Survey of Shotgun Proteomics -- LC-MALDI-TOF/TOF for Shotgun Proteomics -- Fully Automatable Multidimensional Reversed-Phase Liquid Chromatography with Online Tandem Mass Spectrometry -- GeLC-MS/MS Analysis of Complex Protein Mixtures -- IPG Strip-Based Peptide Fractionation for Shotgun Proteomics -- SILAC Yeast: From Labeling to Comprehensive Proteome Quantification -- Analysis of Proteome Dynamics in Mice by Isotopic Labeling -- Stable Isotope Labeling in Mammals (SILAM) -- Analysis of Individual Protein Turnover in Live Animals on a Proteome-Wide Scale -- Determining Protein Subcellular Localization in Mammalian Cell Culture with Biochemical Fractionation and iTRAQ 8-Plex Quantification -- Brain Quantitative Proteomics Combining GeLC-MS and Isotope-Coded Protein Labeling (ICPL) -- Employing TMT Quantification in a Shotgun-MS Platform -- Employing TMT Quantification in Shotgun-MS Proteomic Analysis: A Focus on Skeletal Muscle -- Spectral Counting Label-Free Proteomics -- Quantification of Proteins by Label Free LC-MSE -- Bioinformatics for Proteomics: Opportunities at the Interface Between the Scientists, Their Experiments and the Community -- Identification of DNA Damage Checkpoint-Dependent Protein Interactions in Saccharomyces cerevisiae Using Quantitative Mass Spectrometry -- Application of Shotgun Proteomics for Discovery-Driven Protein-Protein Interaction -- Mapping Protein Complexes Using Covalently Linked Antibodies and Isobaric Mass Tags -- Biomarker Verification Using Selected Reaction Monitoring and Shotgun Proteomics -- 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 -- The Secretome Analysis by High Throughput Proteomics and Multiple Reaction Monitoring (MRM) -- Preparation of Heteroelement-Incorporated and Stable Isotope-Labeled Protein Standards for Quantitative Proteomics -- One-Source Peptide/Phosphopeptide Ratio Standards for Accurate and Site-Specific Determination of the Degree of Phosphorylation -- Quantitative Glycoproteomics for N-Glycoproteome Profiling -- A Practical Recipe to Survey Phosphoproteomes -- Quantitation of the Phosphoproteome Using the Library Assisted eXtracted Ion Chromatogram (LAXIC) Strategy -- Fast, Efficient and Quality-Controlled Phosphopeptide Enrichment from Minute Sample Amounts Using Titanium Dioxide -- Quantifying Small Molecule-Induced Changes in Cellular Protein Expression and Post-Translational Modifications Using Isobaric Mass Tags -- Analysis of Protein Structure by Crosslinking Combined with Mass Spectrometry -- Top Down Proteomics by Means of Orbitrap Mass Spectrometry.

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.