Shotgun proteomics : methods and protocols / edited by Daniel Martins-de-Souza.

Includes bibliographical references and index.

Survey of shotgun proteomics / Fabio Cesar Sousa Nogueira and Gilberto B. Domont -- LC-MALDI-TOF/TOF for shotgun proteomics / Patricia Fernández-Puente [and others] -- Fully automatable multidimensional reversed-phase liquid chromatography with online tandem mass spectrometry / Maggie P.Y. Lam [and others] -- GeLC-MS/MS analysis of complex protein mixtures / Monika Dzieciatkowska, Ryan Hill, and Kirk C. Hansen -- IPG strip-based peptide fractionation for shotgun proteomics / Murat Eravci, Christian Sommer, and Matthias Selbach -- SILAC yeast : from labeling to comprehensive Proteome Quantification / Lyris M.F. de Godoy -- Analysis of proteome dynamics in mice by isotopic labeling / John C. Price and Sina Ghaemmaghami -- Stable isotope labeling in mammals (SILAM) / Daniel B. McClatchy and John R. Yates III -- Analysis of individual protein turnover in live animals on a proteome-wide scale / Stefan Reckow and Christian Webhofer -- 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 -- Brain quantitative proteomics combining GeLC-MS and isotope-coded protein labeling (ICPL) / Giuseppina Maccarrone, Maria Lebar, and Daniel Martins-de-Souza -- Employing TMT quantification in a shotgun-MS platform / Darragh P. O'Brien and John F. Timms -- Employing TMT quantification in shotgun-MS proteomic analysis : a focus on skeletal muscle / Bruno Menezes de Oliveira -- Spectral counting label-free proteomics / Liisa Arike and Lauri Peil -- Quantification of proteins by label-free LC-MSE / Alon Savidor and Yishai Levin -- Bioinformatics for proteomics : opportunities at the interface between the scientists, their experiments, and the community / Marc Vaudel [and others] -- Identification of DNA damage checkpoint-dependent protein interactions in Saccharomyces cerevisiae using quantitative mass spectrometry / Francisco M. Bastos de Oliveira and Marcus B. Smolka -- Application of shotgun proteomics for discovery-driven protein-protein interaction / Livia Goto-Silva [and others] -- Mapping protein complexes using covalently linked antibodies and isobaric mass tags / Antje Dittmann [and others] -- Biomarker verification using selected reaction monitoring and shotgun proteomics / Angel Mauricio Castro-Gamero, Clarice Izumi, and José César Rosa -- 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 [and others] -- Secretome analysis by high-throughput proteomics and multiple reaction monitoring (MRM) / Vitor M. Faça [and others] -- Preparation of heteroelement-incorporated and stable isotope-labeled protein standards for quantitative proteomics / Anna Konopka [and others] -- 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 -- Quantitative glycoproteomics for N-glycoproteome profiling / Sheng Pan -- Practical recipe to survey phosphoproteomes / William C. Edelman [and others] -- Quantitation of the phosphoproteome using the library-assisted eXtracted ion chromatogram (LAXIC) strategy / Justine V. Arrington, Liang Xue, and W. Andy Tao -- Fast, efficient, and quality-controlled phosphopeptide enrichment from minute sample amounts using titanium dioxide / Clarissa Dickhut, Sonja Radau, and René P. Zahedi -- Quantifying small molecule-induced changes in cellular protein expression and posttranslational modifications using isobaric mass tags / Isabelle Becher, Maria Fälth Savitski, and Marcus Bantscheff -- Analysis of protein structure by cross-linking combined with mass spectrometry / Evgeniy V. Petrotchenko [and others] -- Top-down proteomics by means of orbitrap mass spectrometry / Kai Scheffler.

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.

Online resource; title from PDF title page (SpringerLink, viewed May 13, 2014).