Shotgun proteomics
Subtitle: methods and protocols
By: edited by Daniel Martins-de-Souza, Laboratory of Neuroprotemics, Department of Biochemistry, Institute of Biology, State University of the Campinas (UNICAMP), Campinas, Brazil, Max Planck Institute of Psychiatry, Munich, Germany, Research Group of Proteomics, Department of Psychiatry and Psycholtherapy, Ludwig-Maximilians-University of Munich, Munich, Germany, Laboratory of Neurosciences (LIM-27), Institute of Psychiatry, University of Sao Paulo, Sao Paulo, Brazil
Series: Methods in molecular biology -- 1156; Springer protocols; Methods in molecular biology (Clifton, N.J.) -- 1156.; Springer protocols (Series)
Publisher: Humana Press
Published: 2014
Place of publication: New York
Language: eng
Number of pages: 492
ISBN-13: 9781493906840; 9781493906857
Subjects: Proteomics; Laboratory Manuals; Methods; Isotope Labeling
Description: Shotgun Proteomics: Methods and Protocols serves as a vital collection of protocols through which thousands of proteins can be simultaneously identified, quantified, and characterized in a high throughput manner. Beginning with the history of proteomics centered on the vital role of mass spectrometry in its development, this detailed volume continues with chapters on sample pre-fractionation, in vivo and in vitro stable isotope labeling, label-free proteomics, informatics, protein-protein interactions, targeted proteomics, and post-translational modifications. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Practical and comprehensive, Shotgun Proteomics: Methods and Protocols is an ideal and up-to-date guide for researchers seeking to understand the proteome of any given species.
Notes: Includes bibliographical references and index.
Table of contents: title: Survey of shotgun proteomics  -- Fabio Cesar Sousa Nogueira and Gilberto B. Domont; title: LC-MALDI-TOF/TOF for shotgun proteomics  -- Patricia Fernández-Puente ... [et al.]; title: Fully automatable multidimensional reversed-phase liquid chromatography with online tandem mass spectrometry  -- Maggie P.Y. Lam ... [et al.]; title: GeLC-MS/MS analysis of complex protein mixtures  -- Monika Dzieciatkowska, Ryan Hill, and Kirk C. Hansen; title: IPG strip-based peptide fractionation for shotgun proteomics  -- Murat Eravci, Christian Sommer, and Matthias Selbach; title: SILAC yeast : from labeling to comprehensive Proteome Quantification  -- Lyris M. F. de Godoy; title: Analysis of proteome dynamics in mice by isotopic labeling  -- John C. Price and Sina Ghaemmaghami; title: Stable isotope labeling in mammals (SILAM)  -- Daniel B. McClatchy and John R. Yates III; title: Analysis of individual protein turnover in live animals on a proteome-wide scale  -- Stefan Reckow and Christian Webhofer; title: Determining protein subcellular localization in mammalian cell culture with biochemical fractionation and iTRAQ 8-plex quantification  -- Andy Christoforou, Alfonso Martinez Arias, and Kathryn S. Lilley; title: Brain quantitative proteomics combining GeLC-MS and isotope-coded protein labeling (ICPL)  -- Giuseppina Maccarrone, Maria Lebar, and Daniel Martins-de-Souza; title: Employing TMT quantification in a shotgun-MS platform  -- Darragh P. O'Brien and John F. Timms; title: Employing TMT quantification in shotgun-MS proteomic analysis : a focus on skeletal muscle  -- Bruno Menezes de Oliveira; title: Spectral counting label-free proteomics  -- Liisa Arike and Lauri Peil; title: Quantification of proteins by label-free LC-MSE  -- Alon Savidor and Yishai Levin; title: Bioinformatics for proteomics : opportunities at the interface between the scientists, their experiments, and the community  -- Marc Vaudel ... [et al.]; title: Identification of DNA damage checkpoint-dependent protein interactions in Saccharomyces cerevisiae using quantitative mass spectrometry  -- Francisco M. Bastos de Oliveira and Marcus B. Smolka; title: Application of shotgun proteomics for discovery-driven protein-protein interaction  -- Livia Goto-Silva ... [et al.]; title: Mapping protein complexes using covalently linked antibodies and isobaric mass tags  -- Antje Dittmann ... [et al.]; title: Biomarker verification using selected reaction monitoring and shotgun proteomics  -- Angel Mauricio Castro-Gamero, Clarice Izumi, and José César Rosa; title: Use of universal stable isotope labeling by amino acids in cell culture (SILAC)-based selected reaction monitoring (SRM) approach for verification of breast cancer-related protein markers  -- Ning Qing Liu ... [et al.]; title: Secretome analysis by high-throughput proteomics and multiple reaction monitoring (MRM)  -- Vitor M. Faça ... [et al.]; title: Preparation of heteroelement-incorporated and stable isotope-labeled protein standards for quantitative proteomics  -- Anna Konopka ... [et al.]; title: One-source peptide/phosphopeptide ratio standards for accurate and site-specific determination of the degree of phosphorylation  -- Martin E. Boehm, Bettina Hahn, and Wolf D. Lehmann; title: Quantitative glycoproteomics for N-glycoproteome profiling  -- Sheng Pan; title: Practical recipe to survey phosphoproteomes  -- William C. Edelman ... [et al.]; title: Quantitation of the phosphoproteome using the library-assisted eXtracted ion chromatogram (LAXIC) strategy  -- Justine V. Arrington, Liang Xue, and W. Andy Tao; title: Fast, efficient, and quality-controlled phosphopeptide enrichment from minute sample amounts using titanium dioxide  -- Clarissa Dickhut, Sonja Radau, and René P. Zahedi; title: Quantifying small molecule-induced changes in cellular protein expression and posttranslational modifications using isobaric mass tags  -- Isabelle Becher, Maria Fälth Savitski, and Marcus Bantscheff; title: Analysis of protein structure by cross-linking combined with mass spectrometry  -- Evgeniy V. Petrotchenko ... [et al.]; title: Top-down proteomics by means of orbitrap mass spectrometry -- Kai Scheffler.