Proteomics - Technologies, Markets and Companies

Table of Contents

0. Executive Summar 15

1. Basics of Proteomic 17

• Introductio 17
• Histor 17
• Nucleic acids, genes and protein 18
• Genom 18
• DN 19
• RN 19
• MicroRNA 19
• Decoding of mRNA by the ribosom 20
• Gene 20
• Alternative splicin 20
• Transcriptio 21
• Gene regulatio 22
• Gene expressio 22
• Chromati 23
• Protein 23
• Spliceosom 23
• Functions of protein 24
• Inter-relationship of protein, mRNA and DN 24
• Proteomic 25
• Mitochondrial proteom 26
• S-nitrosoproteins in mitochondri 27
• Proteomics and genomic 27
• Classification of proteomic 30
• Levels of functional genomics and various "omics 30
• Glycoproteomic 30
• Transcriptomic 31
• Metabolomic 31
• Cytomic 31
• Phenomic 31
• Proteomics and systems biolog 32

2. Proteomic Technologie 33

• Key technologies driving proteomic 33
• Sample preparatio 34
• New trends in sample preparatio 34
• Pressure Cycling Technolog 35
• Protein separation technologie 35
• High resolution 2D gel electrophoresi 35
• Variations of 2D gel technolog 36
• Limitations of 2DGE and measures to overcome thes 36
• 1-D sodium dodecyl sulfate (SDS) PAG 36
• Capillary electrophoresis system 37
• Head column stacking capillary zone electrophoresi 37
• Removal of albumin and Ig 37
• Companies with protein separation technologie 38
• Protein detectio 39
• Protein identification and characterizatio 39
• Mass spectrometry (MS 39
• Companies involved in mass spectrometr 40
• Electrospray ionizatio 41
• Matrix-Assisted Laser Desorption/Ionization Mass Spectrometr 42
• Cryogenic MALDI- Fourier Transform Mass Spectrometr 43
• Stable-isotope-dilution tandem mass spectrometr 44
• HUPO Gold MS Protein Standar 44
• High performance liquid chromatograph 44
• Multidimensional protein identification technology (MudPIT 44
• Peptide mass fingerprintin 45
• Combination of protein separation technologies with mass spectrometr 45
• Combining capillary electrophoresis with mass spectrometr 45
• 2D PAGE and mass spectrometr 45
• Quantification of low abundance protein 46
• SDS-PAG 46
• Antibodies and proteomic 47
• Detection of fusion protein 47
• Labeling and detection of protein 47
• Fluorescent labeling of proteins in living cell 48
• Combination of microspheres with fluorescenc 48
• Self-labeling protein tag 48
• Analysis of peptide 49
• Differential Peptide Displa 49
• Peptide analyses using NanoLC-M 50
• Protein sequencin 51
• Real-time PCR for protein quantificatio 51
• Functional proteomics: technologies for studying protein functio 52
• Functional genomics by mass spectrometr 52
• RNA-Protein fusion 52
• Designed repeat protein 53
• Application of nanbiotechnology to proteomic 53
• Nanoproteomic 53
• Protein nanocrystallograph 54
• Single-molecule mass spectrometry using a nanopor 54
• Nanoelectrospray ionizatio 54
• Nanoparticle barcode 55
• Biobarcode assay for protein 55
• Resonance Light Scattering technolog 56
• Nanoscale protein analysi 57
• Nanobiotechnology for discovery of protein biomarkers in the bloo 57
• Study of single membrane proteins at subnanometer resolutio 57
• Nanotube-vesicle networks for study of membrane protein 58
• Qdot-nanocrystal 58
• Nanotube electronic biosenso 59
• A nanoscale mechanism for protein engineerin 59
• Protein expression profilin 59
• Cell-based protein assay 60
• Living cell-based assays for protein functio 60
• Companies developing cell-based protein assay 61
• Protein function studie 62
• Transcriptionally Active PC 62
• Protein-protein interaction 62
• Yeast two-hybrid syste 64
• Membrane one-hybrid metho 65
• Protein affinity chromatograph 65
• Phage displa 65
• Fluorescence Resonance Energy Transfe 66
• Bioluminescence Resonance Energy Transfe 66
• Detection Enhanced Ubiquitin Split Protein Sensor technolog 66
• Protein-fragment complementation syste 67
• In vivo study of protein-protein interaction 67
• Computational prediction of interaction 68
• Interactom 68
• Protein-protein interactions and drug discover 69
• Companies with technologies for protein-protein interaction studie 69
• Protein-DNA interactio 70
• Determination of protein structur 70
• X-Ray crystallograph 71
• Nuclear magnetic resonanc 72
• Electron spin resonanc 72
• Prediction of protein structur 73
• Protein tomograph 73
• X-ray scattering-based method for determining the structure of protein 74
• Prediction of protein functio 74
• Three-dimensional proteomics for determination of functio 75
• An algorithm for genome-wide prediction of protein functio 75
• Monitoring protein function by expression profilin 75
• Isotope-coded affinity tag peptide labelin 76
• Differential Proteomic Pannin 76
• Cell map proteomic 77
• Topological proteomic 77
• Organelle or subcellular proteomic 78
• Nucleolar proteomic 78
• Glycoproteomic technologie 79
• High-sensitivity glycoprotein analysi 79
• Fluorescent in vivo imaging of glycoprotein 79
• Integrated approaches for protein characterizatio 79
• Imaging mass spectrometr 80
• IMS technologie 80
• Applications of IM 80
• The protein microscop 81
• Automation and robotics in proteomic 81
• Laser capture microdissectio 82
• Microdissection techniques used for proteomic 82
• Uses of LCM in combination with proteomic technologie 82
• Concluding remarks about applications of proteomic technologie 83
• Precision proteomic 83

3. Protein biochip technolog 85

• Introductio 85
• Types of protein biochip 86
• ProteinChi 86
• Applications and advantages of ProteinChi 87
• ProteinChip Biomarker Syste 87
• Matrix-free ProteinChip Arra 88
• Aptamer-based protein biochi 88
• Fluorescence planar wave guide technology-based protein biochip 89
• Lab-on-a-chip for protein analysi 89
• Microfluidic biochips for proteomic 90
• Protein biochips for high-throughput expressio 91
• Nucleic Acid-Programmable Protein Arra 91
• High-density protein microarray 91
• HPLC-Chip for protein identificatio 91
• Antibody microarray 92
• Integration of protein array and image analysi 92
• Tissue microarray technology for proteomic 92
• Protein biochips in molecular diagnostic 93
• A force-based protein biochi 94
• L1 chip and lipid immobilizatio 94
• Multiplexed Protein Profiling on Microarray 94
• Live cell microarray 95
• ProteinArray Workstatio 95
• Proteome array 96
• The Yeast ProtoArra 96
• ProtoArray™ Human Protein Microarra 96
• TRINECTIN proteome chi 97
• Peptide array 97
• Surface plasmon resonance technolog 98
• Biacore' s SP 98
• FLEX CHI 98
• Combination of surface plasmon resonance and MALDI-TO 99
• Protein chips/microarrays using nanotechnolog 99
• Nanoparticle protein chi 99
• Protein nanobiochi 99
• Protein nanoarray 100
• Self-assembling protein nanoarray 100
• Companies involved in protein biochip/microarray technolog 101

4. Bioinformatics in Relation to Proteomic 105

• Introductio 105
• Bioinformatic tools for proteomic 105
• Testing of SELDI-TOF MS Proteomic Dat 105
• BioImagine' s ProteinMin 106
• Bioinformatics for pharmaceutical applications of proteomic 106
• In silico search of drug targets by Biopendiu 106
• Compugen' s LEAD 107
• DrugScor 107
• Proteochemometric modelin 107
• Integration of genomic and proteomic dat 108
• Proteomic databases: creation and analysi 109
• Introductio 109
• Proteomic database 109
• GenProtE 110
• Human Protein Atla 110
• Human Proteomics Initiativ 111
• International Protein Inde 111
• Proteome map 112
• Protein Structure Initiative - Structural Genomics Knowledgebas 112
• Protein Warehouse Databas 112
• Protein Data Ban 112
• Universal Protein Resourc 113
• Protein interaction database 113
• Biomolecular Interaction Network Databas 114
• ENCOD 114
• Functional Genomics Consortiu 115
• Human Proteinpedi 115
• ProteinCente 115
• Databases of the National Center for Biotechnology Informatio 116
• Bioinformatics for protein identificatio 116
• Application of bioinformatics in functional proteomic 116
• Use of bioinformatics in protein sequencin 116
• Bottom-up protein sequencin 117
• Top-down protein sequencin 118
• Protein structural database approach to drug desig 118
• Bioinformatics for high-throughput proteomic 118
• Companies with bioinformatic tools for proteomic 119

5. Research in Proteomic 121

• Introductio 121
• Applications of proteomics in biological researc 121
• Identification of novel human genes by comparative proteomic 121
• Study of relationship between genes and protein 122
• Structural genomics or structural proteomic 122
• Protein Structure Factor 123
• Protein Structure Initiativ 124
• Studies on protein structure at Argonne National Laborator 124
• Structural Genomics Consortiu 125
• Protein knockou 125
• Antisense approach and proteomic 125
• RNAi and protein knockou 126
• Total knockout of cellular protein 126
• Ribozymes and proteomic 126
• Single molecule proteomic 127
• Single-molecule photon stamping spectroscop 127
• Single nucleotide polymorphism determination by TOF-M 127
• Application of proteomic technologies in systems biolog 128
• Signaling pathways and proteomic 128
• Kinomic 128
• Combinatorial RNAi for quantitative protein network analysi 129
• Proteomics in neuroscience researc 129
• Stem cell proteomic 130
• hESC phosphoproteom 130
• Proteomic studies of mesenchymal stem cell 130
• Proteomics of neural stem cell 131
• Proteome Biology of Stem Cells Initiativ 132
• Proteomic analysis of the cell cycl 132
• Nitric oxide and proteomic 132
• A proteomic method for identification of cysteine S-nitrosylation site 133
• Study of the nitroproteom 133
• Study of the phosphoproteom 133
• Study of the mitochondrial proteom 134
• Proteomic technologies for study of mitochondrial proteomic 134
• Cryptom 135
• Study of protein transport in health and diseas 135
• Proteomics research in the academic secto 135
• Vanderbilt University' s Center for Proteomics and Drug Action 137
• ProteomeBinders initiativ 137

6. Pharmaceutical Applications of Proteomic 139

• Introductio 139
• Current drug discovery process and its limitation 139
• Role of omics in drug discover 140
• Genomics-based drug discover 140
• Metabolomics technologies for drug discover 141
• Role of metabonomics in drug discover 141
• Basis of proteomics approach to drug discover 142
• Proteins and drug actio 142
• Transcription-aided drug desig 143
• Role of proteomic technologies in drug discover 143
• Liquid chromatography-based drug discover 144
• Capture compound mass spectrometr 145
• Protein-expression mapping by 2DG 145
• Role of MALDI mass spectrometry in drug discover 145
• Tissue imaging mass spectrometr 145
• Companies using MALDI for drug discover 147
• Oxford Genome Anatomy Projec 147
• Proteins as drug target 148
• Ligands to capture the purine binding proteom 148
• Chemical probes to interrogate key protein families for drug discover 149
• Global proteomics for pharmacodynamic 149
• CellCartaR proteomics platfor 149
• ZeptoMARK™ protein profiling syste 150
• Role of proteomics in targeting disease pathway 151
• Identification of protein kinases as drug target 151
• Mechanisms of action of kinase inhibitor 151
• G-protein coupled receptors as drug target 152
• Methods of study of GPCR 152
• Cell-based assays for GPC 152
• Companies involved in GPCR-based drug discover 153
• GPCR localization databas 154
• Matrix metalloproteases as drug target 154
• PDZ proteins as drug target 155
• Proteasome as drug targe 155
• Serine hydrolases as drug target 156
• Targeting mTOR signaling pathwa 156
• Targeting caspase-8 for anticancer therapeutic 157
• Bioinformatic analysis of proteomics data for drug discover 158
• Drug design based on structural proteomic 158
• Protein crystallography for determining 3D structure of protein 158
• Automated 3D protein modelin 159
• Drug targeting of flexible dynamic protein 159
• Companies involved in structure-based drug-desig 159
• Integration of genomics and proteomics for drug discover 160
• Ligand-receptor bindin 161
• Role of proteomics in study of ligand-receptor bindin 161
• Aptamer protein bindin 162
• Systematic Evolution of Ligands by Exponential Enrichmen 162
• Aptamers and high-throughput screenin 162
• Nucleic Acid Biotool 163
• Aptamer beacon 163
• Peptide aptamer 164
• Riboreporters for drug discover 164
• Target identification and validatio 164
• Application of mass spectrometry for target identificatio 165
• Gene knockout and gene suppression for validating protein target 165
• Laser-mediated protein knockout for target validatio 165
• Integrated proteomics for drug discover 166
• High-throughput proteomic 166
• Companies involved in high-throughput proteomic 167
• Drug discovery through protein-protein interaction studie 167
• Protein-protein interaction as basis for drug target identificatio 168
• Protein-PCNA interaction as basis for drug desig 168
• Two-hybrid protein interaction technology for target identificatio 169
• Biosensors for detection of small molecule-protein interaction 169
• Protein-protein interaction map 170
• ProNet (Myriad Genetics 170
• Hybrigenics' maps of protein-protein interaction 170
• CellZome' s functional map of protein-protein interaction 171
• Mapping of protein-protein interactions by mass spectrometr 172
• Protein interaction map of Drosophila melanogaste 172
• Protein-interaction map of Wellcome Trust Sanger Institut 172
• Protein-protein interactions as targets for therapeutic interventio 172
• Inhibition of protein-protein interactions by peptide aptamer 173
• Selective disruption of proteins by small molecule 173
• Post-genomic combinatorial biology approac 173
• Differential proteomic 174
• Shotgun proteomic 174
• Chemogenomics/chemoproteomics for drug discover 175
• Chemoproteomics-based drug discover 176
• Companies involved in chemogenomics/chemoproteomic 177
• Activity-based proteomic 178
• Iconix' s DrugMatri 178
• Locus Discovery technolog 178
• Automated ligand identification syste 179
• Expression proteomics: protein level quantificatio 180
• Role of phage antibody libraries in target discover 180
• Analysis of posttranslational modification of proteins by M 180
• Phosphoproteomics for drug discover 181
• Application of glycoproteomics for drug discover 181
• Role of carbohydrates in proteomic 181
• Challenges of glycoproteomic 182
• Companies involved in glycoproteomic 182
• Role of protein microarrays/ biochips for drug discover 183
• Protein microarrays vs DNA microarrays for high-throughput screenin 183
• BIA-MS biochip for protein-protein interaction 184
• ProteinChip with Surface Enhanced Neat Desorptio 184
• Protein-domains microarray 184
• Some limitations of protein biochip 185
• Concluding remarks about role of proteomics in drug discover 185
• RNA versus protein profiling as guide to drug developmen 186
• RNA as drug targe 186
• Combination of RNA and protein profilin 187
• RNA binding protein 187
• Toxicoproteomic 187
• Hepatotoxicit 187
• Nephrotoxicit 188
• Cardiotoxicit 189
• Neurotoxicit 189
• Protein/peptide therapeutic 189
• Peptide-based drug 189
• PhylomerR peptide 190
• Cryptein-based therapeutic 190
• Synthetic proteins and peptides as pharmaceutical 191
• Genetic immunization and proteomic 191
• Proteomics and gene therap 192
• Role of proteomics in clinical drug developmen 192
• Pharmacoproteomic 193
• Role of proteomics in clinical drug safet 193

7. Application of Proteomics in Human Healthcar 195

• Clinical proteomic 196
• Definition and standard 196
• Vermillion' s Clinical Proteomics Progra 196
• Pathophysiology of human disease 197
• Diseases due to misfolding of protein 197
• Mechanism of protein foldin 198
• Nanoproteomics for study of misfolded protein 199
• Therapies for protein misfoldin 199
• Intermediate filament protein 200
• Significance of mitochondrial proteome in human diseas 201
• Proteome of Saccharomyces cerevisiae mitochondri 201
• Rat mitochondrial proteom 201
• Proteomic approaches to biomarker identificatio 202
• The ideal biomarke 202
• Proteomic technologies for biomarker discover 202
• MALDI mass spectrometry for biomarker discover 203
• BAMF™ Technolog 203
• Protein biochips/microarrays and biomarker 204
• Antibody-based biomarker discover 204
• Tumor-specific serum peptidome pattern 204
• Search for protein biomarkers in body fluid 205
• Challenges and strategies for discovey of protein biomarkers in plasm 205
• 3-D structure of CD38 as a biomarke 206
• BD"! Free Flow Electrophoresis Syste 206
• Isotope tags for relative and absolute quantificatio 207
• Plasma protein microparticles as biomarker 207
• Proteome partitionin 208
• Stable isotope tagging method 208
• Technology to measure both the identity and size of the biomarke 208
• SISCAPA method for quantitating proteins and peptides in plasm 209
• Biomarkers in the urinary proteom 209
• Application of proteomics in molecular diagnosi 209
• Proximity ligation assa 210
• Protein pattern 211
• Proteomic tests on body fluid 211
• Cyclical amplification of protein 212
• Applications of proteomics in infection 213
• Role of proteomics in virolog 213
• Study of interaction of proteins with viruse 214
• Role of proteomics in bacteriolog 214
• Epidemiology of bacterial infection 214
• Proteomic approach to bacterial pathogenesi 215
• Vaccines for bacterial infection 215
• Protein profiles associated with bacterial drug resistanc 215
• Analyses of the parasite proteom 216
• Application of proteomics in cystic fibrosi 216
• Oncoproteomic 216
• Application of CellCarta technology for oncolog 218
• Accentuation of differentially expressed proteins using phage technolog 218
• Identification of oncogenic tyrosine kinases using phosphoproteomic 218
• Single-cell protein expression analysis by microfluidic technique 219
• Dynamic cell proteomics in response to a dru 219
• Desorption electrospray ionization for cancer diagnosi 219
• Proteomic analysis of cancer cell mitochondri 219
• Mass spectrometry for identification of oncogenic chimeric protein 220
• Id proteins as targets for cancer therap 220
• Proteomic study of p5 221
• Human Tumor Gene Inde 221
• Integration of cancer genomics and proteomic 221
• Laser capture microdissection technology and cancer proteomic 222
• Cancer tissue proteomic 222
• Use of proteomics in cancers of various organ system 223
• Proteomics of brain tumor 223
• Proteomics of breast cance 224
• Proteomics of colorectal cance 225
• Proteomics of esophageal cance 225
• Proteomics of hepatic cance 226
• Proteomics of leukemi 226
• Proteomics of lung cance 227
• Proteomics of pancreatic cance 227
• Proteomics of prostate cance 228
• Diagnostic use of cancer biomarker 228
• NCI' s Network of Clinical Proteomic Technology Centers for Cancer Researc 230
• Proteomics and tumor immunolog 231
• Proteomics and study of tumor invasivenes 232
• Anticancer drug discovery and developmen 232
• Kinase-targeted drug discovery in oncolog 232
• Anticancer drug targeting: functional proteomics screen of protease 233
• Small molecule inhibitors of cancer-related protein 233
• Role of proteomics in studying drug resistance in cance 234
• Future prospects of oncoproteomic 234
• Companies involved in application of proteomics to oncolog 234
• Application of proteomics in neurological disorder 235
• Neuroproteomic 235
• Prion disease 236
• Proteomics and transmissible spongiform encephalopathie 237
• Proteomics and neurodegenerative disorder 238
• Detection of misfolded protein 240
• Proteomics and glutamate repeat disorder 240
• Proteomics and Huntington' s diseas 240
• Proteomics and Parkinson' s diseas 241
• Proteomics and Alzheimer' s diseas 241
• Common denominators of Alzheimer' s and prion disease 242
• Ion channel link for protein-misfolding diseas 243
• Proteomics and demyelinating disease 243
• Proteomics of amyotrophic lateral sclerosi 243
• Proteomics of spinal muscular atroph 244
• Proteomics of Fabry diseas 244
• Proteomics and GM1 gangliosidosi 244
• Proteomics of CNS traum 245
• Proteomics of CNS agin 246
• Neuroproteomics of psychiatric disorder 246
• Neuroproteomic of cocaine addictio 247
• Neurodiagnostics based on proteomic 247
• Testing for disease-specific proteins in the cerebrospinal flui 247
• Tau protein 248
• CNS tissue proteomic 249
• Diagnosis of CNS disorders by examination of proteins in urin 250
• Diagnosis of CNS disorders by examination of proteins in the bloo 250
• Serum pNF-H as biomarker of CNS damag 251
• Proteomics of BB 252
• Future prospects of neuroproteomics in neurolog 252
• HUPO' s Pilot Brain Proteome Projec 253
• Proteomics of cardiac disorder 253
• Study of cardiac mitochondrial proteome in myocardial ischemi 254
• Cardiac protein database 254
• Proteomics of dilated cardiomyopathy and heart failur 254
• Role of proteomics in heart transplantatio 255
• Future of application of proteomics in cardiolog 255
• Proteomic technologies for research in pulmonary disorder 255
• Application fo proteomics in renal disorder 257
• Diagnosis of renal disorder 257
• Proteomic biomarkers of acute kidney injur 257
• Cystatin C as biomarker of glomerular filtration rat 257
• Protein biomarkers of nephriti 258
• Proteomics and kidney stone 258
• Proteomics of eye disorder 258
• Retinal dystrophie 259
• Use of proteomics in inner ear disorder 259
• Use of proteomics in aging researc 259
• Removal of altered cellular proteins in agin 260
• Proteomics and nutritio 261

8. Commercial Aspects of Proteomic 263

• Potential markets for proteomic technologie 263
• Markets for protein separation technologie 263
• Markets for 2D gel electrophoresi 264
• Trends in protein separation technolgies and effect on marke 265
• Protein biochip market 265
• Mass spectrometry market 265
• Markets for MALDI for drug discover 266
• Markets for nuclear magnetic resonance spectroscop 266
• Market for structure-based drug desig 266
• Bioinformatics markets for proteomic 266
• Markets for protein biomarker 267
• Markets for cell-based protein assay 267
• Business and strategic consideration 267
• Cost of protein structure determinatio 267
• Opinion surveys of the scientist consumers of proteomic technologie 267
• Opinions on mass spectrometr 268
• Opinions on bioinformatics and proteomic database 268
• Systems for in vivo study of protein-protein interaction 268
• Perceptions of the value of protein biochip/microfluidic system 268
• Small versus big companie 269
• Expansion in proteomics according to area of applicatio 269
• Growth trends in cell-based protein assay marke 269
• Challenges for development of cell-based protein assay 269
• Future trends and prospects of cell-based protein assay 270
• Strategic collaboration 270
• Analysis of proteomics collaborations according to types of companie 270
• Types of proteomic collaboration 271
• Proteomics collaborations according to application area 272
• Analysis of proteomics collaborations: types of technologie 272
• Collaborations based on protein biochip technolog 272
• Concluding remarks about proteomic collaboration 273
• Proteomic patent 273
• Market drivers in proteomic 274
• Needs of the pharmaceutical industr 274
• Need for outsourcing proteomic technologie 274
• Funding of proteomic companies and researc 275
• Technical advances in proteomic 275
• Changing trends in healthcare in futur 275
• Challenges facing proteomic 275
• Magnitude and complexity of the tas 275
• Technical challenge 276
• Limitations of proteomic 276
• Limitations of 2DG 276
• Limitations of mass spectrometry technique 277
• Complexity of the pharmaceutical proteomic 277
• Unmet needs in proteomic 277

9. Future of Proteomic 279

• Genomics to proteomic 279
• Faster technologie 279
• FLEXGene repositor 279
• Need for new proteomic technologie 280
• Emerging proteomic technologie 281
• Detection of alternative protein isoform 281
• Direct protein identification in large genomes by mass spectrometr 281
• Proteome identification kits with stacked membrane 281
• Vacuum deposition interfac 282
• In vitro protein biosynthesi 282
• Proteome mining with adenosine triphosphat 282
• Proteome-scale purification of human proteins from bacteri 282
• Proteostasis networ 283
• Cytoproteomic 283
• Subcellular proteomic 283
• Individual cell proteomic 284
• Live cell proteomic 284
• Fluorescent proteins for live-cell imagin 285
• Membrane proteomic 285
• Identification of membrane proteins by tandem MS of protein ion 285
• Solid state NMR for study of nanocrystalline membrane protein 286
• Multiplex proteomic 286
• High-throughput for proteomic 286
• Future directions for protein biochip applicatio 287
• Bioinformatics for proteomic 287
• High-Throughput Crystallography Consortiu 287
• Study of protein folding by IBM' s Blue Gen 288
• Study of proteins by atomic force microscop 288
• Population proteomic 288
• Comparative proteome analysi 289
• Human Proteome Organizatio 289
• Human Salivary Proteom 290
• Academic-commercial collaborations in proteomic 290
• Indiana Centers for Applied Protein Science 290
• Role of proteomics in the healthcare of the futur 291
• Proteomics and molecular medicin 291
• Proteodiagnostic 291
• Proteomics and personalized medicin 292
• Targeting the ubiquitin pathway for personalized therapy of cance 292
• Protein patterns and personalized medicin 292
• Personalizing interferon therapy of hepatitis C viru 294
• Protein biochips and personalized medicin 294
• Combination of diagnostics and therapeutic 294
• Future prospect 295

10. Reference 297

Tables

• Table 1 1: Landmarks in the evolution of proteomic 17
• Table 1 2: Comparison of DNA and protei 24
• Table 1 3: Comparison of mRNA and protei 25
• Table 1 4: Methods of analysis at various levels of functional genomic 30
• Table 2 1: Proteomics technologie 33
• Table 2 2: Protein separation technologies of selected companie 38
• Table 2 3: Companies supplying mass spectrometry instrument 40
• Table 2 4: Companies involved in cell-based protein assay 61
• Table 2 5: Methods used for the study of protein-protein interaction 63
• Table 2 6: A selection of companies involved in protein-protein interaction studie 69
• Table 2 7: Proteomic technologies used with laser capture microdissectio 83
• Table 3 1: Applications of protein biochip technolog 85
• Table 3 2: Selected companies involved in protein biochip/microarray technolog 101
• Table 4 1: Proteomic databases and other Internet sources of proteomics informatio 109
• Table 4 2: Protein interaction databases available on the Interne 113
• Table 4 3: Bioinformatic tools for proteomics from academic source 119
• Table 4 4: Selected companies involved in bioinformatics for proteomic 120
• Table 5 1: Applications of proteomics in basic biological researc 121
• Table 5 2: A sampling of proteomics research projects in academic institution 135
• Table 6 1: Pharmaceutical applications of proteomic 139
• Table 6 2: Selected companies relevant to MALDI-MS for drug discover 147
• Table 6 3: Selected companies involved in GPCR-based drug discover 153
• Table 6 4: Companies involved in drug design based on structural proteomic 159
• Table 6 5: Proteomic companies with high-throughput protein expression technologie 167
• Table 6 6: Selected companies involved in chemogenomics/chemoproteomic 177
• Table 6 7: Companies involved in glycoproteomic technologie 182
• Table 7 1: Applications of proteomics in human healthcar 195
• Table 7 2: Companies involved in applications of proteomics to oncolog 234
• Table 7 3: Neurodegenerative diseases with underlying protein abnormalit 238
• Table 7 4: Disease-specific proteins in the cerebrospinal fluid of patient 247
• Table 7 5: Eye disorders and proteomic approache 258
• Table 8 1: Potential markets for proteomic technologies 2008-201 263
• Table 8 2: 2008 revenues of major companies from protein separation technologie 264
• Table 9 1: Role of proteomics in personalizing strategies for cancer therap 292

Figures

• Figure 1 1: Relationship of DNA, RNA and protein in the cel 25
• Figure 1 2: Protein production pathway from gene expression to functional protein with controls. 28
• Figure 1 3: Parallels between functional genomics and proteomic 28
• Figure 2 1: Proteomics: flow from sample preparation to characterizatio 34
• Figure 2 2: The central role of spectrometry in proteomic 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 assa 56
• Figure 2 6: A diagrammatic presentation of yeast two-hybrid syste 64
• Figure 3 1: ProteinChip Syste 87
• Figure 3 2: Surface plasma resonance (SPR 98
• Figure 4 1: Role of bioinformatics in integrating genomic/proteomic-based drug discover 108
• Figure 4 2: Bottom-up and top-down approaches for protein sequencin 117
• Figure 6 1: Drug discovery proces 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 drug 144
• Figure 6 4: The mTOR pathway 157
• Figure 6 5: Steps in shotgun proteomic 175
• Figure 6 6: Chemogenomic approach to drug discovery (3-Dimensional Pharmaceuticals 176
• Figure 7 1: Relation of oncoproteomics to other technologie 217
• Figure 7 2: A scheme of proteomics applications in CNS drug discovery and developmen 252
• Figure 8 1: Types of companies involved in proteomics collaboration 271
• Figure 8 2: Types of collaborations: R & D, licensing or marketin 271
• Figure 8 3: Proteomics collaborations according to application area 272
• Figure 8 4: Proteomics collaborations according to technologie 272
• Figure 8 5: Unmet needs in proteomic 278
• Figure 9 1: A scheme of the role of proteomics in personalized management of cance 293