Proteome research : concepts, technology and application / M. R. Wilkins ... [and others] (eds.).

Format:

Book

Contributor:

Wilkins, M. R. (Marc R.), 1967-

Series:

Principles and practice

Language:

English

Subjects (All):

Proteomics.

Proteins--Databases.

Proteins.

Post-translational modification.

Proteomics--methods.

Databases, Protein.

Electrophoresis, Gel, Two-Dimensional.

Databases.

Medical Subjects:

Proteomics--methods.

Databases, Protein.

Electrophoresis, Gel, Two-Dimensional.

Physical Description:

xxii, 239 pages : illustrations (some color) ; 24 cm.

Edition:

Second edition.

Place of Publication:

Berlin ; New York : Springer, [2007]

Summary:

Proteomics is a multifaceted, interdisciplinary field which studies the complexity and dynamics of proteins in biological systems. It combines powerful separation and analytical technology with advanced informatics to understand the function of proteins in the cell and in the body. This book provides a clear conceptual description of each facet of proteomics, describes recent advances in technology and thinking in each area, and provides details of how these have been applied to a variety of biological problems. It is written by expert practitioners in the field, from industry, research institutions, and the clinic. It provides junior and experienced researchers with an invaluable proteomic reference, and gives fascinating glimpses of the future of this dynamic field.

Contents:

1 Ten Years of the Proteome / Marc R. Wilkins, Ron D. Appel 1

1.1.1 What's in a Word? 2

1.1.2 Could Things Have Been Different? 3

1.2 Proteomics Is Technology-Driven 3

1.2.1 Protein Separations 3

1.2.2 Mass Spectrometry 5

1.2.3 Making Sense of All the Data 6

1.3 What Has Proteomics Delivered? 8

1.4 What Still Eludes Us? 9

1.5 This Book and Some Conclusions 11

2 Sample Preparation and Prefractionation Techniques for Electrophoresis-Based Proteomics / Ben R. Herbert, Pier Giorgio Righetti, Attilio Citterio, Egisto Boschetti 15

2.2 Conventional Sample Preparation 16

2.3 Artefacts 18

2.3.1 Cysteine Chemistry - Reduction and Alkylation 18

2.3.2 Cysteine Chemistry - [beta]-Elimination 19

2.3.3 Lysine Chemistry - Carbamylation 20

2.4 Multiplexed Approaches to Proteomics 22

2.5 Prefractionation Tools 24

2.5.1 Fractional Centrifugation 24

2.5.2 Chromatographic Techniques 25

2.5.2.1 General Chromatographic Methods 25

2.5.2.2 Sample Fractionation with Stacked Sorbents 26

2.5.3 Electrophoresis-Based Methods 26

2.5.3.1 Continuous Electrophoresis in Free Liquid Films 27

2.5.3.2 Rotationally Stabilised Focusing Apparatus: the Rotofor 28

2.5.3.3 Sample Prefractionation via Multicompartment Electrolysers with Isoelectric Membranes 28

2.5.3.4 Miniaturised Isoelectric Separation Devices 30

2.6 Other Methods for Prefractionation of Samples 30

2.6.1 Depletion of High-Abundance Proteins 30

2.6.2 Equaliser Beads: the Democratic Versus the Plutocratic Proteome 31

3 Protein Identification in Proteomics / Patricia Hernandez, Pierre-Alain Binz, Marc R. Wilkins 41

3.2 Attributes of Proteins Useful for Their Identification 42

3.2.1 Species of Origin 42

3.2.2 Protein Isoelectric Point 42

3.2.3 Protein Mass 42

3.2.4 Partial Sequence or Sequence Tag 43

3.2.5 Protein Amino Acid Composition 43

3.3 Protein Identification by Mass Spectrometry 45

3.3.1 'Top-Down' Versus 'Bottom-Up' Strategies for Protein Identification 45

3.3.2.1 Ionisation 47

3.3.2.2 Mass Analysis 48

3.3.2.3 Instrumentation 50

3.3.3 Protein Identification by Peptide Mass Fingerprinting 51

3.3.3.1 Principle 51

3.3.3.2 Identification and Characterisation of Modified Peptides by Peptide Mass Fingerprinting 53

3.3.3.3 Limitations of Peptide Mass Fingerprinting 55

3.3.4 Tandem Mass Spectrometry Based Identification 56

3.3.4.1 Tandem Mass Spectrometry Spectra 56

3.3.4.2 The 'Peptide Fragment Fingerprinting' Approach 57

3.3.4.3 De Novo Sequencing 60

3.3.4.4 Identification and Characterisation of Peptides with Unexpected Modifications 61

3.3.4.5 Spectral Library Searches 62

3.4 List of Tools and URLs 65

4 Quantitation in Proteomics / Garry L. Corthals, Keith Rose 69

4.2 Non-mass-spectrometric Approaches to Quantitation 70

4.3 Relative Quantitation by Mass Spectrometry 74

4.3.1 Absolute or Relative Quantitation? 76

4.3.2 Introduction of Stable Isotopes Using Chemical Tags 76

4.3.3 Enzyme-Mediated Incorporation of Stable Isotopes 80

4.3.4 Biological Incorporation of Stable Isotopes by Metabolic Labelling 81

4.3.5 Relative Quantitation Without Use of Stable Isotope Labelling 82

4.3.6 Absolute Quantitation by Mass Spectrometry 82

4.4 Analysis of Known Post-translational Modifications 83

4.4.1 Glycosylation 83

4.4.2 Phosphorylation 85

4.4.3 Ubiquitinylation 87

5 One Gene, Many Proteins / Nicolle H. Packer, Andrew A. Gooley, Marc R. Wilkins 95

5.2 An Overview of Modifications: What Are They and Where Do They Occur? 99

5.3 How Do We Find Post-translational Modifications? 100

5.3.1 Separation of Isoforms 100

5.3.2 Detection of Co- and Post-translational Modifications 102

5.3.3 Strategy for the Analysis of Modifications: Top Down Versus Bottom Up 103

5.3.4 Mass Spectrometry for Analysis of Co- and Post-translational Modifications 104

5.4 Analysis of Specific Modifications 105

5.4.1 Acetylation 106

5.4.2 Phosphorylation 106

5.4.3 Ubiquitination and Sumoylation 107

5.4.4 Glycosylation 107

5.5 The Function of Protein Post-translational Modifications: More Than Meets the Eye? 109

5.6 Some Interesting Modification Stories 111

5.6.1 The Erythropoietin Story 111

5.6.2 The Apolipoprotein E Story 113

5.6.3 The Progeria Story 114

5.6.4 The Influenza Story 115

5.7 Future Directions 116

6 Proteome Imaging / Patricia M. Palagi, Daniel Walther, Catherine G. Zimmermann-Ivol, Ron D. Appel 123

6.2 Image Analysis of Two-Dimensional Electrophoresis Gels 124

6.2.1 First Steps in Gel Image Analysis 125

6.2.2 Applications to Different Proteomics Approaches 127

6.2.2.1 Single-Gel Analysis 128

6.2.2.2 Groups of Gels 128

6.2.2.3 Two-Dimensional Difference Gel Electrophoresis 128

6.3 Liquid Chromatography-Mass Spectrometry 130

6.3.1 First Steps in Liquid Chromatography-Mass Spectrometry Image Analysis 130

6.3.2 Applications to Different Proteomics Approaches 131

6.3.2.1 Monitoring Experiments and Post-translational Modifications 131

6.3.2.2 Sample Populations 132

6.4 The Molecular Scanner 134

6.5 Imaging Mass Spectrometry 138

6.5.1 Imaging Mass Spectrometry - Technical Aspects 139

6.5.2 Imaging Mass Spectrometry - Applications 140

7 Data Integration in Proteomics / Frederique Lisacek, Christine Hoogland, Lydie Bougueleret, Amos Bairoch 145

7.2 Integration As Gathering and Cross-Linking Information 148

7.2.1 Selection of Sources and Quantification 148

7.2.1.1 Trends in Databases 148

7.2.1.2 Data Evolution 149

7.2.2 Biology Inspired Cross-Linking 150

7.2.2.1 The UniProt Universal Protein Knowledgebase 150

7.2.2.2 Human Protein Atlas 152

7.2.3 Integrating Elements of the Proteomics Workflow 153

7.2.3.1 High-Throughput Data: Standards and Repositories 153

7.2.3.2 SWISS-2DPAGE 154

7.2.3.3 PeptideAtlas and the Global Proteome Machine 155

7.2.3.4 Other Noteworthy Efforts 156

7.2.4 Integration As a Federated Effort 156

7.2.4.1 Proteomics Servers 156

7.2.4.2 Semantic Web Approach 158

7.3 Integration As Blending of Information 159

7.3.1 Textual Information 159

7.3.2 Ontologies 160

7.3.3 Examples of Visualisation Tools Merging Several Sources 161

7.3.4 From Data Integration to Systems Biology 162

8 Protein-Protein Interactions / Anne-Claude Gavin 169

8.2 Protein-Protein Interactions in Human Diseases: Altered Protein Connectivity Leads to Disorder 170

8.3 Charting Protein-Protein Interactions 172

8.3.1 Characterisation of All Coding Sequences in an Organism 175

8.3.2 Monitoring Binary Interactions: the Yeast Two-Hybrid System 175

8.3.3 Analysis of Protein Complexes by Affinity Purification and Mass Spectrometry 177

8.3.4 Luminescence-Based Mammalian Interactome Mapping 180

8.3.5 Protein Microarrays 180

8.3.6 Data Quality 180

8.4 Biological and Biomedical Applications 181

8.4.1 Charting of Diseases and Pharmacologically Relevant Pathways 181

8.4.2 Lessons Learned from Global Interaction Analyses in Yeast 182

8.4.3 An Emerging Application: the Development of Small-Molecule Protein-Protein Interaction Inhibitors 184

8.5 Future Directions 186

9 Biomedical Applications of Proteomics / Jean-Charles Sanchez, Yohann Coute, Laure Allard, Pierre Lescuyer, Denis F.

Hochstrasser 193

9.2 The Application of Proteomics to Medicine 194

9.3 Disease Diagnosis from Body Fluids 196

9.4 Vascular Diseases 197

9.4.2 Application of Proteomics to Vascular Diseases and Atherosclerosis 198

9.4.3 Application of Proteomics to Cardiovascular Diseases 199

9.4.4 Application of Proteomics to Cerebrovascular Disease 200

9.5 Neurodegenerative Disorders 202

9.5.1 Brain Proteome 202

9.5.2 Proteomic Profiling of Neurodegenerative Disorders 203

9.5.3 Cerebrospinal Fluid Protein Markers 205

9.6 Proteomics and Cancer 206

9.6.1 Biomarker Discovery in Cancer Proteomics 207

9.6.1.1 Tissues 207

9.6.1.2 Primary and Established Cell Lines 208

9.6.2 Proteomic Profiling in Oncology 209

9.6.2.1 Surface-Enhanced Laser Desorption/Ionisation Time-of-Flight Mass Spectrometry 210

9.6.2.2 Protein Microarrays 210

9.6.2.3 Tissue Profiling by Matrix-Assisted Laser Desoprtioon/Ionisation Mass Spectrometry Imaging 210

9.6.3 Use of Proteomics To Define the Tissue of Origin 211

9.7 Toxicopharmacology: the Example of Type 2 Diabetes 211

9.7.2 Pathogenesis of Type 2 Diabetes 212

9.7.3 Treatments of Type 2 Diabetes 213

9.7.4 Proteomics for the Discovery of Treatment Targets for Type 2 Diabetes 213

9.8 Current Limitations and Future Directions of Proteomics for Medicine 215

9.8.1 Preanalytical Issues 215

9.8.2 Analytical Aspects 216

9.8.3 Postanalytical Aspects 217

9.9 Present and Future Directions 217

10 Proteomics: Where to Next? / Keith L. Williams, Denis F. Hochstrasser 223

10.2 The Relevance of-omics to Biology 224

10.3 Technological Developments in Proteomics 225

10.3.1 Characterising Modifications 226

10.3.2 Global Tissue Analysis 226

10.4 The Next Steps for Proteomics: Diagnostics and Drugs 227

10.4.1 Diagnostics 228

10.4.2 Drugs 228.

Notes:

Includes bibliographical references and index.

Previous 'edition' had title: Proteome research : new frontiers in functional genomics. This edition consists of material which was rewritten for this edition, or which is completely new to this edition.

ISBN:

9783540712404

3540712402

3540729100

9783540729105

OCLC:

171111269