When the last edition of this book was published in 2000, the field of proteomics was in its infancy. Now in its adolescence, proteomics is fundamentally transforming biological and medical research. Much of this transformation can be attributed to technological advancements, particularly in mass spectrometry. As a result of these rapid developments that have led to expanded areas of research and innovative applications, an update to Mass Spectrometry of Proteins and Peptides is not only worthwhile, but arguably mandatory. Spanning fields from microbial forensics and clinical applications to protein structure, dynamics and function, the following chapters written by leading experts serve as a forum for presenting some of the latest revolutionizing methods for mass spectrometry-based characterization of proteins and peptides. Staying faithful to the spirit of the Methods in Molecular Biology'„¢ series, all chapters are written in the same format, whereby each chapter opens with a basic description of the method, followed by a description of the protocol and then practical step-by-step instructions to ensure experimental success.Mass Spectrometry of Proteins and Peptides: Methods and Protocols, Second Edition is a valuable resource for novice and seasoned practitioners in the fields of biochemistry, molecular biology, clinical chemistry, immunology, genetic, microbiology and toxicology.

PrefaceContributorsGeneration and Analysis of Multidimensional Protein Identification Technology DatasetsSelene K. Swanson, Laurence Florens and Michael P. WashburnQuantitative Peptide and Protein Profiling by Mass SpectrometryAlexander Schmidt, Birgit Bisle and Thomas KislingerLabel Free Relative Quantitation of Prokaryotic Proteomes Using the Accurate Mass and Time Tag ApproachKim K. HixsonClassical Proteomics: Two-dimensional Electrophoresis/MALDI Mass SpectrometryUrsula Zimny-Arndt, Monika Schmid, Renate Ackermann and Peter R. JungblutThe Use of Difference In-Gel Electrophoresis for Quantitation of Protein ExpressionRajat SapraLiquid-Chromatography-Mass Spectrometry of Thylakoid Membrane ProteinsChristian G. Huber, Anna-Maria Timperio, Hansjörg Toll and Lello ZollaHigh Accuracy Mass Spectrometry in Large-Scale Analysis of Protein PhosphorylationJesper V. Olsen and Boris MacekManual Validation of Peptide Sequence and Sites of Tyrosine Phosphorylation from MS/MS SpectraAmy Nichols and Forest WhiteAssigning Glycosylation Sites and Microheterogeneities in Glycoproteins by Liquid Chromatography/Tandem Mass SpectrometryYehia Mechref, Milan Madera and Milos V. NovotnyStructure Analysis of N-glycoproteinsStefanie Henning, Jasna Peter-Katalinic and Gottfried PohlentzCapillary Zone Electrophoresis-mass Spectrometry for the Characterization of Isoforms of Intact GlycoproteinsChristian Neusüß and Matthias PelzingTop-down Proteomics on a High-field Fourier Transform Ion Cyclotron Resonance Mass spectrometerSéverine A. Ouvry-Patat, Matthew P. Torres, Craig Gelfand, Hung-Hiang Quek, Michael Easterling, J. Paul Speir and Christoph H. Borchers Capillary Isoelectric Focusing/Reversed Phase Liquid Chromatography/Mass SpectrometryCheng S. Lee and Brian M. BalgleyIntegrating Accelerated Tryptic Digestion into Proteomics WorkflowsGordon W. Slysz and David C. SchriemerHydrogen/Deuterium Exchange Mass SpectrometryXuguang Yan and Claudia S. MaierMass Spectrometry Detection and Characterization of Noncovalent Protein ComplexesSheng Yin and Joseph A. LooChemical Cross-linking for Protein-protein Interaction StudiesXiaoting Tang and James E. BruceTissue Analysis with High Resolution Imaging Mass SpectrometryA.F. Maarten Altelaar and Ron M.A. HeerenProteomic Global Profiling for Cancer Biomarker DiscoverySamir HanashAnalysis of Protein Glycosylation and Phosphorylation Using Liquid Phase Separation, Protein Microarray Technology and Mass SpectrometryJia Zhao, Tasneem H. Patwa, Manoj Pal, Weilian Qiu and David M. LubmanTransthyretin Mass Determination for Detection of Transthyretin Familial AmyloidJohn F. O'Brien and H. Robert Bergen, IIICharacterization of Microorganisms by MALDI Mass SpectrometryCatherine E. Petersen, Nancy B. Valentine and Karen L. WahlMass Spectrometric Characterization Of NeuropeptidesStephanie S. DeKeyser, James A. Dowell and Lingjun LiPeptide and Protein Ion/Ion Reactions in Electrodynamic Ion Traps: Tools and MethodsScott A. McLuckeyElectron Capture Dissociation LC/MS/MS for Bottom-Up ProteomicsRoman A. ZubarevTwo-Dimensional Ion Mobility Analyses of Proteins and PeptidesAlexandre A. Shvartsburg, Keqi Tang and Richard D. SmithProteomics for Validation of Automated Gene Model PredictionsKemin Zhou, Ellen A. Panisko, Jon K. Magnuson, Scott E. Baker and Igor V. GrigorievSupport Vector Machines for Improved Peptide Identification from Tandem Mass Spectrometry Database Search Bobbie-Jo M. Webb-Robertson