Phospho-proteomics : methods and protocols / edited by Marjo de Graauw. — [Totowa, N.J.] : Humana, c2009. – (58.17/M592/v.527)

Contents

    Contents
    
    Preface
    Contributors ix
    PART I: PROTEIN PHOSPHORYLATION AND 2D GEL ELECTROPHORESIS
    1. A High-Resolution Two Dimensional Gel- and Pro-Q DPS-Based Proteomics Workflow for Phosphoprotein Identification and Quantitative Profiling
    2. Differential Phosphoprotein Labelling (DIPPL) Using 32p and 33p
    PART II: ENRICHMENT OF PHOSPHOPROTEINS AND PEPTIDES
    3. Identification of Oxidative Stress-Induced Tyrosine Phosphorylated Proteins by Immunoprecipitation and Mass Spectrometry
    4. Enrichment and Characterization of Phosphopeptides by Immobilized Metal Affinity Chromatography (IMAC) and Mass Spectrometry
    5. The Use of Titanium Dioxide Micro-Columns to Selectively Isolate Phosphopeptides from Proteolytic Digests
    6. Enrichment and Separation of Mono- and Multiply Phosphorylated Peptides Using Sequential Elution from IMAC Prior to Mass Spectrometric Analysis
    7. Use of Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) for Phosphotyrosine Protein Identificatiori-and Quantitation
    8. Hydrophilic Interaction Chromatography for Fractionation and Enrichment of the Phosphoproteome
    9. SILAC for Global Phosphoproteomic Analysis 107
    10. Quantitative Phospho-proteomics Based on Soluble Nanopolymers 117
    11. Profiling the Tyrosine Phosphorylation State Using SH2 Domains 131
    PART III: PHOSPHOPROTEIN ANALYSIS BY MASS SPECTROMETRY
    12. An Overview of the Qualitative Analysis of Phosphoproteins by Mass Spectrometry 159
    13. The Analysis of Phosphoproteomes by Selective Labelling and Advanced Mass Spectrometric Techniques 173
    14. On-Line Liquid Chromatography Electron Capture Dissociation for the Characterization of Phosphorylation Sites in Proteins 191
    15. Quantification of Protein Phosphorylation by μLC-ICP-MS 201
    16. Reverse-Phase Diagonal Chromatography for Phosphoproteome Research
    17. Chemical Tagging Strategies for Mass Spectrometry-Based Phospho-proteomics
    PART IV: ARRAYS TO STUDY PROTEIN-PHOSPHORYLATION
    18. Antibody Array Platform to Monitor Protein Tyrosine Phosphorylation in Mammalian Cells 247
    19. Protein Tyrosine Kinase Characterization Based on Fully Automated Synthesis of (Phospho)Peptide Arrays in Microplates 257
    20. Kinome Profiling Using Peptide Arrays in Eukaryotic Cells . .
    PART V: BIOINFORMATICS
    21. ProMoST: A Tool for Calculating the p/and Molecular Mass of Phosphorylated and Modified Proteins on Two-Dimensional Gels
    22. Kinase-Specific Prediction of Protein Phosphorylation Sites
    23. Reconstructing Regulatory Kinase Pathways from Phosphopeptide Data: A Bioinformatics Approach
    Index