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