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Edited by M.R.Wilkins, K.L.Williams, R.D.Appel & D.F.Hochstrasser
Keith L.Williams and Denis F. Hochstrasser
1.1 Proteome: a new word, a new field of biology
1
1.2 The proteome and technology 5
1.2.1 Thinking in two dimensions 6
1.2.2 Further dimensions in protein analysis 8
1.2.3 Information and the proteome 9
1.3 Looking towards new frontiers 10
Acknowledgments 11
References 11
Ben R. Herbert, Jean-Charles Sanchez and Luca Bini
2.1 Introduction 13
2.2 Sample preparation 15
2.2.1 Increasing protein solubility with chaotropes
and surfactants 15
2.2.2 The choice of reducing agent 16
2.2.3 Removal of nucleic acids 16
2.3 Sample loading on IPG gels 18
2.3.1 Sample application during IPG rehydration 18
2.4 Low abundance proteins 19
2.4.1 Cell fractionation and protein prefractionation
20
2.4.2 High protein loads combined with narrow pH gradients
21
2.4.3 Sensitive detection 22
2.5 Basic proteins 24
2.5.1 Separation of basic proteins on IPG gels 24
2.6 Protein quantitation 25
2.7 Future directions for 2-D PAGE 26
2.7.1 Simplifying the IPG-SDS-PAGE interface 27
2.7.2 Fluorescent protein detection 28
2.7.3 High throughput 2-D PAGE 28
2.8 Conclusion 29
Acknowledgments 29
References 30
Marc R. Wilkins and Andrew A. Gooley
3.1 The purpose of protein identification 35
3.2 An overview of protein identification strategies
36
3.3 Primary attributes for protein identification 38
3.3.1 Protein species of origin 38
3.3.2 Protein isoelectric point 38
3.3.3 Protein apparent mass and mass 40
3.3.4 Protein N- and C-terminal sequence tags 41
3.3.5 Extensive N-terminal protein sequence 45
3.4 Secondary attributes for protein identification
46
3.4.1 Attributes of peptides from mass spectrometry
46
3.4.2 Protein amino acid composition 54
3.5 Cross-species protein identification 56
3.6 Future developments and conclusions 60
Acknowledgments 60
References 61
Andrew A. Gooley and Nicolle H. Packer
4.1 Introduction 65
4.2 An overview of modifications: what are they and
where do they occur? 68
4.3 Modifications that influence protein charge on
2-D PAGE 70
4.4 Analysis of co- and post-translational modifications
after 2-D PAGE 70
4.4.1 Presentation of the modified protein 70
4.4.2 Detection of co- and post-translational modifications
74
4.4.3 Analysis of co- and post-translational modifications
76
4.4.4 Mass spectrometry perspectives in the analysis
of protein co- and post-translational modifications 83
4.5 Future directions 86
Acknowledgments 86
References 86
5.1 Introduction 93
5.2 Protein sequence databases 93
5.2.1 SWISS-PROT 95
5.2.2 TrEMBL 100
5.2.3 Completeness and non-redundancy issues 100
5.2.4 Specialised protein sequence databases 102
5.3 Nucleotide sequence databases 103
5.3.1 Hidden treasures 107
5.4 Pattern and profile databases 108
5.4.1 PROSITE 109
5.4.2 BLOCKS 110
5.4.3 PRINTS 112
5.4.4 Pfam 112
5.4.5 Other protein domain databases 112
5.4.6 Towards a unified database of protein families
and domains 114
5.5 2-D PAGE databases 114
5.5.1 SWISS-2DPAGE 115
5.5.2 Other 2-D PAGE databases 116
5.6 Three-dimensional structure databases 116
5.6.1 PDB 117
5.6.2 Swiss-3DImage 119
5.6.3 DSSP, HSSP and FSSP 119
5.7 Post-translational modification databases 119
5.7.1 O-GLYCBASE 120
5.8 Genomic databases 120
5.8.1 OMIM 121
5.9 Metabolic databases 123
5.9.1 Some specific metabolic databases 124
5.10 Conclusions 125
5.10.1 How to access all of this data 125
5.10.2 What future for protein databases? 126
References 129
6.1 Introduction 149
6.2 Past data integration techniques (3300 B.C. - 1993
A.D.) 150
6.2.1 Data exchange on the Internet before WWW 151
6.2.2 Hard media data distribution 152
6.2.3 Local database integration 153
6.2.4 Discussion of standard techniques 154
6.3 Current integration: a Cyber-Encyclopaedia of
the Proteome 154
6.3.1 Cross-references 154
6.3.2 The World-Wide Web 156
6.3.3 Integrated databases on the World-Wide Web 159
6.3.4 Federated proteome databases 162
6.3.5 Discussion of current integration 166
6.4 Integration of databases and analytical methods
166
6.5 The future of proteome database integration 168
6.5.1 Intelligent dedicated search engines 168
6.5.2 Enhanced database integration 169
6.5.3 Automation of database construction 170
6.5.4 Advanced data processing over the Internet 170
6.5.5 Security and confidentiality 171
6.6 Concluding remarks 172
Acknowledgments 172
References 173
Manuel C. Peitsch and Nicolas Guex
7.1 Introduction 177
7.2 Methods and programs 178
7.2.1 Identification of modelling templates 178
7.2.2 Aligning the target sequence with the template
sequence(s) 179
7.2.3 Building the model 179
7.2.4 Model refinement 179
7.2.5 Assessing the model quality 180
7.2.6 Application of protein models 181
7.2.7 Sequence-to-structure workbench 182
7.3 Modelling of Proteomes 182
7.3.1 Large-scale protein modelling 182
7.3.2 Model Repository 183
7.4 Examples 184
7.4.1 Obtaining a 3-D structure from the SWISS-MODEL
Repository 184
7.4.2 Modelling the Fas-ligand protein using the Swiss-PdbViewer
and SWISS-MODEL 184
7.5 Concluding remarks 185
References 186
8.1 Introduction 187
8.2 Biotechnology, genomics and medicine to date 188
8.3 The application of proteomics to medicine 189
8.4 Disease diagnosis from body fluids 190
8.4.1 Glycoproteins in body fluids 191
8.5 Proteomics, toxicology and pharmaceuticals 193
8.5.1 Retinoic acid 195
8.5.2 Glycosylation 196
8.5.3 Phosphorylation 197
8.5.4 Drug adducts and vehicles 198
8.5.5 Other pharmacological treatments 198
8.5.6 Hormones 199
8.6 Generation of complexity in proteomes 200
8.7 Proteomics and cancer 200
8.7.1 Cell cycle and cancer theory 200
8.7.2 Sample preparation 201
8.7.3 Tissue of origin 202
8.7.4 Metastatic potential and cancer treatment 206
8.7.5 Data analysis and automatic diagnosis 206
8.7.6 A return to cell cycle and oncogene products
208
8.8 Current limitations and future directions of proteomics
for medicine 210
References 212
Keith L.Williams and Vitaliano Pallini
9.1 Scope of this chapter 221
9.2 Proteome maps 221
9.2.1 Mollicutes 222
9.2.2 Prokaryotes 222
9.2.3 Eukaryotes 223
9.3 Applications of proteome technology 226
9.3.1 Tracking complexity 226
9.3.2 Immunogenic proteins 227
9.3.3 Improved agricultural products 228
9.3.4 Value added agricultural products 228
9.3.5 Quality control 229
9.4 Concluding remarks 230
References 231
Denis F. Hochstrasser and Keith L.Williams
10.1 Scope of this chapter 233
10.2 Large-scale science: genomics, combinatorial chemistry
and proteomics 233
10.3 Future methodologies in proteomics 234
10.4 Other views of the future of proteomics 236
References 237
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