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. Important areas of application include
cancer (oncoproteomics) and neurological disorders (neuroproteomics). The text
is supplemented with 44 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 220 of these are profiled in the report with 462
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 2012 and are projected to
years 2017 and 2022. The largest expansion will be in bioinformatics and
protein biochip technologies. Important areas of application are cancer and
neurological disorders
Table of Contents
Table of Contents
Part I
0. Executive Summary 17
1. Basics of Proteomics 19
Introduction 19
History 19
Nucleic acids, genes and proteins 20
Genome 20
DNA 21
RNA 21
MicroRNAs 21
Decoding of mRNA by the ribosome 22
Genes 23
Alternative splicing 23
Transcription 24
Gene regulation 24
Gene expression 25
Chromatin 25
Golgi complex 26
Proteins 26
Spliceosome 27
Functions of proteins 27
Inter-relationship of protein, mRNA and DNA 28
Proteomics 29
Mitochondrial proteome 30
S-nitrosoproteins in mitochondria 30
Proteomics and genomics 31
Classification of proteomics 33
Levels of functional genomics and various "omics" 33
Glycoproteomics 34
Transcriptomics 34
Metabolomics 34
Cytomics 35
Phenomics 35
Impact of the genetic factors on the human proteome 35
Proteomics and systems biology 36
Functional synthetic proteins 36
2. Proteomic Technologies 39
Key technologies driving proteomics 39
Sample preparation 40
New trends in sample preparation 40
Pressure Cycling Technology 41
Protein separation technologies 41
High resolution 2DGE 41
Variations of 2D gel technology 42
Limitations of 2DGE and measures to overcome these 42
1-D sodium dodecyl sulfate (SDS) PAGE 42
Capillary electrophoresis systems 43
Head column stacking capillary zone electrophoresis 43
Removal of albumin and IgG 43
SeraFILE™ separations platform 44
Companies with protein separation technologies 44
Protein purification 46
Technologies for protein purification 46
Applications of protein purification 46
Protein detection 46
Protein identification and characterization 47
Mass spectrometry (MS) 47
Companies involved in mass spectrometry 47
Electrospray ionization 48
Desorption electrospray ionization MS 49
Mirosaic 3500 MiD 50
Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry 50
Cryogenic MALDI- Fourier Transform Mass Spectrometry 52
Stable-isotope-dilution tandem mass spectrometry 52
HUPO Gold MS Protein Standard 52
High performance liquid chromatography 53
Multidimensional protein identification technology (MudPIT) 53
Multiple reaction monitoring assays 53
Peptide mass fingerprinting 54
Combination of protein separation technologies with mass spectrometry
54
Combining capillary electrophoresis with mass spectrometry 54
2D PAGE and mass spectrometry 55
Quantification of low abundance proteins 55
SDS-PAGE 55
Antibodies and proteomics 56
Detection of fusion proteins 56
Labeling and detection of proteins 56
Fluorescent labeling of proteins in living cells 57
Combination of microspheres with fluorescence 57
Self-labeling protein tags 57
Analysis of peptides 58
C-terminal peptide analysis 59
Differential Peptide Display 59
Peptide analyses using NanoLC-MS 59
Protein sequencing 60
Real-time PCR for protein quantification 61
Quantitative proteomics 61
MS-based quantitative proteomics 61
MS and cryo-electron tomography 61
Selected reaction monitoring MS 62
Functional proteomics: technologies for studying protein function 62
Functional genomics by mass spectrometry 62
RNA-Protein fusions 63
Designed repeat proteins 63
Application of nanbiotechnology to proteomics 63
Nanoproteomics 64
Protein nanocrystallography 64
Single-molecule mass spectrometry using a nanopore 64
Nanoelectrospray ionization 65
Nanoproteomics for discovery of protein biomarkers in the blood 65
Nanoparticle barcodes 65
Biobarcode assay for proteins 66
Nanopore-based protein sequencing 67
Nanoscale protein analysis 67
Nanoscale mechanism for protein engineering 68
Nanotube electronic biosensor 68
Nanotube-vesicle networks for study of membrane proteins 68
Nanowire transistor for the detection of protein-protein interactions
69
Qdot-nanocrystals 69
Resonance Light Scattering technology 69
Study of single membrane proteins at subnanometer resolution 70
Protein expression profiling 70
Cell-based protein assays 71
Living cell-based assays for protein function 71
Companies developing cell-based protein assays 72
Protein function studies 72
Transcriptionally Active PCR 73
Protein-protein interactions 73
Yeast two-hybrid system 74
Membrane one-hybrid method 75
Protein affinity chromatography 76
Phage display 76
Fluorescence Resonance Energy Transfer 76
Bioluminescence Resonance Energy Transfer 77
Detection Enhanced Ubiquitin Split Protein Sensor technology 77
Protein-fragment complementation system 77
In vivo study of protein-protein interactions 78
Bacterial protein interaction studies for assigning function 78
Computational prediction of interactions 78
Interactome 79
Protein-protein interactions and drug discovery 80
Companies with technologies for protein-protein interaction studies 80
Protein-DNA interaction 81
Determination of protein structure 81
X-Ray crystallography 82
Nuclear magnetic resonance 83
Electron spin resonance 83
Prediction of protein structure 83
Protein tomography 84
X-ray scattering-based method for determining the structure of proteins
84
Prediction of protein function 85
Three-dimensional proteomics for determination of function 85
An algorithm for genome-wide prediction of protein function 86
Monitoring protein function by expression profiling 86
Isotope-coded affinity tag peptide labeling 86
Differential Proteomic Panning 87
Cell map proteomics 87
Topological proteomics 88
Organelle or subcellular proteomics 89
Nucleolar proteomics 89
Glycoproteomic technologies 89
High-sensitivity glycoprotein analysis 89
Fluorescent in vivo imaging of glycoproteins 90
Integrated approaches for protein characterization 90
Imaging mass spectrometry 91
IMS technologies 91
Applications of IMS 91
The protein microscope 92
Tag-Mass IMS 92
Automation and robotics in proteomics 92
Western blot 93
Limitations of WB 93
Innovations in WB 93
Capillary electrophoresis and WB 94
Fluorescent WB 94
Microfluidics and WB 94
Multiplexing WB 95
Applications of Western blot 95
Research applications of Western blot 95
Molecular diagnostic applications of Western blot 96
Companies involved in Western blotting technologies 96
Laser capture microdissection 97
Microdissection techniques used for proteomics 97
Uses of LCM in combination with proteomic technologies 98
Concluding remarks about applications of proteomic technologies 98
Precision proteomics 99
3. Protein biochip technology 101
Introduction 101
Types of protein biochips 102
ProteinChip 102
Applications and advantages of ProteinChip 103
ProteinChip Biomarker System 103
Matrix-free ProteinChip Array 104
Aptamer-based protein biochip 104
Fluorescence planar wave guide technology-based protein biochips 105
Lab-on-a-chip for protein analysis 105
Biochips for peptide arrays 106
Microfluidic biochips for proteomics 106
Protein biochips for high-throughput expression 107
Nucleic Acid-Programmable Protein Array 107
High-density protein microarrays 107
HPLC-Chip for protein identification 108
Antibody microarrays 108
Integration of protein array and image analysis 108
Tissue microarray technology for proteomics 109
Protein biochips in molecular diagnostics 109
A force-based protein biochip 110
L1 chip and lipid immobilization 110
Multiplexed Protein Profiling on Microarrays 110
Live cell microarrays 111
ProteinArray Workstation 111
Proteome arrays 112
The Yeast ProtoArray 112
ProtoArray™ Human Protein Microarray 112
TRINECTIN proteome chip 113
Peptide arrays 113
Surface plasmon resonance technology 114
Biacore's SPR 114
FLEX CHIP 114
Combination of surface plasmon resonance and MALDI-TOF 115
Protein chips/microarrays using nanotechnology 115
Nanoparticle protein chip 115
Protein nanobiochip 116
Protein nanoarrays 116
Self-assembling protein nanoarrays 116
Companies involved in protein biochip/microarray technology 117
4. Bioinformatics in Relation to Proteomics 121
Introduction 121
Bioinformatic tools for proteomics 121
Testing of SELDI-TOF MS Proteomic Data 121
BioImagine's ProteinMine 122
Bioinformatics for pharmaceutical applications of proteomics 122
In silico search of drug targets by Biopendium 122
Compugen's LEADS 123
DrugScore 123
Proteochemometric modeling 123
Integration of genomic and proteomic data 124
Proteomic databases: creation and analysis 125
Introduction 125
Proteomic databases 125
GenProtEC 126
Human Protein Atlas 126
Human Proteomics Initiative 127
International Protein Index 128
Proteome maps 128
Protein Structure Initiative - Structural Genomics Knowledgebase 128
Protein Warehouse Database 128
Protein Data Bank 129
Repository for raw data from proteomics MS 129
Universal Protein Resource 129
Protein interaction databases 130
Biomolecular Interaction Network Database 131
ENCODE 131
Functional Genomics Consortium 131
Human Proteinpedia 132
ProteinCenter 132
Databases of the National Center for Biotechnology Information 132
Bioinformatics for protein identification 133
Application of bioinformatics in functional proteomics 133
Use of bioinformatics in protein sequencing 133
Bottom-up protein sequencing 134
Top-down protein sequencing 135
Protein structural database approach to drug design 135
Bioinformatics for high-throughput proteomics 135
Bioinformatics for protein-protein interactions 136
Companies with bioinformatic tools for proteomics 137
5. Research in Proteomics 139
Introduction 139
Applications of proteomics in biological research 139
Identification of novel human genes by comparative proteomics 139
Study of relationship between genes and proteins 140
Characterization of histone codes 140
Structural genomics or structural proteomics 141
Protein Structure Factory 142
Protein Structure Initiative 142
Studies on protein structure at Argonne National Laboratory 143
Structural Genomics Consortium 143
Protein knockout 144
Antisense approach and proteomics 144
RNAi and protein knockout 144
Total knockout of cellular proteins 144
Ribozymes and proteomics 145
Single molecule proteomics 145
Single-molecule photon stamping spectroscopy 145
Single nucleotide polymorphism determination by TOF-MS 146
Application of proteomic technologies in systems biology 146
Signaling pathways and proteomics 146
Kinomics 147
Combinatorial RNAi for quantitative protein network analysis 147
Proteomics in neuroscience research 147
Stem cell proteomics 148
Comparative proteomic analysis of somatic cells, iPSCs and ESCs 148
hESC phosphoproteome 149
Proteomic studies of mesenchymal stem cells 149
Proteomics of neural stem cells 150
Proteome Biology of Stem Cells Initiative 150
Proteomic analysis of the cell cycle 151
Nitric oxide and proteomics 151
A proteomic method for identification of cysteine S-nitrosylation sites
151
Study of the nitroproteome 152
Study of the phosphoproteome 152
Study of the mitochondrial proteome 153
Proteomic technologies for study of mitochondrial proteomics 153
Cryptome 154
Study of protein transport in health and disease 154
Ancient proteomics 154
Proteomics research in the academic sector 155
Netherlands Proteins@Work 157
ProteomeBinders initiative 157
Rutgers University's Center for Integrative Proteomics Research 157
Vanderbilt University's Center for Proteomics and Drug Actions 158
6. Pharmaceutical Applications of Proteomics 159
Introduction 159
Current drug discovery process and its limitations 159
Role of omics in drug discovery 160
Genomics-based drug discovery 160
Metabolomics technologies for drug discovery 161
Role of metabonomics in drug discovery 161
Basis of proteomics approach to drug discovery 162
Proteins and drug action 162
Transcription-aided drug design 163
Role of proteomic technologies in drug discovery 163
Liquid chromatography-based drug discovery 164
Capture compound mass spectrometry 165
Protein-expression mapping by 2DGE 165
Role of MALDI mass spectrometry in drug discovery 165
Structural proteomics and drug discovery 165
Tissue imaging mass spectrometry 166
Companies using MALDI for drug discovery 167
Oxford Genome Anatomy Project 168
Proteins as drug targets 168
Ligands to capture the purine binding proteome 169
Chemical probes to interrogate key protein families for drug discovery
169
Global proteomics for pharmacodynamics 169
CellCarta® proteomics platform 170
ZeptoMARK™ protein profiling system 170
Role of proteomics in targeting disease pathways 171
Dynamic proteomics 171
Identification of protein kinases as drug targets 171
Mechanisms of action of kinase inhibitors 172
G-protein coupled receptors as drug targets 172
Methods of study of GPCRs 173
Cell-based assays for GPCR 173
Companies involved in GPCR-based drug discovery 174
GPCR localization database 175
Matrix metalloproteases as drug targets 175
PDZ proteins as drug targets 176
Proteasome as drug target 176
Serine hydrolases as drug targets 177
Targeting mTOR signaling pathway 177
Targeting caspase-8 for anticancer therapeutics 178
Bioinformatic analysis of proteomics data for drug discovery 179
Drug design based on structural proteomics 179
Protein crystallography for determining 3D structure of proteins 179
Automated 3D protein modeling 180
Drug targeting of flexible dynamic proteins 180
Companies involved in structure-based drug-design 180
Integration of genomics and proteomics for drug discovery 181
Ligand-receptor binding 182
Role of proteomics in study of ligand-receptor binding 182
Aptamer protein binding 183
Systematic Evolution of Ligands by Exponential Enrichment 183
Aptamers and high-throughput screening 183
Nucleic Acid Biotools 184
Aptamer beacons 184
Peptide aptamers 185
Riboreporters for drug discovery 185
Target identification and validation 185
Application of mass spectrometry for target identification 186
Gene knockout and gene suppression for validating protein targets 186
Laser-mediated protein knockout for target validation 186
Integrated proteomics for drug discovery 187
High-throughput proteomics 187
Companies involved in high-throughput proteomics 188
Drug discovery through protein-protein interaction studies 188
Protein-protein interaction as basis for drug target identification
189
Protein-PCNA interaction as basis for drug design 189
Two-hybrid protein interaction technology for target identification
190
Biosensors for detection of small molecule-protein interactions 190
Protein-protein interaction maps 191
ProNet (Myriad Genetics) 191
Hybrigenics' maps of protein-protein interactions 191
CellZome's functional map of protein-protein interactions 192
Mapping of protein-protein interactions by mass spectrometry 192
Protein interaction map of Drosophila melanogaster 193
Protein-interaction map of Wellcome Trust Sanger Institute 193
Protein-protein interactions as targets for therapeutic intervention
193
Inhibition of protein-protein interactions by peptide aptamers 194
Selective disruption of proteins by small molecules 194
Post-genomic combinatorial biology approach 194
Differential proteomics 195
Shotgun proteomics 195
Chemogenomics/chemoproteomics for drug discovery 196
Chemoproteomics-based drug discovery 197
Companies involved in chemogenomics/chemoproteomics 198
Activity-based proteomics 199
Locus Discovery technology 199
Automated ligand identification system 200
Expression proteomics: protein level quantification 200
Role of phage antibody libraries in target discovery 201
Analysis of posttranslational modification of proteins by MS 201
Phosphoproteomics for drug discovery 202
Application of glycoproteomics for drug discovery 202
Role of carbohydrates in proteomics 202
Challenges of glycoproteomics 203
Companies involved in glycoproteomics 203
Role of protein microarrays/ biochips for drug discovery 204
Protein microarrays vs DNA microarrays for high-throughput screening
204
BIA-MS biochip for protein-protein interactions 204
ProteinChip with Surface Enhanced Neat Desorption 205
Protein-domains microarrays 205
Some limitations of protein biochips 205
Concluding remarks about role of proteomics in drug discovery 206
RNA versus protein profiling as guide to drug development 206
RNA as drug target 206
Combination of RNA and protein profiling 207
RNA binding proteins 208
Toxicoproteomics 208
Hepatotoxicity 208
Nephrotoxicity 209
Cardiotoxicity 209
Neurotoxicity 210
Protein/peptide therapeutics 210
Alphabody technology for improving protein therapeutics 210
Peptide-based drugs 210
Phylomer® peptides 211
Cryptein-based therapeutics 211
Synthetic proteins and peptides as pharmaceuticals 212
Genetic immunization and proteomics 212
Proteomics and gene therapy 213
Role of proteomics in clinical drug development 213
Pharmacoproteomics 214
Role of proteomics in clinical drug safety 214
7. Application of Proteomics in Human Healthcare 215
Introduction 215
Clinical proteomics 216
Definition and standards 216
Vermillion's Clinical Proteomics Program 216
Pathophysiology of human diseases 217
Diseases due to misfolding of proteins 217
Mechanism of protein folding 218
Nanoproteomics for study of misfolded proteins 219
Therapies for protein misfolding 219
Intermediate filament proteins 220
Significance of mitochondrial proteome in human disease 221
Proteome of Saccharomyces cerevisiae mitochondria 221
Rat mitochondrial proteome 221
Proteomic approaches to biomarker identification 222
The ideal biomarker 222
Proteomic technologies for biomarker discovery 222
MALDI mass spectrometry for biomarker discovery 223
BAMF™ Technology 223
Protein biochips/microarrays and biomarkers 224
Affinity proteomics for discovery of biomarkers 224
Antibody array-based biomarker discovery 224
Discovery of biomarkers by MAb microarray profiling 225
Tumor-specific serum peptidome patterns 225
Search for protein biomarkers in body fluids 226
Challenges and strategies for discovey of protein biomarkers in plasma
226
3-D structure of CD38 as a biomarker 227
BD™ Free Flow Electrophoresis System 227
Isotope tags for relative and absolute quantification 227
N-terminal peptide isolation from human plasma 228
Plasma protein microparticles as biomarkers 228
Proteome partitioning 229
SISCAPA method for quantitating proteins and peptides in plasma 229
Stable isotope tagging methods 229
Technology to measure both the identity and size of the biomarker 230
Biomarkers in the urinary proteome 230
Application of proteomics in molecular diagnosis 231
Proximity ligation assay 232
Protein patterns 232
Proteomic tests on body fluids 232
Cyclical amplification of proteins 234
Applications of proteomics in infections 234
MALDI-TOF MS for microbial identification 234
Role of proteomics in virology 235
Study of interaction of proteins with viruses 235
Role of proteomics in bacteriology 236
Epidemiology of bacterial infections 236
Proteomic approach to bacterial pathogenesis 236
Vaccines for bacterial infections 236
Protein profiles associated with bacterial drug resistance 237
Analyses of the parasite proteome 237
Application of proteomics in cystic fibrosis 238
Proteomics of cardiovascular diseases 238
Pathomechanism of cardiovascular diseases 238
Protein misfolding in cardiac dysfunction 239
Study of cardiac mitochondrial proteome in myocardial ischemia 239
Cardiac protein databases 239
Proteomics of dilated cardiomyopathy and heart failure 240
Proteomic biomarkers of cardiovascular diseases 240
Role of proteomics in cardioprotection 241
Role of proteomics in heart transplantation 241
Future of application of proteomics in cardiology 241
Proteomic technologies for research in pulmonary disorders 242
Application of proteomics in renal disorders 243
Diagnosis of renal disorders 243
Proteomic biomarkers of acute kidney injury 243
Cystatin C as biomarker of glomerular filtration rate 244
Protein biomarkers of nephritis 244
Proteomics and kidney stones 244
Proteomics of eye disorders 244
Proteomics of cataract 245
Proteomics of diabetic retinopathy 246
Retinal dystrophies 246
Use of proteomics in inner ear disorders 246
Use of proteomics in aging research 246
Removal of altered cellular proteins in aging 247
Alteration of glycoproteins during aging 248
Proteomics and nutrition 248
8. Oncoproteomics 249
Introduction 249
Proteomic technologies for study of cancer 250
Application of CellCarta technology for oncology 250
Accentuation of differentially expressed proteins using phage technology
250
Cancer tissue proteomics 250
Dynamic cell proteomics in response to a drug 251
Desorption electrospray ionization for cancer diagnosis 251
Id proteins as targets for cancer therapy 252
Identification of oncogenic tyrosine kinases using phosphoproteomics
252
Laser capture microdissection technology and cancer proteomics 252
Mass spectrometry for identification of oncogenic chimeric proteins
253
Proteomic analysis of cancer cell mitochondria 253
Proteomic study of p53 254
Human Tumor Gene Index 254
Integration of cancer genomics and proteomics 254
Role of proteomics in study of cancer stem cell biology 255
Single-cell protein expression analysis by microfluidic techniques 255
Use of proteomics in cancers of various organ systems 255
Proteomics of brain tumors 255
Malignant glial tumors 255
Meningiomas 256
DESI-MS for intraoperative diagnosis of brain tumors 256
Proteomics of breast cancer 257
Integration of proteomic and genomic data for breast cancer 258
Proteomics of colorectal cancer 259
Proteomics of esophageal cancer 259
Proteomics of hepatic cancer 260
Proteomics of leukemia 260
Proteomics of lung cancer 261
Proteomics of pancreatic cancer 261
Proteomics of prostate cancer 262
Diagnostic use of cancer biomarkers 262
Proteomic technologies for tumor biomarkers 263
Nuclear matrix proteins (NMPs) 263
Antiannexins as tumor markers in lung cancer 264
NCI's Network of Clinical Proteomic Technology Centers 264
Proteomics and tumor immunology 265
Proteomics and study of tumor invasiveness 266
Anticancer drug discovery and development 266
Kinase-targeted drug discovery in oncology 266
Anticancer drug targeting: functional proteomics screen of proteases
267
Small molecule inhibitors of cancer-related proteins 267
Role of proteomics in studying drug resistance in cancer 268
Future prospects of oncoproteomics 268
Companies involved in application of proteomics to oncology 268
9. Neuroproteomics 271
Introduction 271
Application of proteomics for the study of nervous system 271
Proteomics of prion diseases 272
Normal function of prions in the brain 272
Diseases due to pathological prion protein 272
Transmissible spongiform encephalopathies 273
Creutzfeld-Jakob disease 273
Bovine spongiform encephalopathy 273
Variant Creutzfeldt-Jakob disease 274
Protein misfolding and neurodegenerative disorders 274
Ion channel link for protein-misfolding disease 274
Detection of misfolded proteins 274
Neurodegenerative disorders with protein abnormalities 275
Alzheimer disease 277
Common denominators of Alzheimer and prion diseases 277
Parkinson disease 278
Amyotrophic lateral sclerosis 278
Proteomics and glutamate repeat disorders 279
Proteomics and Huntington's disease 279
Proteomics and demyelinating diseases 280
Proteomics of neurogenetic disorders 280
Fabry disease 280
GM1 gangliosidosis 281
Quantitative proteomics and familial hemiplegic migraine 281
Proteomics of spinal muscular atrophy 282
Proteomics of CNS trauma 282
Proteomics of traumatic brain injury 282
Chronic traumatic encephalopathy and ALS 283
Proteomics of CNS aging 283
Protein aggregation as a bimarker of aging 283
Neuroproteomics of psychiatric disorders 284
Neuroproteomic of cocaine addiction 285
Neurodiagnostics based on proteomics 285
Disease-specific proteins in the cerebrospinal fluid 285
Tau proteins 286
CNS tissue proteomics 287
Diagnosis of CNS disorders by examination of proteins in urine 288
Diagnosis of CNS disorders by examination of proteins in the blood 288
Serum pNF-H as biomarker of CNS damage 289
Proteomics of BBB 289
Future prospects of neuroproteomics in neurology 290
HUPO's Pilot Brain Proteome Project 291
10. Proteomics Markets 293
Introduction 293
Potential markets for proteomic technologies 293
Bioinformatics markets for proteomics 294
Markets for protein separation technologies 294
Markets for 2D gel electrophoresis 294
Market trends in protein separation technolgies 295
Protein purification markets 295
Mass spectrometry markets 295
Markets for MALDI for drug discovery 296
Markets for nuclear magnetic resonance spectroscopy 296
Market for structure-based drug design 296
Markets for protein biomarkers 297
Markets for cell-based protein assays 297
Protein biochip markets 297
Western blot markets 297
Geographical distribution of proteomics technologies markets 298
Business and strategic considerations 298
Cost of protein structure determination 298
Opinion surveys of the scientist consumers of proteomic technologies
298
Opinions on mass spectrometry 298
Opinions on bioinformatics and proteomic databases 299
Systems for in vivo study of protein-protein interactions 299
Perceptions of the value of protein biochip/microfluidic systems 299
Small versus big companies 299
Expansion in proteomics according to area of application 300
Growth trends in cell-based protein assay market 300
Challenges for development of cell-based protein assays 300
Future trends and prospects of cell-based protein assays 301
Strategic collaborations 301
Analysis of proteomics collaborations according to types of companies
301
Types of proteomic collaborations 302
Proteomics collaborations according to application areas 302
Analysis of proteomics collaborations: types of technologies 303
Collaborations based on protein biochip technology 303
Concluding remarks about proteomic collaborations 304
Proteomic patents 304
Market drivers in proteomics 305
Needs of the pharmaceutical industry 305
Need for outsourcing proteomic technologies 305
Funding of proteomic companies and research 305
Technical advances in proteomics 306
Changing trends in healthcare in future 306
Challenges facing proteomics 306
Magnitude and complexity of the task 306
Technical challenges 307
Limitations of proteomics 307
Limitations of 2DGE 307
Limitations of mass spectrometry techniques 307
Complexity of the pharmaceutical proteomics 308
Unmet needs in proteomics 308
11. Future of Proteomics 311
Genomics to proteomics 311
Faster technologies 311
FLEXGene repository 311
Need for new proteomic technologies 312
Emerging proteomic technologies 313
Detection of alternative protein isoforms 313
Direct protein identification in large genomes by mass spectrometry
313
Proteome identification kits with stacked membranes 313
Vacuum deposition interface 314
In vitro protein biosynthesis 314
Proteome mining with adenosine triphosphate 314
Proteome-scale purification of human proteins from bacteria 314
Proteostasis network 315
Cytoproteomics 315
Subcellular proteomics 315
Individual cell proteomics 316
Live cell proteomics 316
Fluorescent proteins for live-cell imaging 317
Membrane proteomics 317
Identification of membrane proteins by tandem MS of protein ions 317
Solid state NMR for study of nanocrystalline membrane proteins 318
Multiplex proteomics 318
High-throughput for proteomics 318
Future directions for protein biochip application 319
Bioinformatics for proteomics 319
High-Throughput Crystallography Consortium 319
Study of protein folding by IBM's Blue Gene 320
Study of proteins by atomic force microscopy 320
Population proteomics 320
Comparative proteome analysis 321
Human Proteome Organization 321
Cell-based Human Proteome Project 322
Human Salivary Proteome 322
Academic-commercial collaborations in proteomics 323
Indiana Centers for Applied Protein Sciences 323
Role of proteomics in the healthcare of the future 323
Proteomics and molecular medicine 323
Proteodiagnostics 324
Proteomics and personalized medicine 324
Targeting the ubiquitin pathway for personalized therapy of cancer 325
Protein patterns and personalized medicine 325
Personalizing interferon therapy of hepatitis C virus 327
Protein biochips and personalized medicine 327
Combination of diagnostics and therapeutics 328
Future prospects 328
12. References 329
Tables
Table 1-1: Landmarks in the evolution of proteomics 19
Table 1-2: Comparison of DNA and protein 28
Table 1-3: Comparison of mRNA and protein 28
Table 1-4: Methods of analysis at various levels of functional genomics
34
Table 2-1: Proteomics technologies 39
Table 2-2: Protein separation technologies of selected companies 44
Table 2-3: Companies supplying mass spectrometry instruments 47
Table 2-4: Companies involved in cell-based protein assays 72
Table 2-5: Methods used for the study of protein-protein interactions
73
Table 2-6: A selection of companies involved in protein-protein
interaction studies 80
Table 2-7: Companies involved in Western blotting 96
Table 2-8: Proteomic technologies used with laser capture microdissection
98
Table 3-1: Applications of protein biochip technology 101
Table 3-2: Selected companies involved in protein biochip/microarray
technology 117
Table 4-1: Proteomic databases and other Internet sources of proteomics
information 125
Table 4-2: Protein interaction databases available on the Internet
130
Table 4-3: Bioinformatic tools for proteomics from academic sources
136
Table 4-4: Selected companies involved in bioinformatics for proteomics
137
Table 5-1: Applications of proteomics in basic biological research
139
Table 5-2: A sampling of proteomics research projects in academic
institutions 155
Table 6-1: Pharmaceutical applications of proteomics 159
Table 6-2: Selected companies relevant to MALDI-MS for drug discovery
167
Table 6-3: Selected companies involved in GPCR-based drug discovery
174
Table 6-4: Companies involved in drug design based on structural
proteomics 181
Table 6-5: Proteomic companies with high-throughput protein expression
technologies 188
Table 6-6: Selected companies involved in chemogenomics/chemoproteomics
198
Table 6-7: Companies involved in glycoproteomic technologies 203
Table 7-1: Applications of proteomics in human healthcare 215
Table 7-2: Eye disorders and proteomic approaches 245
Table 8-1: Companies involved in applications of proteomics to oncology
269
Table 9-1: Neurodegenerative diseases with underlying protein abnormality
275
Table 9-2: Disease-specific proteins in the cerebrospinal fluid of
patients 285
Table 10-1: Potential markets for proteomic technologies 2012-2022
293
Table 10-2: 2012 revenues of major companies from protein separation
technologies 294
Table 10-3: Geographical distribution of markets for proteomic
technologies 2012-2022 298
Table 11-1: Role of proteomics in personalizing strategies for cancer
therapy 325
Figures
Figure 1-1: A schematic miRNA pathway 22
Figure 1-2: Relationship of DNA, RNA and protein in the cell 29
Figure 1-3: Protein production pathway from gene expression to functional
protein with controls. 31
Figure 1-4: Parallels between functional genomics and proteomics 32
Figure 2-1: Proteomics: flow from sample preparation to characterization
40
Figure 2-2: The central role of spectrometry in proteomics 47
