Proteomics sample preparation / edited by Jorg von Hagen. — Weinheim : Wiley-VCH Verlag GmbH & Co. KGaA, c2008. – (58.17421/P967psp)

Contents

    Contents
    
    Preface
    List of Contributors XXIII
    List of Abbreviations XXXI
    Part I Perspectives in Proteomics Sample Preparation
    1 Introduction 3
    2 General Aspects of Sample Preparation for Comprehensive Proteome Analysis 5
    2.1 The Need for Standards in Proteomics Sample Preparation 5
    2.2 Introduction: The Challenge of Crude Proteome Sample Analysis
    2.3 General Aspects: Parameters which Influence the Sample Preparation Procedure
    2.4 Summary and Perspectives 17
    3 Proteomics: A Philosophical Perspective 21
    3.1 Introduction: "In the Beginning was the Word" 21
    3.2 The Experiment as a Scientific Method and a Tool of Cognition
    3.3 The Experiment as a Method (Tool) of Cognition Within the Scope of Biology. The So-Called "Life Sciences" 26
    3.4 Proteomics as a Cognition-Theoretical Challenge 30
    3.5 Conclusion 36
    Part II Methods 41
    4 Mass Spectrometry 43
    4.1 A Practical Guideline to Electrospray Ionization Mass Spectrometry for Proteomics Application 43
    4.2 Sample Preparation for the Application of MALDI Mass Spectrometry in Proteome Analysis 73
    4.3 Sample Preparation for Label-Free Proteomic Analyses of Body Fluids by Fourier Transform Ion Cyclotron Mass Spectrometry 95
    4.4 Sample Preparation for Differential Proteome Analysis Labeling Technologies for Mass Spectrometry 105
    4.5 Determining Membrane Protein Localization Within Subcellular Compartments Using Stable Isotope Tagging 118
    5 Electrophoresis 129
    5.1 Sample Preparation for Two-Dimensional Gel Electrophoresis 129
    5.2 Sample Preparation for Native Electrophoresis 144
    5.3 Sample Preparation for LC-MS/MS Using Free-Flow Electrophoresis 155
    5.4 Sample Preparation for Capillary Electrophoresis 171
    6 Optical Methods 187
    6.1 High-Throughput Proteomics: Spinning Disc Interferometry(SDI) 187
    6.2 Optical Proteomics on Cell Arrays 208
    6.3 Sample Preparation by Laser Microdissection and Catapulting for Proteome Analysis 219
    6.4 Sample Preparation for Flow Cytometry 234
    7 Chromatography 245
    7.1 Sample Preparation for HPLC-Based Proteome Analysis 245
    7.2 Sample Preparation for Two-Dimensional Phosphopeptide Mapping and Phosphoamino Acid Analysis 265
    8 Structural Proteomics 273
    8.1 Exploring Protein-Ligand Interactions by Solution NMR 273
    8.2 Sample Preparation for Crystallography 281
    9 Interaction Analysis 295
    9.1 Sample Preparation for Protein Complex Analysis by the Tandem Affinity Purification (TAP) Method 295
    9.2 Exploring Membrane Proteomes 303
    10 Post-Translational Modifications 317
    10.1 Sample Preparation for Phosphoproteome Analysis 317
    10.2 Sample Preparation for Analysis of Post-Translational Modifications: Glycosylation 328
    11 Species-Dependent Proteomics 343
    11.1 Sample Preparation and Data Processing in Plant Proteomics 343
    11.2 Sample Preparation for MudPIT with Bacterial Protein Samples 358
    11.3 Sample Preparation for the Cell-Wall Proteome Analysis of Yeast and Fungi 371
    12 The Human Proteosome 379
    12.1 Clinical Proteomics: Sample Preparation and Standardization 379
    12.2 Stem Cell Proteomics 412
    13 Bioinformatics 423
    13.1 Bioinformatics Support for Mass Spectrometric Quality Control 423
    13.2 Use of Physico-Chemical Properties in Peptide and Protein Identification 433
    Index 449