, but is designed as a tutorial aiming to help beginners understand the concept and challenges of MS-based metabolomics. A real case example is taken from the literature to illustrate the application of the metabolomics approach in the field of doping analysis. Challenges and limitations of the approach are then discussed along with future directions in research to cope with these limitations. This tutorial is part of the International Proteomics Tutorial Programme (IPTP18).

  2. Phylogenetic classification and identification of bacteria by mass spectrometry.

    PubMed

    Freiwald, Anja; Sauer, Sascha

    2009-01-01

    Bacteria are a convenient source of intrinsic marker proteins, which can be detected efficiently by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The patterns of protein masses observed can be used for accurate classification and identification of bacteria. Key to the reliability of the method is a robust and standardized procedure for sample preparations, including bacterial culturing, chemical treatment for bacterial cell wall disruption and for protein extraction, and mass spectrometry analysis. The protocol is an excellent alternative to classical microbiological classification and identification procedures, requiring minimal sample preparation efforts and costs. Without cell culturing, the protocol takes in general <1 h.

  3. A Developmental History of Polymer Mass Spectrometry

    ERIC Educational Resources Information Center

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

    2007-01-01

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

  4. Macromolecule Mass Spectrometry: Citation Mining of User Documents

    DTIC Science & Technology

    2006-05-31

    collision - induced dissociation in quadrupole ion trap coupled tandem mass spectrometry. Ion mass spectra analysis of the resulting fragments determines ...Factor 2 ( DISSOCIATION , FRAGMENTS , CID, COLLISIONS , PRECURSOR, TANDEM, MS/MS, ENERGY , CLEAVAGES, IONS , SPECTRA, QUADRAPOLE, TRAP, PATTERNS, PROTONATION...focuses on the use of post- electrospray ionization collision - induced dissociation of macromolecules coupled

  5. Desorption electrospray ionization mass spectrometry of intact bacteria

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Desorption electrospray ionization (DESI) mass spectrometry (MS) was used to differentiate 7 bacterial species based on their measured DESI-mass spectral profile. Both Gram positive and Gram negative bacteria were tested and included Escherichia coli, Staphyloccocus aureus, Enterococcus sp., Bordete...

  6. 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...

  7. Applications of mass spectrometry to structural analysis of marine oligosaccharides.

    PubMed

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

    2014-06-30

    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.

  8. Use of mass spectrometry for imaging metabolites in plants

    SciTech Connect

    Lee, Young-Jin; Perdian, David; Song, Zhihong; Yeung, Edward; Nikolau, Basil

    2012-03-27

    We discuss and illustrate recent advances that have been made to image the distribution of metabolites among cells and tissues of plants using different mass spectrometry technologies. These technologies include matrix-assisted laser desorption ionization, desorption electrospray ionization, and secondary ion mass spectrometry. These are relatively new technological applications of mass spectrometry and they are providing highly spatially resolved data concerning the cellular distribution of metabolites. We discuss the advantages and limitations of each of these mass spectrometric methods, and provide a description of the technical barriers that are currently limiting the technology to the level of single-cell resolution. However, we anticipate that advances in the next few years will increase the resolving power of the technology to provide unprecedented data on the distribution of metabolites at the subcellular level, which will increase our ability to decipher new knowledge concerning the spatial organization of metabolic processes in plants.

  9. Use of Mass spectrometry for imaging metabolites in plants

    SciTech Connect

    Lee, Young Jin; Perdian, David C.; Song, Zhihong; Yeung, Edward S.; Nikolau, Basil

    2012-03-27

    We discuss and illustrate recent advances that have been made to image the distribution of metabolites among cells and tissues of plants using different mass spectrometry technologies. These technologies include matrix-assisted laser desorption ionization, desorption electrospray ionization, and secondary ion mass spectrometry. These are relatively new technological applications of mass spectrometry and they are providing highly spatially resolved data concerning the cellular distribution of metabolites. We discuss the advantages and limitations of each of these mass spectrometric methods, and provide a description of the technical barriers that are currently limiting the technology to the level of single-cell resolution. However, we anticipate that advances in the next few years will increase the resolving power of the technology to provide unprecedented data on the distribution of metabolites at the subcellular level, which will increase our ability to decipher new knowledge concerning the spatial organization of metabolic processes in plants.

  10. 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

  11. Mass Spectrometry-Based Tissue Imaging of Small Molecules

    PubMed Central

    Ferguson, Carly N.; Fowler, Joseph W.M.; Waxer, Jonathan F.; Gatti, Richard A.; Loo, Joseph A.

    2014-01-01

    Mass spectrometry imaging (MSI) of tissue samples is a promising analytical tool that has quickly become associated with biomedical and pharmacokinetic studies. It eliminates several labor-intensive protocols associated with more classical imaging techniques, and provides accurate, histological data at a rapid pace. Because mass spectrometry is used as the readout, MSI can be applied to almost any molecule, especially those that are biologically relevant. Many examples of its utility in the study of peptides and proteins have been reported; here we discuss its value in the mass range of small molecules. We explore its success and potential in the analysis of lipids, medicinals, and metal-based compounds by featuring representative studies from mass spectrometry imaging laboratories around the globe. PMID:24952187

  12. Profiling of Histone Post-Translational Modifications in Mouse Brain with High-Resolution Top-Down Mass Spectrometry.

    PubMed

    Zhou, Mowei; Paša-Tolić, Ljiljana; Stenoien, David L

    2017-02-03

    As histones play central roles in most chromosomal functions including regulation of DNA replication, DNA damage repair, and gene transcription, both their basic biology and their roles in disease development have been the subject of intense study. Because multiple post-translational modifications (PTMs) along the entire protein sequence are potential regulators of histones, a top-down approach, where intact proteins are analyzed, is ultimately required for complete characterization of proteoforms. However, significant challenges remain for top-down histone analysis primarily because of deficiencies in separation/resolving power and effective identification algorithms. Here we used state-of-the-art mass spectrometry and a bioinformatics workflow for targeted data analysis and visualization. The workflow uses ProMex for intact mass deconvolution, MSPathFinder as a search engine, and LcMsSpectator as a data visualization tool. When complemented with the open-modification tool TopPIC, this workflow enabled identification of novel histone PTMs including tyrosine bromination on histone H4 and H2A, H3 glutathionylation, and mapping of conventional PTMs along the entire protein for many histone subunits.

  13. Profiling of Histone Post-Translational Modifications in Mouse Brain with High-Resolution Top-Down Mass Spectrometry

    SciTech Connect

    Zhou, Mowei; Paša-Tolić, Ljiljana; Stenoien, David L.

    2016-12-21

    Histones play central roles in most chromosomal functions and both their basic biology and roles in disease have been the subject of intense study. Since multiple PTMs along the entire protein sequence are potential regulators of histones, a top-down approach, where intact proteins are analyzed, is ultimately required for complete characterization of proteoforms. However, significant challenges remain for top-down histone analysis primarily because of deficiencies in separation/resolving power and effective identification algorithms. Here, we used state of the art mass spectrometry and a bioinformatics workflow for targeted data analysis and visualization. The workflow uses ProMex for intact mass deconvolution, MSPathFinder as search engine, and LcMsSpectator as a data visualization tool. ProMex sums across retention time to maximize sensitivity and accuracy for low abundance species in MS1deconvolution. MSPathFinder searches the MS2 data against protein sequence databases with user-defined modifications. LcMsSpectator presents the results from ProMex and MSPathFinder in a format that allows quick manual evaluation of critical attributes for high-confidence identifications. When complemented with the open-modification tool TopPIC, this workflow enabled identification of novel histone PTMs including tyrosine bromination on histone H4 and H2A, H3 glutathionylation, and mapping of conventional PTMs along the entire protein for many histone subunits.

  14. High-resolution mass spectrometry elucidates metabonate (false metabolite) formation from alkylamine drugs during in vitro metabolite profiling.

    PubMed

    Barbara, Joanna E; Kazmi, Faraz; Muranjan, Seema; Toren, Paul C; Parkinson, Andrew

    2012-10-01

    In vitro metabolite profiling and characterization experiments are widely employed in early drug development to support safety studies. Samples from incubations of investigational drugs with liver microsomes or hepatocytes are commonly analyzed by liquid chromatography/mass spectrometry for detection and structural elucidation of metabolites. Advanced mass spectrometers with accurate mass capabilities are becoming increasingly popular for characterization of drugs and metabolites, spurring changes in the routine workflows applied. In the present study, using a generic full-scan high-resolution data acquisition approach with a time-of-flight mass spectrometer combined with postacquisition data mining, we detected and characterized metabonates (false metabolites) in microsomal incubations of several alkylamine drugs. If a targeted approach to mass spectrometric detection (without full-scan acquisition and appropriate data mining) were employed, the metabonates may not have been detected, hence their formation underappreciated. In the absence of accurate mass data, the metabonate formation would have been incorrectly characterized because the detected metabonates manifested as direct cyanide-trapped conjugates or as cyanide-trapped metabolites formed from the parent drugs by the addition of 14 Da, the mass shift commonly associated with oxidation to yield a carbonyl. This study demonstrates that high-resolution mass spectrometry and the associated workflow is very useful for the detection and characterization of unpredicted sample components and that accurate mass data were critical to assignment of the correct metabonate structures. In addition, for drugs containing an alkylamine moiety, the results suggest that multiple negative controls and chemical trapping agents may be necessary to correctly interpret the results of in vitro experiments.

  15. Direct analysis of samples by mass spectrometry: From elements to bio-molecules using laser ablation inductively couple plasma mass spectrometry and laser desorption/ionization mass spectrometry

    SciTech Connect

    Perdian, David C.

    2009-01-01

    Mass spectrometric methods that are able to analyze solid samples or biological materials with little or no sample preparation are invaluable to science as well as society. Fundamental research that has discovered experimental and instrumental parameters that inhibit fractionation effects that occur during the quantification of elemental species in solid samples by laser ablation inductively coupled plasma mass spectrometry is described. Research that determines the effectiveness of novel laser desorption/ionization mass spectrometric methods for the molecular analysis of biological tissues at atmospheric pressure and at high spatial resolution is also described. A spatial resolution is achieved that is able to analyze samples at the single cell level.

  16. Targeted metabolomics in cultured cells and tissues by mass spectrometry: method development and validation.

    PubMed

    Abdel Rahman, Anas M; Pawling, Judy; Ryczko, Michael; Caudy, Amy A; Dennis, James W

    2014-10-03

    Metabolomics is the identification and quantitation of small bio-molecules (metabolites) in biological samples under various environmental and genetic conditions. Mass spectrometry provides the unique opportunity for targeted identification and quantification of known metabolites by selective reaction monitoring (SRM). However, reproducibility of this approach depends on careful consideration of sample preparation, chemical classes, and stability of metabolites to be evaluated. Herein, we introduce and validate a targeted metabolite profiling workflow for cultured cells and tissues by liquid chromatography-triple quadrupole tandem mass spectrometry. The method requires a one-step extraction of water-soluble metabolites and targeted analysis of central metabolites that include glycolysis, amino acids, nucleotides, citric acid cycle, and the hexosamine biosynthetic pathway. The sensitivity, reproducibility and molecular stability of each targeted metabolite were assessed under experimental conditions. Quantitation of metabolites by peak area ratio was linear with a dilution over a 4 fold dynamic range with minimal deviation R(2)=0.98. Inter- and intra-day precision with cells and tissues had an average coefficient of variation <15% for cultured cell lines, and somewhat higher for mouse liver tissues. The method applied in triplicate measurements readily distinguished immortalized cells from malignant cells, as well as mouse littermates based on their hepatic metabolic profiles.

  17. 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).

  18. Laser electrospray mass spectrometry of adsorbed molecules at atmospheric pressure

    NASA Astrophysics Data System (ADS)

    Brady, John J.; Judge, Elizabeth J.; Simon, Kuriakose; Levis, Robert J.

    2010-02-01

    Atmospheric pressure mass analysis of solid phase biomolecules is performed using laser electrospray mass spectrometry (LEMS). A non-resonant femtosecond duration laser pulse vaporizes native samples at atmospheric pressure for subsequent electrospray ionization and transfer into a mass spectrometer. LEMS was used to detect a complex molecule (irinotecan HCl), a complex mixture (cold medicine formulation with active ingredients: acetaminophen, dextromethorphan HBr and doxylamine succinate), and a biological building block (deoxyguanosine) deposited on steel surfaces without a matrix molecule.

  19. Pharmaceutical metabolite profiling using quadrupole/ion mobility spectrometry/time-of-flight mass spectrometry.

    PubMed

    Chan, Eric C Y; New, Lee Sun; Yap, Chun Wei; Goh, Lin Tang

    2009-02-01

    The use of hybrid quadrupole ion mobility spectrometry time-of-flight mass spectrometry (Q/IMS/TOFMS) in the metabolite profiling of leflunomide (LEF) and acetaminophen (APAP) is presented. The IMS drift times (T(d)) of the drugs and their metabolites were determined in the IMS/TOFMS experiments and correlated with their exact monoisotopic masses and other in silico generated structural properties, such as connolly molecular area (CMA), connolly solvent-excluded volume (CSEV), principal moments of inertia along the X, Y and Z Cartesian coordinates (MI-X, MI-Y and MI-Z), inverse mobility and collision cross-section (CCS). The correlation of T(d) with these parameters is presented and discussed. IMS/TOF tandem mass spectrometry experiments (MS(2) and MS(3)) were successfully performed on the N-acetyl-p-benzoquinoneimine glutathione (NAPQI-GSH) adduct derived from the in vitro microsomal metabolism of APAP. As comparison, similar experiments were also performed using hybrid triple quadrupole linear ion trap mass spectrometry (QTRAPMS) and quadrupole time-of-flight mass spectrometry (QTOFMS). The abilities to resolve the product ions of the metabolite within the drift tube and fragment the ion mobility resolved product ions in the transfer travelling wave-enabled stacked ring ion guide (TWIG) demonstrated the potential applicability of the Q/IMS/TOFMS technique in pharmaceutical metabolite profiling.

  20. Laser mass spectrometry at high vibrational excitation density

    NASA Astrophysics Data System (ADS)

    Haglund, R. F., Jr.; Baltz-Knorr, M.; Ermer, D. R.; Papantonakis, M. R.; Schriver, K. E.

    2003-06-01

    We describe a novel approach to infrared matrix-assisted laser desorption-ionization mass spectrometry using a tunable, picosecond pulse laser to selectively excite specific modes of a solid, thereby creating a high local density of vibrational quanta. The concept is based on recent results from our experiments employing a free-electron laser to explore 'matrix-less' mass spectrometry in which an infrared chromophore intrinsic to the sample, rather than an exogenous matrix, is excited by the laser. Examples from both environmental mass spectrometry and a proteomics-driven research project are presented, showing how the principle of selective vibrational excitation can be used to make possible novel and useful ion generation protocols. We conclude with an analysis of possible mechanisms for the phenomena of infrared desorption, ablation and ionization using very short laser pulses. Prospects for achieving similar results with more conventional laser sources are discussed.

  1. Mass Spectrometry Analysis of Pseudomonas aeruginosa Treated With Azithromycin

    PubMed Central

    Phelan, Vanessa V.; Fang, Jinshu; Dorrestein, Pieter C.

    2015-01-01

    In microbiology, changes in specialized metabolite production (cell-to-cell signaling metabolites, virulence factors and natural products) are measured using phenotypic assays. However, advances in mass spectrometry based techniques including imaging mass spectrometry (IMS) now allow researchers to directly visualize the production of specialized metabolites from microbial colony biofilms. In this study, a combination of IMS and liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to visualize the effect of the macrolide antibiotic azithromycin (AZM) on colony biofilms of Pseudomonas aeruginosa. While previous research suggested that AZM may inhibit cell-to-cell signaling of P. aeruginosa and thereby reducing pathogenicity, we observed no clear decrease in specialized metabolite production. PMID:25801585

  2. Mass Spectrometry Analysis of Pseudomonas aeruginosa Treated with Azithromycin

    NASA Astrophysics Data System (ADS)

    Phelan, Vanessa V.; Fang, Jinshu; Dorrestein, Pieter C.

    2015-06-01

    In microbiology, changes in specialized metabolite production (cell-to-cell signaling metabolites, virulence factors, and natural products) are measured using phenotypic assays. However, advances in mass spectrometry-based techniques including imaging mass spectrometry (IMS) now allow researchers to directly visualize the production of specialized metabolites from microbial colony biofilms. In this study, a combination of IMS and liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to visualize the effect of the macrolide antibiotic azithromycin (AZM) on colony biofilms of Pseudomonas aeruginosa. Although previous research suggested that AZM may inhibit cell-to-cell signaling of P. aeruginosa and thereby reduce pathogenicity, we observed no clear decrease in specialized metabolite production.

  3. Ion mobility–mass spectrometry for structural proteomics

    PubMed Central

    Zhong, Yueyang; Hyung, Suk-Joon; Ruotolo, Brandon T

    2012-01-01

    Ion mobility coupled to mass spectrometry has been an important tool in the fields of chemical physics and analytical chemistry for decades, but its potential for interrogating the structure of proteins and multiprotein complexes has only recently begun to be realized. Today, ion mobility– mass spectrometry is often applied to the structural elucidation of protein assemblies that have failed high-throughput crystallization or NMR spectroscopy screens. Here, we highlight the technology, approaches and data that have led to this dramatic shift in use, including emerging trends such as the integration of ion mobility–mass spectrometry data with more classical (e.g., ‘bottom-up’) proteomics approaches for the rapid structural characterization of protein networks. PMID:22292823

  4. Laser desorption mass spectrometry for biomolecule detection and its applications

    NASA Astrophysics Data System (ADS)

    Winston Chen, C. H.; Sammartano, L. J.; Isola, N. R.; Allman, S. L.

    2001-08-01

    During the past few years, we developed and used laser desorption mass spectrometry for biomolecule detections. Matrix-assisted laser desorption/ionization (MALDI) was successfully used to detect DNA fragments with the size larger than 3000 base pairs. It was also successfully used to sequence DNA with both enzymatic and chemical degradation methods to produce DNA ladders. We also developed MALDI with fragmentation for direct DNA sequencing for short DNA probes. Since laser desorption mass spectrometry for DNA detection has the advantages of fast speed and no need of labeling, it has a great potential for molecular diagnosis for disease and person identification by DNA fingerprinting. We applied laser desorption mass spectrometry to succeed in the diagnosis of cystic fibrosis and several other nerve degenerative diseases such as Huntington's disease. We also succeeded in demonstrating DNA typing for forensic applications.

  5. Laser desorption mass spectrometry for DNA analysis and sequencing

    SciTech Connect

    Chen, C.H.; Taranenko, N.I.; Tang, K.; Allman, S.L.

    1995-03-01

    Laser desorption mass spectrometry has been considered as a potential new method for fast DNA sequencing. Our approach is to use matrix-assisted laser desorption to produce parent ions of DNA segments and a time-of-flight mass spectrometer to identify the sizes of DNA segments. Thus, the approach is similar to gel electrophoresis sequencing using Sanger`s enzymatic method. However, gel, radioactive tagging, and dye labeling are not required. In addition, the sequencing process can possibly be finished within a few hundred microseconds instead of hours and days. In order to use mass spectrometry for fast DNA sequencing, the following three criteria need to be satisfied. They are (1) detection of large DNA segments, (2) sensitivity reaching the femtomole region, and (3) mass resolution good enough to separate DNA segments of a single nucleotide difference. It has been very difficult to detect large DNA segments by mass spectrometry before due to the fragile chemical properties of DNA and low detection sensitivity of DNA ions. We discovered several new matrices to increase the production of DNA ions. By innovative design of a mass spectrometer, we can increase the ion energy up to 45 KeV to enhance the detection sensitivity. Recently, we succeeded in detecting a DNA segment with 500 nucleotides. The sensitivity was 100 femtomole. Thus, we have fulfilled two key criteria for using mass spectrometry for fast DNA sequencing. The major effort in the near future is to improve the resolution. Different approaches are being pursued. When high resolution of mass spectrometry can be achieved and automation of sample preparation is developed, the sequencing speed to reach 500 megabases per year can be feasible.

  6. Purifying protein complexes for mass spectrometry: applications to protein translation.

    PubMed

    Link, Andrew J; Fleischer, Tracey C; Weaver, Connie M; Gerbasi, Vincent R; Jennings, Jennifer L

    2005-03-01

    Proteins control and mediate most of the biological activities in the cell. In most cases, proteins either interact with regulatory proteins or function in large molecular assemblies to carryout biological processes. Understanding the functions of individual proteins requires the identification of these interacting proteins. With its speed and sensitivity, mass spectrometry has become the dominant method for identifying components of protein complexes. This article reviews and discusses various approaches to purify protein complexes and analyze the proteins using mass spectrometry. As examples, methods to isolate and analyze protein complexes responsible for the translation of messenger RNAs into polypeptides are described.

  7. Technical Challenges in Mass Spectrometry-Based Metabolomics

    PubMed Central

    Matsuda, Fumio

    2016-01-01

    Metabolomics is a strategy for analysis, and quantification of the complete collection of metabolites present in biological samples. Metabolomics is an emerging area of scientific research because there are many application areas including clinical, agricultural, and medical researches for the biomarker discovery and the metabolic system analysis by employing widely targeted analysis of a few hundred preselected metabolites from 10–100 biological samples. Further improvement in technologies of mass spectrometry in terms of experimental design for larger scale analysis, computational methods for tandem mass spectrometry-based elucidation of metabolites, and specific instrumentation for advanced bioanalysis will enable more comprehensive metabolome analysis for exploring the hidden secrets of metabolism. PMID:27900235

  8. Xenon purity analysis for EXO-200 via mass spectrometry

    NASA Astrophysics Data System (ADS)

    Dobi, A.; Hall, C.; Slutsky, S.; Yen, Y.-R.; Aharmin, B.; Auger, M.; Barbeau, P. S.; Benitez-Medina, C.; Breidenbach, M.; Cleveland, B.; Conley, R.; Cook, J.; Cook, S.; Counts, I.; Craddock, W.; Daniels, T.; Davis, C. G.; Davis, J.; deVoe, R.; Dixit, M.; Dolinski, M. J.; Donato, K.; Fairbank, W.; Farine, J.; Fierlinger, P.; Franco, D.; Giroux, G.; Gornea, R.; Graham, K.; Gratta, G.; Green, C.; Hagemann, C.; Hall, K.; Hallman, D.; Hargrove, C.; Herrin, S.; Hughes, M.; Hodgson, J.; Juget, F.; Karelin, A.; Kaufman, L. J.; Kuchenkov, A.; Kumar, K.; Leonard, D. S.; Lutter, G.; Mackay, D.; MacLellan, R.; Marino, M.; Mong, B.; Montero Díez, M.; Morgan, P.; Müller, A. R.; Neilson, R.; Odian, A.; O'Sullivan, K.; Piepke, A.; Pocar, A.; Prescott, C. Y.; Pushkin, K.; Rivas, A.; Rollin, E.; Rowson, P. C.; Sabourov, A.; Sinclair, D.; Skarpaas, K.; Stekhanov, V.; Strickland, V.; Swift, M.; Twelker, K.; Vuilleumier, J.-L.; Vuilleumier, J.-M.; Weber, M.; Wichoski, U.; Wodin, J.; Wright, J. D.; Yang, L.

    2012-05-01

    We describe purity measurements of the natural and enriched xenon stockpiles used by the EXO-200 double beta decay experiment based on a mass spectrometry technique. The sensitivity of the spectrometer is enhanced by several orders of magnitude by the presence of a liquid nitrogen cold trap, and many impurity species of interest can be detected at the level of one part-per-billion or better. We have used the technique to screen the EXO-200 xenon before, during, and after its use in our detector, and these measurements have proven useful. This is the first application of the cold trap mass spectrometry technique to an operating physics experiment.

  9. Major roles for minor bacterial lipids identified by mass spectrometry.

    PubMed

    Garrett, Teresa A

    2016-10-17

    Mass spectrometry of lipids, especially those isolated from bacteria, has ballooned over the past two decades, affirming in the process the complexity of the lipidome. With this has come the identification of new and interesting lipid structures. Here is an overview of several novel lipids, from both Gram-negative and Gram-positive bacteria with roles in health and disease, whose structural identification was facilitated using mass spectrometry. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.

  10. Issues and opportunities in accelerator mass spectrometry for stable isotopes.

    PubMed

    Matteson, Sam

    2008-01-01

    Accelerator mass spectrometry (AMS) has developed in the last 30 years many notable applications to the spectrometry of radioisotopes, particularly in radiocarbon dating. The instrumentation science of trace element AMS (TEAMS) that analyzes stable isotopes, also called Accelerator SIMS or MegaSIMS, while unique in many features, has also shared in many of these significant advances and has pushed TEAMS sensitivity to concentration levels surpassing many competing mass spectroscopic technologies. This review examines recent instrumentation developments, the capabilities of the new instrumentation and discernable trends for future development.

  11. Mass spectrometry and inhomogeneous ion optics

    NASA Technical Reports Server (NTRS)

    White, F. A.

    1973-01-01

    Work done in several areas to advance the state of the art of magnetic mass spectrometers is described. The calculations and data necessary for the design of inhomogeneous field mass spectrometers, and the calculation of ion trajectories through such fields are presented. The development and testing of solid state ion detection devices providing the capability of counting single ions is discussed. New techniques in the preparation and operation of thermal-ionization ion sources are described. Data obtained on the concentrations of copper in rainfall and uranium in air samples using the improved thermal ionization techniques are presented. The design of a closed system static mass spectrometer for isotopic analyses is discussed. A summary of instrumental aspects of a four-stage mass spectrometer comprising two electrostatic and two 90 deg. magnetic lenses with a 122-cm radius used to study the interaction of ions with solids is presented.

  12. Structure Determination of Natural Products by Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Biemann, Klaus

    2015-07-01

    I review laboratory research on the development of mass spectrometric methodology for the determination of the structure of natural products of biological and medical interest, which I conducted from 1958 to the end of the twentieth century. The methodology was developed by converting small peptides to their corresponding polyamino alcohols to make them amenable to mass spectrometry, thereby making it applicable to whole proteins. The structures of alkaloids were determined by analyzing the fragmentation of a known alkaloid and then using the results to deduce the structures of related compounds. Heparin-like structures were investigated by determining their molecular weights from the mass of protonated molecular ions of complexes with highly basic, synthetic peptides. Mass spectrometry was also employed in the analysis of lunar material returned by the Apollo missions. A miniaturized gas chromatograph mass spectrometer was sent to Mars on board of the two Viking 1976 spacecrafts.

  13. Structurally selective imaging mass spectrometry by imaging ion mobility-mass spectrometry.

    PubMed

    McLean, John A; Fenn, Larissa S; Enders, Jeffrey R

    2010-01-01

    This chapter describes the utility of structurally based separations combined with imaging mass spectrometry (MS) by ion mobility-MS (IM-MS) approaches. The unique capabilities of combining rapid (mus-ms) IM separations with imaging MS are detailed for an audience ranging from new to potential practitioners in IM-MS technology. Importantly, imaging IM-MS provides the ability to rapidly separate and elucidate various types of endogenous and exogenous biomolecules (e.g., nucleotides, carbohydrates, peptides, and lipids), including isobaric species. Drift tube and traveling wave IM-MS instrumentation are described and specific protocols are presented for calculating ion-neutral collision cross sections (i.e., apparent ion surface area or structure) from experimentally obtained IM-MS data. Special emphasis is placed on the use of imaging IM-MS for the analysis of samples in life sciences research (e.g., thin tissue sections), including selective imaging for peptide/protein and lipid distributions. Future directions for rapid and multiplexed imaging IM-MS/MS are detailed.

  14. Metabolomics by Gas Chromatography-Mass Spectrometry: the combination of targeted and untargeted profiling

    PubMed Central

    Fiehn, Oliver

    2016-01-01

    Gas chromatography-mass spectrometry (GC-MS)-based metabolomics is ideal for identifying and quantitating small molecular metabolites (<650 daltons), including small acids, alcohols, hydroxyl acids, amino acids, sugars, fatty acids, sterols, catecholamines, drugs, and toxins, often using chemical derivatization to make these compounds volatile enough for gas chromatography. This unit shows that on GC-MS- based metabolomics easily allows integrating targeted assays for absolute quantification of specific metabolites with untargeted metabolomics to discover novel compounds. Complemented by database annotations using large spectral libraries and validated, standardized standard operating procedures, GC-MS can identify and semi-quantify over 200 compounds per study in human body fluids (e.g., plasma, urine or stool) samples. Deconvolution software enables detection of more than 300 additional unidentified signals that can be annotated through accurate mass instruments with appropriate data processing workflows, similar to liquid chromatography-MS untargeted profiling (LC-MS). Hence, GC-MS is a mature technology that not only uses classic detectors (‘quadrupole’) but also target mass spectrometers (‘triple quadrupole’) and accurate mass instruments (‘quadrupole-time of flight’). This unit covers the following aspects of GC-MS-based metabolomics: (i) sample preparation from mammalian samples, (ii) acquisition of data, (iii) quality control, and (iv) data processing. PMID:27038389

  15. 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

  16. Analysis of proteins and proteomes by mass spectrometry.

    PubMed

    Mann, M; Hendrickson, R C; Pandey, A

    2001-01-01

    A decade after the discovery of electrospray and matrix-assisted laser desorption ionization (MALDI), methods that finally allowed gentle ionization of large biomolecules, mass spectrometry has become a powerful tool in protein analysis and the key technology in the emerging field of proteomics. The success of mass spectrometry is driven both by innovative instrumentation designs, especially those operating on the time-of-flight or ion-trapping principles, and by large-scale biochemical strategies, which use mass spectrometry to detect the isolated proteins. Any human protein can now be identified directly from genome databases on the basis of minimal data derived by mass spectrometry. As has already happened in genomics, increased automation of sample handling, analysis, and the interpretation of results will generate an avalanche of qualitative and quantitative proteomic data. Protein-protein interactions can be analyzed directly by precipitation of a tagged bait followed by mass spectrometric identification of its binding partners. By these and similar strategies, entire protein complexes, signaling pathways, and whole organelles are being characterized. Posttranslational modifications remain difficult to analyze but are starting to yield to generic strategies.

  17. 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

  18. Electrospray and tandem mass spectrometry in biochemistry.

    PubMed Central

    Griffiths, W J; Jonsson, A P; Liu, S; Rai, D K; Wang, Y

    2001-01-01

    Over the last 20 years, biological MS has changed out of all recognition. This is primarily due to the development in the 1980s of 'soft ionization' methods that permit the ionization and vaporization of large, polar, and thermally labile biomolecules. These developments in ionization mode have driven the design and manufacture of smaller and cheaper mass analysers, making the mass spectrometer a routine instrument in the biochemistry laboratory today. In the present review the revolutionary 'soft ionization' methods will be discussed with particular reference to electrospray. The mass analysis of ions will be described, and the concept of tandem MS introduced. Where appropriate, examples of the application of MS in biochemistry will be provided. Although the present review will concentrate on the MS of peptides/proteins and lipids, all classes of biomolecules can be analysed, and much excellent work has been done in the fields of carbohydrate and nucleic acid biochemistry. PMID:11311115

  19. Lectin chromatography/mass spectrometry discovery workflow identifies putative biomarkers of aggressive breast cancers.

    PubMed

    Drake, Penelope M; Schilling, Birgit; Niles, Richard K; Prakobphol, Akraporn; Li, Bensheng; Jung, Kwanyoung; Cho, Wonryeon; Braten, Miles; Inerowicz, Halina D; Williams, Katherine; Albertolle, Matthew; Held, Jason M; Iacovides, Demetris; Sorensen, Dylan J; Griffith, Obi L; Johansen, Eric; Zawadzka, Anna M; Cusack, Michael P; Allen, Simon; Gormley, Matthew; Hall, Steven C; Witkowska, H Ewa; Gray, Joe W; Regnier, Fred; Gibson, Bradford W; Fisher, Susan J

    2012-04-06

    We used a lectin chromatography/MS-based approach to screen conditioned medium from a panel of luminal (less aggressive) and triple negative (more aggressive) breast cancer cell lines (n=5/subtype). The samples were fractionated using the lectins Aleuria aurantia (AAL) and Sambucus nigra agglutinin (SNA), which recognize fucose and sialic acid, respectively. The bound fractions were enzymatically N-deglycosylated and analyzed by LC-MS/MS. In total, we identified 533 glycoproteins, ∼90% of which were components of the cell surface or extracellular matrix. We observed 1011 glycosites, 100 of which were solely detected in ≥3 triple negative lines. Statistical analyses suggested that a number of these glycosites were triple negative-specific and thus potential biomarkers for this tumor subtype. An analysis of RNaseq data revealed that approximately half of the mRNAs encoding the protein scaffolds that carried potential biomarker glycosites were up-regulated in triple negative vs luminal cell lines, and that a number of genes encoding fucosyl- or sialyltransferases were differentially expressed between the two subtypes, suggesting that alterations in glycosylation may also drive candidate identification. Notably, the glycoproteins from which these putative biomarker candidates were derived are involved in cancer-related processes. Thus, they may represent novel therapeutic targets for this aggressive tumor subtype.

  20. A New Accelerator-Based Mass Spectrometry.

    ERIC Educational Resources Information Center

    Gove, H. E.

    1983-01-01

    Tandem electrostatic accelerators produce beams of positive ions which are used to penetrate atomic nuclei in a target, inducing nuclear reactions whose study elucidates varied properties of the nucleus. Uses of the system, which acts like a mass spectrometer, are discussed. These include radiocarbon dating measurements. (JN)

  1. Mass spectrometry on the surface of Mercury

    NASA Astrophysics Data System (ADS)

    Whitby, J.; Rohner, U.; Benz, W.; Wurz, P.

    2003-04-01

    The proposed Mercury Surface Element of the BepiColombo mission will place a lander on Mercury equipped with a geochemistry instrumentation package. We will discuss the utility of elemental and isotopic analyses of individual mineral grains in the hermean regolith, and present relevant results from a prototype laser-ablation time-of-flight mass spectrometer.

  2. Transformation products of emerging contaminants in the environment and high-resolution mass spectrometry: a new horizon.

    PubMed

    Picó, Yolanda; Barceló, Damià

    2015-08-01

    It is crucial to study the presence of transformation products (TPs) of emerging contaminants that can be potentially found in the environment after biological or chemical degradation. This review focuses on the potential and shortcomings of high-resolution mass spectrometry (HRMS) to identify these TPs, with emphasis on recent developments in mass analyzers, data evaluation, and compound identification workflows and applications. Advances in HRMS technologies, including direct introduction or in-line chromatographic separation modes, ionization techniques, mass analyzers, and detection methods, have led to powerful tools to assess the molecular changes and the opening of new horizons to identify unknown molecules. Advances in HRMS pertaining to the generation of analytical data for the main methods to identify TPs, including nontargeted and targeted approaches as they are applied to elucidate the structure of TPs, are also discussed.

  3. 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.

  4. Mass spectrometry-based proteomics: principles, perspectives, and challenges.

    PubMed

    Wiśniewski, Jacek R

    2008-10-01

    Mass spectrometry-based proteomics is a modern and rapidly developing methodology for qualitative and quantitative characterization of proteins and their posttranslational modification, subcellular localization, and interaction partners. It enables characterization of entire proteomes with unprecedented sensitivity and precision, providing platforms for identification of biomarkers and drug targets.

  5. High-Performance Liquid Chromatography-Mass Spectrometry.

    ERIC Educational Resources Information Center

    Vestal, Marvin L.

    1984-01-01

    Reviews techniques for online coupling of high-performance liquid chromatography with mass spectrometry, emphasizing those suitable for application to nonvolatile samples. Also summarizes the present status, strengths, and weaknesses of various techniques and discusses potential applications of recently developed techniques for combined liquid…

  6. Specialized Gas Chromatography--Mass Spectrometry Systems for Clinical Chemistry.

    ERIC Educational Resources Information Center

    Gochman, Nathan; And Others

    1979-01-01

    A discussion of the basic design and characteristics of gas chromatography-mass spectrometry systems used in clinical chemistry. A comparison of three specific systems: the Vitek Olfax IIA, Hewlett-Packard HP5992, and Du Pont DP-102 are included. (BB)

  7. Multiple parallel mass spectrometry for lipid and vitamin D analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Liquid chromatography (LC) coupled to mass spectrometry (MS) has become the method of choice for analysis of complex lipid samples. Two types of ionization sources have emerged as the most commonly used to couple LC to MS: atmospheric pressure chemical ionization (APCI) and electrospray ionization ...

  8. Diagnosing Prion Diseases: Mass Spectrometry-Based Approaches

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mass spectrometry is an established means of quantitating the prions present in infected hamsters. Calibration curves relating the area ratios of the selected analyte peptides and their oxidized analogs to stable isotope labeled internal standards were prepared. The limit of detection (LOD) and limi...

  9. 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

  10. On-Line Synthesis and Analysis by Mass Spectrometry

    ERIC Educational Resources Information Center

    Bain, Ryan M.; Pulliam, Christopher J.; Raab, Shannon A.; Cooks, R. Graham

    2015-01-01

    In this laboratory experiment, students learn how to use ESI to accelerate chemical synthesis and to couple it with on-line mass spectrometry for structural analysis. The Hantzsch synthesis of symmetric 1,4-dihydropyridines is a classic example of a one-pot reaction in which multiple intermediates can serve to indicate the progress of the reaction…

  11. ENVIRONMENTAL MASS SPECTROMETRY: EMERGING CONTAMINANTS AND CURRENT ISSUES, 2006

    EPA Science Inventory

    This biennial review covers developments in Environmental Mass Spectrometry over the period of 2004-2005. A few significant references that appeared between January and February 2006 are also included. Analytical Chemistry's current policy is to limit reviews to include 100-200 s...

  12. DMS-prefiltered mass spectrometry for the detection of biomarkers

    NASA Astrophysics Data System (ADS)

    Coy, Stephen L.; Krylov, Evgeny V.; Nazarov, Erkinjon G.

    2008-04-01

    Technologies based on Differential Mobility Spectrometry (DMS) are ideally matched to rapid, sensitive, and selective detection of chemicals like biomarkers. Biomarkers linked to exposure to radiation, exposure to CWA's, exposure to toxic materials (TICs and TIMs) and to specific diseases are being examined in a number of laboratories. Screening for these types of exposure can be improved in accuracy and greatly speeded up by using DMS-MS instead of slower techniques like LC-MS and GC-MS. We have performed an extensive series of tests with nanospray-DMS-mass spectroscopy and standalone nanospray-DMS obtaining extensive information on chemistry and detectivity. DMS-MS systems implemented with low-resolution, low-cost, portable mass-spectrometry systems are very promising. Lowresolution mass spectrometry alone would be inadequate for the task, but with DMS pre-filtration to suppress interferences, can be quite effective, even for quantitative measurement. Bio-fluids and digests are well suited to ionization by electrospray and detection by mass-spectrometry, but signals from critical markers are overwhelmed by chemical noise from unrelated species, making essential quantitative analysis impossible. Sionex and collaborators have presented data using DMS to suppress chemical noise, allowing detection of cancer biomarkers in 10,000-fold excess of normal products 1,2. In addition, a linear dynamic range of approximately 2,000 has been demonstrated with accurate quantitation 3. We will review the range of possible applications and present new data on DMS-MS biomarker detection.

  13. Liquid chromatography tandem mass spectrometry in the clinical laboratory.

    PubMed

    Adaway, Joanne E; Keevil, Brian G; Owen, Laura J

    2015-01-01

    Clinical laboratory medicine has seen the introduction and evolution of liquid chromatography tandem mass spectrometry in routine clinical laboratories over the last 10-15 years. There still exists a wide diversity of assays from very esoteric and highly specialist manual assays to more simplified kit-based assays. The technology is not static as manufacturers are continually making improvements. Mass spectrometry is now commonly used in several areas of diagnostics including therapeutic drug monitoring, toxicology, endocrinology, paediatrics and microbiology. Some of the most high throughput analyses or common analytes include vitamin D, immunosuppressant monitoring, androgen measurement and newborn screening. It also offers flexibility for the measurement of analytes in a variety of different matrices which would prove difficult with immunoassays. Unlike immunoassays or high-pressure liquid chromatography assays using ultraviolet or fluorescence detection, mass spectrometry offers better specificity and reduced interferences if attention is paid to potential isobaric compounds. Furthermore, multiplexing, which enables multiple analytes to be measured with the same volume of serum is advantageous, and the requirement for large sample volumes is decreasing as instrument sensitivity increases. There are many emerging applications in the literature. Using mass spectrometry to identify novel isoforms or modified peptides is possible as is quantification of proteins and peptides, with or without protein digests. Future developments by the manufacturers may also include mechanisms to improve the throughput of samples and strategies to decrease the level of skill required by the operators.

  14. Coming to a hospital near you: mass spectrometry imaging

    ScienceCinema

    Bowen, Ben

    2016-07-12

    Berkeley Lab's Ben Bowen discusses "Coming to a hospital near you: mass spectrometry imaging" in this Oct. 28, 2013 talk, which is part of a Science at the Theater event entitled Eight Big Ideas. Go here to watch the entire event with all 8 speakers.

  15. Liquid Chromatography-Mass Spectrometry-based Quantitative Proteomics

    SciTech Connect

    Xie, Fang; Liu, Tao; Qian, Weijun; Petyuk, Vladislav A.; Smith, Richard D.

    2011-07-22

    Liquid chromatography-mass spectrometry (LC-MS)-based quantitative proteomics has become increasingly applied for a broad range of biological applications due to growing capabilities for broad proteome coverage and good accuracy in quantification. Herein, we review the current LC-MS-based quantification methods with respect to their advantages and limitations, and highlight their potential applications.

  16. Colloquium: 100 years of mass spectrometry: Perspectives and future trends

    NASA Astrophysics Data System (ADS)

    Maher, Simon; Jjunju, Fred P. M.; Taylor, Stephen

    2015-01-01

    Mass spectrometry (MS) is widely regarded as the most sensitive and specific general purpose analytical technique. More than a century has passed for MS since the ground-breaking work of Nobel laureate Sir Joseph John Thomson in 1913. This Colloquium aims to (1) give an historical overview of the major instrumentation achievements that have driven mass spectrometry forward in the past century, including those leading up to the initial work of Thomson, (2) provide the nonspecialist with an introduction to MS, and (3) highlight some key applications of MS and explore the current and future trends. Because of the vastness of the subject area and quality of the manifold research efforts that have been undertaken over the last 100 years, which have contributed to the foundations and subsequent advances in mass spectrometry, it should be understood that not all of the key contributions may have been included in this Colloquium. Mass spectrometry has embraced a multitude of scientific disciplines and to recognize all of the achievements is an impossible task, such has been the diverse impact of this invaluable technique. Scientific progress is usually made via the cumulative effort of a large number of researchers; the achievements reported herein are only a representation of that effort.

  17. Coming to a hospital near you: mass spectrometry imaging

    SciTech Connect

    Bowen, Ben

    2013-10-31

    Berkeley Lab's Ben Bowen discusses "Coming to a hospital near you: mass spectrometry imaging" in this Oct. 28, 2013 talk, which is part of a Science at the Theater event entitled Eight Big Ideas. Go here to watch the entire event with all 8 speakers.

  18. MICELLAR ELECTROKINETIC CHROMATOGRAPHY-MASS SPECTROMETRY (R823292)

    EPA Science Inventory

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

  19. Laser ablation sample transfer for mass spectrometry imaging.

    PubMed

    Park, Sung-Gun; Murray, Kermit K

    2015-01-01

    Infrared laser ablation sample transfer (IR-LAST) is a novel ambient sampling technique for mass spectrometry. In this technique, a pulsed mid-IR laser is used to ablate materials that are collected for mass spectrometry analysis; the material can be a solid sample or deposited on a sample target. After collection, the sample can be further separated or analyzed directly by mass spectrometry. For IR-LAST sample transfer tissue imaging using MALDI mass spectrometry, a tissue section is placed on a sample slide and material transferred to a target slide by scanning the tissue sample under a focused laser beam using transmission-mode (back side) IR laser ablation. After transfer, the target slide is analyzed using MALDI imaging. The spatial resolution is approximately 400 μm and limited by the spread of the laser desorption plume. IR-LAST for MALDI imaging provides several new capabilities including ambient sampling, area to spot concentration of ablated material, multiple ablation and analysis from a single section, and direct deposition on matrix-free nanostructured targets.

  20. Analysis of proteins using DIGE and MALDI mass spectrometry

    EPA Science Inventory

    In this work the sensitivity of the quantitative proteomics approach 2D-DIGE/MS (twoDimensional Difference Gel Electrophoresis / Mass Spectrometry) was tested by detecting decreasing amounts of a specific protein at the low picomole and sub-picomole range. Sensitivity of the 2D-D...

  1. Global Mass Spectrometry Based Metabolomics Profiling of Erythrocytes Infected with Plasmodium falciparum

    PubMed Central

    Sana, Theodore R.; Gordon, D. Benjamin; Fischer, Steven M.; Tichy, Shane E.; Kitagawa, Norton; Lai, Cindy; Gosnell, William L.; Chang, Sandra P.

    2013-01-01

    Malaria is a global infectious disease that threatens the lives of millions of people. Transcriptomics, proteomics and functional genomics studies, as well as sequencing of the Plasmodium falciparum and Homo sapiens genomes, have shed new light on this host-parasite relationship. Recent advances in accurate mass measurement mass spectrometry, sophisticated data analysis software, and availability of biological pathway databases, have converged to facilitate our global, untargeted biochemical profiling study of in vitro P. falciparum-infected (IRBC) and uninfected (NRBC) erythrocytes. In order to expand the number of detectable metabolites, several key analytical steps in our workflows were optimized. Untargeted and targeted data mining resulted in detection of over one thousand features or chemical entities. Untargeted features were annotated via matching to the METLIN metabolite database. For targeted data mining, we queried the data using a compound database derived from a metabolic reconstruction of the P. falciparum genome. In total, over one hundred and fifty differential annotated metabolites were observed. To corroborate the representation of known biochemical pathways from our data, an inferential pathway analysis strategy was used to map annotated metabolites onto the BioCyc pathway collection. This hypothesis-generating approach resulted in over-representation of many metabolites onto several IRBC pathways, most prominently glycolysis. In addition, components of the “branched” TCA cycle, partial urea cycle, and nucleotide, amino acid, chorismate, sphingolipid and fatty acid metabolism were found to be altered in IRBCs. Interestingly, we detected and confirmed elevated levels for cyclic ADP ribose and phosphoribosyl AMP in IRBCs, a novel observation. These metabolites may play a role in regulating the release of intracellular Ca2+ during P. falciparum infection. Our results support a strategy of global metabolite profiling by untargeted data

  2. Hadamard Transform Time-of-Flight Mass Spectrometry

    DTIC Science & Technology

    2010-01-26

    collisional activation is similar to the 11 more common collision - induced dissociation (CID), however in SID the...Hines, et al. (1993). "Low-mass ions produced from peptides by high- energy collision - induced dissociation in tandem mass spectrometry." Journal of the...biomolecules." Science 246(4926): 64-72. Galhena, A. S., S. Dagan, et al. (2008). "Surface- Induced Dissociation of Peptides and Protein Complexes in

  3. Accelerator mass spectrometry as a bioanalytical tool for nutritional research

    SciTech Connect

    Vogel, J.S.; Turteltaub, K.W.

    1997-09-01

    Accelerator Mass Spectrometry is a mass spectrometric method of detecting long-lived radioisotopes without regard to their decay products or half-life. The technique is normally applied to geochronology, but recently has been developed for bioanalytical tracing. AMS detects isotope concentrations to parts per quadrillion, quantifying labeled biochemicals to attomole levels in milligram- sized samples. Its advantages over non-isotopeic and stable isotope labeling methods are reviewed and examples of analytical integrity, sensitivity, specificity, and applicability are provided.

  4. Laser Mass Spectrometry in Planetary Science

    SciTech Connect

    Wurz, P.; Whitby, J. A.; Managadze, G. G.

    2009-06-16

    Knowing the chemical, elemental, and isotopic composition of planetary objects allows the study of their origin and evolution within the context of our solar system. Exploration plans in planetary research of several space agencies consider landing spacecraft for future missions. Although there have been successful landers in the past, more landers are foreseen for Mars and its moons, Venus, the jovian moons, and asteroids. Furthermore, a mass spectrometer on a landed spacecraft can assist in the sample selection in a sample-return mission and provide mineralogical context, or identify possible toxic soils on Mars for manned Mars exploration. Given the resources available on landed spacecraft mass spectrometers, as well as any other instrument, have to be highly miniaturised.

  5. Plasma source mass spectrometry in experimental nutrition.

    PubMed

    Barnes, R M

    1998-01-01

    The development and commercial availability of plasma ion source, specifically inductively coupled plasma, mass spectrometers (ICP-MS) have significantly extended the potential application of stable isotopes for nutritional modeling. The status of research and commercial ICP-MS instruments, and their applications and limitations for stable isotopic studies are reviewed. The consequences of mass spectroscopic resolution and measurement sensitivity obtainable with quadrupole, sector, time-of-flight, and trap instruments on stable isotope analysis are examined. Requirements for reliable isotope measurements with practical biological samples including tissues and fluids are considered. The possibility for stable isotope analysis in chemically separated compounds (speciation) also is explored. On-line compound separations by chromatography or electrophoresis, for example, have been combined instrumentally with ICP-MS. Som possibilities and requirements are described for stable isotope speciation analysis.

  6. Laser Mass Spectrometry in Planetary Science

    NASA Astrophysics Data System (ADS)

    Wurz, P.; Whitby, J. A.; Managadze, G. G.

    2009-06-01

    Knowing the chemical, elemental, and isotopic composition of planetary objects allows the study of their origin and evolution within the context of our solar system. Exploration plans in planetary research of several space agencies consider landing spacecraft for future missions. Although there have been successful landers in the past, more landers are foreseen for Mars and its moons, Venus, the jovian moons, and asteroids. Furthermore, a mass spectrometer on a landed spacecraft can assist in the sample selection in a sample-return mission and provide mineralogical context, or identify possible toxic soils on Mars for manned Mars exploration. Given the resources available on landed spacecraft mass spectrometers, as well as any other instrument, have to be highly miniaturised.

  7. Calcium isotope analysis by mass spectrometry.

    PubMed

    Boulyga, Sergei F

    2010-01-01

    The variations in the isotopic composition of calcium caused by fractionation in heterogeneous systems and by nuclear reactions can provide insight into numerous biological, geological, and cosmic processes, and therefore isotopic analysis finds a wide spectrum of applications in cosmo- and geochemistry, paleoclimatic, nutritional, and biomedical studies. The measurement of calcium isotopic abundances in natural samples has challenged the analysts for more than three decades. Practically all Ca isotopes suffer from significant isobaric interferences, whereas low-abundant isotopes can be particularly affected by neighboring major isotopes. The extent of natural variations of stable isotopes appears to be relatively limited, and highly precise techniques are required to resolve isotopic effects. Isotope fractionation during sample preparation and measurements and instrumental mass bias can significantly exceed small isotope abundance variations in samples, which have to be investigated. Not surprisingly, a TIMS procedure developed by Russell et al. (Russell et al., 1978. Geochim Cosmochim Acta 42: 1075-1090) for Ca isotope measurements was considered as revolutionary for isotopic measurements in general, and that approach is used nowadays (with small modifications) for practically all isotopic systems and with different mass spectrometric techniques. Nevertheless, despite several decades of calcium research and corresponding development of mass spectrometers, the available precision and accuracy is still not always sufficient to achieve the challenging goals. The present article discusses figures of merits of presently used analytical methods and instrumentation, and attempts to critically assess their limitations. In Sections 2 and 3, mass spectrometric methods applied to precise stable isotope analysis and to the determination of (41)Ca are described. Section 4 contains a short summary of selected applications, and includes tracer experiments and the potential use

  8. 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.

  9. [New mass spectrometry techniques applied to the study of venoms].

    PubMed

    Auvin-Guette, C

    2002-08-01

    Mass spectrometry is a technique for the analysis and very sensitive identification of molecules. It allows one to determine the mass of the studied product, whether pure or in a mixture, and provides some information on its molecular structure. In the particular case of peptides, this method can, under certain conditions, also provide information on the amino acid sequence. There are two complementary methods in mass spectrometry for the study of the biological molecules: i) ionisation by laser desorption assisted by matrix (MALDI) coupled to a mass analyser of the time of flight type (TOF), which is very effective for the direct study of a mixture of products and ii) ionisation by electronebulisation (ESI) coupled to mass analysers of the quadripolar type and time of flight (Qq-TOF), which allows the interfacing between high phase liquid chromatography and mass spectrometry. These two complementary techniques were already used to draw up toxin charts of snake and spider venoms. The purpose is to be able to characterise species based on an actual peptide print of poisonous gland secretions.

  10. 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…

  11. MASS SPECTROMETRY IMAGING FOR DRUGS AND METABOLITES

    PubMed Central

    Greer, Tyler; Sturm, Robert; Li, Lingjun

    2011-01-01

    Mass spectrometric imaging (MSI) is a powerful analytical technique that provides two- and three-dimensional spatial maps of multiple compounds in a single experiment. This technique has been routinely applied to protein, peptide, and lipid molecules with much less research reporting small molecule distributions, especially pharmaceutical drugs. This review’s main focus is to provide readers with an up-to-date description of the substrates and compounds that have been analyzed for drug and metabolite composition using MSI technology. Additionally, ionization techniques, sample preparation, and instrumentation developments are discussed. PMID:21515430

  12. Fermentation exhaust gas analysis using mass spectrometry

    SciTech Connect

    Buckland, B.; Brix, Fastert, H.; Gbewonyo, K.; Hunt, G.; Jain, D.

    1985-11-01

    A Perkin Elmer MGA-1200 mass spectrometer has been coupled with a mini-computer and a sampling manifold to analyze up to 8 components in the exhaust gases of fermentors. Carbon dioxide, oxygen, and nitrogen are typically analyzed, but ethanol for yeast fermentations can also be tested by heating the line from the fermentor to the sampling manifold. Specifications, operation, and performance of the system are described. The system has been used for process control, the study of fermentation kinetics, and process development. 8 references, 7 figures, 1 table.

  13. Capillary electrophoresis-mass spectrometry of carbohydrates

    PubMed Central

    Zaia, Joseph

    2014-01-01

    The development of methods for capillary electrophoresis (CE) with on-line mass spectrometric detection (CE/MS) is driven by the need for accurate, robust and sensitive glycomics analysis for basic biomedicine, biomarker discovery, and analysis of recombinant protein therapeutics. One important capability is to profile glycan mixtures with respect to the patterns of substituents including sialic acids, acetate, sulfate, phosphate, and other groups. There is additional need for an MS-compatible separation system capable of resolving carbohydrate isomers. This review summarizes applications of CS/MS to analysis of carbohydrates, glycoproteins and glycopeptides that have appeared since 2008. Readers are referred to recent comprehensive reviews covering earlier publications. PMID:23386333

  14. Capillary electrophoresis-mass spectrometry of carbohydrates.

    PubMed

    Zaia, Joseph

    2013-01-01

    The development of methods for capillary electrophoresis (CE) with on-line mass spectrometric detection (CE/MS) is driven by the need for accurate, robust, and sensitive glycomics analysis for basic biomedicine, biomarker discovery, and analysis of recombinant protein therapeutics. One important capability is to profile glycan mixtures with respect to the patterns of substituents including sialic acids, acetate, sulfate, phosphate, and other groups. There is additional need for an MS-compatible separation system capable of resolving carbohydrate isomers. This chapter summarizes applications of CS/MS to analysis of carbohydrates, glycoproteins, and glycopeptides that have appeared since 2008. Readers are referred to recent comprehensive reviews covering earlier publications.

  15. Early discovery drug screening using mass spectrometry.

    PubMed

    Siegel, Marshall M

    2002-01-01

    Electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) mass spectrometric methods useful for early discovery drug screening are reviewed. All methods described involve studies of non-covalent complexes between biopolymer receptors and small molecule ligands formed in the condensed phase. The complexes can be sprayed intact directly into the gas phase by ESI-MS using gentle experimental conditions. Gas phase screening applications are illustrated for drug ligand candidates non-covalently interacting with peptides, proteins, RNA, and DNA. In the condensed phase, the complexes can be also isolated, denatured and analyzed by ESI-MS to identify the small molecule ligands. Condensed phase drug screening examples are illustrated for the ESI-MS ancillary techniques of affinity chromatography, ultrafiltration, ultracentrifugation, gel permeation chromatography (GPC), reverse phase-high performance liquid chromatography (RP-HPLC) and capillary electrophoretic methods. Solid phase drug screening using MALDI-MS is illustrated for small molecule ligands bound to MALDI affinity probe tips and to beads. Since ESI and MALDI principally produce molecular ions, high throughput screening is achieved by analyzing mass indexed mixtures.

  16. Analysis of Milk Oligosaccharides by Mass Spectrometry.

    PubMed

    Wu, Lauren D; Ruhaak, L Renee; Lebrilla, Carlito B

    2017-01-01

    Human milk oligosaccharides (HMOs) are a highly abundant constituent in human milk, and its protective and prebiotic properties have attracted considerable attention. HMOs have been shown to directly and indirectly benefit the overall health of the infant due to a number of functions including serving as a beneficial food for gut bacteria, block to pathogens, and aiding in brain development. Researchers are currently exploring whether these structures may act as possible disease and nutrition biomarkers. Because of this, rapid-throughput methods are desired to investigate biological activity in large patient sets. We have optimized a rapid-throughput protocol to analyze human milk oligosaccharides using micro-volumes of human breast milk for nutritional biomarkers. This method may additionally be applied to other biological fluid substrates such as plasma, urine, and feces. The protocol involves lipid separation via centrifugation, protein precipitation using ethanol, alditol reduction with sodium borohydride, and a final solid-phase extraction purification step using graphitized carbon cartridges. Samples are analyzed using HPLC-Chip/TOF-MS and data filtered on Agilent MassHunter using an in-house library. Individual structural identification is matched against a previously developed HMO library using accurate mass and retention time. Using this method will allow in-depth characterization and profiling of HMOs in large patient sets, and will ease the process of discovering significant nutritional biomarkers in human milk.

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

    SciTech Connect

    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/MS 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.

  18. Complete Hexose Isomer Identification with Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Nagy, Gabe; Pohl, Nicola L. B.

    2015-04-01

    The first analytical method is presented for the identification and absolute configuration determination of all 24 aldohexose and 2-ketohexose isomers, including the D and L enantiomers for allose, altrose, galactose, glucose, gulose, idose, mannose, talose, fructose, psicose, sorbose, and tagatose. Two unique fixed ligand kinetic method combinations were discovered to create significant enough energetic differences to achieve chiral discrimination among all 24 hexoses. Each of these 24 hexoses yields unique ratios of a specific pair of fragment ions that allows for simultaneous determination of identification and absolute configuration. This mass spectrometric-based methodology can be readily employed for accurate identification of any isolated monosaccharide from an unknown biological source. This work provides a key step towards the goal of complete de novo carbohydrate analysis.

  19. Advances in structure elucidation of small molecules using mass spectrometry

    PubMed Central

    Fiehn, Oliver

    2010-01-01

    The structural elucidation of small molecules using mass spectrometry plays an important role in modern life sciences and bioanalytical approaches. This review covers different soft and hard ionization techniques and figures of merit for modern mass spectrometers, such as mass resolving power, mass accuracy, isotopic abundance accuracy, accurate mass multiple-stage MS(n) capability, as well as hybrid mass spectrometric and orthogonal chromatographic approaches. The latter part discusses mass spectral data handling strategies, which includes background and noise subtraction, adduct formation and detection, charge state determination, accurate mass measurements, elemental composition determinations, and complex data-dependent setups with ion maps and ion trees. The importance of mass spectral library search algorithms for tandem mass spectra and multiple-stage MS(n) mass spectra as well as mass spectral tree libraries that combine multiple-stage mass spectra are outlined. The successive chapter discusses mass spectral fragmentation pathways, biotransformation reactions and drug metabolism studies, the mass spectral simulation and generation of in silico mass spectra, expert systems for mass spectral interpretation, and the use of computational chemistry to explain gas-phase phenomena. A single chapter discusses data handling for hyphenated approaches including mass spectral deconvolution for clean mass spectra, cheminformatics approaches and structure retention relationships, and retention index predictions for gas and liquid chromatography. The last section reviews the current state of electronic data sharing of mass spectra and discusses the importance of software development for the advancement of structure elucidation of small molecules. Electronic supplementary material The online version of this article (doi:10.1007/s12566-010-0015-9) contains supplementary material, which is available to authorized users. PMID:21289855

  20. Estimating the Efficiency of Phosphopeptide Identification by Tandem Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Hsu, Chuan-Chih; Xue, Liang; Arrington, Justine V.; Wang, Pengcheng; Paez Paez, Juan Sebastian; Zhou, Yuan; Zhu, Jian-Kang; Tao, W. Andy

    2017-03-01

    Mass spectrometry has played a significant role in the identification of unknown phosphoproteins and sites of phosphorylation in biological samples. Analyses of protein phosphorylation, particularly large scale phosphoproteomic experiments, have recently been enhanced by efficient enrichment, fast and accurate instrumentation, and better software, but challenges remain because of the low stoichiometry of phosphorylation and poor phosphopeptide ionization efficiency and fragmentation due to neutral loss. Phosphoproteomics has become an important dimension in systems biology studies, and it is essential to have efficient analytical tools to cover a broad range of signaling events. To evaluate current mass spectrometric performance, we present here a novel method to estimate the efficiency of phosphopeptide identification by tandem mass spectrometry. Phosphopeptides were directly isolated from whole plant cell extracts, dephosphorylated, and then incubated with one of three purified kinases—casein kinase II, mitogen-activated protein kinase 6, and SNF-related protein kinase 2.6—along with 16O4- and 18O4-ATP separately for in vitro kinase reactions. Phosphopeptides were enriched and analyzed by LC-MS. The phosphopeptide identification rate was estimated by comparing phosphopeptides identified by tandem mass spectrometry with phosphopeptide pairs generated by stable isotope labeled kinase reactions. Overall, we found that current high speed and high accuracy mass spectrometers can only identify 20%-40% of total phosphopeptides primarily due to relatively poor fragmentation, additional modifications, and low abundance, highlighting the urgent need for continuous efforts to improve phosphopeptide identification efficiency.

  1. Identification of metabolites of hexazinone by mass spectrometry.

    PubMed

    Reiser, R W; Belasco, I J; Rhodes, R C

    1983-11-01

    The metabolites of hexazinone [3-cyclohexyl-6-(dimethylamino)-1-methyl-1,3,5-triazine-2,4(1H,3H)-dione ] obtained in the rat and in plants were identified by mass spectrometry. Rat urine metabolites were identified from direct probe spectra obtained on metabolites separated by thin-layer chromatography. Sugarcane metabolites were identified by gas chromatography mass spectrometry of the trimethylsilyl derivatives. The major metabolic routes were found to be hydroxylation of the cyclohexyl group and demethylation. All identifications were confirmed by synthesis and direct comparison of chromatographic data and mass spectra. Hexazinone is metabolized quickly and extensively in the biological systems studied, and is relatively nonpersistent in the environment.

  2. Recent developments in Penning-trap mass spectrometry

    NASA Astrophysics Data System (ADS)

    Block, M.

    2016-06-01

    Penning-trap mass spectrometry provides atomic masses with the highest precision. At accelerator-based on-line facilities it is applied to investigate exotic radionuclides in the context of tests of fundamental symmetries, nuclear structure studies, and nuclear astrophysics research. Recent progress in slowing down radioactive ion-beams in buffer-gas cells in combination with advanced ion-manipulation techniques has paved the way to reach nuclides ever-more far from stability. In this endeavor many efforts are underway to increase the sensitivity, the efficiency, and the precision of Penning-trap mass spectrometry. In this article some recent experimental developments are addressed with the focus on the phase-imaging ion-cyclotron-resonance technique and the Fourier transform ion-cyclotron-resonance technique.

  3. Determination of 135Cs by accelerator mass spectrometry

    NASA Astrophysics Data System (ADS)

    MacDonald, C. M.; Charles, C. R. J.; Zhao, X.-L.; Kieser, W. E.; Cornett, R. J.; Litherland, A. E.

    2015-10-01

    The ratio of anthropogenic 135Cs and 137Cs isotopes is characteristic of a uranium fission source. This research evaluates the technique of isotope dilution (yield tracing) for the purpose of quantifying 135Cs by accelerator mass spectrometry with on-line isobar separation. Interferences from Ba, Zn2, and isotopes of equal mass to charge ratios were successfully suppressed. However, some sample crosstalk from source contamination remains. The transmission and di-fluoride ionization efficiencies of Cs isotopes were found to be 8 × 10-3 and 1.7 × 10-7 respectively. This quantification of 135Cs using yield tracing by accelerator mass spectrometry shows promise for future environmental sample analysis once the issues of sample crosstalk and low efficiency can be resolved.

  4. Electrochemistry-mass spectrometry in drug metabolism and protein research.

    PubMed

    Permentier, Hjalmar P; Bruins, Andries P; Bischoff, Rainer

    2008-01-01

    The combination of electrochemistry coupled on-line to mass spectrometry (EC-MS) forms a powerful analytical technique with unique applications in the fields of drug metabolism and proteomics. In this review the latest developments are surveyed from both instrumental and application perspectives. The limitations and solutions for coupling an electrochemical system to a mass spectrometer are discussed. The electrochemical mimicking of drug metabolism, specifically by Cytochrome P450, is high-lighted as an application with high biomedical relevance. The EC-MS analysis of proteins also has promising new applications for both proteomics research and biomarker discovery. EC-MS has furthermore advantages for improved analyte detection with mass spectrometry, both for small molecules and large biomolecules. Finally, potential future directions of development of the technique are briefly discussed.

  5. Trends in biochemical and biomedical applications of mass spectrometry

    NASA Astrophysics Data System (ADS)

    Gelpi, Emilio

    1992-09-01

    This review attempts an in-depth evaluation of progress and achievements made since the last 11th International Mass Spectrometry Conference in the application of mass spectrometric techniques to biochemistry and biomedicine. For this purpose, scientific contributions in this field at major international meetings have been monitored, together with an extensive appraisal of literature data covering the period from 1988 to 1991. A bibliometric evaluation of the MEDLINE database for this period provides a total of almost 4000 entries for mass spectrometry. This allows a detailed study of literature and geographical sources of the most frequent applications, of disciplines where mass spectrometry is most active and of types of sample and instrumentation most commonly used. In this regard major efforts according to number of publications (over 100 literature reports) are concentrated in countries like Canada, France, Germany, Italy, Japan, Sweden, UK and the USA. Also, most of the work using mass spectrometry in biochemistry and biomedicine is centred on studies on biotransformation, metabolism, pharmacology, pharmacokinetics and toxicology, which have been carried out on samples of blood, urine, plasma and tissue, by order of frequency of use. Human and animal studies appear to be evenly distributed in terms of the number of reports published in the literature in which the authors make use of experimental animals or describe work on human samples. Along these lines, special attention is given to the real usefulness of mass spectrometry (MS) technology in routine medical practice. Thus the review concentrates on evaluating the progress made in disease diagnosis and overall patient care. As regards prevailing techniques, GCMS continues to be the mainstay of the state of the art methods for multicomponent analysis, stable isotope tracer studies and metabolic profiling, while HPLC--MS and tandem MS are becoming increasingly important in biomedical research. However

  6. Microscale mass spectrometry systems, devices and related methods

    DOEpatents

    Ramsey, John Michael

    2016-06-21

    Mass spectrometry systems or assemblies therefore include an ionizer that includes at least one planar conductor, a mass analyzer with a planar electrode assembly, and a detector comprising at least one planar conductor. The ionizer, the mass analyzer and the detector are attached together in a compact stack assembly. The stack assembly has a perimeter that bounds an area that is between about 0.01 mm.sup.2 to about 25 cm.sup.2 and the stack assembly has a thickness that is between about 0.1 mm to about 25 mm.

  7. An introduction to quadrupole-time-of-flight mass spectrometry.

    PubMed

    Chernushevich, I V; Loboda, A V; Thomson, B A

    2001-08-01

    A brief introduction is presented to the basic principles and application of a quadrupole-time-of-flight (TOF) tandem mass spectrometer. The main features of reflecting TOF instruments with orthogonal injection of ions are discussed. Their operation and performance are compared with those of triple quadrupoles with electrospray ionization and matrix-assisted laser desorption/ionization (MALDI) TOF mass spectrometers. Examples and recommendations are provided for all major operational modes: mass spectrometry (MS) and tandem MS (MS/MS), precursor ion scans and studies of non-covalent complexes. Basic algorithms for liquid chromatography/MS/MS automation are discussed and illustrated by two applications.

  8. Rapid discrimination of bacteria by paper spray mass spectrometry.

    PubMed

    Hamid, Ahmed M; Jarmusch, Alan K; Pirro, Valentina; Pincus, David H; Clay, Bradford G; Gervasi, Gaspard; Cooks, R Graham

    2014-08-05

    Paper spray mass spectrometry ambient ionization is utilized for rapid discrimination of bacteria without sample preparation. Bacterial colonies were smeared onto filter paper precut to a sharp point, then wetted with solvent and held at a high potential. Charged droplets released by field emission were sucked into the mass spectrometer inlet and mass spectra were recorded. Sixteen different species representing eight different genera from Gram-positive and Gram-negative bacteria were investigated. Phospholipids were the predominant species observed in the mass spectra in both the negative and positive ion modes. Multivariate data analysis based on principal component analysis, followed by linear discriminant analysis, allowed bacterial discrimination. The lipid information in the negative ion mass spectra proved useful for species level differentiation of the investigated Gram-positive bacteria. Gram-negative bacteria were differentiated at the species level by using a numerical data fusion strategy of positive and negative ion mass spectra.

  9. Small system for tritium accelerator mass spectrometry

    DOEpatents

    Roberts, Mark L.; Davis, Jay C.

    1993-01-01

    Apparatus for ionizing and accelerating a sample containing isotopes of hydrogen and detecting the ratios of hydrogen isotopes contained in the sample is disclosed. An ion source generates a substantially linear ion beam including ions of tritium from the sample. A radio-frequency quadrupole accelerator is directly coupled to and axially aligned with the source at an angle of substantially zero degrees. The accelerator accelerates species of the sample having different mass to different energy levels along the same axis as the ion beam. A spectrometer is used to detect the concentration of tritium ions in the sample. In one form of the invention, an energy loss spectrometer is used which includes a foil to block the passage of hydrogen, deuterium and .sup.3 He ions, and a surface barrier or scintillation detector to detect the concentration of tritium ions. In another form of the invention, a combined momentum/energy loss spectrometer is used which includes a magnet to separate the ion beams, with Faraday cups to measure the hydrogen and deuterium and a surface barrier or scintillation detector for the tritium ions.

  10. Small system for tritium accelerator mass spectrometry

    DOEpatents

    Roberts, M.L.; Davis, J.C.

    1993-02-23

    Apparatus for ionizing and accelerating a sample containing isotopes of hydrogen and detecting the ratios of hydrogen isotopes contained in the sample is disclosed. An ion source generates a substantially linear ion beam including ions of tritium from the sample. A radio-frequency quadrupole accelerator is directly coupled to and axially aligned with the source at an angle of substantially zero degrees. The accelerator accelerates species of the sample having different mass to different energy levels along the same axis as the ion beam. A spectrometer is used to detect the concentration of tritium ions in the sample. In one form of the invention, an energy loss spectrometer is used which includes a foil to block the passage of hydrogen, deuterium and [sup 3]He ions, and a surface barrier or scintillation detector to detect the concentration of tritium ions. In another form of the invention, a combined momentum/energy loss spectrometer is used which includes a magnet to separate the ion beams, with Faraday cups to measure the hydrogen and deuterium and a surface barrier or scintillation detector for the tritium ions.

  11. "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...

  12. 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 ...

  13. The role of ion mobility spectrometry-mass spectrometry in the analysis of protein reference standards.

    PubMed

    Pritchard, Caroline; O'Connor, Gavin; Ashcroft, Alison E

    2013-08-06

    To achieve comparability of measurement results of protein amount of substance content between clinical laboratories, suitable reference materials are required. The impact on measurement comparability of potential differences in the tertiary and quaternary structure of protein reference standards is as yet not well understood. With the use of human growth hormone as a model protein, the potential of ion mobility spectrometry-mass spectrometry as a tool to assess differences in the structure of protein reference materials and their interactions with antibodies has been investigated here.

  14. Electrospray Ionization Mass Spectrometry of hexanitrohexaazaisowurtzitane (CL-20)

    SciTech Connect

    Campbell, James A.; Szecsody, Jim E.; Devary, Brooks J.; Valenzuela, Blandina R.

    2007-09-03

    Hexanitrohexaazaisowurtzitane, (C6H6N12O12, MW 438) {CL-20}, is a high-energy propellent that has been recently developed and successfully tested (Nielsen et al. 1998). CL-20 releases more energy on ignition and is more stable to accidental detonation than currently used energetic materials. It is expected to replace many of the energetic materials currently being used by the Department of Defense (DoD). The EPA method 8330 (EPA 1997) for the analysis of explosives and metabolites in soils calls for the use of UV/Vis detection. High performance liquid chromatography has been used to quantify CL-20 and precursor concentration (Bazaki et al. 1998`) at relatively high concentrations. Fourier transform infrared (FTIR) spectroscopy has been used to identify different crystal forms of CL-20 (4 isomers; Kim et al. 1998). Campbell et al. (1997) utilized particle beam mass spectrometry for the analysis of enzymatic degradation of explosives. Introduction and recent improvements of ionization techniques such as electrospray (ES) have allowed the mass spectrometer to become more widely used in liquid chromatography. Schilling(1996) also examined explosive components and metabolites using electrospray (ES) and atmospheric pressure chemical ionization (APCI) liquid chromatography/mass spectrometry (LC/MS). Schilling’s results showed that compared to thermospray LC/MS, APCI and ES were more sensitive than thermospray by at least an order of magnitude. 1,3,5-trinitro-1,3,5-triazacyclohexane (RDX), 10 nitroso-RDX metabolites, and other munitions in ground water have been analyzed using solid phase extraction and isotope dilution liquid chromatography-APCI mass spectrometry (Cassada et al. 1999). The method detection limits indicate that nitramine and nitroaromatic compounds can be routinely determined in ground water samples using electrospray LC/MS with concentration techniques utilizing solid-phase extraction. Miller et al. (1996) studied nitrated explosives with mobile phase

  15. Characterization of Bacteria by Particle Beam Mass Spectrometry

    PubMed Central

    Sinha, Mahadeva P.; Platz, Robert M.; Friedlander, Sheldon K.; Vilker, Vincent L.

    1985-01-01

    A technique is described for detecting and characterizing bacteria on a single-particle basis by mass spectrometry. The method involves generation of a particle beam of single whole cells which are rapidly volatilized and ionized in vacuum in the ion source of a quadrupole mass spectrometer. The particle beam can be generated, with minimal sample handling, from a naturally occurring aerosol or from a solution of bacteria that can be dispersed as an aerosol. The mass spectrum is generated by successively measuring the average intensities of different mass peaks. The average intensity is obtained by measuring the ion intensity distribution at the particular mass (m/e) for ion pulses from more than 1,000 bacteria particles. Bacillus cereus, Bacillus subtilis, and Pseudomonas putida samples were analyzed to test the capability of the instrument for differentiating among species of bacteria. Significant ion-intensity information was produced over the m/e range of 50 to 300, an improvement over previous pyrolysis-mass spectrometry results. The complex mass spectra contained a few unique peaks which could be used for the differentiation of the bacteria. A statistical analysis of the variations in peak intensities among the three bacteria provided a quantitative measure of the reproducibility of the instrument and its ability to differentiate among bacteria. The technique could lead to a new rapid method for the analysis of microorganisms and could be used for the detection of airborne pathogens on a continuous, real-time basis. Images PMID:16346802

  16. 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.

  17. Cortisol production rates measured by liquid chromatography/mass spectrometry

    SciTech Connect

    Esteban, N.V.; Yergey, A.L. )

    1990-04-01

    Cortisol production rates (FPRs) in physiologic and pathologic states in humans have been investigated over the past 30 years. However, there has been conflicting evidence concerning the validity of the currently accepted value of FPRs in humans (12 to 15 mg/m2/d) as determined by radiotracer methodology. The present study reviews previous methods proposed for the measurement of FPRs in humans and discusses the applications of the first method for the direct determination of 24-hour plasma FPRs during continuous administration of a stable isotope, using a thermospray high-pressure liquid chromatography-mass spectrometry technique. The technique is fast, sensitive, and, unlike gas chromatography-mass spectrometry methods, does not require derivatization, allowing on-line detection and quantification of plasma cortisol after a simple extraction procedure. The results of determination of plasma FPRs by stable tracer/mass spectrometry are directly in units of mass/time and, unlike radiotracer methods, are independent of any determination of volume of distribution or cortisol concentration. Our methodology offers distinct advantages over radiotracer techniques in simplicity and reliability since only single measurements of isotope ratios are required. The technique was validated in adrenalectomized patients. Circadian variations in daily FRPs were observed in normal volunteers, and, to date, results suggest a lower FRP in normal children and adults than previously believed. 88 references.

  18. DNA analysis by MALDI-TOF mass spectrometry.

    PubMed

    Gut, Ivo Glynne

    2004-05-01

    The last decade has seen an increased demand for high-throughput DNA analysis. This is mainly due to the human genome sequencing project that is now completed. Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry was pinpointed early on as a technology that could be of great use for sequence variation analysis in the post-genome sequencing era. Applications developed first on this platform were for SNP genotyping. Several strategies for allele-discrimination (hybridization, cleavage, ligation, and primer extension) were combined with MALDI-TOF mass spectrometric detection. Nowadays, in practice, only primer extension methods are applied for large-scale SNP genotyping studies with MALDI-TOF detection. Problems surrounding the integration of SNP genotyping by MALDI-TOF mass spectrometry at high throughput are largely mastered now. Mass spectrometry geared presentations at the HUGO Mutation Detection Meeting in Palm Cove, Australia almost exclusively focused on novel applications that go beyond standard SNP genotyping. These applications are more demanding in terms of chemistry and molecular biology. Molecular haplotyping, expression profiling, DNA methylation analysis, and mutation detection are now being demonstrated.

  19. Identification of carbohydrate anomers using ion mobility-mass spectrometry

    NASA Astrophysics Data System (ADS)

    Hofmann, J.; Hahm, H. S.; Seeberger, P. H.; Pagel, K.

    2015-10-01

    Carbohydrates are ubiquitous biological polymers that are important in a broad range of biological processes. However, owing to their branched structures and the presence of stereogenic centres at each glycosidic linkage between monomers, carbohydrates are harder to characterize than are peptides and oligonucleotides. Methods such as nuclear magnetic resonance spectroscopy can be used to characterize glycosidic linkages, but this technique requires milligram amounts of material and cannot detect small amounts of coexisting isomers. Mass spectrometry, on the other hand, can provide information on carbohydrate composition and connectivity for even small amounts of sample, but it cannot be used to distinguish between stereoisomers. Here, we demonstrate that ion mobility-mass spectrometry--a method that separates molecules according to their mass, charge, size, and shape--can unambiguously identify carbohydrate linkage-isomers and stereoisomers. We analysed six synthetic carbohydrate isomers that differ in composition, connectivity, or configuration. Our data show that coexisting carbohydrate isomers can be identified, and relative concentrations of the minor isomer as low as 0.1 per cent can be detected. In addition, the analysis is rapid, and requires no derivatization and only small amounts of sample. These results indicate that ion mobility-mass spectrometry is an effective tool for the analysis of complex carbohydrates. This method could have an impact on the field of carbohydrate synthesis similar to that of the advent of high-performance liquid chromatography on the field of peptide assembly in the late 1970s.

  20. Advances in 193 nm excimer lasers for mass spectrometry applications

    NASA Astrophysics Data System (ADS)

    Delmdahl, Ralph; Esser, Hans-Gerd; Bonati, Guido

    2016-03-01

    Ongoing progress in mass analysis applications such as laser ablation inductively coupled mass spectrometry of solid samples and ultraviolet photoionization mediated sequencing of peptides and proteins is to a large extent driven by ultrashort wavelength excimer lasers at 193 nm. This paper will introduce the latest improvements achieved in the development of compact high repetition rate excimer lasers and elaborate on the impact on mass spectrometry instrumentation. Various performance and lifetime measurements obtained in a long-term endurance test over the course of 18 months will be shown and discussed in view of the laser source requirements of different mass spectrometry tasks. These sampling type applications are served by excimer lasers delivering pulsed 193 nm output of several mJ as well as fast repetition rates which are already approaching one Kilohertz. In order to open up the pathway from the laboratory to broader market industrial use, sufficient component lifetimes and long-term stable performance behavior have to be ensured. The obtained long-term results which will be presented are based on diverse 193 nm excimer laser tube improvements aiming at e.g. optimizing the gas flow dynamics and have extended the operational life the laser tube for the first time over several billion pulses even under high duty-cycle conditions.

  1. Suspected-target pesticide screening using gas chromatography-quadrupole time-of-flight mass spectrometry with high resolution deconvolution and retention index/mass spectrum library.

    PubMed

    Zhang, Fang; Wang, Haoyang; Zhang, Li; Zhang, Jing; Fan, Ruojing; Yu, Chongtian; Wang, Wenwen; Guo, Yinlong

    2014-10-01

    A strategy for suspected-target screening of pesticide residues in complicated matrices was exploited using gas chromatography in combination with hybrid quadrupole time-of-flight mass spectrometry (GC-QTOF MS). The screening workflow followed three key steps of, initial detection, preliminary identification, and final confirmation. The initial detection of components in a matrix was done by a high resolution mass spectrum deconvolution; the preliminary identification of suspected pesticides was based on a special retention index/mass spectrum (RI/MS) library that contained both the first-stage mass spectra (MS(1) spectra) and retention indices; and the final confirmation was accomplished by accurate mass measurements of representative ions with their response ratios from the MS(1) spectra or representative product ions from the second-stage mass spectra (MS(2) spectra). To evaluate the applicability of the workflow in real samples, three matrices of apple, spinach, and scallion, each spiked with 165 test pesticides in a set of concentrations, were selected as the models. The results showed that the use of high-resolution TOF enabled effective extractions of spectra from noisy chromatograms, which was based on a narrow mass window (5 mDa) and suspected-target compounds identified by the similarity match of deconvoluted full mass spectra and filtering of linear RIs. On average, over 74% of pesticides at 50 ng/mL could be identified using deconvolution and the RI/MS library. Over 80% of pesticides at 5 ng/mL or lower concentrations could be confirmed in each matrix using at least two representative ions with their response ratios from the MS(1) spectra. In addition, the application of product ion spectra was capable of confirming suspected pesticides with specificity for some pesticides in complicated matrices. In conclusion, GC-QTOF MS combined with the RI/MS library seems to be one of the most efficient tools for the analysis of suspected-target pesticide residues

  2. New Types of Ionization Sources for Mass Spectrometry

    SciTech Connect

    2008-12-01

    The purpose of this Cooperative Research and Development Agreement (CRADA) between UT-Battelle (Contractor) and MDS Sciex (Participant) and ESA, Inc. (Participant) is to research, develop and apply new types of ionization sources and sampling/inlet systems for analytical mass spectrometry making use of the Participants state-of-the-art atmospheric sampling mass spectrometry electrochemical cell technology instrumentation and ancillary equipment. The two overriding goals of this research project are: to understand the relationship among the various instrumental components and operational parameters of the various ion sources and inlet systems under study, the chemical nature of the gases, solvents, and analytes in use, and the nature and abundances of the ions ultimately observed in the mass spectrometer; and to develop new and better analytical and fundamental applications of these ion sources and inlet systems or alternative sources and inlets coupled with mass spectrometry on the basis of the fundamental understanding obtained in Goal 1. The end results of this work are expected to be: (1) an expanded utility for the ion sources and inlet systems under study (such as the analysis of new types of analytes) and the control or alteration of the ionic species observed in the gas-phase; (2) enhanced instrument performance as judged by operational figures-of-merit such as dynamic range, detection limits, susceptibility to matrix signal suppression and sensitivity; and (3) novel applications (such as surface sampling with electrospray) in both applied and fundamental studies. The research projects outlined herein build upon work initiated under the previous CRADA between the Contractor and MDS Sciex on ion sources and inlet systems for mass spectrometry. Specific ion source and inlet systems for exploration of the fundamental properties and practical implementation of these principles are given.

  3. Utility of Ion Mobility Mass Spectrometry for Drug-to-Antibody Ratio Measurements in Antibody-Drug Conjugates

    NASA Astrophysics Data System (ADS)

    Huang, Richard Y.-C.; Deyanova, Ekaterina G.; Passmore, David; Rangan, Vangipuram; Deshpande, Shrikant; Tymiak, Adrienne A.; Chen, Guodong

    2015-06-01

    Antibody-drug conjugates (ADCs) are emerging modalities in the pharmaceutical industry. Characterization of ADC's drug-to-antibody ratio (DAR) becomes a key assessment because of its importance in ADC efficacy and safety. DAR characterization by conventional intact protein MS analysis, however, is challenging because of high heterogeneity of ADC samples. The analysis often requires protein deglycosylation, disulfide-bond reduction, or partial fragmentation. In this study, we illustrate the practical utility of ion mobility mass spectrometry (IM-MS) in a routine LC/MS workflow for DAR measurements. This strategy allows analyte "cleanup" in the gas phase, providing significant improvement of signal-to-noise ratios of ADC intact mass spectra for accurate DAR measurements. In addition, protein drift time analysis offers a new dimension in monitoring the changes of DAR in lot-to-lot analysis.

  4. Distinguishing between the metabolome and xenobiotic exposome in environmental field samples analysed by direct-infusion mass spectrometry based metabolomics and lipidomics.

    PubMed

    Southam, Andrew D; Lange, Anke; Al-Salhi, Raghad; Hill, Elizabeth M; Tyler, Charles R; Viant, Mark R

    2014-01-01

    Environmental metabolomics is increasingly used to investigate organismal responses to complex chemical mixtures, including waste water effluent (WWE). In parallel, increasingly sensitive analytical methods are being used in metabolomics studies, particularly mass spectrometry. This introduces a considerable, yet overlooked, challenge that high analytical sensitivity will not only improve the detection of endogenous metabolites in biological specimens but also exogenous chemicals. If these often unknown xenobiotic features are not removed from the "biological" dataset, they will bias the interpretation and could lead to incorrect conclusions about the biotic response. Here we illustrate and validate a novel workflow classifying the origin of peaks detected in biological samples as: endogenous, xenobiotics, or metabolised xenobiotics. The workflow is demonstrated using direct infusion mass spectrometry-based metabolomic analysis of testes from roach exposed to different concentrations of a complex WWE. We show that xenobiotics and their metabolic products can be detected in roach testes (including triclosan, chloroxylenol and chlorophene), and that these compounds have a disproportionately high level of statistical significance within the total (bio)chemical changes induced by the WWE. Overall we have demonstrated that this workflow extracts more information from an environmental metabolomics study of complex mixture exposures than was possible previously.

  5. Quantification of proteins in urine samples using targeted mass spectrometry methods.

    PubMed

    Khristenko, Nina; Domon, Bruno

    2015-01-01

    Numerous clinical proteomics studies are focused on the development of biomarkers to improve either diagnostics for early disease detection or the monitoring of the response to the treatment. Although, a wealth of biomarker candidates are available, their evaluation and validation in a true clinical setup remains challenging. In biomarkers evaluation studies, a panel of proteins of interest are systematically analyzed in a large cohort of samples. However, in spite of the latest progresses in mass spectrometry, the consistent detection of pertinent proteins in high complex biological samples is still a challenging task. Thus, targeted LC-MS/MS methods are better suited for the systematic analysis of biomarkers rather than shotgun approaches. This chapter describes the workflow used to perform targeted quantitative analyses of proteins in urinary samples. The peptides, as surrogates of the protein of interest, are commonly measured using a triple quadrupole mass spectrometers operated in selected reaction monitoring (SRM) mode. More recently, the advances in targeted LC-MS/MS analysis based on parallel reaction monitoring (PRM) performed on a quadrupole-orbitrap instrument have allowed to increase the specificity and selectivity of the measurements.

  6. Characterization and identification of clinically relevant microorganisms using rapid evaporative ionization mass spectrometry.

    PubMed

    Strittmatter, Nicole; Rebec, Monica; Jones, Emrys A; Golf, Ottmar; Abdolrasouli, Alireza; Balog, Julia; Behrends, Volker; Veselkov, Kirill A; Takats, Zoltan

    2014-07-01

    Rapid evaporative ionization mass spectrometry (REIMS) was investigated for its suitability as a general identification system for bacteria and fungi. Strains of 28 clinically relevant bacterial species were analyzed in negative ion mode, and corresponding data was subjected to unsupervised and supervised multivariate statistical analyses. The created supervised model yielded correct cross-validation results of 95.9%, 97.8%, and 100% on species, genus, and Gram-stain level, respectively. These results were not affected by the resolution of the mass spectral data. Blind identification tests were performed for strains cultured on different culture media and analyzed using different instrumental platforms which led to 97.8-100% correct identification. Seven different Escherichia coli strains were subjected to different culture conditions and were distinguishable with 88% accuracy. In addition, the technique proved suitable to distinguish five pathogenic Candida species with 98.8% accuracy without any further modification to the experimental workflow. These results prove that REIMS is sufficiently specific to serve as a culture condition-independent tool for the identification and characterization of microorganisms.

  7. Advances in liquid chromatography-high-resolution mass spectrometry for quantitative and qualitative environmental analysis.

    PubMed

    Aceña, Jaume; Stampachiacchiere, Serena; Pérez, Sandra; Barceló, Damià

    2015-08-01

    This review summarizes the advances in environmental analysis by liquid chromatography-high-resolution mass spectrometry (LC-HRMS) during the last decade and discusses different aspects of their application. LC-HRMS has become a powerful tool for simultaneous quantitative and qualitative analysis of organic pollutants, enabling their quantitation and the search for metabolites and transformation products or the detection of unknown compounds. LC-HRMS provides more information than low-resolution (LR) MS for each sample because it can accurately determine the mass of the molecular ion and its fragment ions if it can be used for MS-MS. Another advantage is that the data can be processed using either target analysis, suspect screening, retrospective analysis, or non-target screening. With the growing popularity and acceptance of HRMS analysis, current guidelines for compound confirmation need to be revised for quantitative and qualitative purposes. Furthermore, new commercial software and user-built libraries are required to mine data in an efficient and comprehensive way. The scope of this critical review is not to provide a comprehensive overview of the many studies performed with LC-HRMS in the field of environmental analysis, but to reveal its advantages and limitations using different workflows.

  8. Peakbin selection in mass spectrometry data using a consensus approach with estimation of distribution algorithms.

    PubMed

    Armañanzas, Rubén; Saeys, Yvan; Inza, Iñaki; García-Torres, Miguel; Bielza, Concha; van de Peer, Yves; Larrañaga, Pedro

    2011-01-01

    Progress is continuously being made in the quest for stable biomarkers linked to complex diseases. Mass spectrometers are one of the devices for tackling this problem. The data profiles they produce are noisy and unstable. In these profiles, biomarkers are detected as signal regions (peaks), where control and disease samples behave differently. Mass spectrometry (MS) data generally contain a limited number of samples described by a high number of features. In this work, we present a novel class of evolutionary algorithms, estimation of distribution algorithms (EDA), as an efficient peak selector in this MS domain. There is a trade-of f between the reliability of the detected biomarkers and the low number of samples for analysis. For this reason, we introduce a consensus approach, built upon the classical EDA scheme, that improves stability and robustness of the final set of relevant peaks. An entire data workflow is designed to yield unbiased results. Four publicly available MS data sets (two MALDI-TOF and another two SELDI-TOF) are analyzed. The results are compared to the original works, and a new plot (peak frequential plot) for graphically inspecting the relevant peaks is introduced. A complete online supplementary page, which can be found at http://www.sc.ehu.es/ccwbayes/members/ruben/ms, includes extended info and results, in addition to Matlab scripts and references.

  9. 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…

  10. Fourier Transform Mass Spectrometry: The Transformation of Modern Environmental Analyses

    PubMed Central

    Lim, Lucy; Yan, Fangzhi; Bach, Stephen; Pihakari, Katianna; Klein, David

    2016-01-01

    Unknown compounds in environmental samples are difficult to identify using standard mass spectrometric methods. Fourier transform mass spectrometry (FTMS) has revolutionized how environmental analyses are performed. With its unsurpassed mass accuracy, high resolution and sensitivity, researchers now have a tool for difficult and complex environmental analyses. Two features of FTMS are responsible for changing the face of how complex analyses are accomplished. First is the ability to quickly and with high mass accuracy determine the presence of unknown chemical residues in samples. For years, the field has been limited by mass spectrometric methods that were based on knowing what compounds of interest were. Secondly, by utilizing the high resolution capabilities coupled with the low detection limits of FTMS, analysts also could dilute the sample sufficiently to minimize the ionization changes from varied matrices. PMID:26784175

  11. Establishing Drug Resistance in Microorganisms by Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Demirev, Plamen A.; Hagan, Nathan S.; Antoine, Miquel D.; Lin, Jeffrey S.; Feldman, Andrew B.

    2013-08-01

    A rapid method to determine drug resistance in bacteria based on mass spectrometry is presented. In it, a mass spectrum of an intact microorganism grown in drug-containing stable isotope-labeled media is compared with a mass spectrum of the intact microorganism grown in non-labeled media without the drug present. Drug resistance is determined by predicting characteristic mass shifts of one or more microorganism biomarkers using bioinformatics algorithms. Observing such characteristic mass shifts indicates that the microorganism is viable even in the presence of the drug, thus incorporating the isotopic label into characteristic biomarker molecules. The performance of the method is illustrated on the example of intact E. coli, grown in control (unlabeled) and 13C-labeled media, and analyzed by MALDI TOF MS. Algorithms for data analysis are presented as well.

  12. Establishing drug resistance in microorganisms by mass spectrometry.

    PubMed

    Demirev, Plamen A; Hagan, Nathan S; Antoine, Miquel D; Lin, Jeffrey S; Feldman, Andrew B

    2013-08-01

    A rapid method to determine drug resistance in bacteria based on mass spectrometry is presented. In it, a mass spectrum of an intact microorganism grown in drug-containing stable isotope-labeled media is compared with a mass spectrum of the intact microorganism grown in non-labeled media without the drug present. Drug resistance is determined by predicting characteristic mass shifts of one or more microorganism biomarkers using bioinformatics algorithms. Observing such characteristic mass shifts indicates that the microorganism is viable even in the presence of the drug, thus incorporating the isotopic label into characteristic biomarker molecules. The performance of the method is illustrated on the example of intact E. coli, grown in control (unlabeled) and (13)C-labeled media, and analyzed by MALDI TOF MS. Algorithms for data analysis are presented as well.

  13. Characterization of acyl chain position in unsaturated phosphatidylcholines using differential mobility-mass spectrometry[S

    PubMed Central

    Maccarone, Alan T.; Duldig, Jackson; Mitchell, Todd W.; Blanksby, Stephen J.; Duchoslav, Eva; Campbell, J. Larry

    2014-01-01

    Glycerophospholipids (GPs) that differ in the relative position of the two fatty acyl chains on the glycerol backbone (i.e., sn-positional isomers) can have distinct physicochemical properties. The unambiguous assignment of acyl chain position to an individual GP represents a significant analytical challenge. Here we describe a workflow where phosphatidylcholines (PCs) are subjected to ESI for characterization by a combination of differential mobility spectrometry and MS (DMS-MS). When infused as a mixture, ions formed from silver adduction of each phospholipid isomer {e.g., [PC (16:0/18:1) + Ag]+ and [PC (18:1/16:0) + Ag]+} are transmitted through the DMS device at discrete compensation voltages. Varying their relative amounts allows facile and unambiguous assignment of the sn-positions of the fatty acyl chains for each isomer. Integration of the well-resolved ion populations provides a rapid method (< 3 min) for relative quantification of these lipid isomers. The DMS-MS results show excellent agreement with established, but time-consuming, enzymatic approaches and also provide superior accuracy to methods that rely on MS alone. The advantages of this DMS-MS method in identification and quantification of GP isomer populations is demonstrated by direct analysis of complex biological extracts without any prior fractionation. PMID:24939921

  14. Plasma-based ambient ionization mass spectrometry in bioanalytical sciences.

    PubMed

    Smoluch, Marek; Mielczarek, Przemyslaw; Silberring, Jerzy

    2016-01-01

    Plasma-based ambient ionization mass spectrometry techniques are gaining growing interest due to their specific features, such as the need for little or no sample preparation, its high analysis speed, and the ambient experimental conditions. Samples can be analyzed in gas, liquid, or solid forms. These techniques allow for a wide range of applications, like warfare agent detection, chemical reaction control, mass spectrometry imaging, polymer identification, and food safety monitoring, as well as applications in biomedical science, e.g., drug and pharmaceutical analysis, medical diagnostics, biochemical analysis, etc. Until now, the main drawback of plasma-based techniques is their quantitative aspect, but a lot of efforts have been done to improve this obstacle.

  15. Protein identification using nano liquid chromatography-tandem mass spectrometry.

    PubMed

    Negroni, Luc

    2007-01-01

    Tandem mass spectrometry is an efficient technique for the identification of peptides on the basis of their fragmentation pattern (MS/MS scan). It can generate individual spectra for each peptide, thereby creating a powerful tool for protein identification on the basis of peptide characterization. This important advance in automatic data acquisition has allowed an efficient association between liquid chromatography and tandem mass spectrometry, and the use of nanocolumns and nanoelectrospray ionization has dramatically increased the efficiency of this method. Now large sets of peptides can be identified at a femtomole level. At the end of the process, batch processing of the MS/MS spectra produces peptide lists that identify purified proteins or protein mixtures with high confidence.

  16. Challenges ahead for mass spectrometry and proteomics applications in epigenetics.

    PubMed

    Kessler, Benedikt M

    2010-02-01

    Inheritance of biological information to future generations depends on the replication of DNA and the Mendelian principle of distribution of genes. In addition, external and environmental factors can influence traits that can be propagated to offspring, but the molecular details of this are only beginning to be understood. The discoveries of DNA methylation and post-translational modifications on chromatin and histones provided entry points for regulating gene expression, an area now defined as epigenetics and epigenomics. Mass spectrometry turned out to be instrumental in uncovering molecular details involved in these processes. The central role of histone post-translational modifications in epigenetics related biological processes has revitalized mass spectrometry based investigations. In this special report, current approaches and future challenges that lay ahead due to the enormous complexity are discussed.

  17. Analytical validation of accelerator mass spectrometry for pharmaceutical development

    PubMed Central

    Keck, Bradly D; Ognibene, Ted; Vogel, John S

    2011-01-01

    The validation parameters for pharmaceutical analyses were examined for the accelerator mass spectrometry measurement of 14C/C ratio, independent of chemical separation procedures. The isotope ratio measurement was specific (owing to the 14C label), stable across samples storage conditions for at least 1 year, linear over four orders of magnitude with an analytical range from 0.1 Modern to at least 2000 Modern (instrument specific). Furthermore, accuracy was excellent (between 1 and 3%), while precision expressed as coefficient of variation was between 1 and 6% determined primarily by radiocarbon content and the time spent analyzing a sample. Sensitivity, expressed as LOD and LLOQ was 1 and 10 attomoles of 14C, respectively (which can be expressed as compound equivalents) and for a typical small molecule labeled at 10% incorporated with 14C corresponds to 30 fg equivalents. Accelerator mass spectrometry provides a sensitive, accurate and precise method of measuring drug compounds in biological matrices. PMID:21083256

  18. Quantitative aspects of inductively coupled plasma mass spectrometry

    NASA Astrophysics Data System (ADS)

    Bulska, Ewa; Wagner, Barbara

    2016-10-01

    Accurate determination of elements in various kinds of samples is essential for many areas, including environmental science, medicine, as well as industry. Inductively coupled plasma mass spectrometry (ICP-MS) is a powerful tool enabling multi-elemental analysis of numerous matrices with high sensitivity and good precision. Various calibration approaches can be used to perform accurate quantitative measurements by ICP-MS. They include the use of pure standards, matrix-matched standards, or relevant certified reference materials, assuring traceability of the reported results. This review critically evaluates the advantages and limitations of different calibration approaches, which are used in quantitative analyses by ICP-MS. Examples of such analyses are provided. This article is part of the themed issue 'Quantitative mass spectrometry'.

  19. Analysis of Protein O-GlcNAcylation by Mass Spectrometry.

    PubMed

    Ma, Junfeng; Hart, Gerald W

    2017-02-02

    O-linked β-D-N-acetyl glucosamine (O-GlcNAc) addition (O-GlcNAcylation), a post-translational modification of serine/threonine residues of proteins, is involved in diverse cellular metabolic and signaling pathways. Aberrant O-GlcNAcylation underlies the initiation and progression of multiple chronic diseases including diabetes, cancer, and neurodegenerative diseases. Numerous methods have been developed for the analysis of protein O-GlcNAcylation, but instead of discussing the classical biochemical techniques, this unit covers O-GlcNAc characterization by combining several enrichment methods and mass spectrometry detection techniques [including collision-induced dissociation (CID), higher energy collision dissociation (HCD), and electron transfer dissociation (ETD) mass spectrometry]. © 2017 by John Wiley & Sons, Inc.

  20. 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

  1. Sharing and community curation of mass spectrometry data with GNPS

    PubMed Central

    Nguyen, Don Duy; Watrous, Jeramie; Kapono, Clifford A; Luzzatto-Knaan, Tal; Porto, Carla; Bouslimani, Amina; Melnik, Alexey V; Meehan, Michael J; Liu, Wei-Ting; Crüsemann, Max; Boudreau, Paul D; Esquenazi, Eduardo; Sandoval-Calderón, Mario; Kersten, Roland D; Pace, Laura A; Quinn, Robert A; Duncan, Katherine R; Hsu, Cheng-Chih; Floros, Dimitrios J; Gavilan, Ronnie G; Kleigrewe, Karin; Northen, Trent; Dutton, Rachel J; Parrot, Delphine; Carlson, Erin E; Aigle, Bertrand; Michelsen, Charlotte F; Jelsbak, Lars; Sohlenkamp, Christian; Pevzner, Pavel; Edlund, Anna; McLean, Jeffrey; Piel, Jörn; Murphy, Brian T; Gerwick, Lena; Liaw, Chih-Chuang; Yang, Yu-Liang; Humpf, Hans-Ulrich; Maansson, Maria; Keyzers, Robert A; Sims, Amy C; Johnson, Andrew R.; Sidebottom, Ashley M; Sedio, Brian E; Klitgaard, Andreas; Larson, Charles B; P., Cristopher A Boya; Torres-Mendoza, Daniel; Gonzalez, David J; Silva, Denise B; Marques, Lucas M; Demarque, Daniel P; Pociute, Egle; O'Neill, Ellis C; Briand, Enora; Helfrich, Eric J. N.; Granatosky, Eve A; Glukhov, Evgenia; Ryffel, Florian; Houson, Hailey; Mohimani, Hosein; Kharbush, Jenan J; Zeng, Yi; Vorholt, Julia A; Kurita, Kenji L; Charusanti, Pep; McPhail, Kerry L; Nielsen, Kristian Fog; Vuong, Lisa; Elfeki, Maryam; Traxler, Matthew F; Engene, Niclas; Koyama, Nobuhiro; Vining, Oliver B; Baric, Ralph; Silva, Ricardo R; Mascuch, Samantha J; Tomasi, Sophie; Jenkins, Stefan; Macherla, Venkat; Hoffman, Thomas; Agarwal, Vinayak; Williams, Philip G; Dai, Jingqui; Neupane, Ram; Gurr, Joshua; Rodríguez, Andrés M. C.; Lamsa, Anne; Zhang, Chen; Dorrestein, Kathleen; Duggan, Brendan M; Almaliti, Jehad; Allard, Pierre-Marie; Phapale, Prasad; Nothias, Louis-Felix; Alexandrov, Theodore; Litaudon, Marc; Wolfender, Jean-Luc; Kyle, Jennifer E; Metz, Thomas O; Peryea, Tyler; Nguyen, Dac-Trung; VanLeer, Danielle; Shinn, Paul; Jadhav, Ajit; Müller, Rolf; Waters, Katrina M; Shi, Wenyuan; Liu, Xueting; Zhang, Lixin; Knight, Rob; Jensen, Paul R; Palsson, Bernhard O; Pogliano, Kit; Linington, Roger G; Gutiérrez, Marcelino; Lopes, Norberto P; Gerwick, William H; Moore, Bradley S; Dorrestein, Pieter C; Bandeira, Nuno

    2017-01-01

    The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry techniques are well-suited to high-throughput characterization of natural products, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social molecular networking (GNPS, http://gnps.ucsd.edu), an open-access knowledge base for community wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of ‘living data’ through continuous reanalysis of deposited data. PMID:27504778

  2. Quantitative aspects of inductively coupled plasma mass spectrometry.

    PubMed

    Bulska, Ewa; Wagner, Barbara

    2016-10-28

    Accurate determination of elements in various kinds of samples is essential for many areas, including environmental science, medicine, as well as industry. Inductively coupled plasma mass spectrometry (ICP-MS) is a powerful tool enabling multi-elemental analysis of numerous matrices with high sensitivity and good precision. Various calibration approaches can be used to perform accurate quantitative measurements by ICP-MS. They include the use of pure standards, matrix-matched standards, or relevant certified reference materials, assuring traceability of the reported results. This review critically evaluates the advantages and limitations of different calibration approaches, which are used in quantitative analyses by ICP-MS. Examples of such analyses are provided.This article is part of the themed issue 'Quantitative mass spectrometry'.

  3. Analytical validation of accelerator mass spectrometry for pharmaceutical development.

    PubMed

    Keck, Bradly D; Ognibene, Ted; Vogel, John S

    2010-03-01

    The validation parameters for pharmaceutical analyses were examined for the accelerator mass spectrometry measurement of (14)C/C ratio, independent of chemical separation procedures. The isotope ratio measurement was specific (owing to the (14)C label), stable across samples storage conditions for at least 1 year, linear over four orders of magnitude with an analytical range from 0.1 Modern to at least 2000 Modern (instrument specific). Furthermore, accuracy was excellent (between 1 and 3%), while precision expressed as coefficient of variation was between 1 and 6% determined primarily by radiocarbon content and the time spent analyzing a sample. Sensitivity, expressed as LOD and LLOQ was 1 and 10 attomoles of (14)C, respectively (which can be expressed as compound equivalents) and for a typical small molecule labeled at 10% incorporated with (14)C corresponds to 30 fg equivalents. Accelerator mass spectrometry provides a sensitive, accurate and precise method of measuring drug compounds in biological matrices.

  4. Characterization of a model Phillips catalyst by mass spectrometry.

    PubMed

    Di Croce, Pascal Gabriel; Aubriet, Frédéric; Chéty-Gimondo, Rachel; Muller, Jean-François; Grange, Paul

    2004-01-01

    A model Phillips catalyst for ethylene polymerization, prepared by spin coating a Cr(III)(Cr(acac)3) precursor on a silicon wafer, was submitted to an oxidative activation. Laser ablation Fourier transform mass spectrometry provided direct information on molecular species at the silicon wafer surface during activation. At 350 degrees C the chromium precursor was degraded, while chromium oxide species were formed. The chromium concentration decreased with temperature. The activated model catalyst was active for ethylene polymerization. Using complementary techniques (Fourier transform infrared spectroscopy, laser desorption/ionization mass spectrometry), the polymer was identified as crystalline polyethylene. After 1 h of polymerization at 160 degrees C, dome-like structures were observed by atomic force microscopy. Their morphologies were constituted of regions of parallel aligned lamellae of polymer.

  5. What accelerator mass spectrometry can do for solar physics

    NASA Astrophysics Data System (ADS)

    Newkirk, Gordon

    1984-11-01

    We review some of the empirical aspects of the solar magnetic activity and the convective dynamo models developed to account for the magnetic cycle. Alternative hypotheses which have recently emerged are sketched. Possible applications of accelerator mass spectrometry to solar physics and the important questions that proxy data on past solar activity might answer are evaluated. The National Center for Atmospheric Research is sponsored by the National Science Foundation.

  6. Dissociation techniques in mass spectrometry-based proteomics.

    PubMed

    Jones, Andrew W; Cooper, Helen J

    2011-09-07

    The field of proteomics, the large-scale analysis of proteins, has undergone a huge expansion over the past decade. Mass spectrometry-based proteomics relies on the dissociation of peptide and/or protein ions to provide information on primary sequence and sites of post-translational modifications. Fragmentation techniques include collision-induced dissociation, electron capture dissociation and electron transfer dissociation. Here, we describe each of these techniques and their use in proteomics. The principles, advantages, limitations, and applications are discussed.

  7. ESI and MALDI Mass Spectrometry of Large POSS Oligomers (Preprint)

    DTIC Science & Technology

    2010-03-10

    induced dissociation of peptides and protein complexes in a quadrupole/time-of-flight mass spectrometer. Anal. Chem., 80 (2008) 1425-1436. [43] A...spectrometry has been quite successful in studying large conventional polymers or biopolymers including DNA and peptides [26-32]. This methodology...with or without pulsing the nitrogen collision gas in the selected ion path. Electrospray (nanospray) ionization (ESI)-MS. Polymer samples were

  8. Accelerator mass spectrometry for quantitative in vivo tracing

    SciTech Connect

    Vogel, J S

    2005-04-19

    Accelerator mass spectrometry (AMS) counts individual rare, usually radio-, isotopes such as radiocarbon at high efficiency and specificity in milligram-sized samples. AMS traces very low chemical doses ({micro}g) and radiative doses (100 Bq) of isotope labeled compounds in animal models and directly in humans for pharmaceutical, nutritional, or toxicological research. Absorption, metabolism, distribution, binding, and elimination are all quantifiable with high precision after appropriate sample definition.

  9. Targeting Synaptic Pathology with a Novel Affinity Mass Spectrometry Approach*

    PubMed Central

    Brinkmalm, Ann; Brinkmalm, Gunnar; Honer, William G.; Moreno, Julie A.; Jakobsson, Joel; Mallucci, Giovanna R.; Zetterberg, Henrik; Blennow, Kaj; Öhrfelt, Annika

    2014-01-01

    We report a novel strategy for studying synaptic pathology by concurrently measuring levels of four SNARE complex proteins from individual brain tissue samples. This method combines affinity purification and mass spectrometry and can be applied directly for studies of SNARE complex proteins in multiple species or modified to target other key elements in neuronal function. We use the technique to demonstrate altered levels of presynaptic proteins in Alzheimer disease patients and prion-infected mice. PMID:24973420

  10. Charge Prediction of Lipid Fragments in Mass Spectrometry

    SciTech Connect

    Schrom, Brian T.; Kangas, Lars J.; Ginovska, Bojana; Metz, Thomas O.; Miller, John H.

    2011-12-18

    An artificial neural network is developed for predicting which fragment is charged and which fragment is neutral for lipid fragment pairs produced from a liquid chromatography tandem mass spectrometry simulation process. This charge predictor is integrated into software developed at PNNL for in silico spectra generation and identification of metabolites known as Met ISIS. To test the effect of including charge prediction in Met ISIS, 46 lipids are used which show a reduction in false positive identifications when the charge predictor is utilized.

  11. Tissue Imaging Using Nanospray Desorption Electrospray Ionization Mass Spectrometry

    SciTech Connect

    Laskin, Julia; Heath, Brandi S.; Roach, Patrick J.; Cazares, Lisa H.; Semmes, O. John

    2012-01-03

    We present the first results showing the ambient imaging of biological samples in their native environment using nanospray desorption ionization (nanoDESI) mass spectrometry. NanoDESI is an ambient pressure ionization technique that enables precise control of ionization of molecules from substrates. We demonstrate highly sensitive and robust analysis of tissue samples with high spatial resolution (<12 {mu}m) without sample preparation, which will be essential for applications in clinical diagnostics, drug discovery, molecular biology, and biochemistry.

  12. Computational and Statistical Analysis of Protein Mass Spectrometry Data

    PubMed Central

    Noble, William Stafford; MacCoss, Michael J.

    2012-01-01

    High-throughput proteomics experiments involving tandem mass spectrometry produce large volumes of complex data that require sophisticated computational analyses. As such, the field offers many challenges for computational biologists. In this article, we briefly introduce some of the core computational and statistical problems in the field and then describe a variety of outstanding problems that readers of PLoS Computational Biology might be able to help solve. PMID:22291580

  13. Application of MALDI Mass Spectrometry in Natural Products Analysis.

    PubMed

    Silva, Ricardo; Lopes, Norberto Peporine; Silva, Denise Brentan

    2016-05-01

    This article presents the utility of mass spectrometry with a MALDI ionization source in natural products analysis. The advantages and drawbacks of this technique for natural products analyses will be presented and discussed. In addition, the structural determination of secondary metabolites using MALDI-MS/MS will be explored, which can guide MALDI experimental methods and stimulate new research in this area. Finally, several important approaches for MALDI data processing will be discussed.

  14. Sheathless interface for coupling capillary electrophoresis with mass spectrometry

    DOEpatents

    Wang, Chenchen; Tang, Keqi; Smith, Richard D.

    2014-06-17

    A sheathless interface for coupling capillary electrophoresis (CE) with mass spectrometry is disclosed. The sheathless interface includes a separation capillary for performing CE separation and an emitter capillary for electrospray ionization. A portion of the emitter capillary is porous or, alternatively, is coated to form an electrically conductive surface. A section of the emitter capillary is disposed within the separation capillary, forming a joint. A metal tube, containing a conductive liquid, encloses the joint.

  15. Macromolecule mass spectrometry: citation mining of user documents.

    PubMed

    Kostoff, Ronald N; Bedford, Clifford D; del Río, J Antonio; Cortes, Héctor D; Karypis, George

    2004-03-01

    Identifying research users, applications, and impact is important for research performers, managers, evaluators, and sponsors. Identification of the user audience and the research impact is complex and time consuming due to the many indirect pathways through which fundamental research can impact applications. This paper identified the literature pathways through which two highly-cited papers of 2002 Chemistry Nobel Laureates Fenn and Tanaka impacted research, technology development, and applications. Citation Mining, an integration of citation bibliometrics and text mining, was applied to the >1600 first generation Science Citation Index (SCI) citing papers to Fenn's 1989 Science paper on Electrospray Ionization for Mass Spectrometry, and to the >400 first generation SCI citing papers to Tanaka's 1988 Rapid Communications in Mass Spectrometry paper on Laser Ionization Time-of-Flight Mass Spectrometry. Bibliometrics was performed on the citing papers to profile the user characteristics. Text mining was performed on the citing papers to identify the technical areas impacted by the research, and the relationships among these technical areas.

  16. Triboelectric nanogenerators for sensitive nano-coulomb molecular mass spectrometry.

    PubMed

    Li, Anyin; Zi, Yunlong; Guo, Hengyu; Wang, Zhong Lin; Fernández, Facundo M

    2017-02-27

    Ion sources for molecular mass spectrometry are usually driven by direct current power supplies with no user control over the total charges generated. Here, we show that the output of triboelectric nanogenerators (TENGs) can quantitatively control the total ionization charges in mass spectrometry. The high output voltage of TENGs can generate single- or alternating-polarity ion pulses, and is ideal for inducing nanoelectrospray ionization (nanoESI) and plasma discharge ionization. For a given nanoESI emitter, accurately controlled ion pulses ranging from 1.0 to 5.5 nC were delivered with an onset charge of 1.0 nC. Spray pulses can be generated at a high frequency of 17 Hz (60 ms in period) and the pulse duration is adjustable on-demand between 60 ms and 5.5 s. Highly sensitive (∼0.6 zeptomole) mass spectrometry analysis using minimal sample (18 pl per pulse) was achieved with a 10 pg ml(-1) cocaine sample. We also show that native protein conformation is conserved in TENG-ESI, and that patterned ion deposition on conductive and insulating surfaces is possible.

  17. Mass spectrometry theory and application to adrenal diseases.

    PubMed

    Wooding, Kerry M; Auchus, Richard J

    2013-05-22

    The diagnosis and management of adrenal diseases hinge upon accurate determination of hormone concentrations in blood and other body fluids. The advent of immunoassays for various steroid hormones has enabled the remarkable progress in adrenal disease over the last several decades, with some limitation. Sequential immunoassay of single analytes is a tedious process, which requires aliquots for each assay. In many complex adrenal diseases, including adrenal cancer and congenital adrenal hyperplasia, the patterns or ratios of multiple steroids rather than the value of any one steroid is more relevant. Although gas chromatography/mass spectrometry of urinary steroid metabolites has been employed to profile steroid production, throughput is slow, and availability is sparse. Recent generations of liquid chromatography-tandem mass spectrometry instruments (LC-MS/MS) provide the throughput and sensitivity required to measure many steroids simultaneously using small samples for commercial and research uses. Even in the best hands, however, LC-MS/MS suffers from limitations and requires diligent attention to detail during method development and implementation. This article reviews the theory, instrumentation principles and terminology, and practical application of mass spectrometry to clinical adrenal disorders.

  18. Mass spectrometry of peptides and proteins from human blood.

    PubMed

    Zhu, Peihong; Bowden, Peter; Zhang, Du; Marshall, John G

    2011-01-01

    It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.

  19. Multidimensional Mass Spectrometry of Synthetic Polymers and Advanced Materials.

    PubMed

    Wesdemiotis, Chrys

    2017-02-01

    Multidimensional mass spectrometry interfaces a suitable ionization technique and mass analysis (MS) with fragmentation by tandem mass spectrometry (MS(2) ) and an orthogonal online separation method. Separation choices include liquid chromatography (LC) and ion-mobility spectrometry (IMS), in which separation takes place pre-ionization in the solution state or post-ionization in the gas phase, respectively. The MS step provides elemental composition information, while MS(2) exploits differences in the bond stabilities of a polymer, yielding connectivity and sequence information. LC conditions can be tuned to separate by polarity, end-group functionality, or hydrodynamic volume, whereas IMS adds selectivity by macromolecular shape and architecture. This Minireview discusses how selected combinations of the MS, MS(2) , LC, and IMS dimensions can be applied, together with the appropriate ionization method, to determine the constituents, structures, end groups, sequences, and architectures of a wide variety of homo- and copolymeric materials, including multicomponent blends, supramolecular assemblies, novel hybrid materials, and large cross-linked or nonionizable polymers.

  20. Significant advancement of mass spectrometry imaging for food chemistry.

    PubMed

    Yoshimura, Yukihiro; Goto-Inoue, Naoko; Moriyama, Tatsuya; Zaima, Nobuhiro

    2016-11-01

    Food contains various compounds that have an impact on our daily lives. Many technologies have been established to analyze these molecules of interest in foods. However, the analysis of the spatial distribution of these compounds in foods using conventional technology, such as high-performance liquid chromatography-mass spectrometry or gas chromatography-mass spectrometry is difficult. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is considered an ideal complementary approach. MALDI-MSI is a two-dimensional MALDI-MS technology that can detect compounds in a tissue section without extraction, purification, separation, or labeling. MALDI-MSI can be used to visualize the spatial distribution of chemical compounds or biomolecules in foods. Although the methodology of MALDI-MSI in food science is not yet fully established, the versatility of MALDI-MSI is expected to open a new frontier in food science. Herein, we describe the principles and applications of MALDI-MSI in food science and related fields.

  1. Visualization of lipid droplet composition by direct organelle mass spectrometry.

    PubMed

    Horn, Patrick J; Ledbetter, Nicole R; James, Christopher N; Hoffman, William D; Case, Charlene R; Verbeck, Guido F; Chapman, Kent D

    2011-02-04

    An expanding appreciation for the varied functions of neutral lipids in cellular organisms relies on a more detailed understanding of the mechanisms of lipid production and packaging into cytosolic lipid droplets (LDs). Conventional lipid profiling procedures involve the analysis of tissue extracts and consequently lack cellular or subcellular resolution. Here, we report an approach that combines the visualization of individual LDs, microphase extraction of lipid components from droplets, and the direct identification of lipid composition by nanospray mass spectrometry, even to the level of a single LD. The triacylglycerol (TAG) composition of LDs from several plant sources (mature cotton (Gossypium hirsutum) embryos, roots of cotton seedlings, and Arabidopsis thaliana seeds and leaves) were examined by direct organelle mass spectrometry and revealed the heterogeneity of LDs derived from different plant tissue sources. The analysis of individual LDs makes possible organellar resolution of molecular compositions and will facilitate new studies of LD biogenesis and functions, especially in combination with analysis of morphological and metabolic mutants. Furthermore, direct organelle mass spectrometry could be applied to the molecular analysis of other subcellular compartments and macromolecules.

  2. Characterization of individual particles in gaseous media by mass spectrometry

    NASA Technical Reports Server (NTRS)

    Sinha, M. P.

    1990-01-01

    An introduction is given to a system for particle analysis by mass spectrometry (PAMS) which employs particle-beam techniques to measure mass spectra on a continuous real-time basis. The system is applied to particles of both organic and inorganic compounds, and the measurements give the chemical characteristics of particles in mixtures and indicate source apportionment. The PAMS system can be used for process control and studying heterogeneous/catalytic reactions in particles, and can be fitted to study the real-time attributes of PAMS.

  3. High Resolution Double-Focusing Isotope Ratio Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Radke, J.; Deerberg, M.; Hilkert, A.; Schlüter, H.-J.; Schwieters, J.

    2012-04-01

    In recent years isotope ratio mass spectrometry has extended to the capability of quantifying very small isotope signatures related with low abundances and simultaneously detecting molecular masses such as isotopomers and isotopologues containing clumped isotopes. Some of those applications are limited by molecular interferences like different gas molecules with the same nominal mass, e.g. Ar/O2, adducts of the same molecule or of different molecules, and very small isotope abundances. The Thermo Scientific MAT 253 ULTRA is the next generation of high precision gas isotope ratio mass spectrometry, which combines a 10 KV gas ionization source (Thermo Scientific MAT 253) with a double focusing multi-collector mass analyzer (Thermo Scientific Neptune) and reduces those limitations by measuring isotope ratios on a larger dynamic range with high precision. Small ion beam requirements and high sensitivity are achieved by signal-to-noise improvements through enhanced ion beam amplification in faraday cups and ion counters. Interfering backgrounds, e.g. interfering isotopologues or isobaric ions of contaminants, are dramatically decreased by a dynamic range increase combined with high evacuation leading to undisturbed ion transmission through the double-focusing analyser. Furthermore, automated gain calibration for mathematical baseline corrections, switchable detector arrays, ion source control, analyser focusing and full data export is controlled under Isodat data control. New reference/sample strategies are under investigation besides incorporation of the continuous-flow technique and its versatile inlet devices. We are presenting first results and applications of the MAT 253 Ultra.

  4. Liquid chromatography/microspray mass spectrometry for bacterial investigations.

    PubMed

    Krishnamurthy, T; Davis, M T; Stahl, D C; Lee, T D

    1999-01-01

    Cellular proteins (biomarkers) specific to any individual microorganism, determined by the direct mass spectral analysis of the corresponding intact cellular suspension, can be applied for the rapid and specific identification of the organisms present in unknown samples. The components of the bacterial suspensions, after a rapid separation over a C18 reversed-phase microcapillary column, were directly subjected to on-line electrospray ionization followed by analysis using an ion trap tandem mass spectrometer. This approach is equally effective for gram-positive as well as gram-negative bacteria but has a distinct advantage over our earlier reported method involving matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). During electrospray ionitation mass spectrometry (ESI-MS), liquid samples can be directly analyzed and there is the potential for developing tandem mass spectral methods for more specific identification of the individual organisms present in crude bacterial mixtures. The total analysis time leading to unambiguous bacterial identification in samples was less than 10 minutes and the results were quite reproducible. Miniaturization of the instrumentation along with total automation of this simple process could have immense impact on field operations. Routine, rapid, cost-effective field monitoring of environmental samples, agricultural products, samples from food processing, industrial sites and health institutions for suspected bacterial contamination could be a reality in the near future. Potential utility in biological, medical, bioprocessing, pharmaceutical, and other industrial research is also enormous.

  5. Performance metrics for evaluating system suitability in liquid chromatography—Mass spectrometry peptide mass mapping of protein therapeutics and monoclonal antibodies

    PubMed Central

    Zhou, Mowei; Gucinski, Ashley C; Boyne, Michael T

    2015-01-01

    The use of liquid chromatography – mass spectrometry (LC-MS) for the characterization of proteins can provide a plethora of information related to their structure, including amino acid sequence determination and analysis of posttranslational modifications. The variety of LC-MS based applications has led to the use of LC-MS characterization of therapeutic proteins and monoclonal antibodies as an integral part of the regulatory approval process. However, the improper use of an LC-MS system, related to intrinsic instrument limitations, improper tuning parameters, or poorly optimized methods may result in the production of low quality data. Improper system performance may arise from subtle changes in operating conditions that limit the ability to detect low abundance species. To address this issue, we systematically evaluated LC-MS/MS operating parameters to identify a set of metrics that can be used in a workflow to determine if a system is suitable for its intended purpose. Development of this workflow utilized a bovine serum albumin (BSA) digest standard spiked with synthetic peptides present at 0.1% to 100% of the BSA digest peptide concentration to simulate the detection of low abundance species using a traditional bottom-up workflow and data-dependent MS2 acquisition. BSA sequence coverage, a commonly used indicator for instrument performance did not effectively identify settings that led to limited dynamic range or poorer absolute mass accuracy on 2 separate LC-MS systems. Additional metrics focusing on the detection limit and sensitivity for peptide identification were determined to be necessary to establish system suitability for protein therapeutic characterization by LC-MS. PMID:26218711

  6. Determination of accurate protein monoisotopic mass with the most abundant mass measurable using high-resolution mass spectrometry.

    PubMed

    Chen, Ya-Fen; Chang, C Allen; Lin, Yu-Hsuan; Tsay, Yeou-Guang

    2013-09-01

    While recent developments in mass spectrometry enable direct evaluation of monoisotopic masses (M(mi)) of smaller compounds, protein M(mi) is mostly determined based on its relationship to average mass (Mav). Here, we propose an alternative approach to determining protein M(mi) based on its correlation with the most abundant mass (M(ma)) measurable using high-resolution mass spectrometry. To test this supposition, we first empirically calculated M(mi) and M(ma) of 6158 Escherichia coli proteins, which helped serendipitously uncover a linear correlation between these two protein masses. With the relationship characterized, liquid chromatography-mass spectrometry was employed to measure M(ma) of protein samples in its ion cluster with the highest signal in the mass spectrum. Generally, our method produces a short series of likely M(mi) in 1-Da steps, and the probability of each likely M(mi) is assigned statistically. It is remarkable that the mass error of this M(mi) is as miniscule as a few parts per million, indicating that our method is capable of determining protein M(mi) with high accuracy. Benefitting from the outstanding performance of modern mass spectrometry, our approach is a significant improvement over others and should be of great utility in the rapid assessment of protein primary structures.

  7. Measurement of the 135Cs half-life with accelerator mass spectrometry and inductively coupled plasma mass spectrometry

    NASA Astrophysics Data System (ADS)

    MacDonald, C. M.; Cornett, R. J.; Charles, C. R. J.; Zhao, X. L.; Kieser, W. E.

    2016-01-01

    The isotope 135Cs is quoted as having a half-life of 2.3 Myr. However, there are three published values ranging from 1.8 to 3 Myr. This research reviews previous measurements and reports a new measurement of the half-life using newly developed accelerator mass spectrometry (AMS) and inductively coupled plasma mass spectrometry (ICPMS) techniques along with β and γ radiometric analysis. The half-life was determined to be (1.6 ±0.6 ) ×106 yr by AMS and (1.3 ±0.2 ) ×106 yr by ICPMS with 95% confidence. The two values agree with each other but differ from the accepted value by ˜40 % .

  8. Direct infusion mass spectrometry or liquid chromatography mass spectrometry for human metabonomics? A serum metabonomic study of kidney cancer.

    PubMed

    Lin, Lin; Yu, Quan; Yan, Xiaomei; Hang, Wei; Zheng, Jiaxin; Xing, Jinchun; Huang, Benli

    2010-11-01

    Serum samples from kidney cancer patients and healthy controls were analyzed by both direct infusion mass spectrometry (DIMS) and liquid chromatography-mass spectrometry (LC-MS) with a high resolution ESI-Q-TOFMS. The classification and biomarker discovery capacities of the two methods were compared, and MS/MS experiments were carried out to identify potential biomarkers. DIMS had comparable classification and prediction capabilities to LC-MS but consumed only ~5% of the analysis time. With regard to biomarker discovery, twenty-three variables were found as potential biomarkers by DIMS, and 48 variables were obtained by LC-MS. DIMS is recommended to be a fast diagnostic method for kidney cancer, while LC-MS is necessary when comprehensive screening of biomarkers is required.

  9. Analysis of polar lipids in the serum from rats fed shiitake by liquid chromatography-mass spectrometry/mass spectrometry.

    PubMed

    Yu, Shanggong; Peng, Min; Ronis, Martin; Badger, Thomas; Fang, Nianbai

    2010-12-22

    Consumption of a shiitake mushroom diet has been reported to have effects on serum phospholipids. However, much less is known about the effect on serum polar lipids including lysophospholipids and free fatty acids. In the present study, the effects of a shiitake diet were evaluated on the basis of identification and quantification of individual polar lipid components in rat serum using liquid chromatography-mass spectrometry/mass spectrometry. By comparison with standards and published data, 50 lysophospholipids and 32 free fatty acids were identified, and the concentrations of 27 polar lipids in rat serum were determined. Shiitake diets decreased the levels of all individual polar lipid components in the serum of male rat. The total level of serum polar lipids in males fed 4% shiitake diets (1365.71 mol/L) was significantly lower than that of the control (2270.26 mol/L). However, shiitake diets did not significantly affect the levels of serum polar lipids in female rats.

  10. Neuropeptide Signaling in Crustaceans Probed by Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Liang, Zhidan

    Neuropeptides are one of the most diverse classes of signaling molecules whose identities and functions are not yet fully understood. They have been implicated in the regulation of a wide range of physiological processes, including feeding-related and motivated behaviors, and also environmental adaptations. In this work, improved mass spectrometry-based analytical platforms were developed and applied to the crustacean systems to characterize signaling molecules. This dissertation begins with a review of mass spectrometry-based neuropeptide studies from both temporal- and spatial-domains. This review is then followed by several chapters detailing a few research projects related to the crustacean neuropeptidomic characterization and comparative analysis. The neuropeptidome of crayfish, Orconectes rusticus is characterized for the first time using mass spectrometry-based tools. In vivo microdialysis sampling technique offers the capability of direct sampling from extracellular space in a time-resolved manner. It is used to investigate the secreted neuropeptide and neurotransmitter content in Jonah crab, Cancer borealis, in this work. A new quantitation strategy using alternative mass spectrometry data acquisition approach is developed and applied for the first time to quantify neuropeptides. Coupling of this method with microdialysis enables the study of neuropeptide dynamics concurrent with different behaviors. Proof-of-principle experiments validating this approach have been carried out in Jonah crab, Cancer borealis to study feeding- and circadian rhythm-related neuropeptide changes using micoridialysis in a time-resolved manner. This permits a close correlation between behavioral and neurochemical changes, providing potential candidates for future validation of regulatory roles. In addition to providing spatial information, mass spectrometry imaging (MSI) technique enables the characterization of signaling molecules while preserving the temporal resolution. A

  11. Fast characterization of cheeses by dynamic headspace-mass spectrometry.

    PubMed

    Pérès, Christophe; Denoyer, Christian; Tournayre, Pascal; Berdagué, Jean-Louis

    2002-03-15

    This study describes a rapid method to characterize cheeses by analysis of their volatile fraction using dynamic headspace-mass spectrometry. Major factors governing the extraction and concentration of the volatile components were first studied. These components were extracted from the headspace of the cheeses in a stream of helium and concentrated on a Tenax TA trap. They were then desorbed by heating and injected directly into the source of a mass spectrometer via a short deactivated silica transfer line. The mass spectra of the mixture of volatile components were considered as fingerprints of the analyzed substances. Forward stepwise factorial discriminant analysis afforded a limited number of characteristic mass fragments that allowed a good classification of the batches of cheeses studied.

  12. A Proof of Concept to Bridge the Gap between Mass Spectrometry Imaging, Protein Identification and Relative Quantitation: MSI~LC-MS/MS-LF

    PubMed Central

    Théron, Laëtitia; Centeno, Delphine; Coudy-Gandilhon, Cécile; Pujos-Guillot, Estelle; Astruc, Thierry; Rémond, Didier; Barthelemy, Jean-Claude; Roche, Frédéric; Feasson, Léonard; Hébraud, Michel; Béchet, Daniel; Chambon, Christophe

    2016-01-01

    Mass spectrometry imaging (MSI) is a powerful tool to visualize the spatial distribution of molecules on a tissue section. The main limitation of MALDI-MSI of proteins is the lack of direct identification. Therefore, this study focuses on a MSI~LC-MS/MS-LF workflow to link the results from MALDI-MSI with potential peak identification and label-free quantitation, using only one tissue section. At first, we studied the impact of matrix deposition and laser ablation on protein extraction from the tissue section. Then, we did a back-correlation of the m/z of the proteins detected by MALDI-MSI to those identified by label-free quantitation. This allowed us to compare the label-free quantitation of proteins obtained in LC-MS/MS with the peak intensities observed in MALDI-MSI. We managed to link identification to nine peaks observed by MALDI-MSI. The results showed that the MSI~LC-MS/MS-LF workflow (i) allowed us to study a representative muscle proteome compared to a classical bottom-up workflow; and (ii) was sparsely impacted by matrix deposition and laser ablation. This workflow, performed as a proof-of-concept, suggests that a single tissue section can be used to perform MALDI-MSI and protein extraction, identification, and relative quantitation. PMID:28248242

  13. Emerging mass spectrometry techniques for the direct analysis of microbial colonies

    PubMed Central

    Fang, Jinshu; Dorrestein, Pieter C.

    2014-01-01

    One of the emerging areas in microbiology is detecting specialized metabolites produced by microbial colonies and communities with mass spectrometry. In this review/perspective, we illustrate the emerging mass spectrometry methodologies that enable the interrogation of specialized metabolites directly from microbial colonies. Mass spectrometry techniques such as imaging mass spectrometry and real-time mass spectrometry allow two and three dimensional visualization of the distribution of metabolites, often with minimal sample pretreatment. The speed in which molecules are captured using these methods requires the development of new molecular visualization tools such as molecular networking. Together, these tools are beginning to provide unprecedented insight into the chemical world that microbes experience. PMID:25064218

  14. Classification of natural resins by liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry using chemometric analysis.

    PubMed

    Rhourrhi-Frih, B; West, C; Pasquier, L; André, P; Chaimbault, P; Lafosse, M

    2012-09-21

    Twenty-six resins from six botanical sources belonging to the class Magnoliopsida were compared based on gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry data. The extracts were analysed by GC after silylation and by reversed phase LC combined with atmospheric pressure photoionisation (APPI) mass spectrometry. The chromatograms were re-organized in data matrices, where each sample was represented by a single column comprising 2755 observations (intensity, time, m/z) in GC-MS and 360 observations in LC-MS. A simple comparison of resin fingerprints was attempted by organizing data according to a three dimensional bubble chart (retention time against m/z where each point was a bubble which size represented the ion intensity) where it is possible to easily superimpose the fingerprints. Thus the common and different species can be easily observed enabling to classify the resins. Hierarchical cluster analysis based on characteristics of GC-MS and LC-MS profiles affords a complete description of the classes of the resins and shows that 26 resins are divided into five main clusters Commiphora mukul, Daniella oliveri, Gardenia gummifera, Canarium madagascariensis, Boswellia dalzielii and Boswellia serrata, respectively. In conclusion, the proposed method has been applied to three other resinous samples from the Burseraceae family to evaluate their alteration state.

  15. Resonance enhanced multiphoton ionization/secondary neutral mass spectrometry and cesium attachment secondary ion mass spectrometry of bronze : a comparison.

    SciTech Connect

    McCann, M. P.; Calaway, W. F.; Pellin, M. J.; Veryovkin, I. V.; Constantinides, I.; Adriaens, A.; Adams, F.; Materials Science Division; Sam Houston State Univ.; Univ. of Antwerp

    2002-05-01

    Archaeologists have considerable interests in ancient bronzes. They want to know how these alloys were produced and how they corroded with time. Modern bronzes, with compositions very close to that of some ancient bronzes, have been produced and two methods were examined to characterize one of these modern bronzes. Analysis of this modern bronze using resonance enhanced multiphoton ionization/secondary neutral mass spectrometry (REMPI/SNMS) is examined in detail and compared to cesium attachment secondary ion mass spectrometry (CsAMS) results. Both REMPI/SNMS and CsAMS were used to quantify the composition of Fe, Ni and Mn in a modern quaternary bronze designed to serve as a certified reference material for an ancient bronze. Both methods exhibit reduced matrix effects when compared to secondary ion mass spectrometry (SIMS) and thus quantification should be simplified. It was found that when relative sensitivity factors obtained from a standard bronze material are used to calibrate the instruments, the REMPI/SNMS measurements yield results that were more sensitive and more accurate.

  16. Quantitative mass spectrometry of unconventional human biological matrices

    NASA Astrophysics Data System (ADS)

    Dutkiewicz, Ewelina P.; Urban, Pawel L.

    2016-10-01

    The development of sensitive and versatile mass spectrometric methodology has fuelled interest in the analysis of metabolites and drugs in unconventional biological specimens. Here, we discuss the analysis of eight human matrices-hair, nail, breath, saliva, tears, meibum, nasal mucus and skin excretions (including sweat)-by mass spectrometry (MS). The use of such specimens brings a number of advantages, the most important being non-invasive sampling, the limited risk of adulteration and the ability to obtain information that complements blood and urine tests. The most often studied matrices are hair, breath and saliva. This review primarily focuses on endogenous (e.g. potential biomarkers, hormones) and exogenous (e.g. drugs, environmental contaminants) small molecules. The majority of analytical methods used chromatographic separation prior to MS; however, such a hyphenated methodology greatly limits analytical throughput. On the other hand, the mass spectrometric methods that exclude chromatographic separation are fast but suffer from matrix interferences. To enable development of quantitative assays for unconventional matrices, it is desirable to standardize the protocols for the analysis of each specimen and create appropriate certified reference materials. Overcoming these challenges will make analysis of unconventional human biological matrices more common in a clinical setting. This article is part of the themed issue 'Quantitative mass spectrometry'.

  17. Surface Ionization and Soft Landing Techniques in Mass Spectrometry

    SciTech Connect

    Futrell, Jean H.; Laskin, Julia

    2010-04-01

    The advent of soft ionization techniques, notably electrospray and laser desorption ionization methods, has extended mass spectrometric methods to large molecules and molecular complexes. This both greatly expands appli¬cations of mass spectrometry and makes the activation and dissociation of complex ions an integral part of large molecule mass spectrometry. A corollary of the much greater number of internal degrees of freedom and high density of states associated with molecular complexity is that internal energies much higher than the dissociation energies for competing fragmentation processes are required for observable fragmentation in time scales sampled by mass spectrometers. This article describes the kinetics of surface-induced dissociation (SID), a particularly efficient activation method for complex ions. Two very important characteristics of SID are very rapid, sub-picosecond activation and precise control of ion internal energy by varying ion collision energy. The nature of the surface plays an important role in SID, determining both efficiency and mechanism of ion activation. Surface composition and morphology strongly influence the relative importance of competing reactions of SID, ion capture (soft-landing), surface reaction and neutralization. The important features of SID and ion soft-landing are described briefly in this review and more fully in the recommended reading list.

  18. ATP synthases: cellular nanomotors characterized by LILBID mass spectrometry

    PubMed Central

    Hoffmann, Jan; Sokolova, Lucie; Preiss, Laura; Hicks, David B.; Krulwich, Terry A.; Morgner, Nina; Wittig, Ilka; Schägger, Hermann; Meier, Thomas; Brutschy, Bernd

    2010-01-01

    Mass spectrometry of membrane protein complexes is still a methodological challenge due to hydrophobic and hydrophilic parts of the species and the fact that all subunits are bound non-covalently together. The present study with the novel laser induced liquid bead ion desorption mass spectrometry (LILBID-MS) reports on the determination of the subunit composition of the F1Fo-ATP synthase from Bacillus pseudofirmus OF4, that of both bovine heart and, for the first time, of human heart mitochondrial F1Fo-ATP synthases. Under selected buffer conditions the mass of the intact F1Fo-ATP synthase of B. pseudofirmus OF4 could be measured, allowing the analysis of complex subunit stoichiometry. The agreement with theoretical masses derived from sequence databases is very good. A comparison of the ATP synthase subunit composition of 5 different ATPases reveals differences in the complexity of eukaryotic and bacterial ATP synthases. However, whereas the overall construction of eukaryotic enzymes is more complex than the bacterial ones, functionally important subunits are conserved among all ATPases. PMID:20820587

  19. Linking high resolution mass spectrometry data with exposure ...

    EPA Pesticide Factsheets

    There is a growing need in the field of exposure science for monitoring methods that rapidly screen environmental media for suspect contaminants. Measurement and analysis platforms, based on high resolution mass spectrometry (HRMS), now exist to meet this need. Here we describe results of a study that links HRMS data with exposure predictions from the U.S. EPA's ExpoCast™ program and in vitro bioassay data from the U.S. interagency Tox21 consortium. Vacuum dust samples were collected from 56 households across the U.S. as part of the American Healthy Homes Survey (AHHS). Sample extracts were analyzed using liquid chromatography time-of-flight mass spectrometry (LC–TOF/MS) with electrospray ionization. On average, approximately 2000 molecular features were identified per sample (based on accurate mass) in negative ion mode, and 3000 in positive ion mode. Exact mass, isotope distribution, and isotope spacing were used to match molecular features with a unique listing of chemical formulas extracted from EPA's Distributed Structure-Searchable Toxicity (DSSTox) database. A total of 978 DSSTox formulas were consistent with the dust LC–TOF/molecular feature data (match score ≥ 90); these formulas mapped to 3228 possible chemicals in the database. Correct assignment of a unique chemical to a given formula required additional validation steps. Each suspect chemical was prioritized for follow-up confirmation using abundance and detection frequency results, along wi

  20. Ultratrace Analysis of Uranium and Plutonium By Mass Spectrometry

    SciTech Connect

    Wacker, John F.; Wogman, Ned A.; Olsen, Khris B.; Petersen, Steven L.; Farmer, O T.; Kelley, James M.; Eiden, Greg C.; Maiti, Tapas C.

    2003-01-01

    At the Pacific Northwest National Laboratory (PNNL), we have developed highly sensitive methods to analyze uranium and plutonium in environmental samples. The development of an ultratrace analysis capability for measuring uranium and plutonium has arisen from a need to detect and characterize environmental samples for signatures associated with nuclear industry processes. Our most sensitive well-developed methodologies employ thermal ionization mass spectrometry (TIMS), however, recent advances in inductively coupled plasma mass spectrometry (ICP-MS) have shown considerable promise for use in detecting uranium and plutonium at ultratrace levels. The work at PNNL has included the development of both chemical separation and purification techniques, as well as the development of mass spectrometric instrumentation and techniques. At the heart of our methodology for TIMS analysis is a procedure that utilizes 100-microliter-volumes of analyte for chemical processing to purify, separate, and load actinide elements into resin beads for subsequent mass spectrometric analysis. The resin bead technique has been combined with a thorough knowledge of the physicochemistry of thermal ion emission to achieve femtogram detection limits for the TIMS analysis of plutonium in environmental samples.

  1. Use of MALDI Mass Spectrometry for Identification of Microbes

    NASA Astrophysics Data System (ADS)

    Wilkins, C. L.; Stump, M.; Jones, J.; Lay, J. O.; Fleming, R.

    2003-12-01

    Recently, it has been demonstrated that bacteria can be characterized using whole cells and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). However, identification of specific bacterial proteins usually requires analysis of cellular fractions or purified extracts. This presentation will discuss the first application of Fourier transform mass spectrometry (FTMS) to analysis of bacterial proteins directly from whole cells. In this research it is seen that accurate mass MALDI-FTMS can be used to characterize specific ribosomal proteins directly from Escherichia coli cells. Using the high-accuracy mass measurements and high resolution isotope profile data thus available it is possible to confirm posttranslational modifications proposed previously on the basis of low resolution mass measurements. In our initial work, ribosomal proteins from E. coli whole cells were observed with errors of less than 27 ppm. This was accomplished directly from whole cells without fractionation, concentration, or overt overexpression of characteristic cellular proteins. More recently, by use of carbon and nitrogen isotopically-depleted growth media additional E. coli proteins have been identified with even smaller mass measurement errors. MALDI FTMS also provided information regarding E. coli lipids in the low-mass region. Although ions with m/z values below 1000 were previously observed by FTMS of whole cells, the work to be presented was the first report of detection of ions in the 5000 to 10 000 m/z range by MALDI-FTMS using whole cells. The implications of these results for genus, species, and strain assignments of such organisms will be discussed.

  2. Invited review article: Recent developments in isotope-ratio mass spectrometry for geochemistry and cosmochemistry.

    PubMed

    Ireland, Trevor R

    2013-01-01

    Mass spectrometry is fundamental to measurements of isotope ratios for applications in isotope geochemistry, geochronology, and cosmochemistry. Magnetic-sector mass spectrometers are most common because these provide the best precision in isotope ratio measurements. Where the highest precision is desired, chemical separation followed by mass spectrometric analysis is carried out with gas (noble gas and stable isotope mass spectrometry), liquid (inductively coupled plasma mass spectrometry), or solid (thermal ionization mass spectrometry) samples. Developments in in situ analysis, including ion microprobes and laser ablation inductively coupled plasma mass spectrometry, have opened up issues concerning homogeneity according to domain size, and allow ever smaller amounts of material to be analyzed. While mass spectrometry is built solidly on developments in the 20th century, there are new technologies that will push the limits in terms of precision, accuracy, and sample efficiency. Developments of new instruments based on time-of-flight mass spectrometers could open up the ultimate levels of sensitivity per sample atom.

  3. Intact MicroRNA Analysis Using High Resolution Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Kullolli, Majlinda; Knouf, Emily; Arampatzidou, Maria; Tewari, Muneesh; Pitteri, Sharon J.

    2014-01-01

    MicroRNAs (miRNAs) are small single-stranded non-coding RNAs that post-transcriptionally regulate gene expression, and play key roles in the regulation of a variety of cellular processes and in disease. New tools to analyze miRNAs will add understanding of the physiological origins and biological functions of this class of molecules. In this study, we investigate the utility of high resolution mass spectrometry for the analysis of miRNAs through proof-of-concept experiments. We demonstrate the ability of mass spectrometry to resolve and separate miRNAs and corresponding 3' variants in mixtures. The mass accuracy of the monoisotopic deprotonated peaks from various miRNAs is in the low ppm range. We compare fragmentation of miRNA by collision-induced dissociation (CID) and by higher-energy collisional dissociation (HCD) which yields similar sequence coverage from both methods but additional fragmentation by HCD versus CID. We measure the linear dynamic range, limit of detection, and limit of quantitation of miRNA loaded onto a C18 column. Lastly, we explore the use of data-dependent acquisition of MS/MS spectra of miRNA during online LC-MS and demonstrate that multiple charge states can be fragmented, yielding nearly full sequence coverage of miRNA on a chromatographic time scale. We conclude that high resolution mass spectrometry allows the separation and measurement of miRNAs in mixtures and a standard LC-MS setup can be adapted for online analysis of these molecules.

  4. Analysis of fluticasone propionate in induced sputum by mass spectrometry.

    PubMed

    Hagan, John B; Taylor, Robert L; Kita, Hirohito; Singh, Ravinder J

    2011-01-01

    Although evaluation of induced sputum has shown promise as a marker of eosinophilic airway inflammation in asthmatic subjects, most studies, to date, do not adequately address the potential effect that inhaled corticosteroids may have on sputum eosinophilia. This study was designed to prospectively evaluate analysis of fluticasone propionate (FP) in whole sputum by mass spectrometry as a tool to determine recent administration of inhaled FP. Induced sputum of nonsmoking asthmatic subjects was prospectively analyzed 16-24 hours after witnessed administration of orally inhaled FP. FP was extracted from whole sputum via an acetonitrile protein precipitation followed by methylene chloride liquid extraction of the supernatant (AB 4000; AB Sciex). A portion of the reconstituted sample was analyzed by liquid chromatography tandem mass spectrometry using a triple quad tandem mass spectrometer. Results were compared with those from nonsmoking asthmatic subjects not receiving inhaled FP. Twenty-two asthmatic subjects on FP and 9 asthmatic subjects without FP underwent sputum induction 16-24 hours following witnessed administration of FP. Sufficient sputum for analysis was obtained from 30 of 31 subjects. FP was detected in 22 of 22 asthmatic subjects receiving FP (range, 29-133,000 pg/mL) and was undetectable in 8 of 8 subjects not receiving FP. The sensitivity and specificity of tandem mass spectrometry's ability to detect FP in sputum was 100% and 100%, respectively. Analysis of FP in induced sputum is a reliable method to verify recent administration of inhaled FP. Induced asthmatic sputum from one induction may be used to concomitantly assess sputum eosinophilia as well as recent administration of FP.

  5. Intact MicroRNA Analysis Using High Resolution Mass Spectrometry

    PubMed Central

    Kullolli, Majlinda; Knouf, Emily; Arampatzidou, Maria; Tewari, Muneesh; Pitteri, Sharon J.

    2014-01-01

    MicroRNAs (miRNAs) are small single-stranded non-coding RNAs that post-transcriptionally regulate gene expression, and play key roles in the regulation of a variety of cellular processes and in disease. New tools to analyze miRNAs will add understanding of the physiological origins and biological functions of this class of molecules. In this study we investigate the utility of high resolution mass spectrometry for the analysis of miRNAs through proof-of-concept experiments. We demonstrate the ability of mass spectrometry to resolve and separate miRNAs and corresponding 3′ variants in mixtures. The mass accuracy of the monoisotopic deprotonated peaks from various miRNAs is in the low ppm range. We compare fragmentation of miRNA by collision-induced dissociation (CID) and by higher-energy collisional dissociation (HCD) which yields similar sequence coverage from both methods but additional fragmentation by HCD versus CID. We measure the linear dynamic range, limit of detection, and limit of quantitation of miRNA loaded onto a C18 column. Lastly we explore the use of data dependent acquisition of MS/MS spectra of miRNA during online LC-MS and demonstrate that multiple charge states can be fragmented, yielding nearly full sequence coverage of miRNA on a chromatographic time scale. We conclude that high resolution mass spectrometry allows the separation and measurement of miRNAs in mixtures and a standard LC-MS setup can be adapted for online analysis of these molecules. PMID:24174127

  6. Constraining Anthropogenic and Biogenic Emissions Using Chemical Ionization Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Spencer, Kathleen M.

    Numerous gas-phase anthropogenic and biogenic compounds are emitted into the atmosphere. These gases undergo oxidation to form other gas-phase species and particulate matter. Whether directly or indirectly, primary pollutants, secondary gas-phase products, and particulate matter all pose health and environmental risks. In this work, ambient measurements conducted using chemical ionization mass spectrometry are used as a tool for investigating regional air quality. Ambient measurements of peroxynitric acid (HO2NO2) were conducted in Mexico City. A method of inferring the rate of ozone production, PO3, is developed based on observations of HO2NO 2, NO, and NO2. Comparison of this observationally based PO3 to a highly constrained photochemical box model indicates that regulations aimed at reducing ozone levels in Mexico City by reducing NOx concentrations may be effective at higher NO x levels than predicted using accepted photochemistry. Measurements of SO2 and particulate sulfate were conducted over the Los Angeles basin in 2008 and are compared to measurements made in 2002. A large decrease in SO2 concentration and a change in spatial distribution are observed. Nevertheless, only a modest reduction in sulfate concentration is observed at ground sites within the basin. Possible explanations for these trends are investigated. Two techniques, single and triple quadrupole chemical ionization mass spectrometry, were used to quantify ambient concentrations of biogenic oxidation products, hydroxyacetone and glycolaldehyde. The use of these techniques demonstrates the advantage of triple quadrupole mass spectrometry for separation of mass analogues, provided the collision-induced daughter ions are sufficiently distinct. Enhancement ratios of hydroxyacetone and glycolaldehyde in Californian biomass burning plumes are presented as are concentrations of these compounds at a rural ground site downwind of Sacramento.

  7. Mass spectrometry-based identification of allergens from Curvularia pallescens, a prevalent aerospore in India.

    PubMed

    Dey, Debarati; Saha, Bodhisattwa; Sircar, Gaurab; Ghosal, Kavita; Bhattacharya, Swati Gupta

    2016-07-01

    The worldwide prevalence of fungal allergy in recent years has augmented mining allergens from yet unexplored ones. Curvularia pallescens (CP) being a dominant aerospore in India and a major sensitiser on a wide range of allergic population, pose a serious threat to human health. Therefore, we aimed to identify novel allergens from CP in our present study. A cohort of 22 CP-sensitised patients was selected by positive Skin prick grade. Individual sera exhibited elevated specific IgE level and significant histamine release on a challenge with antigenic extract of CP. First gel-based profiling of CP proteome was done by 1- and 2-dimensional gel. Parallel 1- and 2-dimensional immunoblot were performed applying individual as well as pooled patient sera. Identification of the sero-reactive spots from the 2-dimensional gel was found to be challenging as CP was not previously sequenced. Hence, mass spectrometry-based proteomic workflow consisting of conventional database search was not alone sufficient. Therefore, de novo sequencing preceded homology search was implemented for further identification. Altogether 11 allergenic proteins including Brn-1, vacuolar protease, and fructose-bis-phosphate aldolase were identified with high statistical confidence (p<0.05). This is the first study to report on any allergens from CP. This kind of proteome-based analysis provided a catalogue of CP allergens that would lead an improved way of diagnosis and therapy of CP-related allergy.

  8. Xylose Migration During Tandem Mass Spectrometry of N-Linked Glycans

    NASA Astrophysics Data System (ADS)

    Hecht, Elizabeth S.; Loziuk, Philip L.; Muddiman, David C.

    2017-01-01

    Understanding the rearrangement of gas-phase ions via tandem mass spectrometry is critical to improving manual and automated interpretation of complex datasets. N-glycan analysis may be carried out under collision induced (CID) or higher energy collision dissociation (HCD), which favors cleavage at the glycosidic bond. However, fucose migration has been observed in tandem MS, leading to the formation of new bonds over four saccharide units away. In the following work, we report the second instance of saccharide migration ever to occur for N-glycans. Using horseradish peroxidase as a standard, the beta-1,2 xylose was observed to migrate from a hexose to a glucosamine residue on the (Xyl)Man3GlcNac2 glycan. This investigation was followed up in a complex N-linked glycan mixture derived from stem differentiating xylem tissue, and the rearranged product ion was observed for 75% of the glycans. Rearrangement was not favored in isomeric glycans with a core or antennae fucose and unobserved in glycans predicted to have a permanent core-fucose modification. As the first empirical observation of this rearrangement, this work warrants dissemination so it may be searched in de novo sequencing glycan workflows.

  9. SWATH Mass Spectrometry Performance Using Extended Peptide MS/MS Assay Libraries.

    PubMed

    Wu, Jemma X; Song, Xiaomin; Pascovici, Dana; Zaw, Thiri; Care, Natasha; Krisp, Christoph; Molloy, Mark P

    2016-07-01

    The use of data-independent acquisition methods such as SWATH for mass spectrometry based proteomics is usually performed with peptide MS/MS assay libraries which enable identification and quantitation of peptide peak areas. Reference assay libraries can be generated locally through information dependent acquisition, or obtained from community data repositories for commonly studied organisms. However, there have been no studies performed to systematically evaluate how locally generated or repository-based assay libraries affect SWATH performance for proteomic studies. To undertake this analysis, we developed a software workflow, SwathXtend, which generates extended peptide assay libraries by integration with a local seed library and delivers statistical analysis of SWATH-quantitative comparisons. We designed test samples using peptides from a yeast extract spiked into peptides from human K562 cell lysates at three different ratios to simulate protein abundance change comparisons. SWATH-MS performance was assessed using local and external assay libraries of varying complexities and proteome compositions. These experiments demonstrated that local seed libraries integrated with external assay libraries achieve better performance than local assay libraries alone, in terms of the number of identified peptides and proteins and the specificity to detect differentially abundant proteins. Our findings show that the performance of extended assay libraries is influenced by the MS/MS feature similarity of the seed and external libraries, while statistical analysis using multiple testing corrections increases the statistical rigor needed when searching against large extended assay libraries.

  10. Analyzing the posttranslational modification status of Notch using mass spectrometry.

    PubMed

    Kakuda, Shinako; Haltiwanger, Robert S

    2014-01-01

    Notch is modified by multiple types of posttranslational modifications, most of which are known to affect Notch function. The extracellular domain (ECD) is modified with N-glycosylation and at least three types of O-glycosylation (O-fucose, O-glucose, and O-GlcNAc), while the intracellular domain is hydroxylated, phosphorylated, and ubiquitinated. In order to analyze the structure and function of the O-glycans decorating the ECD, we have developed semiquantitative mass spectral methods for identifying modifications at individual sites on Notch that are generally applicable to most posttranslational modifications. Here we describe the expression and purification of Notch ECD fragments, digestion of the fragments with proteases to prepare for mass spectral analysis, and identification of peptides modified with O-glycans using mass spectrometry.

  11. Revealing Higher Order Protein Structure Using Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Chait, Brian T.; Cadene, Martine; Olinares, Paul Dominic; Rout, Michael P.; Shi, Yi

    2016-06-01

    The development of rapid, sensitive, and accurate mass spectrometric methods for measuring peptides, proteins, and even intact protein assemblies has made mass spectrometry (MS) an extraordinarily enabling tool for structural biology. Here, we provide a personal perspective of the increasingly useful role that mass spectrometric techniques are exerting during the elucidation of higher order protein structures. Areas covered in this brief perspective include MS as an enabling tool for the high resolution structural biologist, for compositional analysis of endogenous protein complexes, for stoichiometry determination, as well as for integrated approaches for the structural elucidation of protein complexes. We conclude with a vision for the future role of MS-based techniques in the development of a multi-scale molecular microscope.

  12. Mass spectrometry technology at the Jet Propulsion Laboratory (JPL)

    NASA Technical Reports Server (NTRS)

    Giffin, C. E.

    1985-01-01

    Recent developments in the field of mass spectrometry taking place at the Caltech Jet Propulsion Laboratory are highlighted. The pertinent research and development is aimed at producing an ultrahigh sensitivity mass spectrograph for both spaceflight and terrestrial applications. The unique aspect of the JPL developed technology is an integrating focal plane ion detector that obviates the need for spectral scanning since all ions over a wide mass range are monitored simultaneously. The ion detector utilizes electro-optical technology and is therefore referred to as an Electro-Optical Ion Detector (EOID). A technical description of the JPL MS/EOID, some of the current applications, and its potential benefits for internal contamination analysis are discussed.

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

    DOE PAGES

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

    2017-03-29

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

  14. Apparatus for studying premixed laminar flames using mass spectrometry and fiber-optic spectrometry

    NASA Astrophysics Data System (ADS)

    Olsson, Jim O.; Andersson, Lars L.; Lenner, Magnus; Simonson, Margaret

    1990-03-01

    An integrated flat-flame/ microprobe sampling quadrupole mass spectrometer system, complemented by optical spectrometry based on optical fibers, is presented. The short microprobe sampling line (total 25 cm) is directly connected to an open ion source closely flanked by two nude cryopumps (900 l/s) yielding a background pressure of 10-9 Torr and a sampling pressure of about 10-5 Torr. Due to this improved microprobe system, mass spectrometry can be used for analysis of stable species (including fuel, O2, H2O, CO2, CO, and Ar) with less disturbance of the sample than with a conventional microprobe with a back pressure of about 1 Torr. Optical spectrometry is used for the study of emission from important radical species (such as C2, CH, and OH). The system is proposed as a complement to more conventional flat-flame/MBMS systems in which the sampling cone can effect the experimental system. Details are provided concerning the configuration of the whole system ranging from gas delivery to data evaluation. Test data are presented for a 16% methanol/68% oxygen/16% argon flame studied at a pressure of 40 Torr, to elucidate the special features of this system.

  15. Miniaturized Digestion and Extraction of Surface Proteins from Candida albicans following Treatment with Histatin 5 for Mass Spectrometry Analysis

    PubMed Central

    Fan, Shirley; Xiao, Yizhi; Siqueira, Walter L.

    2016-01-01

    A common approach to isolate surface proteins from fungal and bacterial cells is to perform a proteolytic cleavage of proteins on the surface of intact cells suspended in solution. This paper describes miniaturization of this technique, in which cells are adhered on glass surfaces, and all sample treatments are conducted at μL volumes. Specifically, Candida albicans cells were attached onto HSA-coated glass slides. By depositing the appropriate reagent solutions on the adhered cells, we successfully performed cell washing, treatment with antifugal peptide, Histatin 5, and a proteolysis on intact cells with trypsin. The resulting peptides were subsequently analysed by mass spectrometry. In general, the data obtained was similar to that collected with suspended cells in much larger sample volumes. However, our miniaturized workflow offers the benefit of greatly reducing the consumption of cells and reagents. PMID:28044106

  16. 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…

  17. The role of mass spectrometry in atomic weight determinations.

    PubMed

    De Laeter, John R

    2009-01-01

    The 1914 Nobel Prize for Chemistry was awarded to Theodore Richards, whose work provided an insight into the history of the birth and evolution of matter as embedded in the atomic weights. However, the secret to unlocking the hieroglyphics contained in the atomic weights is revealed by a study of the relative abundances of the isotopes. A consistent set of internationally accepted atomic weights has been a goal of the scientific community for over a century. Atomic weights were originally determined by chemical stoichiometry--the so-called "Harvard Method," but this methodology has now been superseded by the "physical method," in which the isotopic composition and atomic masses of the isotopes comprising an element are used to calculate the atomic weight with far greater accuracy than before. The role of mass spectrometry in atomic weight determinations was initiated by the discovery of isotopes by Thomson, and established by the pioneering work of Aston, Dempster, and Nier using sophisticated mass spectrographs. The advent of the sector field mass spectrometer in 1947, revolutionized the application of mass spectrometry for both solids and gases to other fields of science including atomic weights. Subsequently, technological advances in mass spectrometry have enabled atomic masses to be determined with an accuracy better than one part in 10(7), whilst the absolute isotopic composition of many elements has been determined to produce accurate values of their atomic weights. Conversely, those same technological developments have revealed significant variations in the isotope abundances of many elements caused by a variety of physiochemical mechanisms in natural materials. Although these variations were initially seen as an impediment to the accuracy with which atomic weights could be determined, it was quickly realized that nature had provided a new tool to investigate physiochemical and biogeochemical mechanisms in nature, which could be exploited by precise and

  18. Capillary zone electrophoresis-mass spectrometry of peptides and proteins

    SciTech Connect

    Loo, J.A.; Udseth, H.R.; Smith, R.D.

    1989-05-01

    Capillary zone electrophoresis (CZE) is attracting extensive attention as a fast, high resolution analytical and micro-preparative separations technique for systems of biological interest. In zone electrophoresis, a column is filled with a single electrolyte having a specific conductivity. The mixture of substances to be separated is applied as a narrow band to the head of a buffer filled column in a band whose width is much less than the length of the column and at a concentration too low to affect the buffer conductivity. An electric field is then applied across the length of the column and the individual substances migrate and separate according to their net electrophoretic velocities. Zone electrophoresis carried out in small diameter (<100 ..mu..m) fused silica capillaries is a relatively new approach to the high resolution separation of aqueous samples. Very small volume samples (picoliter range) with separation efficiencies on the order of 10/sup 6/ theoretical plates for amino acids have been achieved. The method can be further enhanced by the dynamic combination of detection sensitivity and selectivity offered by mass spectrometry (MS). The on-line marriage of mass spectrometry to CZE is accomplished by an atmospheric pressure electrospray ionization source interface. Our research efforts have demonstrated that proteins with MW's greater than 100 kDa can be analyzed using a conventional quadrupole mass spectrometer with an upper m/z limit of only 1700. 6 refs.

  19. Accelerator Mass Spectrometry for Measurement of Long-Lived Radioisotopes

    NASA Astrophysics Data System (ADS)

    Elmore, David; Phillips, Fred M.

    1987-05-01

    Particle accelerators, such as those built for research in nuclear physics, can also be used together with magnetic and electrostatic mass analyzers to measure rare isotopes at very low abundance ratios. All molecular ions can be eliminated when accelerated to energies of millions of electron volts. Some atomic isobars can be eliminated with the use of negative ions; others can be separated at high energies by measuring their rate of energy loss in a detector. The long-lived radioisotopes 10Be, 14C, 26Al, 36Cl, and 129I can now be measured in small natural samples having isotopic abundances in the range 10-12 to 10-15 and as few as 105 atoms. In the past few years, research applications of accelerator mass spectrometry have been concentrated in the earth sciences (climatology, cosmochemistry, environmental chemistry, geochronology, glaciology, hydrology, igneous petrogenesis, minerals exploration, sedimentology, and volcanology), in anthropology and archeology (radiocarbon dating), and in physics (searches for exotic particles and measurement of half-lives). In addition, accelerator mass spectrometry may become an important tool for the materials and biological sciences.

  20. Resonance ionization mass spectrometry for isotopic abundance measurements

    NASA Technical Reports Server (NTRS)

    Miller, C. M.

    1986-01-01

    Resonance ionization mass spectrometry (RIMS) is a relatively new laser-based technique for the determination of isotopic abundances. The resonance ionization process depends upon the stepwise absorption of photons from the laser, promoting atoms of the element of interest through progressively higher electronic states until an ion is formed. Sensitivity arises from the efficiency of the resonant absorption process when coupled with the power available from commercial laser sources. Selectivity derives naturally from the distinct electronic structure of different elements. This isobaric discrimination has provided the major impetus for development of the technique. Resonance ionization mass spectrometry was used for analysis of the isotopic abundances of the rare earth lutetium. Isobaric interferences from ytterbium severely effect the ability to measure small amounts of the neutron-deficient Lu isotopes by conventional mass spectrometric techniques. Resonance ionization for lutetium is performed using a continuous-wave laser operating at 452 nm, through a sequential two-photon process, with one photon exciting the intermediate resonance and the second photon causing ionization. Ion yields for microgram-sized quantities of lutetium lie between 10(6) and 10(7) ions per second, at overall ionization efficiencies approaching 10(-4). Discrimination factors against ytterbium greater than 10(6) have been measured. Resonance ionization for technetium is also being explored, again in response to an isobaric interference, molybdenum. Because of the relatively high ionization potential for Tc, three-photon, two-color RIMS processes are being developed.

  1. Capillary isoelectric focusing-electrospray mass spectrometry for protein analysis

    SciTech Connect

    Tang, Q.; Harrata, A.K.; Lee, C.S.

    1995-10-01

    On-line combination of capillary isoelectric focusing (CIEF) with electrospray mass spectrometry (ESMS) as a two-dimensional separation system is demonstrated. Mixtures of model proteins including cytochrome c (horse heart), myoglobin (horse heart), and carbonic anhydrase II (bovine erythrocyte) are focused and cathodically mobilized in a polyacrylamide-coated capillary. At the end of CIEF capillary, the mobilized protein zones are analyzed by mass spectrometry coupled on-line to an electrospray interface with a coaxial sheath flow configuration. The effects of carrier ampholyte concentration on the CIEF separation and the protein electrospray ionization mass spectra are presented and discussed. In this study, the focusing effect of CIEF permits analysis of very dilute protein samples. A typical concentration factor of 50-100 times is observed. The concentration detection limit of myoglobin for a full-scan CIEF-ESMS analysis is in the range of 10{sup -7} M, 2 orders of magnitude over that possible with normal capillary zone electrophoresis ESMS. 35 refs., 5 figs., 2 tabs.

  2. Direct and Convenient Mass Spectrometry Sampling with Ambient Flame Ionization

    PubMed Central

    Liu, Xiao-Pan; Wang, Hao-Yang; Zhang, Jun-Ting; Wu, Meng-Xi; Qi, Wan-Shu; Zhu, Hui; Guo, Yin-Long

    2015-01-01

    Recent innovations in ambient ionization technology for the direct analysis of various samples in their native environment facilitate the development and applications of mass spectrometry in natural science. Presented here is a novel, convenient and flame-based ambient ionization method for mass spectrometric analysis of organic compounds, termed as the ambient flame ionization (AFI) ion source. The key features of AFI ion source were no requirement of (high) voltages, laser beams and spray gases, but just using small size of n-butane flame (height approximately 1 cm, about 500 oC) to accomplish the rapid desorption and ionization for direct analysis of gaseous-, liquid- and solid-phase organic compounds, as well as real-world samples. This method has high sensitivity with a limit of detection of 1 picogram for propyphenazone, which allows consuming trace amount of samples. Compared to previous ionization methods, this ion source device is extremely simple, maintain-free, low-cost, user–friendly so that even an ordinary lighter (with n-butane as fuel) can achieve efficient ionization. A new orientation to mass spectrometry ion source exploitation might emerge from such a convenient, easy and inexpensive AFI ion source. PMID:26582511

  3. Botulinum Neurotoxin Detection and Differentiation by Mass Spectrometry

    PubMed Central

    Moura, Hercules; Boyer, Anne E.; Woolfitt, Adrian R.; Kalb, Suzanne R.; Pavlopoulos, Antonis; McWilliams, Lisa G.; Schmidt, Jurgen G.; Martinez, Rodolfo A.; Ashley, David L.

    2005-01-01

    Botulinum neurotoxins (BoNTs) are proteases that cleave specific cellular proteins essential for neurotransmitter release. Seven BoNT serotypes (A–G) exist; 4 usually cause human botulism (A, B, E, and F). We developed a rapid, mass spectrometry–based method (Endopep-MS) to detect and differentiate active BoNTs A, B, E, and F. This method uses the highly specific protease activity of the toxins with target peptides specific for each toxin serotype. The product peptides derived from the endopeptidase activities of BoNTs are detected by matrix-assisted laser-desorption ionization time-of-flight mass spectrometry. In buffer, this method can detect toxin equivalents of as little as 0.01 mouse lethal dose (MLD)50 and concentrations as low as 0.62 MLD50/mL. A high-performance liquid chromatography–tandem mass spectrometry method for quantifying active toxin, where the amount of toxin can be correlated to the amount of product peptides, is also described. PMID:16318699

  4. Characterization of botulinum progenitor toxins by mass spectrometry.

    PubMed

    Hines, Harry B; Lebeda, Frank; Hale, Martha; Brueggemann, Ernst E

    2005-08-01

    Botulinum toxin analysis has renewed importance. This study included the use of nanochromatography-nanoelectrospray-mass spectrometry/mass spectrometry to characterize the protein composition of botulinum progenitor toxins and to assign botulinum progenitor toxins to their proper serotype and strain by using currently available sequence information. Clostridium botulinum progenitor toxins from strains Hall, Okra, Stockholm, MDPH, Alaska, and Langeland and 89 representing serotypes A through G, respectively, were reduced, alkylated, digested with trypsin, and identified by matching the processed product ion spectra of the tryptic peptides to proteins in accessible databases. All proteins known to be present in progenitor toxins from each serotype were identified. Additional proteins, including flagellins, ORF-X1, and neurotoxin binding protein, not previously reported to be associated with progenitor toxins, were present also in samples from several serotypes. Protein identification was used to assign toxins to a serotype and strain. Serotype assignments were accurate, and strain assignments were best when either sufficient nucleotide or amino acid sequence data were available. Minor difficulties were encountered using neurotoxin-associated protein identification for assigning serotype and strain. This study found that combined nanoscale chromatographic and mass spectrometric techniques can characterize C. botulinum progenitor toxin protein composition and that serotype/strain assignments based upon these proteins can provide accurate serotype and, in most instances, strain assignments using currently available information. Assignment accuracy will continue to improve as more nucleotide/amino acid sequence information becomes available for different botulinum strains.

  5. Accelerator mass spectrometry for measurement of long-lived radioisotopes.

    PubMed

    Elmore, D; Phillips, F M

    1987-05-01

    Particle accelerators, such as those built for research in nuclear physics, can also be used together with magnetic and electrostatic mass analyzers to measure rare isotopes at very low abundance ratios. All molecular ions can be eliminated when accelerated to energies of millions of electron volts. Some atomic isobars can be eliminated with the use of negative ions; others can be separated at high energies by measuring their rate of energy loss in a detector. The long-lived radioisotopes (10)Be, (14)C,(26)A1, 36Cl, and (129)1 can now be measured in small natural samples having isotopic abundances in the range 10(-12) to 10(- 5) and as few as 10(5) atoms. In the past few years, research applications of accelerator mass spectrometry have been concentrated in the earth sciences (climatology, cosmochemistry, environmental chemistry, geochronology, glaciology, hydrology, igneous petrogenesis, minerals exploration, sedimentology, and volcanology), in anthropology and archeology (radiocarbon dating), and in physics (searches for exotic particles and measurement of halflives). In addition, accelerator mass spectrometry may become an important tool for the materials and biological sciences.

  6. Analysis of metal-EDTA complexes by electrospray mass spectrometry

    SciTech Connect

    Baron, D.; Hering, J.G.

    1998-07-01

    Solutions of the strong complexing agent ethylenediaminetetraacetic acid (EDTA) and Cu, Pb, Cd, Al, and Fe(III) were examined by electrospray mass spectrometry (ES/MS). Uncomplexed EDTA and metal-EDTA complexes survive the electrospray process intact and can be detected simultaneously by mass spectrometry. Best sensitivity was achieved in the positive ion mode in which EDTA and EDTA-metal complexes (present in solution as anions) were detected as protonated species with a single positive charge. Except for the protonation, the aqueous metal-EDTA complexes are preserved and neither fragmentation of complexes nor formation of clusters with more than one metal or ligand were observed in the mass spectra. Detection limits are between approximately 1 to 2 {micro}M for uncomplexed EDTA and for the Cu-EDTA and Pb-EDTA complexes, with a linear range up to 10{sup {minus}4} M. Calibrations based on solutions with equimolar concentrations of EDTA and Cu or Pb can be used to quantify EDTA-metal complexes in solutions with excess EDTA or metal, and in solutions with more than one metal present. Isotopic signatures of metals in the metal-ligand complexes are preserved, allowing the identification of the metal in a metal-ligand complex. Isotopic signatures of metals can therefore aid in the identification of metal-ligand complexes in unknown samples.

  7. Laser desorption mass spectrometry for point mutation detection

    SciTech Connect

    Taranenko, N.I.; Chung, C.N.; Zhu, Y.F.

    1996-10-01

    A point mutation can be associated with the pathogenesis of inherited or acquired diseases. Laser desorption mass spectrometry coupled with allele specific polymerase chain reaction (PCR) was first used for point mutation detection. G551D is one of several mutations of the cystic fibrosis transmembrane conductance regulator (CFTR) gene present in 1-3% of the mutant CFTR alleles in most European populations. In this work, two different approaches were pursued to detect G551D point mutation in the cystic fibrosis gene. The strategy is to amplify the desired region of DNA template by PCR using two primers that overlap one base at the site of the point mutation and which vary in size. If the two primers based on the normal sequence match the target DNA sequence, a normal PCR product will be produced. However, if the alternately sized primers that match the mutant sequence recognize the target DNA, an abnormal PCR product will be produced. Thus, the mass spectrometer can be used to identify patients that are homozygous normal, heterozygous for a mutation or homozygous abnormal at a mutation site. Another approach to identify similar mutations is the use of sequence specific restriction enzymes which respond to changes in the DNA sequence. Mass spectrometry is used to detect the length of the restriction fragments generated by digestion of a PCR generated target fragment. 21 refs., 10 figs., 2 tabs.

  8. Laser desorption mass spectrometry for point mutation detection

    SciTech Connect

    Taranenko, N.I.; Chung, C.N.; Zhu, Y.F.

    1996-12-31

    A point mutation can be associated with the pathogenesis of inherited or acquired diseases. Laser desorption mass spectrometry coupled with allele specific polymerase chain reaction (PCR) was first used for point mutation detection. G551D is one of several mutations of the cystic fibrosis transmembrane conductance regulator (CFTR) gene present in 1-3% of the mutant CFTR alleles in most European populations. In this work, two different approaches were pursued to detect G551D point mutation in the cystic fibrosis gene. The strategy is to amplify the desired region of DNA template by PCR using two primers that overlap one base at the site of the point mutation and which vary in size. If the two primers based on the normal sequence match the target DNA sequence, a normal PCR product will be produced. However, if the alternately sized primers that match the mutant sequence recognize the target DNA, an abnormal PCR product will be produced. Thus, the mass spectrometer can be used to identify patients that are homozygous normal, heterozygous for a mutation or homozygous abnormal at a mutation site. Another approach to identify similar mutations is the use of sequence specific restriction enzymes which respond to changes in the DNA sequence. Mass spectrometry is used to detect the length of the restriction fragments by digestion of a PCR generated target fragment. 21 refs., 10 figs., 2 tabs.

  9. Towards airborne nanoparticle mass spectrometry with nanomechanical string resonators

    NASA Astrophysics Data System (ADS)

    Schmid, Silvan; Kurek, Maksymilian; Boisen, Anja

    2013-06-01

    Airborne nanoparticles can cause severe harm when inhaled. Therefore, small and cheap portable airborne nanoparticle monitors are highly demanded by authorities and the nanoparticle producing industry. We propose to use nanomechanical resonators to build the next generation cheap and portable airborne nanoparticle sensors. Recently, nanomechanical mass spectrometry was established. One of the biggest challenges of nanomechanical sensors is the low efficiency of diffusion-based sampling. We developed an inertial-based sampling method that enables the efficient sampling of airborne nanoparticles on a nanomechanical sensor operating directly in air. We measured a sampling rate of over 1000 particles per second, for 28 nm silica nanoparticles with a concentration of 380000 #/cm3, collected on a 500 nm wide nanomechanical string resonator. We show that it is possible to reach a saturated sampling regime in which 100% of all nanoparticles are captured that are owing in the projection of the nanostring. We further show that it is possible to detect single airborne nanoparticles by detecting 50 nm Au particles with a 250 nm wide string resonator. Our resonators are currently operating in the first bending mode. Mass spectrometry of airborne nanoparticles requires the simultaneous operation in the first and second mode, which can be implemented in the transduction scheme of the resonator. The presented results lay the cornerstone for the realization of a portable airborne nanoparticle mass spectrometer.

  10. Rapid Analysis of Isobaric Exogenous Metabolites by Differential Mobility Spectrometry Mass Spectrometry

    SciTech Connect

    Parson, Whitney B; Schneider, Bradley B; Kertesz, Vilmos; Corr, Jay; Covey, Thomas R.; Van Berkel, Gary J

    2011-01-01

    The direct separation of isobaric glucuronide metabolites from propranolol dosed tissue extracts by differential mobility spectrometry mass spectrometry (DMS-MS) with the use of a polar gas-phase chemical modifier was demonstrated. The DMS gas-phase separation was able to resolve the isobaric metabolites with separation times on the order of ms instead of mins to hrs typically required when using pre-ionization chromatographic separation methods. Direct separation of isobaric metabolites from the complex tissue extract was validated using standards as well as implementing an HPLC separation prior to the DMS-MS analysis to pre-separate the species of interest. The ability to separate isobaric exogenous metabolites directly from a complex tissue extract is expected to facilitate the drug development process by increasing analytical throughput without the requirement for pre-ionization cleanup or separation strategies.

  11. Uncovering biologically significant lipid isomers with liquid chromatography, ion mobility spectrometry and mass spectrometry

    SciTech Connect

    Kyle, Jennifer E.; Zhang, Xing; Weitz, Karl K.; Monroe, Matthew E.; Ibrahim, Yehia M.; Moore, Ronald J.; Cha, Jeeyeon; Sun, Xiaofei; Lovelace, Erica S.; Wagoner, Jessica; Polyak, Stephen J.; Metz, Thomas O.; Dey, Sudhansu K.; Smith, Richard D.; Burnum-Johnson, Kristin E.; Baker, Erin S.

    2016-01-01

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

  12. Uncovering Biologically Significant Lipid Isomers with Liquid Chromatography, Ion Mobility Spectrometry and Mass Spectrometry

    PubMed Central

    Kyle, Jennifer E.; Zhang, Xing; Weitz, Karl K.; Monroe, Matthew E.; Ibrahim, Yehia M.; Moore, Ronald J.; Cha, Jeeyeon; Sun, Xiaofei; Lovelace, Erica S.; Wagoner, Jessica; Polyak, Stephen J.; Metz, Thomas O.; Dey, Sudhansu K.; Smith, Richard D.; Burnum-Johnson, Kristin E.; Baker, Erin S.

    2016-01-01

    Understanding how biological molecules are generated, metabolized and eliminated in living systems is important for interpreting processes such as immune response and disease pathology. While genomic and proteomic studies have provided vast amounts of information over the last several decades, interest in lipidomics has also grown due to improved analytical technologies revealing altered lipid metabolism in type 2 diabetes, cancer, and lipid storage disease. Mass spectrometry (MS) measurements are currently the dominant approach for characterizing the lipidome by providing detailed information on the spatial and temporal composition of lipids. However, interpreting lipids’ biological roles is challenging due to the existence of numerous structural and stereoisomers (i.e. distinct acyl chain and double-bond positions), which are often unresolvable using present approaches. Here we show that combining liquid chromatography (LC) and structurally-based ion mobility spectrometry (IMS) measurement with MS analyses distinguishes lipid isomers and allows insight into biological and disease processes. PMID:26734689

  13. Fast Screening of Polycyclic Aromatic Hydrocarbons using Trapped Ion Mobility Spectrometry - Mass Spectrometry

    PubMed Central

    Castellanos, A.; Benigni, P.; Hernandez, D. R.; DeBord, J. D.; Ridgeway, M. E.; Park, M. A.

    2014-01-01

    In the present paper, we showed the advantages of trapped ion mobility spectrometry coupled too mass spectrometry (TIMS-MS) combined with theoretical calculations for fast identification (millisecond timescale) of polycyclic aromatic hydrocarbons (PAH) compounds from complex mixtures. Accurate PAH collision cross sections (CCS, in nitrogen as a bath gas) are reported for the most commonly encountered PAH compounds and the ability to separate PAH geometric isomers is shown for three isobaric pairs with mobility resolution exceeding 150 (3–5 times higher than conventional IMS devices). Theoretical candidate structures (optimized at the DFT/B3LYP level) are proposed for the most commonly encountered PAH compounds showing good agreement with the experimental CCS values (<5%). The potential of TIMS-MS for the separation and identification of PAH compounds from complex mixtures without the need of lengthy pre-separation steps is illustrated for the case of a complex soil mixture. PMID:25558291

  14. Analysis of wastewater samples by direct combination of thin-film microextraction and desorption electrospray ionization mass spectrometry.

    PubMed

    Strittmatter, Nicole; Düring, Rolf-Alexander; Takáts, Zoltán

    2012-09-07

    An analysis method for aqueous samples by the direct combination of C18/SCX mixed mode thin-film microextraction (TFME) and desorption electrospray ionization mass spectrometry (DESI-MS) was developed. Both techniques make analytical workflow simpler and faster, hence the combination of the two techniques enables considerably shorter analysis time compared to the traditional liquid chromatography mass spectrometry (LC-MS) approach. The method was characterized using carbamazepine and triclosan as typical examples for pharmaceuticals and personal care product (PPCP) components which draw increasing attention as wastewater-derived environmental contaminants. Both model compounds were successfully detected in real wastewater samples and their concentrations determined using external calibration with isotope labeled standards. Effects of temperature, agitation, sample volume, and exposure time were investigated in the case of spiked aqueous samples. Results were compared to those of parallel HPLC-MS determinations and good agreement was found through a three orders of magnitude wide concentration range. Serious matrix effects were observed in treated wastewater, but lower limits of detection were still found to be in the low ng L(-1) range. Using an Orbitrap mass spectrometer, the technique was found to be ideal for screening purposes and led to the detection of various different PPCP components in wastewater treatment plant effluents, including beta-blockers, nonsteroidal anti-inflammatory drugs, and UV filters.

  15. Calibration using constrained smoothing with applications to mass spectrometry data.

    PubMed

    Feng, Xingdong; Sedransk, Nell; Xia, Jessie Q

    2014-06-01

    Linear regressions are commonly used to calibrate the signal measurements in proteomic analysis by mass spectrometry. However, with or without a monotone (e.g., log) transformation, data from such functional proteomic experiments are not necessarily linear or even monotone functions of protein (or peptide) concentration except over a very restricted range. A computationally efficient spline procedure improves upon linear regression. However, mass spectrometry data are not necessarily homoscedastic; more often the variation of measured concentrations increases disproportionately near the boundaries of the instruments measurement capability (dynamic range), that is, the upper and lower limits of quantitation. These calibration difficulties exist with other applications of mass spectrometry as well as with other broad-scale calibrations. Therefore the method proposed here uses a functional data approach to define the calibration curve and also the limits of quantitation under the two assumptions: (i) that the variance is a bounded, convex function of concentration; and (ii) that the calibration curve itself is monotone at least between the limits of quantitation, but not necessarily outside these limits. Within this paradigm, the limit of detection, where the signal is definitely present but not measurable with any accuracy, is also defined. An iterative approach draws on existing smoothing methods to account simultaneously for both restrictions and is shown to achieve the global optimal convergence rate under weak conditions. This approach can also be implemented when convexity is replaced by other (bounded) restrictions. Examples from Addona et al. (2009, Nature Biotechnology 27, 663-641) both motivate and illustrate the effectiveness of this functional data methodology when compared with the simpler linear regressions and spline techniques.

  16. Future Directions of Structural Mass Spectrometry using Hydroxyl Radical Footprinting

    SciTech Connect

    J Kiselar; M Chance

    2011-12-31

    Hydroxyl radical protein footprinting coupled to mass spectrometry has been developed over the last decade and has matured to a powerful method for analyzing protein structure and dynamics. It has been successfully applied in the analysis of protein structure, protein folding, protein dynamics, and protein-protein and protein-DNA interactions. Using synchrotron radiolysis, exposure of proteins to a 'white' X-ray beam for milliseconds provides sufficient oxidative modification to surface amino acid side chains, which can be easily detected and quantified by mass spectrometry. Thus, conformational changes in proteins or protein complexes can be examined using a time-resolved approach, which would be a valuable method for the study of macromolecular dynamics. In this review, we describe a new application of hydroxyl radical protein footprinting to probe the time evolution of the calcium-dependent conformational changes of gelsolin on the millisecond timescale. The data suggest a cooperative transition as multiple sites in different molecular subdomains have similar rates of conformational change. These findings demonstrate that time-resolved protein footprinting is suitable for studies of protein dynamics that occur over periods ranging from milliseconds to seconds. In this review, we also show how the structural resolution and sensitivity of the technology can be improved as well. The hydroxyl radical varies in its reactivity to different side chains by over two orders of magnitude, thus oxidation of amino acid side chains of lower reactivity are more rarely observed in such experiments. Here we demonstrate that the selected reaction monitoring (SRM)-based method can be utilized for quantification of oxidized species, improving the signal-to-noise ratio. This expansion of the set of oxidized residues of lower reactivity will improve the overall structural resolution of the technique. This approach is also suggested as a basis for developing hypothesis

  17. Molecular scavengers as carriers of analytes for mass spectrometry identification.

    PubMed

    Smoluch, Marek; Ceglowski, Michal; Kurczewska, Joanna; Babij, Michal; Gotszalk, Teodor; Silberring, Jerzy; Schroeder, Grzegorz

    2014-11-18

    Storage and preconcentration of various molecules by molecular scavengers for thermal desorption and identification by mass spectrometry is presented. A dielectric barrier discharge ionization source combined with a heating element for the chemical characterization of amines and organic acids, initially trapped by molecular scavengers, is described. The developed technique can be applied for preconcentration of minute amounts of molecules in liquid and gaseous phases, as well as their transportation and thorough analysis. The method, operating at ambient pressure, can also be complementary to electron impact ionization, with no need for sample derivatization.

  18. Considerations for electron capture dissociation efficiency in FTICR mass spectrometry

    NASA Astrophysics Data System (ADS)

    Gorshkov, Michael V.; Masselon, Christophe D.; Nikolaev, Eugene N.; Udseth, Harold R.; Pasa-Tolic, Ljiljana; Smith, Richard D.

    2004-05-01

    An experimental approach for increasing the efficiency of Electron Capture Dissociation (ECD) with Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) is presented. The approach is based on manipulating the spatial distribution of an ion cloud inside an FTICR trap during electron irradiation, which is realized by using both on-resonance pre-excitation of the ions and sustained off-resonance irradiation (SORI). The achieved fragmentation efficiency is compared with the theoretical prediction. This method may be useful in biological applications of FTICR, such as identification of posttranslational modifications in proteins and de novo sequencing, where the ECD technique is most applicable.

  19. Toward Digital Staining using Imaging Mass Spectrometry and Random Forests

    PubMed Central

    Hanselmann, Michael; Köthe, Ullrich; Kirchner, Marc; Renard, Bernhard Y.; Amstalden, Erika R.; Glunde, Kristine; Heeren, Ron M. A.; Hamprecht, Fred A.

    2009-01-01

    We show on Imaging Mass Spectrometry (IMS) data that the Random Forest classifier can be used for automated tissue classification and that it results in predictions with high sensitivities and positive predictive values, even when inter-sample variability is present in the data. We further demonstrate how Markov Random Fields and vector-valued median filtering can be applied to reduce noise effects to further improve the classification results in a post-hoc smoothing step. Our study gives clear evidence that digital staining by means of IMS constitutes a promising complement to chemical staining techniques. PMID:19469555

  20. Web Resources for Mass Spectrometry-based Proteomics

    PubMed Central

    Chen, Tao; Zhao, Jie; Ma, Jie; Zhu, Yunping

    2015-01-01

    With the development of high-resolution and high-throughput mass spectrometry (MS) technology, a large quantum of proteomic data is continually being generated. Collecting and sharing these data are a challenge that requires immense and sustained human effort. In this report, we provide a classification of important web resources for MS-based proteomics and present rating of these web resources, based on whether raw data are stored, whether data submission is supported, and whether data analysis pipelines are provided. These web resources are important for biologists involved in proteomics research. PMID:25721607

  1. Applications of ambient mass spectrometry in high-throughput screening.

    PubMed

    Li, Li-Ping; Feng, Bao-Sheng; Yang, Jian-Wang; Chang, Cui-Lan; Bai, Yu; Liu, Hu-Wei

    2013-06-07

    The development of rapid screening and identification techniques is of great importance for drug discovery, doping control, forensic identification, food safety and quality control. Ambient mass spectrometry (AMS) allows rapid and direct analysis of various samples in open air with little sample preparation. Recently, its applications in high-throughput screening have been in rapid progress. During the past decade, various ambient ionization techniques have been developed and applied in high-throughput screening. This review discusses typical applications of AMS, including DESI (desorption electrospray ionization), DART (direct analysis in real time), EESI (extractive electrospray ionization), etc., in high-throughput screening (HTS).

  2. Vaporization Studies of Olivine via Knudsen Effusion Mass Spectrometry

    NASA Technical Reports Server (NTRS)

    Costa, G. C. C.; Jacobson, N. S.

    2014-01-01

    Olivine is the major mineral in the Earth's upper mantle occurring predominantly in igneous rocks and has been identified in meteorites, asteroids, the Moon and Mars. Among many other important applications in planetary and materials sciences, the thermodynamic properties of vapor species from olivine are crucial as input parameters in computational modelling of the atmospheres of hot, rocky exoplanets (lava planets). There are several weight loss studies of olivine vaporization in the literature and one Knudsen Effusion Mass Spectrometry (KEMS) study. In this study, we examine a forsterite-rich olivine (93% forsterite and 7% fayalite, Fo93Fa7) with KEMS to further understand its vaporization and thermodynamic properties.

  3. Solid support resins and affinity purification mass spectrometry.

    PubMed

    Havis, Spencer; Moree, Wilna J; Mali, Sujina; Bark, Steven J

    2017-02-28

    Co-affinity purification-mass spectrometry (CoAP-MS) is a primary technology for elucidating the protein-protein interactions that form the basis of all biological processes. A critical component of CoAP-MS is the affinity purification (AP) of the bait protein, usually by immobilization of an antibody to a solid-phase resin. This Minireview discusses common resins, reagents, tagging methods, and their consideration for successful AP of tagged proteins. We discuss our experiences with different solid supports, their impact in AP experiments, and propose areas where chemistry can advance this important technology.

  4. Drug confirmation by mass spectrometry: Identification criteria and complicating factors.

    PubMed

    Yuan, Chao; Chen, Derrick; Wang, Sihe

    2015-01-01

    Drug confirmation by mass spectrometry coupled with chromatography is essential to toxicology, doping control, pain management, and workplace drug testing. High confidence in this technology is due to its superior specificity and sensitivity. However, there are challenges associated with drug confirmation, and proper setup and validation of these assays are important in assuring high-quality results. In this article, assay parameters required for drug confirmation are summarized based on recent scientific publications, various established guidelines, and our own practical experience. Factors affecting the result quality and correct results interpretation are critically reviewed. Several emerging technologies and their potential applications are briefly explored.

  5. Small sample Accelerator Mass Spectrometry for biomedical applications

    NASA Astrophysics Data System (ADS)

    Salehpour, M.; Håkansson, K.; Possnert, G.

    2015-10-01

    The Accelerator Mass Spectrometry activities at Uppsala University include a group dedicated to the biomedical applications, involving natural level samples, as well as 14C-labeled substances requiring separate handling and preparation. For most applications sufficient sample amounts are available but many applications are limited to samples sizes in the μg-range. We have developed a preparation procedure for small samples biomedical applications, where a few μg C can be analyzed, albeit with compromised precision. The latest results for the small sample AMS method are shown and some of the biomedical activities at our laboratory are presented.

  6. Mass spectrometry cancer data classification using wavelets and genetic algorithm.

    PubMed

    Nguyen, Thanh; Nahavandi, Saeid; Creighton, Douglas; Khosravi, Abbas

    2015-12-21

    This paper introduces a hybrid feature extraction method applied to mass spectrometry (MS) data for cancer classification. Haar wavelets are employed to transform MS data into orthogonal wavelet coefficients. The most prominent discriminant wavelets are then selected by genetic algorithm (GA) to form feature sets. The combination of wavelets and GA yields highly distinct feature sets that serve as inputs to classification algorithms. Experimental results show the robustness and significant dominance of the wavelet-GA against competitive methods. The proposed method therefore can be applied to cancer classification models that are useful as real clinical decision support systems for medical practitioners.

  7. Rapid Identification of Vector-Borne Flaviviruses by Mass Spectrometry

    DTIC Science & Technology

    2010-01-01

    replicates of 10. All six mosquito-borne primer sets (VIR2215, VIR2217, VIR2211, VIR2216, VIR1026, VIR1028) had 100% sensitivity (10/10 reactions were...borne Flavivirus RT-PCR primer pairs. From a known West Nile virus (WNV) titer, the RNA was serially diluted ten-fold. Ten replicates were performed...mass spectrometry, Molecular and Cellular Probes (2010), doi:10.1016/j.mcp.2010.04.003 alphaviruses (assuming that 30 genome equivalents is approxi

  8. Epidemiological typing of Klebsiella pneumoniae by pyrolysis mass spectrometry.

    PubMed

    Jackson, R M; Heginbothom, M L; Magee, J T

    1997-01-01

    Thirteen isolates of ceftazidime-resistant Klebsiella pneumoniae from a suspected cross-infection outbreak involving patients on an intensive care unit and a haematology ward were examined in pyrolysis-mass spectrometry (Py-MS), along with eight concurrent non-outbreak-associated clinical isolates of klebsiellae as controls. Py-MS showed tight clustering of the suspected outbreak isolates, suggesting cross-infection with a single strain. Non-outbreak isolates were clearly distinct from one another and from the outbreak strain. The results confirm that Py-MS is a powerful tool for rapid strain comparison in investigations of cross-infection incidents.

  9. Clusters of Monoisotopic Elements for Calibration in (TOF) Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Kolářová, Lenka; Prokeš, Lubomír; Kučera, Lukáš; Hampl, Aleš; Peňa-Méndez, Eladia; Vaňhara, Petr; Havel, Josef

    2017-03-01

    Precise calibration in TOF MS requires suitable and reliable standards, which are not always available for high masses. We evaluated inorganic clusters of the monoisotopic elements gold and phosphorus (Au n +/Au n - and P n +/P n -) as an alternative to peptides or proteins for the external and internal calibration of mass spectra in various experimental and instrumental scenarios. Monoisotopic gold or phosphorus clusters can be easily generated in situ from suitable precursors by laser desorption/ionization (LDI) or matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Their use offers numerous advantages, including simplicity of preparation, biological inertness, and exact mass determination even at lower mass resolution. We used citrate-stabilized gold nanoparticles to generate gold calibration clusters, and red phosphorus powder to generate phosphorus clusters. Both elements can be added to samples to perform internal calibration up to mass-to-charge ( m/z) 10-15,000 without significantly interfering with the analyte. We demonstrated the use of the gold and phosphorous clusters in the MS analysis of complex biological samples, including microbial standards and total extracts of mouse embryonic fibroblasts. We believe that clusters of monoisotopic elements could be used as generally applicable calibrants for complex biological samples.

  10. Characterization of polymer decomposition products by laser desorption mass spectrometry

    NASA Technical Reports Server (NTRS)

    Pallix, Joan B.; Lincoln, Kenneth A.; Miglionico, Charles J.; Roybal, Robert E.; Stein, Charles; Shively, Jon H.

    1993-01-01

    Laser desorption mass spectrometry has been used to characterize the ash-like substances formed on the surfaces of polymer matrix composites (PMC's) during exposure on LDEF. In an effort to minimize fragmentation, material was removed from the sample surfaces by laser desorption and desorbed neutrals were ionized by electron impact. Ions were detected in a time-of-flight mass analyzer which allows the entire mass spectrum to be collected for each laser shot. The method is ideal for these studies because only a small amount of ash is available for analysis. Three sets of samples were studied including C/polysulfone, C/polyimide and C/phenolic. Each set contains leading and trailing edge LDEF samples and their respective controls. In each case, the mass spectrum of the ash shows a number of high mass peaks which can be assigned to fragments of the associated polymer. These high mass peaks are not observed in the spectra of the control samples. In general, the results indicate that the ash is formed from decomposition of the polymer matrix.

  11. Clusters of Monoisotopic Elements for Calibration in (TOF) Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Kolářová, Lenka; Prokeš, Lubomír; Kučera, Lukáš; Hampl, Aleš; Peňa-Méndez, Eladia; Vaňhara, Petr; Havel, Josef

    2016-12-01

    Precise calibration in TOF MS requires suitable and reliable standards, which are not always available for high masses. We evaluated inorganic clusters of the monoisotopic elements gold and phosphorus (Au n +/Au n - and P n +/P n -) as an alternative to peptides or proteins for the external and internal calibration of mass spectra in various experimental and instrumental scenarios. Monoisotopic gold or phosphorus clusters can be easily generated in situ from suitable precursors by laser desorption/ionization (LDI) or matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Their use offers numerous advantages, including simplicity of preparation, biological inertness, and exact mass determination even at lower mass resolution. We used citrate-stabilized gold nanoparticles to generate gold calibration clusters, and red phosphorus powder to generate phosphorus clusters. Both elements can be added to samples to perform internal calibration up to mass-to-charge (m/z) 10-15,000 without significantly interfering with the analyte. We demonstrated the use of the gold and phosphorous clusters in the MS analysis of complex biological samples, including microbial standards and total extracts of mouse embryonic fibroblasts. We believe that clusters of monoisotopic elements could be used as generally applicable calibrants for complex biological samples.

  12. Clusters of Monoisotopic Elements for Calibration in (TOF) Mass Spectrometry.

    PubMed

    Kolářová, Lenka; Prokeš, Lubomír; Kučera, Lukáš; Hampl, Aleš; Peňa-Méndez, Eladia; Vaňhara, Petr; Havel, Josef

    2017-03-01

    Precise calibration in TOF MS requires suitable and reliable standards, which are not always available for high masses. We evaluated inorganic clusters of the monoisotopic elements gold and phosphorus (Au n(+)/Au n(-) and P n(+)/P n(-)) as an alternative to peptides or proteins for the external and internal calibration of mass spectra in various experimental and instrumental scenarios. Monoisotopic gold or phosphorus clusters can be easily generated in situ from suitable precursors by laser desorption/ionization (LDI) or matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Their use offers numerous advantages, including simplicity of preparation, biological inertness, and exact mass determination even at lower mass resolution. We used citrate-stabilized gold nanoparticles to generate gold calibration clusters, and red phosphorus powder to generate phosphorus clusters. Both elements can be added to samples to perform internal calibration up to mass-to-charge (m/z) 10-15,000 without significantly interfering with the analyte. We demonstrated the use of the gold and phosphorous clusters in the MS analysis of complex biological samples, including microbial standards and total extracts of mouse embryonic fibroblasts. We believe that clusters of monoisotopic elements could be used as generally applicable calibrants for complex biological samples. Graphical Abstract ᅟ.

  13. Incorporating Biological Mass Spectrometry into Undergraduate Teaching Labs, Part 1: Identifying Proteins Based on Molecular Mass

    ERIC Educational Resources Information Center

    Arnquist, Isaac J.; Beussman, Douglas J.

    2007-01-01

    Biological mass spectrometry is an important analytical technique in drug discovery, proteomics, and research at the biology-chemistry interface. Currently, few hands-on opportunities exist for undergraduate students to learn about this technique. With the 2002 Nobel Prize being awarded, in part, for the development of biological mass…

  14. Accurate Mass Assignment of Native Protein Complexes Detected by Electrospray Mass Spectrometry

    PubMed Central

    Liepold, Lars O.; Oltrogge, Luke M.; Suci, Peter; Douglas, Trevor; Young, Mark J.

    2009-01-01

    Correct charge state assignment is crucial to assigning an accurate mass to supramolecular complexes analyzed by electrospray mass spectrometry. Conventional charge state assignment techniques fall short of reliably and unambiguously predicting the correct charge state for many supramolecular complexes. We provide an explanation of the shortcomings of the conventional techniques and have developed a robust charge state assignment method that is applicable to all spectra. PMID:19103497

  15. Distance-of-Flight Mass Spectrometry: What, Why, and How?

    NASA Astrophysics Data System (ADS)

    Dennis, Elise A.; Gundlach-Graham, Alexander W.; Ray, Steven J.; Enke, Christie G.; Hieftje, Gary M.

    2016-11-01

    Distance-of-flight mass spectrometry (DOFMS) separates ions of different mass-to-charge ( m/ z) by the distance they travel in a given time after acceleration. Like time-of-flight mass spectrometry (TOFMS), separation and mass assignment are based on ion velocity. However, DOFMS is not a variant of TOFMS; different methods of ion focusing and detection are used. In DOFMS, ions are driven orthogonally, at the detection time, onto an array of detectors parallel to the flight path. Through the independent detection of each m/ z, DOFMS can provide both wider dynamic range and increased throughput for m/ z of interest compared with conventional TOFMS. The iso-mass focusing and detection of ions is achieved by constant-momentum acceleration (CMA) and a linear-field ion mirror. Improved energy focus (including turn-around) is achieved in DOFMS, but the initial spatial dispersion of ions remains unchanged upon detection. Therefore, the point-source nature of surface ionization techniques could put them at an advantage for DOFMS. To date, three types of position-sensitive detectors have been used for DOFMS: a microchannel plate with a phosphorescent screen, a focal plane camera, and an IonCCD array; advances in detector technology will likely improve DOFMS figures-of-merit. In addition, the combination of CMA with TOF detection has provided improved resolution and duty factor over a narrow m/ z range (compared with conventional, single-pass TOFMS). The unique characteristics of DOFMS can enable the intact collection of large biomolecules, clusters, and organisms. DOFMS might also play a key role in achieving the long-sought goal of simultaneous MS/MS.

  16. 3-D imaging mass spectrometry of protein distributions in mouse Neurofibromatosis 1 (NF1)-associated optic glioma.

    PubMed

    Anderson, David M G; Van de Plas, Raf; Rose, Kristie L; Hill, Salisha; Schey, Kevin L; Solga, Anne C; Gutmann, David H; Caprioli, Richard M

    2016-10-21

    Neurofibromatosis type 1 (NF1) is a common neurogenetic disorder, in which affected individuals develop tumors of the nervous system. Children with NF1 are particularly prone to brain tumors (gliomas) involving the optic pathway that can result in impaired vision. Since tumor formation and expansion requires a cooperative tumor microenvironment, it is important to identify the cellular and acellular components associated with glioma development and growth. In this study, we used 3-D matrix assisted laser desorption ionization imaging mass spectrometry (MALDI IMS) to measure the distributions of multiple molecular species throughout optic nerve tissue in mice with and without glioma, and to explore their spatial relationships within the 3-D volume of the optic nerve and chiasm. 3-D IMS studies often involve extensive workflows due to the high volume of sections required to generate high quality 3-D images. Herein, we present a workflow for 3-D data acquisition and volume reconstruction using mouse optic nerve tissue. The resulting 3-D IMS data yield both molecular similarities and differences between glioma-bearing and wild-type (WT) tissues, including protein distributions localizing to different anatomical subregions.

  17. Chemo-informatic strategy for imaging mass spectrometry-based hyperspectral profiling of lipid signatures in colorectal cancer

    PubMed Central

    Veselkov, Kirill A.; Mirnezami, Reza; Strittmatter, Nicole; Goldin, Robert D.; Kinross, James; Speller, Abigail V. M.; Abramov, Tigran; Jones, Emrys A.; Darzi, Ara; Holmes, Elaine; Nicholson, Jeremy K.; Takats, Zoltan

    2014-01-01

    Mass spectrometry imaging (MSI) provides the opportunity to investigate tumor biology from an entirely novel biochemical perspective and could lead to the identification of a new pool of cancer biomarkers. Effective clinical translation of histology-driven MSI in systems oncology requires precise colocalization of morphological and biochemical features as well as advanced methods for data treatment and interrogation. Currently proposed MSI workflows are subject to several limitations, including nonoptimized raw data preprocessing, imprecise image coregistration, and limited pattern recognition capabilities. Here we outline a comprehensive strategy for histology-driven MSI, using desorption electrospray ionization that covers (i) optimized data preprocessing for improved information recovery; (ii) precise image coregistration; and (iii) efficient extraction of tissue-specific molecular ion signatures for enhanced biochemical distinction of different tissue types. The proposed workflow has been used to investigate region-specific lipid signatures in colorectal cancer tissue. Unique lipid patterns were observed using this approach according to tissue type, and a tissue recognition system using multivariate molecular ion patterns allowed highly accurate (>98%) identification of pixels according to morphology (cancer, healthy mucosa, smooth muscle, and microvasculature). This strategy offers unique insights into tumor microenvironmental biochemistry and should facilitate compilation of a large-scale tissue morphology-specific MSI spectral database with which to pursue next-generation, fully automated histological approaches. PMID:24398526

  18. Single Cell Proteomics with Ultra-High Sensitivity Mass Spectrometry

    SciTech Connect

    Frank, M

    2005-02-16

    This project was a joint LDRD project between PAT, CMS and NAI with the objective to develop an instrument that analyzes the biochemical composition of single cells in real-time using bioaerosol mass spectrometry (BAMS) combined with advanced laser desorption and ionization techniques. Applications include both biological defense, fundamental cell biology and biomedical research. BAMS analyzes the biochemical composition of single, micrometer-sized particles (such as bacterial cells or spores) that can be directly sampled from air or a suspension. BAMS is based on an earlier development of aerosol time of flight mass spectrometry (ATOFMS) by members of our collaboration [1,2]. Briefly, in ATOFMS and BAMS aerosol particles are sucked directly from the atmosphere into vacuum through a series of small orifices. As the particles approach the ion source region of the mass spectrometer, they cross and scatter light from two CW laser beams separated by a known distance. The timing of the two bursts of scattered light created by each ''tracked'' particle reveals the speed, location and size of the particle. This information then enables the firing of a high-intensity laser such that the resulting laser pulse desorbs and ionizes molecules from the tracked particle just as it reaches the center of the ion source region. The full spectrum of ions is then measured using a time-of-flight mass spectrometer. The ability to rapidly analyze individual particles is clearly applicable to the rapid detection of aerosolized biological warfare agents so long as agent particles can be made to produce mass spectra that are distinct from the spectra of harmless background particles. The pattern of ions formed is determined by the properties of the laser pulse, the particle, and, in aerosol matrix-assisted laser desorption/ionization (MALDI), also the MALDI matrix used. As a result, it is critical that the properties of the laser pulses used for desorption and ionization be carefully chosen

  19. A modular and adaptive mass spectrometry-based platform for support of bioprocess development toward optimal host cell protein clearance.

    PubMed

    Walker, Donald E; Yang, Feng; Carver, Joseph; Joe, Koman; Michels, David A; Yu, X Christopher

    2017-03-27

    A modular and adaptive mass spectrometry (MS)-based platform was developed to provide fast, robust and sensitive host cell protein (HCP) analytics to support process development. This platform relies on one-dimensional ultra-high performance liquid chromatography (1D UHPLC) combined with several different MS data acquisition strategies to meet the needs of purification process development. The workflow was designed to allow HCP composition and quantitation for up to 20 samples per day, a throughput considered essential for real time bioprocess development support. With data-dependent acquisition (DDA), the 1D UHPLC-MS/MS method had excellent speed and demonstrated robustness in detecting unknown HCPs at ≥ 50 ng/mg (ppm) level. Combining 1D UHPLC with sequential window acquisition of all theoretical spectra (SWATH) MS enabled simultaneous detection and quantitation of all HCPs in single-digit ng/mg range within 1 hour, demonstrating for the first time the benefit of SWATH MS as a technique for HCP analysis. As another alternative, a targeted MS approach can be used to track the clearance of specific known HCP under various process conditions. This study highlights the importance of designing a robust LC-MS/MS workflow that not only allows HCP discovery, but also affords greatly improved process knowledge and capability in HCP removal. As an orthogonal and complementary detection approach to traditional HCP analysis by enzyme-linked immunosorbent assay, the reported LC-MS/MS workflow supports the development of bioprocesses with optimal HCP clearance and the production of safe and high quality therapeutic biopharmaceuticals.

  20. Gated Trapped Ion Mobility Spectrometry Coupled to Fourier Transform Ion Cyclotron Resonance Mass Spectrometry.

    PubMed

    Ridgeway, Mark E; Wolff, Jeremy J; Silveira, Joshua A; Lin, Cheng; Costello, Catherine E; Park, Melvin A

    2016-09-01

    Analysis of molecules by ion mobility spectrometry coupled with mass spectrometry (IMS-MS) provides chemical information on the three dimensional structure and mass of the molecules. The coupling of ion mobility to trapping mass spectrometers has historically been challenging due to the large differences in analysis time between the two devices. In this paper we present a modification of the trapped ion mobility (TIMS) analysis scheme termed "Gated TIMS" that allows efficient coupling to a Fourier Transform Ion Cyclotron Resonance (FT-ICR) analyzer. Analyses of standard compounds and the influence of source conditions on the TIMS distributions produced by ion mobility spectra of labile ubiquitin protein ions are presented. Ion mobility resolving powers up to 100 are observed. Measured collisional cross sections of ubiquitin ions are in excellent qualitative and quantitative agreement to previous measurements. Gated TIMS FT-ICR produces results comparable to those acquired using TIMS/time-of-flight MS instrument platforms as well as numerous drift tube IMS-MS studies published in the literature.

  1. Characterization of a Distributed Plasma Ionization Source (DPIS) for Ion Mobility Spectrometry and Mass Spectrometry

    SciTech Connect

    Waltman, Melanie J.; Dwivedi, Prabha; Hill, Herbert; Blanchard, William C.; Ewing, Robert G.

    2008-10-15

    A recently developed atmospheric pressure ionization source, a distributed plasma ionization source (DPIS), was characterized and compared to commonly used atmospheric pressure ionization sources with both mass spectrometry and ion mobility spectrometry. The source consisted of two electrodes of different sizes separated by a thin dielectric. Application of a high RF voltage across the electrodes generated plasma in air yielding both positive and negative ions depending on the polarity of the applied potential. These reactant ions subsequently ionized the analyte vapors. The reactant ions generated were similar to those created in a conventional point-to-plane corona discharge ion source. The positive reactant ions generated by the source were mass identified as being solvated protons of general formula (H2O)nH+ with (H2O)2H+ as the most abundant reactant ion. The negative reactant ions produced were mass identified primarily as CO3-, NO3-, NO2-, O3- and O2- of various relative intensities. The predominant ion and relative ion ratios varied depending upon source construction and supporting gas flow rates. A few compounds including drugs, explosives and environmental pollutants were selected to evaluate the new ionization source. The source was operated continuously for several months and although deterioration was observed visually, the source continued to produce ions at a rate similar that of the initial conditions. The results indicated that the DPIS may have a longer operating life than a conventional corona discharge.

  2. Characterization of a distributed plasma ionization source (DPIS) for ion mobility spectrometry and mass spectrometry.

    PubMed

    Waltman, Melanie J; Dwivedi, Prabha; Hill, Herbert H; Blanchard, William C; Ewing, Robert G

    2008-10-19

    A recently developed atmospheric pressure ionization source, a distributed plasma ionization source (DPIS), was characterized and compared to commonly used atmospheric pressure ionization sources with both mass spectrometry (MS) and ion mobility spectrometry (IMS). The source consisted of two electrodes of different sizes separated by a thin dielectric. Application of a high RF voltage across the electrodes generated plasma in air yielding both positive and negative ions. These reactant ions subsequently ionized the analyte vapors. The reactant ions generated were similar to those created in a conventional point-to-plane corona discharge ion source. The positive reactant ions generated by the source were mass identified as being solvated protons of general formula (H(2)O)(n)H(+) with (H(2)O)(2)H(+) as the most abundant reactant ion. The negative reactant ions produced were mass identified primarily as CO(3)(-), NO(3)(-), NO(2)(-), O(3)(-) and O(2)(-) of various relative intensities. The predominant ion and relative ion ratios varied depending upon source construction and supporting gas flow rates. A few compounds including drugs, explosives and amines were selected to evaluate the new ionization source. The source was operated continuously for 3 months and although surface deterioration was observed visually, the source continued to produce ions at a rate similar that of the initial conditions.

  3. Steroid profiling by gas chromatography-mass spectrometry and high performance liquid chromatography-mass spectrometry for adrenal diseases.

    PubMed

    McDonald, Jeffrey G; Matthew, Susan; Auchus, Richard J

    2011-12-01

    The ability to measure steroid hormone concentrations in blood and urine specimens is central to the diagnosis and proper treatment of adrenal diseases. The traditional approach has been to assay each steroid hormone, precursor, or metabolite using individual aliquots of serum, each with a separate immunoassay. For complex diseases, such as congenital adrenal hyperplasia and adrenocortical cancer, in which the assay of several steroids is essential for management, this approach is time consuming and costly, in addition to using large amounts of serum. Gas chromatography/mass spectrometry profiling of steroid metabolites in urine has been employed for many years but only in a small number of specialized laboratories and suffers from slow throughput. The advent of commercial high-performance liquid chromatography instruments coupled to tandem mass spectrometers offers the potential for medium- to high-throughput profiling of serum steroids using small quantities of sample. Here, we review the physical principles of mass spectrometry, the instrumentation used for these techniques, the terminology used in this field and applications to steroid analysis.

  4. Mass Spectrometry of Polymer Electrolyte Membrane Fuel Cells

    PubMed Central

    Ostroverkh, Anna; Fiala, Roman; Rednyk, Andrii; Matolín, Vladimír

    2016-01-01

    The chemical analysis of processes inside fuel cells under operating conditions in either direct or inverted (electrolysis) mode and their correlation with potentiostatic measurements is a crucial part of understanding fuel cell electrochemistry. We present a relatively simple yet powerful experimental setup for online monitoring of the fuel cell exhaust (of either cathode or anode side) downstream by mass spectrometry. The influence of a variety of parameters (composition of the catalyst, fuel type or its concentration, cell temperature, level of humidification, mass flow rate, power load, cell potential, etc.) on the fuel cell operation can be easily investigated separately or in a combined fashion. We demonstrate the application of this technique on a few examples of low-temperature (70°C herein) polymer electrolyte membrane fuel cells (both alcohol- and hydrogen-fed) subjected to a wide range of conditions. PMID:28042492

  5. Mass Spectrometry of Polymer Electrolyte Membrane Fuel Cells.

    PubMed

    Johánek, Viktor; Ostroverkh, Anna; Fiala, Roman; Rednyk, Andrii; Matolín, Vladimír

    2016-01-01

    The chemical analysis of processes inside fuel cells under operating conditions in either direct or inverted (electrolysis) mode and their correlation with potentiostatic measurements is a crucial part of understanding fuel cell electrochemistry. We present a relatively simple yet powerful experimental setup for online monitoring of the fuel cell exhaust (of either cathode or anode side) downstream by mass spectrometry. The influence of a variety of parameters (composition of the catalyst, fuel type or its concentration, cell temperature, level of humidification, mass flow rate, power load, cell potential, etc.) on the fuel cell operation can be easily investigated separately or in a combined fashion. We demonstrate the application of this technique on a few examples of low-temperature (70°C herein) polymer electrolyte membrane fuel cells (both alcohol- and hydrogen-fed) subjected to a wide range of conditions.

  6. Isolation and mass spectrometry of transcription factor complexes.

    PubMed

    Sebastiaan Winkler, G; Lacomis, Lynne; Philip, John; Erdjument-Bromage, Hediye; Svejstrup, Jesper Q; Tempst, Paul

    2002-03-01

    Protocols are described that enable the isolation of novel proteins associated with a known protein and the subsequent identification of these proteins by mass spectrometry. We review the basics of nanosample handling and of two complementary approaches to mass analysis, and provide protocols for the entire process. The protein isolation procedure is rapid and based on two high-affinity chromatography steps. The method does not require previous knowledge of complex composition or activity and permits subsequent biochemical characterization of the isolated factor. As an example, we provide the procedures used to isolate and analyze yeast Elongator, a histone acetyltransferase complex important for transcript elongation, which led to the identification of three novel subunits.

  7. Testing and Validation of Computational Methods for Mass Spectrometry.

    PubMed

    Gatto, Laurent; Hansen, Kasper D; Hoopmann, Michael R; Hermjakob, Henning; Kohlbacher, Oliver; Beyer, Andreas

    2016-03-04

    High-throughput methods based on mass spectrometry (proteomics, metabolomics, lipidomics, etc.) produce a wealth of data that cannot be analyzed without computational methods. The impact of the choice of method on the overall result of a biological study is often underappreciated, but different methods can result in very different biological findings. It is thus essential to evaluate and compare the correctness and relative performance of computational methods. The volume of the data as well as the complexity of the algorithms render unbiased comparisons challenging. This paper discusses some problems and challenges in testing and validation of computational methods. We discuss the different types of data (simulated and experimental validation data) as well as different metrics to compare methods. We also introduce a new public repository for mass spectrometric reference data sets ( http://compms.org/RefData ) that contains a collection of publicly available data sets for performance evaluation for a wide range of different methods.

  8. Field gas chromatography-mass spectrometry for fast analysis.

    PubMed

    Makas, Alexei L; Troshkov, Mikhail L

    2004-02-05

    The objective of this presentation is to demonstrate the original device and procedure for fast gas chromatography-mass spectrometry (GC-MS) analysis of gaseous and liquid samples and to discuss its features and capabilities. The concept was developed in order to expand the range of compounds suitable for GC separation and to reduce the time of analysis. Field GC-MS, consisting of original "concentrator-thermodesorber" (CTD) unit, multiple module GC system and compact magnetic mass spectrometer with powerful two-stage vacuum system and multicollector ion detector, is represented. The whole weight of the device is 90 kg. Power consumption is 250 W. The device and analytical procedures allow high speed screening of toxic substances in air and extracts within 100 s per sample. The examples of applications are described, including fast screening of tributyl phosphate (TBP) in air at low ppt level at the rate 1 sample/min.

  9. Statistical design of quantitative mass spectrometry-based proteomic experiments.

    PubMed

    Oberg, Ann L; Vitek, Olga

    2009-05-01

    We review the fundamental principles of statistical experimental design, and their application to quantitative mass spectrometry-based proteomics. We focus on class comparison using Analysis of Variance (ANOVA), and discuss how randomization, replication and blocking help avoid systematic biases due to the experimental procedure, and help optimize our ability to detect true quantitative changes between groups. We also discuss the issues of pooling multiple biological specimens for a single mass analysis, and calculation of the number of replicates in a future study. When applicable, we emphasize the parallels between designing quantitative proteomic experiments and experiments with gene expression microarrays, and give examples from that area of research. We illustrate the discussion using theoretical considerations, and using real-data examples of profiling of disease.

  10. Mass Spectrometry of Protein Complexes: From Origins to Applications

    NASA Astrophysics Data System (ADS)

    Mehmood, Shahid; Allison, Timothy M.; Robinson, Carol V.

    2015-04-01

    Now routine is the ability to investigate soluble and membrane protein complexes in the gas phase of a mass spectrometer while preserving folded structure and ligand-binding properties. Several recent transformative developments have occurred to arrive at this point. These include advances in mass spectrometry instrumentation, particularly with respect to resolution; the ability to study intact membrane protein complexes released from detergent micelles; and the use of protein unfolding in the gas phase to obtain stability parameters. Together, these discoveries are providing unprecedented information on the compositional heterogeneity of biomacromolecules, the unfolding trajectories of multidomain proteins, and the stability imparted by ligand binding to both soluble and membrane-embedded protein complexes. We review these recent breakthroughs, highlighting the challenges that had to be overcome and the physicochemical insight that can now be gained from studying proteins and their assemblies in the gas phase.

  11. High pressure (>1 atm) electrospray ionization mass spectrometry.

    PubMed

    Chen, Lee Chuin; Mandal, Mridul Kanti; Hiraoka, Kenzo

    2011-03-01

    High pressure electrospray ionization mass spectrometry has been performed by pressurizing a custom made ion source chamber with compressed air to a pressure higher than the atmospheric pressure. The ion source was coupled to a commercial time-of-flight mass spectrometer using a nozzle-skimmer arrangement. The onset voltage for the electrospray of aqueous solution was found to be independent on the operating pressure. The onset voltage for the corona discharge, however, increased with the rise of pressure following the Paschen's law. Thus, besides having more working gas for the desolvation process, gaseous breakdown could also be avoided by pressurizing the ESI ion source with air to an appropriate level. Stable electrospray ionization has been achieved for the sample solution with high surface tension such as pure water in both positive and negative ion modes. Fragmentation of labile compounds during the ionization process could also be reduced by optimizing the operating pressure of the ion source.

  12. Structural Characterization of Carbohydrates by Fourier Transform Tandem Mass Spectrometry

    PubMed Central

    Zhou, Wen; Håkansson, Kristina

    2012-01-01

    Fourier transform tandem mass spectrometry (MS/MS) provides high mass accuracy, high sensitivity, and analytical versatility and has therefore emerged as an indispensable tool for structural elucidation of biomolecules. Glycosylation is one of the most common posttranslational modifications, occurring in ~50% of proteins. However, due to the structural diversity of carbohydrates, arising from non-template driven biosynthesis, achievement of detailed structural insight is highly challenging. This review briefly discusses carbohydrate sample preparation and ionization methods, and highlights recent developments in alternative high-resolution MS/MS strategies, including infrared multiphoton dissociation (IRMPD), electron capture dissociation (ECD), and electron detachment dissociation (EDD), for carbohydrates with a focus on glycans and proteoglycans from mammalian glycoproteins. PMID:22389641

  13. Quantification of antidepressants using gas chromatography-mass spectrometry.

    PubMed

    Winecker, Ruth E

    2010-01-01

    Antidepressants are of great interest to clinical and forensic toxicologists as they are frequently used in suicidal gestures; they can be the source of drug interactions and some have narrow therapeutic indices making the potential for toxicity more likely. There are five categories of antidepressants based on function and/or structure. These are monoamine oxidase inhibitors (MAOI), cyclic antidepressants including tricyclic and tetracyclic compounds (TCA), selective serotonin reuptake inhibitors (SSRI), serotonin-norepinephrine reuptake inhibitors (SNRI), and atypical compounds. This method is designed to detect the presence of antidepressant drugs in blood/serum, urine, and tissue specimens using gas chromatography/mass spectrometry (GC/MS) following liquid-liquid extraction (LLE) and identified by relative retention times and mass spectra.

  14. Mass spectrometry. [in organic ion and biorganic chemistry and medicine

    NASA Technical Reports Server (NTRS)

    Burlingame, A. L.; Cox, R. E.; Derrick, P. J.

    1974-01-01

    Review of the present status of mass spectrometry in the light of pertinent recent publications spanning the period from December 1971 to January 1974. Following an initial survey of techniques, instruments, and computer applications, a sharp distinction is made between the chemistry of organic (radical-)ions and analytical applications in biorganic chemistry and medicine. The emphasis is on the chemistry of organic (radical-)ions at the expense of inorganic, organometallic, and surface ion chemistry. Biochemistry and medicine are chosen because of their contemporary importance and because of the stupendous contributions of mass spectroscopy to these fields in the past two years. In the review of gas-phase organic ion chemistry, special attention is given to studies making significant contributions to the understanding of ion chemistry.

  15. Analysis of protein composition using multidimensional chromatography and mass spectrometry.

    PubMed

    Link, Andrew J; Washburn, Michael P

    2014-11-03

    Multidimensional liquid chromatography of peptides produced by protease digestion of complex protein mixtures followed by tandem mass spectrometry can be coupled with automated database searching to identify large numbers of proteins in complex samples. These methods avoid the limitations of gel electrophoresis and in-gel digestions by directly identifying protein mixtures in solution. One method used extensively is named Multidimensional Protein Identification Technology (MudPIT), where reversed-phase chromatography and strong cation-exchange chromatography are coupled directly in a microcapillary column. This column is then placed in line between an HPLC and a mass spectrometer for complex mixture analysis. MudPIT remains a powerful approach for analyzing complex mixtures like whole proteomes and protein complexes. MudPIT is used for quantitative proteomic analysis of complex mixtures to generate novel biological insights.

  16. Sequencing of Oligourea Foldamers by Tandem Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Bathany, Katell; Owens, Neil W.; Guichard, Gilles; Schmitter, Jean-Marie

    2013-03-01

    This study is focused on sequence analysis of peptidomimetic helical oligoureas by means of tandem mass spectrometry, to build a basis for de novo sequencing for future high-throughput combinatorial library screening of oligourea foldamers. After the evaluation of MS/MS spectra obtained for model compounds with either MALDI or ESI sources, we found that the MALDI-TOF-TOF instrument gave more satisfactory results. MS/MS spectra of oligoureas generated by decay of singly charged precursor ions show major ion series corresponding to fragmentation across both CO-NH and N'H-CO urea bonds. Oligourea backbones fragment to produce a pattern of a, x, b, and y type fragment ions. De novo decoding of spectral information is facilitated by the occurrence of low mass reporter ions, representative of constitutive monomers, in an analogous manner to the use of immonium ions for peptide sequencing.

  17. Mass Spectrometry for Planetary Probes: Past, Present and Future

    NASA Technical Reports Server (NTRS)

    Niemann, Hasso B.; Harpold, Dan N.; Jamieson, Brian G.; Mahaffy, Paul R.

    2005-01-01

    Atmospheric entry probes present a unique opportunity for performing quantitative analysis of extra-terrestrial atmospheres in cases where remote sensing alone may not be sufficient and measurements with balloons or aircraft is not practical. An entry probe can provide a complete vertical profile of atmospheric parameters including chemical composition, which cannot be obtained with most other techniques. There are, however, unique challenges associated with building instruments for an entry probe, as compared to orbiters, landers, or rovers. Conditions during atmospheric entry are extreme, there are inherent time constraints due to the short duration of the experiment, and the instrument experiences rapid environmental changes in temperature and pressure as it descends. In addition, there are resource limitations, i.e. mass, power, size and bandwidth. Finally, the demands on the instrument design are determined in large part by conditions (pressure, temperature, composition) unique to the particular body under study, and as a result there is no one-size-fits-all instrument for an atmospheric probe. Many of these requirements can be more easily met by miniaturizing the probe instrument. Our experience building mass spectrometers for atmospheric entry probes leads us to believe that the time is right for a fundamental change in the way spaceflight mass spectrometers are built. The emergence over the past twenty years of Micro-electro- mechanical Systems (MEMS), utilizing lithographic semiconductor fabrication techniques to produce instrument systems in miniature, holds great promise for application to spaceflight mass spectrometry. A highly miniaturized, high performance and low-power mass spectrometer would be an enormous benefit to future entry probe missions, allowing, for example, parallel measurements (e.g., multiple simultaneous gas chromatographic analyses and direct atmospheric leaks.) Such an instrument would also enable mass spectrometry on board small

  18. Charge detection mass spectrometry: Instrumentation & applications to viruses

    NASA Astrophysics Data System (ADS)

    Pierson, Elizabeth E.

    For over three decades, electrospray ionization (ESI) has been used to ionize non-covalent complexes and subsequently transfer the intact ion into the gas phase for mass spectrometry (MS) analysis. ESI generates a distribution of multiple charged ions, resulting in an m/z spectrum comprised of a series of peaks, known as a charge state envelope. To obtain mass information, the number of charges for each peak must be deduced. For smaller biological analytes like peptides, the charge states are sufficiently resolved and this process is straightforward. For macromolecular complexes exceeding ~100 kDa, this process is complicated by the broadening and shifting of charge states due to incomplete desolvation, salt adduction, and inherent mass heterogeneity. As the analyte mass approaches the MDa regime, the m/z spectrum is often comprised of a broad distribution of unresolved charge states. In such cases, mass determination is precluded. Charge detection mass spectrometry (CDMS) is an emerging MS technique for determining the masses of heterogeneous, macromolecular complexes. In CDMS, the m/z and z of single ions are measured concurrently so that mass is easily calculated. With this approach, deconvolution of an m/z spectrum is unnecessary. This measurement is carried out by passing macroions through a conductive cylinder. The induced image charge on the cylindrical detector provides information about m/z and z: the m/z is related to its time-of-flight through the detector, and the z is related to the intensity of the image charge. We have applied CDMS to study the self-assembly of virus capsids. Late-stage intermediates in the assembly of hepatitis B virus, a devastating human pathogen, have been identified. This is the first time that such intermediates have been detected and represent a significant advancement towards understanding virus capsid assembly. CDMS has also been used to identify oversized, non-icosahedral polymorphs in the assembly of woodchuck hepatitis

  19. Electrospray ionization tandem mass spectrometry of ammonium cationized polyethers.

    PubMed

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

    2011-05-01

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

  20. Electrospray Ionization Tandem Mass Spectrometry of Ammonium Cationized Polyethers

    NASA Astrophysics Data System (ADS)

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

    2011-05-01

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

  1. High Resolution Mass Spectrometry of Polyfluorinated Polyether-Based Formulation

    NASA Astrophysics Data System (ADS)

    Dimzon, Ian Ken; Trier, Xenia; Frömel, Tobias; Helmus, Rick; Knepper, Thomas P.; de Voogt, Pim

    2016-02-01

    High resolution mass spectrometry (HRMS) was successfully applied to elucidate the structure of a polyfluorinated polyether (PFPE)-based formulation. The mass spectrum generated from direct injection into the MS was examined by identifying the different repeating units manually and with the aid of an instrument data processor. Highly accurate mass spectral data enabled the calculation of higher-order mass defects. The different plots of MW and the nth-order mass defects (up to n = 3) could aid in assessing the structure of the different repeating units and estimating their absolute and relative number per molecule. The three major repeating units were -C2H4O-, -C2F4O-, and -CF2O-. Tandem MS was used to identify the end groups that appeared to be phosphates, as well as the possible distribution of the repeating units. Reversed-phase HPLC separated of the polymer molecules on the basis of number of nonpolar repeating units. The elucidated structure resembles the structure in the published manufacturer technical data. This analytical approach to the characterization of a PFPE-based formulation can serve as a guide in analyzing not just other PFPE-based formulations but also other fluorinated and non-fluorinated polymers. The information from MS is essential in studying the physico-chemical properties of PFPEs and can help in assessing the risks they pose to the environment and to human health.

  2. Mass Spectrometry of Atmospheric Pressure Surface Wave Discharges

    NASA Astrophysics Data System (ADS)

    Ridenti, M. A.; Souza-Corrêa, J. A.; Amorim, J.

    2016-05-01

    By applying mass spectrometry techniques, we carried out measurements of ionic mass spectrum and their energy distribution in order to investigate an atmospheric argon discharge by using a surfatron surface-wave device. The mass and energy distribution measurements were performed with fixed flow rate (2.5 SLM) of pure argon gas (99.999%) and different Ar-O2 gas mixture compositions (99-1, 98-2 and 97-3). The mass spectra and energy distributions were recorded for Ar+, O+, O+ 2, N+ and N2 +. The axial distribution profiles of ionic mass and their energy were obtained for different experimental conditions as a function of the plasma length. The results showed that the peak of the positive ion energy distributions shifted to higher energies and also that the distribution width increased as the distance between the sampling orifice and the launcher gap was increased. It was also found that under certain experimental conditions the ion flux of atomic species were higher than the ion flux of their diatomic counterpart. The motivation of this study was to obtain a better understanding of a surface wave discharge in atmospheric pressure that may play a key role on new second generation biofuel technologies.

  3. 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.

  4. 37th British Mass Spectrometry Society annual meeting.

    PubMed

    Wright, Patricia; Eckers, Christine

    2017-03-01

    The 37th British Mass Spectrometry Society (BMSS) annual meeting took place over a brilliantly sunny 3 days by the sea in the historic Eastbourne Winter Gardens on the south coast of England. It was held between 13 and 15 September 2016. Two-hundred attendees enjoyed a conference covering all aspects of MS with speakers drawn from across Europe and North America. The BMSS is particularly proud of the encouragement it offers students and early career scientists, both financially in the form of travel grants and also in terms of opportunities to present at an international level in a supportive atmosphere. Further encouragement to newcomers to the field is offered in the form of the Barber Prize for best oral presentation and the Bordoli Prize for the best poster. This year's winners were Patrick Knight (University of Leeds), the Bordoli Prize for the poster 'Characterising the Interaction of Ataxin-3 and the Poly-Glutamine Aggregation Inhibitor QBP1'; Lisa Deininger (Sheffield Hallam University), the Barber Prize for 'Out Damned Spot! Bottom Up Proteomics for the Analysis of Bloodied Fingermarks'. In addition, the Delegates Choice for best poster went to Hannah Britt (Durham University) for 'Monitoring Reactions of Small Molecules with Cell Membranes by Liquid Chromatography-Mass Spectrometry'. For services to the MS community, Professor Gareth Brenton (Swansea University) was awarded the BMSS Medal; Professor Alison Ashcroft (Leeds University) and Anna Upton (former BMSS administrator) were given lifetime membership of the BMSS.

  5. An efficient data format for mass spectrometry-based proteomics.

    PubMed

    Shah, Anuj R; Davidson, Jennifer; Monroe, Matthew E; Mayampurath, Anoop M; Danielson, William F; Shi, Yan; Robinson, Aaron C; Clowers, Brian H; Belov, Mikhail E; Anderson, Gordon A; Smith, Richard D

    2010-10-01

    The diverse range of mass spectrometry (MS) instrumentation along with corresponding proprietary and nonproprietary data formats has generated a proteomics community driven call for a standardized format to facilitate management, processing, storing, visualization, and exchange of both experimental and processed data. To date, significant efforts have been extended towards standardizing XML-based formats for mass spectrometry data representation, despite the recognized inefficiencies associated with storing large numeric datasets in XML. The proteomics community has periodically entertained alternate strategies for data exchange, e.g., using a common application programming interface or a database-derived format. However, these efforts have yet to gain significant attention, mostly because they have not demonstrated significant performance benefits over existing standards, but also due to issues such as extensibility to multidimensional separation systems, robustness of operation, and incomplete or mismatched vocabulary. Here, we describe a format based on standard database principles that offers multiple benefits over existing formats in terms of storage size, ease of processing, data retrieval times, and extensibility to accommodate multidimensional separation systems.

  6. An efficient data format for mass spectrometry based proteomics

    SciTech Connect

    Shah, Anuj R.; Davidson, Jennifer L.; Monroe, Matthew E.; Mayampurath, Anoop M.; Danielson, William F.; Shi, Yan; Robinson, Aaron C.; Clowers, Brian H.; Belov, Mikhail E.; Anderson, Gordon A.; Smith, Richard D.

    2010-10-01

    The diverse range of mass spectrometry (MS) instrumentation along with corresponding proprietary and non-proprietary data formats has generated a proteomics community driven call for a standardized format to facilitate management, processing, storing, visualization, and exchange of both experimental and processed data. To date, significant efforts have been extended towards standardizing XML-based formats for mass spectrometry data representation, despite the recognized inefficiencies associated with storing large numeric datasets in XML. The proteomics community has periodically entertained alternate strategies for data exchange, e.g., using a common application programming interface or a database-derived format. However these efforts have yet to garner significant attention, mostly because they haven’t illustrated significant performance benefits over existing standards, but also due to issues such as extensibility to multi-dimensional separation systems, robustness of operation, and incomplete or mismatched vocabulary. Here, we describe a format based on standard database principles that offers multiple benefits over existing formats in terms of storage size, ease of processing, data retrieval times and extensibility to accommodate multi-dimensional separation systems.

  7. High resolution MALDI imaging mass spectrometry of retinal tissue lipids.

    PubMed

    Anderson, David M G; Ablonczy, Zsolt; Koutalos, Yiannis; Spraggins, Jeffrey; Crouch, Rosalie K; Caprioli, Richard M; Schey, Kevin L

    2014-08-01

    Matrix assisted laser desorption ionization imaging mass spectrometry (MALDI IMS) has the ability to provide an enormous amount of information on the abundances and spatial distributions of molecules within biological tissues. The rapid progress in the development of this technology significantly improves our ability to analyze smaller and smaller areas and features within tissues. The mammalian eye has evolved over millions of years to become an essential asset for survival, providing important sensory input of an organism's surroundings. The highly complex sensory retina of the eye is comprised of numerous cell types organized into specific layers with varying dimensions, the thinnest of which is the 10 μm retinal pigment epithelium (RPE). This single cell layer and the photoreceptor layer contain the complex biochemical machinery required to convert photons of light into electrical signals that are transported to the brain by axons of retinal ganglion cells. Diseases of the retina, including age-related macular degeneration (AMD), retinitis pigmentosa, and diabetic retinopathy, occur when the functions of these cells are interrupted by molecular processes that are not fully understood. In this report, we demonstrate the use of high spatial resolution MALDI IMS and FT-ICR tandem mass spectrometry in the Abca4(-/-) knockout mouse model of Stargardt disease, a juvenile onset form of macular degeneration. The spatial distributions and identity of lipid and retinoid metabolites are shown to be unique to specific retinal cell layers.

  8. NMR and mass spectrometry of phosphorus in wetlands

    USGS Publications Warehouse

    El-Rifai, H.; Heerboth, M.; Gedris, T.E.; Newman, S.; Orem, W.; Cooper, W.T.

    2008-01-01

    There is at present little information on the long-term stability of phosphorus sequestered in wetlands. Phosphorus sequestered during high loading periods may be relatively unstable and easily remobilized following changes in nutrient status or hydrological regime, but the chemical forms of sequestered phosphorus that do remobilize are largely unknown at this time. A lack of suitable analytical techniques has contributed to this dearth of knowledge regarding the stability of soil organic phosphorus. We analysed phosphorus in soils from the 'head' of Rescue Strand tree island and an adjacent marsh in the Florida Everglades by 31P nuclear magnetic resonance (NMR) spectroscopy and high-resolution mass spectrometry. Tree islands are important areas of biodiversity within the Everglades and offer a unique opportunity to study phosphorus sequestration because they are exposed to large phosphorus loads and appear to be natural nutrient sinks. The 31P NMR profiling of extracts from surface and sediment samples in the tree island indicates that phosphorus input to Rescue Strand tree island soils is mostly in the form of inorganic ortho-phosphate and is either refractory when deposited or rapidly recycled by the native vegetation into a stable phosphorus pool largely resistant to re-utilization by plants or microbes. Mass spectrometry revealed the presence of inositol hexakisphosphate, a common organic monophosphate ester not previously observed in Everglades' soils. ?? 2008 The Authors.

  9. Mass spectrometry-based proteomics: existing capabilities and future directions

    SciTech Connect

    Angel, Thomas E.; Aryal, Uma K.; Hengel, Shawna M.; Baker, Erin Shammel; Kelly, Ryan T.; Robinson, Errol W.; Smith, Richard D.

    2012-05-21

    Mass spectrometry-based proteomics provides a means for identification, characterization, and quantification of biomolecules that are integral components of the processes essential for life. Characterization of proteins present in a biological system at the proteome and sub-proteomes (e.g., the phosphoproteome, proteoglycome, or degradome/peptidome) levels provides a foundation for understanding fundamental aspects as well as potentially a range of translational applications. Emerging technologies such as ion mobility separations coupled with mass spectrometry and microchip-based - proteome measurements combined with continued enhancement of MS instrumentation and separation techniques, such as reversed phase liquid chromatography and potentially capillary electrophoresis, show great promise for both broad undirected as well as targeted measurements and will be critical for e.g., the proteome-wide characterization of post translational modifications and identification, or the verification, and validation of potential biomarkers of disease. MS-based proteomics is also increasingly demonstrating great potential for contributing to our understanding of the dynamics, reactions, and roles proteins and peptides play advancing our understanding of biology on a system wide level for a wide range of applications, from investigations of microbial communities, bioremediation, and human health and disease states alike.

  10. Unexpected Analyte Oxidation during Desorption Electrospray Ionization - Mass Spectrometry

    SciTech Connect

    Pasilis, Sofie P; Kertesz, Vilmos; Van Berkel, Gary J

    2008-01-01

    During the analysis of surface spotted analytes using desorption electrospray ionization mass spectrometry (DESI-MS), abundant ions are sometimes observed that appear to be the result of oxygen addition reactions. In this investigation, the effect of sample aging, the ambient lab environment, spray voltage, analyte surface concentration, and surface type on this oxidative modification of spotted analytes, exemplified by tamoxifen and reserpine, during analysis by desorption electrospray ionization mass spectrometry was studied. Simple exposure of the samples to air and to ambient lighting increased the extent of oxidation. Increased spray voltage lead also to increased analyte oxidation, possibly as a result of oxidative species formed electrochemically at the emitter electrode or in the gas - phase by discharge processes. These oxidative species are carried by the spray and impinge on and react with the sampled analyte during desorption/ionization. The relative abundance of oxidized species was more significant for analysis of deposited analyte having a relatively low surface concentration. Increasing spray solvent flow rate and addition of hydroquinone as a redox buffer to the spray solvent were found to decrease, but not entirely eliminate, analyte oxidation during analysis. The major parameters that both minimize and maximize analyte oxidation were identified and DESI-MS operational recommendations to avoid these unwanted reactions are suggested.

  11. LASER DESORPTION IONIZATION MASS SPECTROMETRY ON SILICON NANOWELL ARRAYS

    PubMed Central

    Gulbakan, Basri; Park, Dooho; Kang, Myungchan; Kececi, Kaan; Martin, Charles R.; Powell, David H.; Tan, Weihong

    2010-01-01

    This paper describes a new technique for fabrication of nanostructured porous silicon (pSi) for laser desorption ionization mass spectrometry. Porous silicon nanowell arrays were prepared by argon plasma etching through an alumina mask. Porous silicon prepared in this way proved to be an excellent substrate for desorption/ionization on silicon (DIOS) mass spectrometry (MS) using adenosine, Pro-Leu-Gly tripeptide and [Des-Arg9]-bradykinin as the model compounds. It also allows the analyses of complex biological samples such as a tryptic digest of bovine serum albumin, and a carnitine standard mixture. Nanowell array surfaces were also used for direct quantification of the illicit drug fentanyl in red blood cell extracts. This method also allows full control of the surface features. MS results suggested that the pore depth has significant effect on the ion signals. Significant improvement in the ionization was observed by increasing the pore depth from 10 nm to 50 nm. These substrates are useful for laser desorption ionization in both the atmospheric pressure and vacuum regimes. PMID:20731384

  12. Quantitation of DNA adducts by stable isotope dilution mass spectrometry

    PubMed Central

    Tretyakova, Natalia; Goggin, Melissa; Janis, Gregory

    2012-01-01

    Exposure to endogenous and exogenous chemicals can lead to the formation of structurally modified DNA bases (DNA adducts). If not repaired, these nucleobase lesions can cause polymerase errors during DNA replication, leading to heritable mutations potentially contributing to the development of cancer. Due to their critical role in cancer initiation, DNA adducts represent mechanism-based biomarkers of carcinogen exposure, and their quantitation is particularly useful for cancer risk assessment. DNA adducts are also valuable in mechanistic studies linking tumorigenic effects of environmental and industrial carcinogens to specific electrophilic species generated from their metabolism. While multiple experimental methodologies have been developed for DNA adduct analysis in biological samples – including immunoassay, HPLC, and 32P-postlabeling – isotope dilution high performance liquid chromatography-electrospray ionization-tandem mass spectrometry (HPLC-ESI-MS/MS) generally has superior selectivity, sensitivity, accuracy, and reproducibility. As typical DNA adducts concentrations in biological samples are between 0.01 – 10 adducts per 108 normal nucleotides, ultrasensitive HPLC-ESI-MS/MS methodologies are required for their analysis. Recent developments in analytical separations and biological mass spectrometry – especially nanoflow HPLC, nanospray ionization MS, chip-MS, and high resolution MS – have pushed the limits of analytical HPLC-ESI-MS/MS methodologies for DNA adducts, allowing researchers to accurately measure their concentrations in biological samples from patients treated with DNA alkylating drugs and in populations exposed to carcinogens from urban air, drinking water, cooked food, alcohol, and cigarette smoke. PMID:22827593

  13. Analysis of hazardous biological material by MALDI mass spectrometry

    SciTech Connect

    KL Wahl; KH Jarman; NB Valentine; MT Kingsley; CE Petersen; ST Cebula; AJ Saenz

    2000-03-21

    Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-MS) has become a valuable tool for analyzing microorganisms. The speed with which data can be obtained from MALDI-MS makes this a potentially important tool for biological health hazard monitoring and forensic applications. The excitement in the mass spectrometry community in this potential field of application is evident by the expanding list of research laboratories pursuing development of MALDI-MS for bacterial identification. Numerous research groups have demonstrated the ability to obtain unique MALDI-MS spectra from intact bacterial cells and bacterial cell extracts. The ability to differentiate strains of the same species has been investigated. Reproducibility of MALDI-MS spectra from bacterial species under carefully controlled experimental conditions has also been demonstrated. Wang et al. have reported on interlaboratory reproducibility of the MALDI-MS analysis of several bacterial species. However, there are still issues that need to be addressed, including the careful control of experimental parameters for reproducible spectra and selection of optimal experimental parameters such as solvent and matrix.

  14. Bio-Aerosol Detection Using Mass Spectrometry: Public Health Applications

    SciTech Connect

    Ludvigson, Laura D.

    2004-01-01

    I recently spent a summer as an intern at the Lawrence Livermore National Laboratory. I worked on a project involving the real-time, reagentless, single cell detection of aerosolized pathogens using a novel mass spectrometry approach called Bio-Aerosol Mass Spectrometry (BAMS). Based upon preliminary results showing the differentiation capabilities of BAMS, I would like to explore the development and use of this novel detection system in the context of both environmental and clinical sample pathogen detection. I would also like to explore the broader public health applications that a system such as BAMS might have in terms of infectious disease prevention and control. In order to appreciate the potential of this instrument, I will demonstrate the need for better pathogen detection methods, and outline the instrumentation, data analysis and preliminary results that lead me toward a desire to explore this technology further. I will also discuss potential experiments for the future along with possible problems that may be encountered along the way.

  15. Use of Tritium Accelerator Mass Spectrometry for Tree Ring Analysis

    PubMed Central

    LOVE, ADAM H.; HUNT, JAMES R.; ROBERTS, MARK L.; SOUTHON, JOHN R.; CHIARAPPA - ZUCCA, MARINA L.; DINGLEY, KAREN H.

    2010-01-01

    Public concerns over the health effects associated with low-level and long-term exposure to tritium released from industrial point sources have generated the demand for better methods to evaluate historical tritium exposure levels for these communities. The cellulose of trees accurately reflects the tritium concentration in the source water and may contain the only historical record of tritium exposure. The tritium activity in the annual rings of a tree was measured using accelerator mass spectrometry to reconstruct historical annual averages of tritium exposure. Milligram-sized samples of the annual tree rings from a Tamarix located at the Nevada Test Site are used for validation of this methodology. The salt cedar was chosen since it had a single source of tritiated water that was well-characterized as it varied over time. The decay-corrected tritium activity of the water in which the salt cedar grew closely agrees with the organically bound tritium activity in its annual rings. This demonstrates that the milligram-sized samples used in tritium accelerator mass spectrometry are suited for reconstructing anthropogenic tritium levels in the environment. PMID:12144257

  16. High Resolution MALDI Imaging Mass Spectrometry of Retinal Tissue Lipids

    PubMed Central

    Anderson, David M. G.; Ablonczy, Zsolt; Koutalos, Yiannis; Spraggins, Jeffrey; Crouch, Rosalie K.; Caprioli, Richard M.; Schey, Kevin L.

    2014-01-01

    Matrix assisted laser desorption ionization imaging mass spectrometry (MALDI IMS) has the ability to provide an enormous amount of information on the abundances and spatial distributions of molecules within biological tissues. The rapid progress in the development of this technology significantly improves our ability to analyze smaller and smaller areas and features within tissues. The mammalian eye has evolved over millions of years to become an essential asset for survival, providing important sensory input of an organism’s surroundings. The highly complex sensory retina of the eye is comprised of numerous cell types organized into specific layers with varying dimensions, the thinnest of which is the 10 μm retinal pigment epithelium (RPE). This single cell layer and the photoreceptor layer contain the complex biochemical machinery required to convert photons of light into electrical signals that are transported to the brain by axons of retinal ganglion cells. Diseases of the retina including age related macular degeneration (AMD), retinitis pigmentosa, and diabetic retinopathy occur when the functions of these cells are interrupted by molecular processes that are not fully understood. In this report, we demonstrate the use of high spatial resolution MALDI IMS and FT-ICR tandem mass spectrometry in the Abca4−/− knockout mouse model of Stargardt disease, a juvenile onset form of macular degeneration. The spatial distributions and identity of lipid and retinoid metabolites are shown to be unique to specific retinal cell layers. PMID:24819461

  17. Data-Independent Microbial Metabolomics with Ambient Ionization Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Rath, Christopher M.; Yang, Jane Y.; Alexandrov, Theodore; Dorrestein, Pieter C.

    2013-08-01

    Atmospheric ionization methods are ideally suited for prolonged MS/MS analysis. Data-independent MS/MS is a complementary technique for analysis of biological samples as compared to data-dependent analysis. Here, we pair data-independent MS/MS with the ambient ionization method nanospray desorption electrospray ionization (nanoDESI) for untargeted analysis of bacterial metabolites. Proof-of-principle data and analysis are illustrated by sampling Bacillus subtilis and Pseudomonas aeruginosa directly from Petri dishes. We found that this technique enables facile comparisons between strains via MS and MS/MS plots which can be translated to chemically informative molecular maps through MS/MS networking. The development of novel techniques to characterize microbial metabolites allows rapid and efficient analysis of metabolic exchange factors. This is motivated by our desire to develop novel techniques to explore the role of interspecies interactions in the environment, health, and disease. This is a contribution to honor Professor Catherine C. Fenselau in receiving the prestigious ASMS Award for a Distinguished Contribution in Mass Spectrometry for her pioneering work on microbial mass spectrometry.

  18. High Resolution MALDI Imaging Mass Spectrometry of Retinal Tissue Lipids

    NASA Astrophysics Data System (ADS)

    Anderson, David M. G.; Ablonczy, Zsolt; Koutalos, Yiannis; Spraggins, Jeffrey; Crouch, Rosalie K.; Caprioli, Richard M.; Schey, Kevin L.

    2014-08-01

    Matrix assisted laser desorption ionization imaging mass spectrometry (MALDI IMS) has the ability to provide an enormous amount of information on the abundances and spatial distributions of molecules within biological tissues. The rapid progress in the development of this technology significantly improves our ability to analyze smaller and smaller areas and features within tissues. The mammalian eye has evolved over millions of years to become an essential asset for survival, providing important sensory input of an organism's surroundings. The highly complex sensory retina of the eye is comprised of numerous cell types organized into specific layers with varying dimensions, the thinnest of which is the 10 μm retinal pigment epithelium (RPE). This single cell layer and the photoreceptor layer contain the complex biochemical machinery required to convert photons of light into electrical signals that are transported to the brain by axons of retinal ganglion cells. Diseases of the retina, including age-related macular degeneration (AMD), retinitis pigmentosa, and diabetic retinopathy, occur when the functions of these cells are interrupted by molecular processes that are not fully understood. In this report, we demonstrate the use of high spatial resolution MALDI IMS and FT-ICR tandem mass spectrometry in the Abca4 -/- knockout mouse model of Stargardt disease, a juvenile onset form of macular degeneration. The spatial distributions and identity of lipid and retinoid metabolites are shown to be unique to specific retinal cell layers.

  19. Expanded newborn screening by mass spectrometry: New tests, future perspectives.

    PubMed

    Ombrone, Daniela; Giocaliere, Elisa; Forni, Giulia; Malvagia, Sabrina; la Marca, Giancarlo

    2016-01-01

    Tandem mass spectrometry (MS/MS) has become a leading technology used in clinical chemistry and has shown to be particularly sensitive and specific when used in newborn screening (NBS) tests. The success of tandem mass spectrometry is due to important advances in hardware, software and clinical applications during the last 25 years. MS/MS permits a very rapid measurement of many metabolites in different biological specimens by using filter paper spots or directly on biological fluids. Its use in NBS give us the chance to identify possible treatable metabolic disorders even when asymptomatic and the benefits gained by this type of screening is now recognized worldwide. Today the use of MS/MS for second-tier tests and confirmatory testing is promising especially in the early detection of new disorders such as some lysosomal storage disorders, ADA and PNP SCIDs, X-adrenoleucodistrophy (X-ALD), Wilson disease, guanidinoacetate methyltransferase deficiency (GAMT), and Duchenne muscular dystrophy. The new challenge for the future will be reducing the false positive rate by using second-tier tests, avoiding false negative results by using new specific biomarkers and introducing new treatable disorders in NBS programs.

  20. Laser desorption ionization mass spectrometry on silicon nanowell arrays.

    PubMed

    Gulbakan, Basri; Park, Dooho; Kang, Myungchan; Kececi, Kaan; Martin, Charles R; Powell, David H; Tan, Weihong

    2010-09-15

    This paper describes a new technique for fabrication of nanostructured porous silicon (pSi) for laser desorption ionization mass spectrometry. Porous silicon nanowell arrays were prepared by argon plasma etching through an alumina mask. Porous silicon prepared in this way proved to be an excellent substrate for desorption/ionization on silicon (DIOS) mass spectrometry (MS) using adenosine, Pro-Leu-Gly tripeptide, and [Des-Arg(9)]-bradykinin as the model compounds. It also allows the analyses of complex biological samples such as a tryptic digest of bovine serum albumin and a carnitine standard mixture. Nanowell array surfaces were also used for direct quantification of the illicit drug fentanyl in red blood cell extracts. This method also allows full control of the surface features. MS results suggested that the pore depth has a significant effect on the ion signals. Significant improvement in the ionization was observed by increasing the pore depth from 10 to 50 nm. These substrates are useful for laser desorption ionization in both the atmospheric pressure and vacuum regimes.