Introducing Proteomics: From Concepts to Sample Separation, Mass Spectrometry and Data Analysis

Preface ix

Acknowledgements xi

1 Introduction 1

1.1 What Are the Tasks in Proteomics? 1

1.2 Challenges in Proteomics 5

1.3 Proteomics in Relation to Other -omics and System Biology 10

1.4 Some General Applications of Proteomics 12

1.5 Structure of the Book 18

References 18

2 Separation and Detection Technologies 21

2.1 Introduction to Experimental Strategies in Proteomics 21

2.2 Gel-Based Separation 31

2.3 Visualization and Analysis of Proteins/Peptides in Gels 40

2.4 Gel-Free Separation Technologies 54

2.5 Visualization of Proteins/Peptides from Hyphenated Methods 74

2.6 Chips in Proteomic Applications 81

References 81

3 Analysis of Peptides/Proteins by Mass Spectrometry 83

3.1 Basic Principles of Mass Spectrometry for Proteomics 83

3.2 Ionization Methods for Small Amounts of Biomolecules 101

3.3 Mass Analyzers and Mass Spectrometers 116

3.4 Concluding Remarks on Mass Analyzers for Proteomics 170

References 170

4 Analysis and Interpretation of Mass Spectrometric and Proteomic Data 173

4.1 Introduction 173

4.2 Analysis of MS Data 174

4.3 Analysis of MS/MS Data 192

4.4 Quantification of LC MS and MS/MS Data from Complex Samples 209

4.5 Bioinformatic Approaches for Mass Spectrometric Proteome Data Analysis 213

References 218

5 Strategies in Proteomics 221

5.1 Imaging Mass Spectrometry 221

5.2 Qualitative Proteomics 223

5.3 Differential and Quantitative Proteomics 234

5.4 Analysis of Posttranslational Modifications 257

5.5 Interaction Proteomics 261

5.6 Proteomics as Part of Integrated Approaches 266

References 271

Index 275