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Market Research Report

Proteomics - Technologies, Markets and Companies

Published by Jain Pharmabiotech Contact us : +1-860-674-8796
Published 2009/11 Content info  
Product code JAI70918
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Description TOC

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
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