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> Proteomics - Technologies, Markets and Companies
Market Research Report
Proteomics - Technologies, Markets and Companies
Published by
Jain Pharmabiotech
Published
2009/11
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JAI70918
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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
Real-time PCR for protein quantification 51
MS-based quantitative proteomics 52
Functional proteomics: technologies for studying protein function 52
Functional genomics by mass spectrometry 52
RNA-Protein fusions 53
Designed repeat proteins 53
Application of nanbiotechnology to proteomics 53
Nanoproteomics 54
Protein nanocrystallography 54
Single-molecule mass spectrometry using a nanopore 54
Nanoelectrospray ionization 55
Nanoparticle barcodes 55
Biobarcode assay for proteins 56
Resonance Light Scattering technology 57
Nanoscale protein analysis 57
Nanobiotechnology for discovery of protein biomarkers in the blood 58
Study of single membrane proteins at subnanometer resolution 58
Nanotube-vesicle networks for study of membrane proteins 58
Qdot-nanocrystals 59
Nanotube electronic biosensor 59
A nanoscale mechanism for protein engineering 59
Protein expression profiling 60
Cell-based protein assays 60
Living cell-based assays for protein function 61
Companies developing cell-based protein assays 61
Protein function studies 62
Transcriptionally Active PCR 62
Protein-protein interactions 62
Yeast two-hybrid system 64
Membrane one-hybrid method 65
Protein affinity chromatography 66
Phage display 66
Fluorescence Resonance Energy Transfer 66
Bioluminescence Resonance Energy Transfer 66
Detection Enhanced Ubiquitin Split Protein Sensor technology 67
Protein-fragment complementation system 67
In vivo study of protein-protein interactions 67
Computational prediction of interactions 68
Interactome 68
Protein-protein interactions and drug discovery 69
Companies with technologies for protein-protein interaction studies 69
Protein-DNA interaction 70
Determination of protein structure 71
X-Ray crystallography 71
Nuclear magnetic resonance 72
Electron spin resonance 73
Prediction of protein structure 73
Protein tomography 73
X-ray scattering-based method for determining the structure of proteins 74
Prediction of protein function 74
Three-dimensional proteomics for determination of function 75
An algorithm for genome-wide prediction of protein function 75
Monitoring protein function by expression profiling 76
Isotope-coded affinity tag peptide labeling 76
Differential Proteomic Panning 77
Cell map proteomics 77
Topological proteomics 77
Organelle or subcellular proteomics 78
Nucleolar proteomics 79
Glycoproteomic technologies 79
High-sensitivity glycoprotein analysis 79
Fluorescent in vivo imaging of glycoproteins 79
Integrated approaches for protein characterization 80
Imaging mass spectrometry 80
IMS technologies 80
Applications of IMS 81
The protein microscope 81
Automation and robotics in proteomics 82
Laser capture microdissection 82
Microdissection techniques used for proteomics 82
Uses of LCM in combination with proteomic technologies 83
Concluding remarks about applications of proteomic technologies 83
Precision proteomics 84
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 115
Human Proteinpedia 115
ProteinCenter 115
Databases of the National Center for Biotechnology Information 116
Bioinformatics for protein identification 116
Application of bioinformatics in functional proteomics 116
Use of bioinformatics in protein sequencing 116
Bottom-up protein sequencing 117
Top-down protein sequencing 118
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
hESC phosphoproteome 130
Proteomic studies of mesenchymal stem cells 130
Proteomics of neural stem cells 131
Proteome Biology of Stem Cells Initiative 132
Proteomic analysis of the cell cycle 132
Nitric oxide and proteomics 132
A proteomic method for identification of cysteine S-nitrosylation sites 133
Study of the nitroproteome 133
Study of the phosphoproteome 133
Study of the mitochondrial proteome 134
Proteomic technologies for study of mitochondrial proteomics 134
Cryptome 135
Study of protein transport in health and disease 135
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
Mechanisms of action of kinase inhibitors 151
G-protein coupled receptors as drug targets 152
Methods of study of GPCRs 152
Cell-based assays for GPCR 152
Companies involved in GPCR-based drug discovery 153
GPCR localization database 154
Matrix metalloproteases as drug targets 154
PDZ proteins as drug targets 155
Proteasome as drug target 155
Serine hydrolases as drug targets 156
Targeting mTOR signaling pathway 156
Targeting caspase-8 for anticancer therapeutics 157
Bioinformatic analysis of proteomics data for drug discovery 158
Drug design based on structural proteomics 158
Protein crystallography for determining 3D structure of proteins 158
Automated 3D protein modeling 159
Drug targeting of flexible dynamic proteins 159
Companies involved in structure-based drug-design 159
Integration of genomics and proteomics for drug discovery 160
Ligand-receptor binding 161
Role of proteomics in study of ligand-receptor binding 161
Aptamer protein binding 162
Systematic Evolution of Ligands by Exponential Enrichment 162
Aptamers and high-throughput screening 162
Nucleic Acid Biotools 163
Aptamer beacons 163
Peptide aptamers 164
Riboreporters for drug discovery 164
Target identification and validation 164
Application of mass spectrometry for target identification 165
Gene knockout and gene suppression for validating protein targets 165
Laser-mediated protein knockout for target validation 165
Integrated proteomics for drug discovery 166
High-throughput proteomics 166
Companies involved in high-throughput proteomics 167
Drug discovery through protein-protein interaction studies 167
Protein-protein interaction as basis for drug target identification 168
Protein-PCNA interaction as basis for drug design 168
Two-hybrid protein interaction technology for target identification 169
Biosensors for detection of small molecule-protein interactions 169
Protein-protein interaction maps 170
ProNet (Myriad Genetics) 170
Hybrigenics' maps of protein-protein interactions 170
CellZome' s functional map of protein-protein interactions 171
Mapping of protein-protein interactions by mass spectrometry 172
Protein interaction map of Drosophila melanogaster 172
Protein-interaction map of Wellcome Trust Sanger Institute 172
Protein-protein interactions as targets for therapeutic intervention 172
Inhibition of protein-protein interactions by peptide aptamers 173
Selective disruption of proteins by small molecules 173
Post-genomic combinatorial biology approach 173
Differential proteomics 174
Shotgun proteomics 174
Chemogenomics/chemoproteomics for drug discovery 175
Chemoproteomics-based drug discovery 176
Companies involved in chemogenomics/chemoproteomics 177
Activity-based proteomics 178
Iconix' s DrugMatrix 178
Locus Discovery technology 178
Automated ligand identification system 179
Expression proteomics: protein level quantification 180
Role of phage antibody libraries in target discovery 180
Analysis of posttranslational modification of proteins by MS 180
Phosphoproteomics for drug discovery 181
Application of glycoproteomics for drug discovery 181
Role of carbohydrates in proteomics 181
Challenges of glycoproteomics 182
Companies involved in glycoproteomics 182
Role of protein microarrays/ biochips for drug discovery 183
Protein microarrays vs DNA microarrays for high-throughput screening 183
BIA-MS biochip for protein-protein interactions 184
ProteinChip with Surface Enhanced Neat Desorption 184
Protein-domains microarrays 184
Some limitations of protein biochips 185
Concluding remarks about role of proteomics in drug discovery 185
RNA versus protein profiling as guide to drug development 186
RNA as drug target 186
Combination of RNA and protein profiling 187
RNA binding proteins 187
Toxicoproteomics 187
Hepatotoxicity 187
Nephrotoxicity 188
Cardiotoxicity 189
Neurotoxicity 189
Protein/peptide therapeutics 189
Peptide-based drugs 189
PhylomerR peptides 190
Cryptein-based therapeutics 190
Synthetic proteins and peptides as pharmaceuticals 191
Genetic immunization and proteomics 191
Proteomics and gene therapy 192
Role of proteomics in clinical drug development 192
Pharmacoproteomics 193
Role of proteomics in clinical drug safety 193
7. Application of Proteomics in Human Healthcare 195
Clinical proteomics 196
Definition and standards 196
Vermillion' s Clinical Proteomics Program 196
Pathophysiology of human diseases 197
Diseases due to misfolding of proteins 197
Mechanism of protein folding 198
Nanoproteomics for study of misfolded proteins 199
Therapies for protein misfolding 199
Intermediate filament proteins 200
Significance of mitochondrial proteome in human disease 201
Proteome of Saccharomyces cerevisiae mitochondria 201
Rat mitochondrial proteome 201
Proteomic approaches to biomarker identification 202
The ideal biomarker 202
Proteomic technologies for biomarker discovery 202
MALDI mass spectrometry for biomarker discovery 203
BAMF™ Technology 203
Protein biochips/microarrays and biomarkers 204
Antibody-based biomarker discovery 204
Tumor-specific serum peptidome patterns 204
Search for protein biomarkers in body fluids 205
Challenges and strategies for discovey of protein biomarkers in plasma 205
3-D structure of CD38 as a biomarker 206
BD"! Free Flow Electrophoresis System 206
Isotope tags for relative and absolute quantification 207
Plasma protein microparticles as biomarkers 207
Proteome partitioning 208
Stable isotope tagging methods 208
Technology to measure both the identity and size of the biomarker 208
SISCAPA method for quantitating proteins and peptides in plasma 209
Biomarkers in the urinary proteome 209
Application of proteomics in molecular diagnosis 209
Proximity ligation assay 210
Protein patterns 211
Proteomic tests on body fluids 211
Cyclical amplification of proteins 212
Applications of proteomics in infections 213
Role of proteomics in virology 213
Study of interaction of proteins with viruses 214
Role of proteomics in bacteriology 214
Epidemiology of bacterial infections 214
Proteomic approach to bacterial pathogenesis 215
Vaccines for bacterial infections 215
Protein profiles associated with bacterial drug resistance 215
Analyses of the parasite proteome 216
Application of proteomics in cystic fibrosis 216
Oncoproteomics 216
Application of CellCarta technology for oncology 218
Accentuation of differentially expressed proteins using phage technology 218
Identification of oncogenic tyrosine kinases using phosphoproteomics 218
Single-cell protein expression analysis by microfluidic techniques 219
Dynamic cell proteomics in response to a drug 219
Desorption electrospray ionization for cancer diagnosis 219
Proteomic analysis of cancer cell mitochondria 219
Mass spectrometry for identification of oncogenic chimeric proteins 220
Id proteins as targets for cancer therapy 220
Proteomic study of p53 221
Human Tumor Gene Index 221
Integration of cancer genomics and proteomics 221
Laser capture microdissection technology and cancer proteomics 222
Cancer tissue proteomics 222
Use of proteomics in cancers of various organ systems 223
Proteomics of brain tumors 223
Proteomics of breast cancer 224
Proteomics of colorectal cancer 225
Proteomics of esophageal cancer 225
Proteomics of hepatic cancer 226
Proteomics of leukemia 226
Proteomics of lung cancer 227
Proteomics of pancreatic cancer 227
Proteomics of prostate cancer 228
Diagnostic use of cancer biomarkers 228
NCI' s Network of Clinical Proteomic Technology Centers for Cancer Research 230
Proteomics and tumor immunology 231
Proteomics and study of tumor invasiveness 232
Anticancer drug discovery and development 232
Kinase-targeted drug discovery in oncology 232
Anticancer drug targeting: functional proteomics screen of proteases 233
Small molecule inhibitors of cancer-related proteins 233
Role of proteomics in studying drug resistance in cancer 234
Future prospects of oncoproteomics 234
Companies involved in application of proteomics to oncology 234
Application of proteomics in neurological disorders 235
Neuroproteomics 235
Prion diseases 236
Proteomics and transmissible spongiform encephalopathies 237
Proteomics and neurodegenerative disorders 238
Detection of misfolded proteins 240
Proteomics and glutamate repeat disorders 240
Proteomics and Huntington' s disease 240
Proteomics and Parkinson' s disease 241
Proteomics and Alzheimer' s disease 241
Common denominators of Alzheimer' s and prion diseases 242
Ion channel link for protein-misfolding disease 243
Proteomics and demyelinating diseases 243
Proteomics of amyotrophic lateral sclerosis 243
Proteomics of spinal muscular atrophy 244
Proteomics of Fabry disease 244
Proteomics and GM1 gangliosidosis 244
Proteomics of CNS trauma 245
Proteomics of CNS aging 246
Neuroproteomics of psychiatric disorders 246
Neuroproteomic of cocaine addiction 247
Neurodiagnostics based on proteomics 247
Testing for disease-specific proteins in the cerebrospinal fluid 247
Tau proteins 248
CNS tissue proteomics 249
Diagnosis of CNS disorders by examination of proteins in urine 250
Diagnosis of CNS disorders by examination of proteins in the blood 250
Serum pNF-H as biomarker of CNS damage 251
Proteomics of BBB 252
Future prospects of neuroproteomics in neurology 252
HUPO' s Pilot Brain Proteome Project 253
Proteomics of cardiac disorders 253
Study of cardiac mitochondrial proteome in myocardial ischemia 254
Cardiac protein databases 254
Proteomics of dilated cardiomyopathy and heart failure 254
Role of proteomics in heart transplantation 255
Future of application of proteomics in cardiology 255
Proteomic technologies for research in pulmonary disorders 255
Application fo proteomics in renal disorders 257
Diagnosis of renal disorders 257
Proteomic biomarkers of acute kidney injury 257
Cystatin C as biomarker of glomerular filtration rate 257
Protein biomarkers of nephritis 258
Proteomics and kidney stones 258
Proteomics of eye disorders 258
Retinal dystrophies 259
Use of proteomics in inner ear disorders 259
Use of proteomics in aging research 260
Removal of altered cellular proteins in aging 260
Proteomics and nutrition 261
8. Commercial Aspects of Proteomics 263
Introduction 263
Potential markets for proteomic technologies 263
Geographical distribution of proteomics technologies markets 264
Markets for protein separation technologies 264
Markets for 2D gel electrophoresis 265
Trends in protein separation technolgies and effect on market 265
Protein biochip markets 265
Mass spectrometry markets 266
Markets for MALDI for drug discovery 266
Markets for nuclear magnetic resonance spectroscopy 266
Market for structure-based drug design 267
Bioinformatics markets for proteomics 267
Markets for protein biomarkers 267
Markets for cell-based protein assays 267
Business and strategic considerations 268
Cost of protein structure determination 268
Opinion surveys of the scientist consumers of proteomic technologies 268
Opinions on mass spectrometry 268
Opinions on bioinformatics and proteomic databases 268
Systems for in vivo study of protein-protein interactions 269
Perceptions of the value of protein biochip/microfluidic systems 269
Small versus big companies 269
Expansion in proteomics according to area of application 269
Growth trends in cell-based protein assay market 270
Challenges for development of cell-based protein assays 270
Future trends and prospects of cell-based protein assays 270
Strategic collaborations 271
Analysis of proteomics collaborations according to types of companies 271
Types of proteomic collaborations 272
Proteomics collaborations according to application areas 272
Analysis of proteomics collaborations: types of technologies 272
Collaborations based on protein biochip technology 273
Concluding remarks about proteomic collaborations 273
Proteomic patents 274
Market drivers in proteomics 274
Needs of the pharmaceutical industry 274
Need for outsourcing proteomic technologies 275
Funding of proteomic companies and research 275
Technical advances in proteomics 275
Changing trends in healthcare in future 276
Challenges facing proteomics 276
Magnitude and complexity of the task 276
Technical challenges 276
Limitations of proteomics 277
Limitations of 2DGE 277
Limitations of mass spectrometry techniques 277
Complexity of the pharmaceutical proteomics 277
Unmet needs in proteomics 278
9. Future of Proteomics 279
Genomics to proteomics 279
Faster technologies 279
FLEXGene repository 279
Need for new proteomic technologies 280
Emerging proteomic technologies 281
Detection of alternative protein isoforms 281
Direct protein identification in large genomes by mass spectrometry 281
Proteome identification kits with stacked membranes 281
Vacuum deposition interface 282
In vitro protein biosynthesis 282
Proteome mining with adenosine triphosphate 282
Proteome-scale purification of human proteins from bacteria 282
Proteostasis network 283
Cytoproteomics 283
Subcellular proteomics 283
Individual cell proteomics 284
Live cell proteomics 284
Fluorescent proteins for live-cell imaging 285
Membrane proteomics 285
Identification of membrane proteins by tandem MS of protein ions 285
Solid state NMR for study of nanocrystalline membrane proteins 286
Multiplex proteomics 286
High-throughput for proteomics 286
Future directions for protein biochip application 287
Bioinformatics for proteomics 287
High-Throughput Crystallography Consortium 287
Study of protein folding by IBM' s Blue Gene 288
Study of proteins by atomic force microscopy 288
Population proteomics 288
Comparative proteome analysis 289
Human Proteome Organization 289
Human Salivary Proteome 290
Academic-commercial collaborations in proteomics 290
Indiana Centers for Applied Protein Sciences 290
Role of proteomics in the healthcare of the future 291
Proteomics and molecular medicine 291
Proteodiagnostics 291
Proteomics and personalized medicine 292
Targeting the ubiquitin pathway for personalized therapy of cancer 292
Protein patterns and personalized medicine 292
Personalizing interferon therapy of hepatitis C virus 294
Protein biochips and personalized medicine 294
Combination of diagnostics and therapeutics 295
Future prospects 295
10. References 297
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 61
Table 2 5: Methods used for the study of protein-protein interactions 63
Table 2 6: A selection of companies involved in protein-protein interaction studies 69
Table 2 7: Proteomic technologies used with laser capture microdissection 83
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 120
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 167
Table 6 6: Selected companies involved in chemogenomics/chemoproteomics 177
Table 6 7: Companies involved in glycoproteomic technologies 182
Table 7 1: Applications of proteomics in human healthcare 195
Table 7 2: Companies involved in applications of proteomics to oncology 234
Table 7 3: Neurodegenerative diseases with underlying protein abnormality 238
Table 7 4: Disease-specific proteins in the cerebrospinal fluid of patients 247
Table 7 5: Eye disorders and proteomic approaches 259
Table 8 1: Potential markets for proteomic technologies 2008-2018 263
Table 8 2: Geographical distribution of markets for proteomic technologies 2008-2018 264
Table 8 3: 2008 revenues of major companies from protein separation technologies 264
Table 9 1: Role of proteomics in personalizing strategies for cancer therapy 292
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 56
Figure 2 6: A diagrammatic presentation of yeast two-hybrid system 64
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 117
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 157
Figure 6 5: Steps in shotgun proteomics 175
Figure 6 6: Chemogenomic approach to drug discovery (3-Dimensional Pharmaceuticals) 176
Figure 7 1: Relation of oncoproteomics to other technologies 217
Figure 7 2: A scheme of proteomics applications in CNS drug discovery and development 253
Figure 8 1: Types of companies involved in proteomics collaborations 271
Figure 8 2: Types of collaborations: R & D, licensing or marketing 272
Figure 8 3: Proteomics collaborations according to application areas 272
Figure 8 4: Proteomics collaborations according to technologies 273
Figure 8 5: Unmet needs in proteomics 278
Figure 9 1: A scheme of the role of proteomics in personalized management of cancer 294
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