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