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Quantitative methods in proteomics / edited by Katrin Marcus. — New York : Humana Press ;Springer, c2012. – (58.17/M592/v.893)

Contents

    Contents
    
    Preface
    Contributors
    PART I PLANNING A PROTEOMIC EXPERIMEN'I
    1 Important Issues in Planning a Proteomics Experiment: Statistical Considerations of Quantitative Proteomic Data
    PART II QUANTITATIVE PROTEOMICS: GEL-BASED METHODS
    2 The Whereabouts of 2D Gels in Quantitative Proteomics 25
    3 Proteome Analysis with Classical 2D-PAGE 37
    4 Fast and Sensitive Coomassie Staining in Quantitative Proteomics 47
    5 Silver Staining of2D Electrophoresis Gels 61
    6 Differential Proteome Analysis Using 2D-DIGE 75
    PART III QUANTITATIVE PROTEOMICS: MS-BASED METHODS
    7 Quantitative Mass Spectrometry-Based Proteomics: An Overview 85
    8 Robust Workflow for iTRAQ-Based Peptide and Protein Quantification 101
    9 Relative Protein Quantification by MS/MS Using the Tandem Mass Tag Technology l15
    10 A Rapid Approach for Isobaric Peptide Termini Labeling 129
    11 Isotope-Coded Protein Label 143
    12 Hydroponic Isotope Labeling of Entire Plants and High-Performance Mass Spectrometry for Quantitative Plant Proteomics 155
    13 In Vivo Quantitative Proteome Profiling: Planning and Evaluation of SILAC Experiments 175
    14 SILAC for the Study of Mammalian Cell Lines and Yeast Protein Complexes 201
    15 Post-digestion 1~O Exchange/Labeling for Quantitative Shotgun Proteomics of Membrane Proteins 223
    16 Application of Label-Free Proteomics for Differential Analysis of Lung Carcinoma Cell Line A549 241
    17 Absolute Quantification of Proteins Using Standard Peptides and Multiple Reaction Monitoring 249
    18 Absolute Multiplexed Protein Quantification Using QconCAT Technology 267
    19 A Practical Guide to the FLEXIQuant Method 295
    20 Label-Free Protein Quantitation Using Weighted Spectral Counting 321
    PART IV SPECIFIC METHODS -- DETECTION AND QUANTIFICATION OF POST-TRANSLATIONAL MODIFICATIONS
    21 Discovering the Phosphoproteome of the Hydrophobic Cytochrome c Oxidase Membrane Protein Complex 345
    22 KiC Assay: A Quantitative Mass Spectrometry-Based Approach
    23 Robust and High-Throughput Sample Preparation for (Semi-)Quantitative Analysis of N-Glycosylation Profiles from Plasma Samples 371
    24 Quantitative Redox Proteomics: The NOxICAT Method 387
    25 Quantitative Analysis of S-Nitrosylated Proteins 405
    26 Analysis of Ubiquitinated Proteome by Quantitative Mass Spectrometry 417
    27 Identification of Endogenous SUMO1 Accepter Sites by Mass Spectrometry 431
    PART V DATA ANALYSIS and SOFTWARE TOOLS
    28 Search and Decoy: The Automatic Identification of Mass Spectra 445
    29 Software Tools for MS-Based Quantitative Proteomics: A Brief Overview 489
    30 iTRAQ Data Interpretation 501
    31 MSQuant: A Platform for Stable Isotope-Based Quantitative Proteomics 511
    Erratum
    Index