1;Preface to Second Edition;6 2;Foreword to Second Edition;7 3;Contributors;10 4;Contents;13 5;1 Ten Years of the Proteome;19 5.1;Abstract;19 5.2;1.1 Introduction to the Proteome;19 5.3;1.2 Proteomics Is Technology-Driven;21 5.4;1.3 What Has Proteomics Delivered?;26 5.5;1.4 What Still Eludes Us?;27 5.6;1.5 This Book and Some Conclusions;29 5.7;References;29 6;2 Sample Preparation and Prefractionation Techniques for Electrophoresis- Based Proteomics;32 6.1;Abstract;32 6.2;2.1 Introduction;32 6.3;2.2 Conventional Sample Preparation;33 6.4;2.3 Artefacts;35 6.5;2.4 Multiplexed Approaches to Proteomics;39 6.6;2.5 Prefractionation Tools;41 6.7;2.6 Other Methods for Prefractionation of Samples;47 6.8;2.7 Conclusions;52 6.9;References;53 7;3 Protein Identification in Proteomics;58 7.1;Abstract;58 7.2;3.1 Introduction;58 7.3;3.2 Attributes of Proteins Useful for Their Identification;59 7.4;3.3 Protein Identification by Mass Spectrometry;62 7.5;3.4 List of Tools and URLs;82 7.6;3.5 Concluding Remarks;82 7.7;References;83 8;4 Quantitation in Proteomics;85 8.1;Abstract;85 8.2;4.1 Introduction;85 8.3;4.2 Non-mass-spectrometric Approaches to Quantitation;86 8.4;4.3 Relative Quantitation by Mass Spectrometry;90 8.5;4.4 Analysis of Known Post-translational Modifications;99 8.6;4.5 Conclusions;103 8.7;References;104 9;5 One Gene, Many Proteins;110 9.1;Abstract;110 9.2;5.1 Introduction;110 9.3;5.2 An Overview of Modifications: What Are They and Where Do They Occur?;114 9.4;5.3 How Do We Find Post-translational Modifications?;115 9.5;5.4 Analysis of Specific Modifications;120 9.6;5.5 The Function of Protein Post-translational Modifications: More Than Meets the Eye?;124 9.7;5.6 Some Interesting Modification Stories;126 9.8;5.7 Future Directions;131 9.9;References;131 10;6 Proteome Imaging;137 10.1;Abstract;137 10.2;6.1 Introduction;137 10.3;6.2 Image Analysis of Two-Dimensional Electrophoresis Gels;138 10.4;6.3 Liquid Chromatography-Mass Spectrometry;144 10.5;6.4 The Molecular Scanner;148 10.6;6.5 Imaging Mass Spectrometry;152 10.7;6.6 Conclusion;155 10.8;References;156 11;7 Data Integration in Proteomics;159 11.1;Abstract;159 11.2;7.1 Introduction;159 11.3;7.2 Integration As Gathering and Cross-Linking Information;162 11.4;7.3 Integration As Blending of Information;173 11.5;7.4 Concluding Remarks;178 11.6;References;178 12;8 Protein-Protein Interactions;183 12.1;Abstract;183 12.2;8.1 Introduction;183 12.3;8.2 Protein-Protein Interactions in Human Diseases: Altered Protein Connectivity Leads to Disorder;184 12.4;8.3 Charting Protein-Protein Interactions;186 12.5;8.4 Biological and Biomedical Applications;195 12.6;8.5 Future Directions;200 12.7;References;201 13;9 Biomedical Applications of Proteomics;207 13.1;Abstract;207 13.2;9.1 Introduction;207 13.3;9.2 The Application of Proteomics to Medicine;208 13.4;9.3 Disease Diagnosis from Body Fluids;210 13.5;9.4 Vascular Diseases;211 13.6;9.5 Neurodegenerative Disorders;216 13.7;9.6 Proteomics and Cancer;220 13.8;9.7 Toxicopharmacology: the Example of Type 2 Diabetes;225 13.9;9.8 Current Limitations and Future Directions of Proteomics for Medicine;229 13.10;9.9 Present and Future Directions;231 13.11;References;231 14;10 Proteomics: Where to Next?;236 14.1;Abstract;236 14.2;10.1 Introduction;236 14.3;10.2 The Relevance of -omics to Biology;237 14.4;10.3 Technological Developments in Proteomics;238 14.5;10.4 The Next Steps for Proteomics: Diagnostics and Drugs;240 14.6;10.5 Conclusions;242 14.7;References;242 15;Index;244