蛋白體學：技術・市場・企業

Abstract

Summary

This report describes and evaluates the proteomic technologies that will play an important role in drug discovery, molecular diagnostics and practice of medicine in the post-genomic era - the first decade of the 21st century. Most commonly used technologies are 2D gel electrophoresis for protein separation and analysis of proteins by mass spectrometry. Microanalytical protein characterization with multidimentional liquid chromatography/mass spectrometry improves the throughput and reliability of peptide mapping. Matrix-Assisted Laser Desorption Mass Spectrometry (MALDI-MS) has become a widely used method for determination of biomolecules including peptides, proteins. Functional proteomics technologies include yeast two-hybrid system for studying protein- protein interactions. Establishing a proteomics platform in the industrial setting initially requires implementation of a series of robotic systems to allow a high-throughput approach for analysis and identification of differences observed on 2D electrophoresis gels. Protein chips are also proving to be useful. Proteomic technologies are now being integrated into the drug discovery process as complimentary to genomic approaches. Toxicoproteomics, i.e. the evaluation of protein expression for understanding of toxic events, is an important application of proteomics in preclincial drug safety. Use of bioinformatics is essential for analyzing the massive amount of data generated from both genomics and proteomics.

Proteomics is providing a better understanding of pathomechanisms of human diseases. Analysis of different levels of gene expression in healthy and diseased tissues by proteomic approaches is as important as the detection of mutations and polymorphisms at the genomic level and may be of more value in designing a rational therapy. Protein distribution / characterization in body tissues and fluids, in health as well as in disease, is the basis of the use of proteomic technologies for molecular diagnostics. Proteomics will play an important role in medicine of the future which will be personalized and will combine diagnostics with therapeutics.The text is supplemented with 42 tables, 27 figures and over 500 selected references from the literature.

The number of companies involved in proteomics has increased remarkably during the past few years. More than 300 companies have been identified to be involved in proteomics and 212 of these are profiled in the report with 470 collaborations.

The markets for proteomic technologies are difficult to estimate as they are not distinct but overlap with those of genomics, gene expression, high throughput screening, drug discovery and molecular diagnostics. Markets for proteomic technologies are analyzed for the year 2008 and are projected to years 2013 and 2018. The largest expansion will be in bioinformatics and protein biochip technologies. Important areas of application are cancer and neurological disorders

Table of Contents

0. Executive Summary 15

1. Basics of Proteomics 17

• Introduction 17
• History 17
• Nucleic acids, genes and proteins 18
• Genome 18
• DNA 19
• RNA 19
• MicroRNAs 19
• Decoding of mRNA by the ribosome 20
• Genes 20
• Alternative splicing 20
• Transcription 21
• Gene regulation 22
• Gene expression 22
• Chromatin 23
• Proteins 23
• Spliceosome 23
• Functions of proteins 24
• Inter-relationship of protein, mRNA and DNA 24
• Proteomics 25
• Mitochondrial proteome 26
• S-nitrosoproteins in mitochondria 27
• Proteomics and genomics 27
• Classification of proteomics 30
• Levels of functional genomics and various "omics" 30
• Glycoproteomics 30
• Transcriptomics 31
• Metabolomics 31
• Cytomics 31
• Phenomics 31
• Proteomics and systems biology 32

2. Proteomic Technologies 33

• Key technologies driving proteomics 33
• Sample preparation 34
• New trends in sample preparation 34
• Pressure Cycling Technology 35
• Protein separation technologies 35
• High resolution 2D gel electrophoresis 35
• Variations of 2D gel technology 36
• Limitations of 2DGE and measures to overcome these 36
• 1-D sodium dodecyl sulfate (SDS) PAGE 36
• Capillary electrophoresis systems 37
• Head column stacking capillary zone electrophoresis 37
• Removal of albumin and IgG 37
• Companies with protein separation technologies 38
• Protein detection 39
• Protein identification and characterization 39
• Mass spectrometry (MS) 39
• Companies involved in mass spectrometry 40
• Electrospray ionization 41
• Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry 42
• Cryogenic MALDI- Fourier Transform Mass Spectrometry 43
• Stable-isotope-dilution tandem mass spectrometry 44
• HUPO Gold MS Protein Standard 44
• High performance liquid chromatography 44
• Multidimensional protein identification technology (MudPIT) 44
• Peptide mass fingerprinting 45
• Combination of protein separation technologies with mass spectrometry 45
• Combining capillary electrophoresis with mass spectrometry 45
• 2D PAGE and mass spectrometry 45
• Quantification of low abundance proteins 46
• SDS-PAGE 46
• Antibodies and proteomics 47
• Detection of fusion proteins 47
• Labeling and detection of proteins 47
• Fluorescent labeling of proteins in living cells 48
• Combination of microspheres with fluorescence 48
• Self-labeling protein tags 48
• Analysis of peptides 49
• Differential Peptide Display 49
• Peptide analyses using NanoLC-MS 50
• Protein sequencing 51
• Functional proteomics: technologies for studying protein function 51
• Functional genomics by mass spectrometry 52
• RNA-Protein fusions 52
• Designed repeat proteins 52
• Application of nanbiotechnology to proteomics 53
• Nanoproteomics 53
• Protein nanocrystallography 53
• Single-molecule mass spectrometry using a nanopore 54
• Nanoelectrospray ionization 54
• Nanoparticle barcodes 54
• Biobarcode assay for proteins 55
• Resonance Light Scattering technology 56
• Nanoscale protein analysis 56
• Nanobiotechnology for discovery of protein biomarkers in the blood 57
• Study of single membrane proteins at subnanometer resolution 57
• Nanotube-vesicle networks for study of membrane proteins 57
• Qdot-nanocrystals 58
• Nanotube electronic biosensor 58
• A nanoscale mechanism for protein engineering 58
• Protein expression profiling 59
• Cell-based protein assays 59
• Living cell-based assays for protein function 60
• Companies developing cell-based protein assays 60
• Protein function studies 61
• Transcriptionally Active PCR 61
• Protein-protein interactions 62
• Yeast two-hybrid system 63
• Membrane one-hybrid method 65
• Protein affinity chromatography 65
• Phage display 65
• Fluorescence Resonance Energy Transfer 65
• Bioluminescence Resonance Energy Transfer 66
• Detection Enhanced Ubiquitin Split Protein Sensor technology 66
• Protein-fragment complementation system 66
• In vivo study of protein-protein interactions 67
• Computational prediction of interactions 67
• Interactome 68
• Protein-protein interactions and drug discovery 68
• Companies with technologies for protein-protein interaction studies 69
• Protein-DNA interaction 70
• Determination of protein structure 70
• X-Ray crystallography 71
• Nuclear magnetic resonance 71
• Electron spin resonance 72
• Prediction of protein structure 72
• Protein tomography 73
• Prediction of protein function 73
• Three-dimensional proteomics for determination of function 74
• An algorithm for genome-wide prediction of protein function 74
• Monitoring protein function by expression profiling 74
• Isotope-coded affinity tag peptide labeling 75
• Differential Proteomic Panning 75
• Cell map proteomics 76
• Topological proteomics 76
• Organelle or subcellular proteomics 77
• Nucleolar proteomics 77
• Glycoproteomic technologies 78
• High-sensitivity glycoprotein analysis 78
• Fluorescent in vivo imaging of glycoproteins 78
• Integrated approaches for protein characterization 78
• Imaging mass spectrometry 79
• IMS technologies 79
• Applications of IMS 80
• The protein microscope 80
• Automation and robotics in proteomics 80
• Laser capture microdissection 81
• Microdissection techniques used for proteomics 81
• Uses of LCM in combination with proteomic technologies 82
• Concluding remarks about applications of proteomic technologies 82
• Precision proteomics 83

3. Protein biochip technology 85

• Introduction 85
• Types of protein biochips 86
• ProteinChip 86
• Applications and advantages of ProteinChip 87
• ProteinChip Biomarker System 87
• Matrix-free ProteinChip Array 88
• Aptamer-based protein biochip 88
• Fluorescence planar wave guide technology-based protein biochips 89
• Lab-on-a-chip for protein analysis 89
• Microfluidic biochips for proteomics 90
• Protein biochips for high-throughput expression 91
• Nucleic Acid-Programmable Protein Array 91
• High-density protein microarrays 91
• HPLC-Chip for protein identification 91
• Antibody microarrays 92
• Integration of protein array and image analysis 92
• Tissue microarray technology for proteomics 92
• Protein biochips in molecular diagnostics 93
• A force-based protein biochip 94
• L1 chip and lipid immobilization 94
• Multiplexed Protein Profiling on Microarrays 94
• Live cell microarrays 95
• ProteinArray Workstation 95
• Proteome arrays 96
• The Yeast ProtoArray 96
• ProtoArray™ Human Protein Microarray 96
• TRINECTIN proteome chip 97
• Peptide arrays 97
• Surface plasmon resonance technology 98
• Biacore' s SPR 98
• FLEX CHIP 98
• Combination of surface plasmon resonance and MALDI-TOF 99
• Protein chips/microarrays using nanotechnology 99
• Nanoparticle protein chip 99
• Protein nanobiochip 99
• Protein nanoarrays 100
• Self-assembling protein nanoarrays 100
• Companies involved in protein biochip/microarray technology 101

4. Bioinformatics in Relation to Proteomics 105

• Introduction 105
• Bioinformatic tools for proteomics 105
• Testing of SELDI-TOF MS Proteomic Data 105
• BioImagine' s ProteinMine 106
• Bioinformatics for pharmaceutical applications of proteomics 106
• In silico search of drug targets by Biopendium 106
• Compugen' s LEADS 107
• DrugScore 107
• Proteochemometric modeling 107
• Integration of genomic and proteomic data 108
• Proteomic databases: creation and analysis 109
• Introduction 109
• Proteomic databases 109
• GenProtEC 110
• Human Protein Atlas 110
• Human Proteomics Initiative 111
• International Protein Index 111
• Proteome maps 112
• Protein Structure Initiative - Structural Genomics Knowledgebase 112
• Protein Warehouse Database 112
• Protein Data Bank 112
• Universal Protein Resource 113
• Protein interaction databases 113
• Biomolecular Interaction Network Database 114
• ENCODE 114
• Functional Genomics Consortium 114
• Human Proteinpedia 115
• ProteinCenter 115
• Databases of the National Center for Biotechnology Information 115
• Application of bioinformatics in functional proteomics 116
• Use of bioinformatics in protein sequencing 116
• Bottom-up protein sequencing 116
• Top-down protein sequencing 117
• Protein structural database approach to drug design 118
• Bioinformatics for high-throughput proteomics 118
• Companies with bioinformatic tools for proteomics 119

5. Research in Proteomics 121

• Introduction 121
• Applications of proteomics in biological research 121
• Identification of novel human genes by comparative proteomics 121
• Study of relationship between genes and proteins 122
• Structural genomics or structural proteomics 122
• Protein Structure Factory 123
• Protein Structure Initiative 124
• Studies on protein structure at Argonne National Laboratory 124
• Structural Genomics Consortium 125
• Protein knockout 125
• Antisense approach and proteomics 125
• RNAi and protein knockout 126
• Total knockout of cellular proteins 126
• Ribozymes and proteomics 126
• Single molecule proteomics 127
• Single-molecule photon stamping spectroscopy 127
• Single nucleotide polymorphism determination by TOF-MS 127
• Application of proteomic technologies in systems biology 128
• Signaling pathways and proteomics 128
• Kinomics 128
• Combinatorial RNAi for quantitative protein network analysis 129
• Proteomics in neuroscience research 129
• Stem cell proteomics 130
• Proteomic studies of mesenchymal stem cells 130
• Proteomics of neural stem cells 130
• Proteome Biology of Stem Cells Initiative 131
• Proteomic analysis of the cell cycle 132
• Nitric oxide and proteomics 132
• A proteomic method for identification of cysteine S-nitrosylation sites 132
• Study of the nitroproteome 132
• Study of the phosphoproteome 133
• Study of the mitochondrial proteome 133
• Proteomic technologies for study of mitochondrial proteomics 134
• Cryptome 134
• Study of protein transport in health and disease 134
• Proteomics research in the academic sector 135
• Vanderbilt University' s Center for Proteomics and Drug Actions 137
• ProteomeBinders initiative 137

6. Pharmaceutical Applications of Proteomics 139

• Introduction 139
• Current drug discovery process and its limitations 139
• Role of omics in drug discovery 140
• Genomics-based drug discovery 140
• Metabolomics technologies for drug discovery 141
• Role of metabonomics in drug discovery 141
• Basis of proteomics approach to drug discovery 142
• Proteins and drug action 142
• Transcription-aided drug design 143
• Role of proteomic technologies in drug discovery 143
• Liquid chromatography-based drug discovery 144
• Capture compound mass spectrometry 145
• Protein-expression mapping by 2DGE 145
• Role of MALDI mass spectrometry in drug discovery 145
• Tissue imaging mass spectrometry 145
• Companies using MALDI for drug discovery 147
• Oxford Genome Anatomy Project 147
• Proteins as drug targets 148
• Ligands to capture the purine binding proteome 148
• Chemical probes to interrogate key protein families for drug discovery 149
• Global proteomics for pharmacodynamics 149
• CellCartaR proteomics platform 149
• ZeptoMARK™ protein profiling system 150
• Role of proteomics in targeting disease pathways 151
• Identification of protein kinases as drug targets 151
• G-protein coupled receptors as drug targets 151
• Methods of study of GPCRs 151
• Cell-based assays for GPCR 152
• Companies involved in GPCR-based drug discovery 153
• GPCR localization database 153
• Matrix metalloproteases as drug targets 154
• PDZ proteins as drug targets 154
• Proteasome as drug target 155
• Serine hydrolases as drug targets 155
• Targeting mTOR signaling pathway 156
• Bioinformatic analysis of proteomics data for drug discovery 157
• Drug design based on structural proteomics 157
• Protein crystallography for determining 3D structure of proteins 157
• Automated 3D protein modeling 158
• Drug targeting of flexible dynamic proteins 158
• Companies involved in structure-based drug-design 159
• Integration of genomics and proteomics for drug discovery 160
• Ligand-receptor binding 160
• Role of proteomics in study of ligand-receptor binding 160
• Aptamer protein binding 161
• Systematic Evolution of Ligands by Exponential Enrichment 161
• Aptamers and high-throughput screening 162
• Nucleic Acid Biotools 162
• Aptamer beacons 162
• Peptide aptamers 163
• Riboreporters for drug discovery 163
• Target identification and validation 164
• Application of mass spectrometry for target identification 164
• Gene knockout and gene suppression for validating protein targets 164
• Laser-mediated protein knockout for target validation 165
• Integrated proteomics for drug discovery 165
• High-throughput proteomics 165
• Companies involved in high-throughput proteomics 166
• Drug discovery through protein-protein interaction studies 167
• Protein-protein interaction as basis for drug target identification 167
• Protein-PCNA interaction as basis for drug design 168
• Two-hybrid protein interaction technology for target identification 168
• Biosensors for detection of small molecule-protein interactions 169
• Protein-protein interaction maps 169
• ProNet (Myriad Genetics) 169
• Hybrigenics' maps of protein-protein interactions 170
• CellZome' s functional map of protein-protein interactions 170
• Mapping of protein-protein interactions by mass spectrometry 171
• Protein interaction map of Drosophila melanogaster 171
• Protein-interaction map of Wellcome Trust Sanger Institute 171
• Protein-protein interactions as targets for therapeutic intervention 172
• Inhibition of protein-protein interactions by peptide aptamers 172
• Selective disruption of proteins by small molecules 172
• Post-genomic combinatorial biology approach 172
• Differential proteomics 173
• Shotgun proteomics 173
• Chemogenomics/chemoproteomics for drug discovery 174
• Chemoproteomics-based drug discovery 175
• Companies involved in chemogenomics/chemoproteomics 176
• Activity-based proteomics 177
• Iconix' s DrugMatrix 177
• Locus Discovery technology 177
• Automated ligand identification system 178
• Expression proteomics: protein level quantification 178
• Role of phage antibody libraries in target discovery 179
• Analysis of posttranslational modification of proteins by MS 179
• Phosphoproteomics for drug discovery 180
• Application of glycoproteomics for drug discovery 180
• Role of carbohydrates in proteomics 180
• Challenges of glycoproteomics 181
• Companies involved in glycoproteomics 181
• Role of protein microarrays/ biochips for drug discovery 182
• Protein microarrays vs DNA microarrays for high-throughput screening 182
• BIA-MS biochip for protein-protein interactions 182
• ProteinChip with Surface Enhanced Neat Desorption 183
• Protein-domains microarrays 183
• Some limitations of protein biochips 183
• Concluding remarks about role of proteomics in drug discovery 184
• RNA versus protein profiling as guide to drug development 184
• RNA as drug target 184
• Combination of RNA and protein profiling 185
• RNA binding proteins 186
• Toxicoproteomics 186
• Hepatotoxicity 186
• Nephrotoxicity 187
• Cardiotoxicity 187
• Neurotoxicity 188
• Protein/peptide therapeutics 188
• Peptide-based drugs 188
• PhylomerR peptides 189
• Cryptein-based therapeutics 189
• Synthetic proteins and peptides as pharmaceuticals 190
• Genetic immunization and proteomics 190
• Proteomics and gene therapy 191
• Role of proteomics in clinical drug development 191
• Pharmacoproteomics 191
• Role of proteomics in clinical drug safety 192

7. Application of Proteomics in Human Healthcare 193

• Clinical proteomics 194
• Definition and standards 194
• Vermillion' s Clinical Proteomics Program 194
• Pathophysiology of human diseases 195
• Diseases due to misfolding of proteins 195
• Mechanism of protein folding 196
• Nanoproteomics for study of misfolded proteins 197
• Therapies for protein misfolding 197
• Intermediate filament proteins 198
• Significance of mitochondrial proteome in human disease 199
• Proteome of Saccharomyces cerevisiae mitochondria 199
• Rat mitochondrial proteome 199
• Proteomic approaches to biomarker identification 200
• The ideal biomarker 200
• Proteomic technologies for biomarker discovery 200
• MALDI mass spectrometry for biomarker discovery 201
• BAMF™ Technology 201
• Protein biochips/microarrays and biomarkers 202
• Antibody-based biomarker discovery 202
• Tumor-specific serum peptidome patterns 202
• Search for protein biomarkers in body fluids 203
• Challenges and strategies for discovey of protein biomarkers in plasma 203
• 3-D structure of CD38 as a biomarker 204
• BD"! Free Flow Electrophoresis System 204
• Isotope tags for relative and absolute quantification 205
• Proteome partitioning 205
• Stable isotope tagging methods 205
• Technology to measure both the identity and size of the biomarker 206
• SISCAPA method for quantitating proteins and peptides in plasma 206
• Biomarkers in the urinary proteome 207
• Application of proteomics in molecular diagnosis 207
• Proximity ligation assay 208
• Protein patterns 208
• Proteomic tests on body fluids 209
• Cyclical amplification of proteins 210
• Applications of proteomics in infections 210
• Role of proteomics in virology 211
• Study of interaction of proteins with viruses 211
• Role of proteomics in bacteriology 211
• Epidemiology of bacterial infections 212
• Proteomic approach to bacterial pathogenesis 212
• Vaccines for bacterial infections 212
• Protein profiles associated with bacterial drug resistance 213
• Analyses of the parasite proteome 213
• Application of proteomics in cystic fibrosis 213
• Oncoproteomics 214
• Application of CellCarta technology for oncology 215
• Accentuation of differentially expressed proteins using phage technology 215
• Identification of oncogenic tyrosine kinases using phosphoproteomics 216
• Single-cell protein expression analysis by microfluidic techniques 216
• Dynamic cell proteomics in response to a drug 216
• Desorption electrospray ionization for cancer diagnosis 216
• Proteomic analysis of cancer cell mitochondria 217
• Mass spectrometry for identification of oncogenic chimeric proteins 217
• Id proteins as targets for cancer therapy 218
• Proteomic study of p53 218
• Human Tumor Gene Index 218
• Integration of cancer genomics and proteomics 219
• Laser capture microdissection technology and cancer proteomics 219
• Cancer tissue proteomics 220
• Use of proteomics in cancers of various organ systems 220
• Proteomics of brain tumors 220
• Proteomics of breast cancer 221
• Proteomics of colorectal cancer 222
• Proteomics of esophageal cancer 223
• Proteomics of hepatic cancer 223
• Proteomics of leukemia 223
• Proteomics of lung cancer 224
• Proteomics of pancreatic cancer 224
• Proteomics of prostate cancer 225
• Diagnostic use of cancer biomarkers 226
• NCI' s Network of Clinical Proteomic Technology Centers for Cancer Research 227
• Proteomics and tumor immunology 229
• Proteomics and study of tumor invasiveness 229
• Anticancer drug discovery and development 229
• Kinase-targeted drug discovery in oncology 229
• Anticancer drug targeting: functional proteomics screen of proteases 230
• Small molecule inhibitors of cancer-related proteins 231
• Role of proteomics in studying drug resistance in cancer 231
• Future prospects of oncoproteomics 232
• Companies involved in application of proteomics to oncology 232
• Application of proteomics in neurological disorders 233
• Neuroproteomics 233
• Prion diseases 233
• Proteomics and transmissible spongiform encephalopathies 234
• Proteomics and neurodegenerative disorders 235
• Detection of misfolded proteins 237
• Proteomics and glutamate repeat disorders 237
• Proteomics and Huntington' s disease 238
• Proteomics and Alzheimer' s disease 238
• Common denominators of Alzheimer' s and prion diseases 239
• Ion channel link for protein-misfolding disease 240
• Proteomics and demyelinating diseases 240
• Proteomics of amyotrophic lateral sclerosis 240
• Proteomics of spinal muscular atrophy 241
• Proteomics of Fabry disease 241
• Proteomics and GM1 gangliosidosis 241
• Proteomics of CNS trauma 242
• Proteomics of CNS aging 243
• Neuroproteomics of psychiatric disorders 243
• Neuroproteomic of cocaine addiction 244
• Neurodiagnostics based on proteomics 244
• Testing for disease-specific proteins in the cerebrospinal fluid 244
• Tau proteins 245
• CNS tissue proteomics 246
• Diagnosis of CNS disorders by examination of proteins in urine 247
• Diagnosis of CNS disorders by examination of proteins in the blood 248
• Serum pNF-H as biomarker of CNS damage 248
• Proteomics of BBB 249
• Future prospects of neuroproteomics in neurology 249
• HUPO' s Pilot Brain Proteome Project 250
• Proteomics of cardiac disorders 250
• Cardiac protein databases 251
• Proteomics of dilated cardiomyopathy and heart failure 251
• Role of proteomics in heart transplantation 251
• Future of application of proteomics in cardiology 252
• Proteomic technologies for research in pulmonary disorders 252
• Proteomics of eye disorders 253
• Retinal dystrophies 254
• Use of proteomics in inner ear disorders 254
• Use of proteomics in aging research 255
• Removal of altered cellular proteins in aging 255
• Proteomics and nutrition 256

8. Commercial Aspects of Proteomics 257

• Potential markets for proteomic technologies 257
• Markets for protein separation technologies 257
• Markets for 2D gel electrophoresis 258
• Trends in protein separation technolgies and effect on market 259
• Protein biochip markets 259
• Mass spectrometry markets 259
• Markets for MALDI for drug discovery 260
• Markets for nuclear magnetic resonance spectroscopy 260
• Market for structure-based drug design 260
• Bioinformatics markets for proteomics 260
• Markets for protein biomarkers 261
• Markets for cell-based protein assays 261
• Business and strategic considerations 261
• Cost of protein structure determination 261
• Opinion surveys of the scientist consumers of proteomic technologies 261
• Opinions on mass spectrometry 262
• Opinions on bioinformatics and proteomic databases 262
• Systems for in vivo study of protein-protein interactions 262
• Perceptions of the value of protein biochip/microfluidic systems 262
• Small versus big companies 263
• Expansion in proteomics according to area of application 263
• Growth trends in cell-based protein assay market 263
• Challenges for development of cell-based protein assays 263
• Future trends and prospects of cell-based protein assays 264
• Strategic collaborations 264
• Analysis of proteomics collaborations according to types of companies 264
• Types of proteomic collaborations 265
• Proteomics collaborations according to application areas 266
• Analysis of proteomics collaborations: types of technologies 266
• Collaborations based on protein biochip technology 266
• Concluding remarks about proteomic collaborations 267
• Proteomic patents 267
• Market drivers in proteomics 268
• Needs of the pharmaceutical industry 268
• Need for outsourcing proteomic technologies 268
• Funding of proteomic companies and research 269
• Technical advances in proteomics 269
• Changing trends in healthcare in future 269
• Challenges facing proteomics 269
• Magnitude and complexity of the task 269
• Technical challenges 270
• Limitations of proteomics 270
• Limitations of 2DGE 270
• Limitations of mass spectrometry techniques 271
• Complexity of the pharmaceutical proteomics 271
• Unmet needs in proteomics 271

9. Future of Proteomics 273

• Genomics to proteomics 273
• Faster technologies 273
• FLEXGene repository 273
• Need for new proteomic technologies 274
• Emerging proteomic technologies 275
• Detection of alternative protein isoforms 275
• Direct protein identification in large genomes by mass spectrometry 275
• Proteome identification kits with stacked membranes 275
• Vacuum deposition interface 276
• In vitro protein biosynthesis 276
• Proteome mining with adenosine triphosphate 276
• Proteome-scale purification of human proteins from bacteria 276
• Proteostasis network 277
• Cytoproteomics 277
• Subcellular proteomics 277
• Individual cell proteomics 278
• Live cell proteomics 278
• Fluorescent proteins for live-cell imaging 279
• Membrane proteomics 279
• Identification of membrane proteins by tandem MS of protein ions 279
• Solid state NMR for study of nanocrystalline membrane proteins 280
• Multiplex proteomics 280
• High-throughput for proteomics 280
• Future directions for protein biochip application 281
• Bioinformatics for proteomics 281
• High-Throughput Crystallography Consortium 281
• Study of protein folding by IBM' s Blue Gene 282
• Study of proteins by atomic force microscopy 282
• Population proteomics 282
• Comparative proteome analysis 283
• Human Proteome Organization 283
• Human Salivary Proteome 284
• Academic-commercial collaborations in proteomics 284
• Indiana Centers for Applied Protein Sciences 284
• Role of proteomics in the healthcare of the future 285
• Proteomics and molecular medicine 285
• Proteodiagnostics 285
• Proteomics and personalized medicine 286
• Targeting the ubiquitin pathway for personalized therapy of cancer 286
• Protein patterns and personalized medicine 286
• Personalizing interferon therapy of hepatitis C virus 288
• Protein biochips and personalized medicine 288
• Combination of diagnostics and therapeutics 288
• Future prospects 289

10. References 291

Tables

• Table 1 1: Landmarks in the evolution of proteomics 17
• Table 1 2: Comparison of DNA and protein 24
• Table 1 3: Comparison of mRNA and protein 25
• Table 1 4: Methods of analysis at various levels of functional genomics 30
• Table 2 1: Proteomics technologies 33
• Table 2 2: Protein separation technologies of selected companies 38
• Table 2 3: Companies supplying mass spectrometry instruments 40
• Table 2 4: Companies involved in cell-based protein assays 60
• Table 2 5: Methods used for the study of protein-protein interactions 62
• Table 2 6: A selection of companies involved in protein-protein interaction studies 69
• Table 2 7: Proteomic technologies used with laser capture microdissection 82
• Table 3 1: Applications of protein biochip technology 85
• Table 3 2: Selected companies involved in protein biochip/microarray technology 101
• Table 4 1: Proteomic databases and other Internet sources of proteomics information 109
• Table 4 2: Protein interaction databases available on the Internet 113
• Table 4 3: Bioinformatic tools for proteomics from academic sources 119
• Table 4 4: Selected companies involved in bioinformatics for proteomics 119
• Table 5 1: Applications of proteomics in basic biological research 121
• Table 5 2: A sampling of proteomics research projects in academic institutions 135
• Table 6 1: Pharmaceutical applications of proteomics 139
• Table 6 2: Selected companies relevant to MALDI-MS for drug discovery 147
• Table 6 3: Selected companies involved in GPCR-based drug discovery 153
• Table 6 4: Companies involved in drug design based on structural proteomics 159
• Table 6 5: Proteomic companies with high-throughput protein expression technologies 166
• Table 6 6: Selected companies involved in chemogenomics/chemoproteomics 176
• Table 6 7: Companies involved in glycoproteomic technologies 181
• Table 7 1: Applications of proteomics in human healthcare 193
• Table 7 2: Companies involved in applications of proteomics to oncology 232
• Table 7 3: Neurodegenerative diseases with underlying protein abnormality 235
• Table 7 4: Disease-specific proteins in the cerebrospinal fluid of patients 244
• Table 7 5: Eye disorders and proteomic approaches 254
• Table 8 1: Potential markets for proteomic technologies 2008-2018 257
• Table 8 2: 2008 revenues of major companies from protein separation technologies 258
• Table 9 1: Role of proteomics in personalizing strategies for cancer therapy 286

Figures

• Figure 1 1: Relationship of DNA, RNA and protein in the cell 25
• Figure 1 2: Protein production pathway from gene expression to functional protein with controls. 28
• Figure 1 3: Parallels between functional genomics and proteomics 28
• Figure 2 1: Proteomics: flow from sample preparation to characterization 34
• Figure 2 2: The central role of spectrometry in proteomics 40
• Figure 2 3: Electrospray ionization (ESI) 41
• Figure 2 4: Matrix-Assisted Laser Desorption/Ionization (MALDI) 42
• Figure 2 5: Scheme of bio-bar-code assay 55
• Figure 2 6: A diagrammatic presentation of yeast two-hybrid system 63
• Figure 3 1: ProteinChip System 87
• Figure 3 2: Surface plasma resonance (SPR) 98
• Figure 4 1: Role of bioinformatics in integrating genomic/proteomic-based drug discovery 108
• Figure 4 2: Bottom-up and top-down approaches for protein sequencing 116
• Figure 6 1: Drug discovery process 140
• Figure 6 2: Regulatory changes induced by drugs and implemented at the proteins level. 143
• Figure 6 3: Relation of proteome to genome, diseases and drugs 144
• Figure 6 4: The mTOR pathways 156
• Figure 6 5: Steps in shotgun proteomics 174
• Figure 6 6: Chemogenomic approach to drug discovery (3-Dimensional Pharmaceuticals) 175
• Figure 7 1: Relation of oncoproteomics to other technologies 214
• Figure 7 2: A scheme of proteomics applications in CNS drug discovery and development 250
• Figure 8 1: Types of companies involved in proteomics collaborations 265
• Figure 8 2: Types of collaborations: R & D, licensing or marketing 265
• Figure 8 3: Proteomics collaborations according to application areas 266
• Figure 8 4: Proteomics collaborations according to technologies 266
• Figure 8 5: Unmet needs in proteomics 272
• Figure 9 1: A scheme of the role of proteomics in personalized management of cancer 287