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Reportlinker Adds Proteomics - Technologies, Markets and Companies

NEW YORK, Sept. 7 /PRNewswire/ -- announces that a new market research report is available in its catalogue:

Proteomics - Technologies, Markets and Companies

SummaryThis 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 preclinical drug safety. Use of bioinformatics is essential for analyzing the massive amount of data generated from both genomics and proteomics.

Proteomics is providing a better understanding of pathomechanisms of human diseases. Analysis of different levels of gene expression in healthy and diseased tissues by proteomic approaches is as important as the detection of mutations and polymorphisms at the genomic level and may be of more value in designing a rational therapy. Protein distribution / characterization in body tissues and fluids, in health as well as in disease, is the basis of the use of proteomic technologies for molecular diagnostics. Proteomics will play an important role in medicine of the future which will be personalized and will combine diagnostics with therapeutics. The text is supplemented with 43 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 217 of these are profiled in the report with 471 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 2009 and are projected to years 2014 and 2019. The largest expansion will be in bioinformatics and protein biochip technologies. Important areas of application are cancer and neurological disorders

TABLE OF CONTENTS0.Executive Summary15

1.Basics of Proteomics17



Nucleic acids, genes and proteins18





Decoding of mRNA by the ribosome20


Alternative splicing21


Gene regulation22

Gene expression23




Functions of proteins24

Inter-relationship of protein, mRNA and DNA25


Mitochondrial proteome27

S-nitrosoproteins in mitochondria27

Proteomics and genomics28

Classification of proteomics30

Levels of functional genomics and various "omics"30






Proteomics and systems biology32

2.Proteomic Technologies35

Key technologies driving proteomics35

Sample preparation36

New trends in sample preparation36

Pressure Cycling Technology37

Protein separation technologies37

High resolution 2D gel electrophoresis37

Variations of 2D gel technology38

Limitations of 2DGE and measures to overcome these38

1-D sodium dodecyl sulfate (SDS) PAGE38

Capillary electrophoresis systems39

Head column stacking capillary zone electrophoresis39

Removal of albumin and IgG39

Companies with protein separation technologies40

Protein detection41

Protein identification and characterization41

Mass spectrometry (MS)41

Companies involved in mass spectrometry42

Electrospray ionization43

Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry44

Cryogenic MALDI- Fourier Transform Mass Spectrometry45

Stable-isotope-dilution tandem mass spectrometry46

HUPO Gold MS Protein Standard46

High performance liquid chromatography46

Multidimensional protein identification technology (MudPIT)46

Peptide mass fingerprinting47

Combination of protein separation technologies with mass spectrometry47

Combining capillary electrophoresis with mass spectrometry47

2D PAGE and mass spectrometry47

Quantification of low abundance proteins48


Antibodies and proteomics49

Detection of fusion proteins49

Labeling and detection of proteins49

Fluorescent labeling of proteins in living cells50

Combination of microspheres with fluorescence50

Self-labeling protein tags50

Analysis of peptides51

C-terminal peptide analysis51

Differential Peptide Display52

Peptide analyses using NanoLC-MS52

Protein sequencing53

Real-time PCR for protein quantification54

Quantitative proteomics54

MS-based quantitative proteomics54

MS and cryo-electron tomography54

Functional proteomics: technologies for studying protein function55

Functional genomics by mass spectrometry55

RNA-Protein fusions55

Designed repeat proteins55

Application of nanbiotechnology to proteomics56


Protein nanocrystallography56

Single-molecule mass spectrometry using a nanopore57

Nanoelectrospray ionization57

Nanoparticle barcodes58

Biobarcode assay for proteins58

Nanobiotechnology for discovery of protein biomarkers in the blood59

Nanoscale protein analysis59

Nanoscale mechanism for protein engineering60

Nanotube electronic biosensor60

Nanotube-vesicle networks for study of membrane proteins61

Nanowire transistor for the detection of protein-protein interactions61


Resonance Light Scattering technology62

Study of single membrane proteins at subnanometer resolution62

Protein expression profiling62

Cell-based protein assays63

Living cell-based assays for protein function64

Companies developing cell-based protein assays64

Protein function studies65

Transcriptionally Active PCR65

Protein-protein interactions65

Yeast two-hybrid system67

Membrane one-hybrid method68

Protein affinity chromatography68

Phage display68

Fluorescence Resonance Energy Transfer69

Bioluminescence Resonance Energy Transfer69

Detection Enhanced Ubiquitin Split Protein Sensor technology69

Protein-fragment complementation system69

In vivo study of protein-protein interactions70

Computational prediction of interactions70


Protein-protein interactions and drug discovery72

Companies with technologies for protein-protein interaction studies72

Protein-DNA interaction73

Determination of protein structure73

X-Ray crystallography74

Nuclear magnetic resonance75

Electron spin resonance75

Prediction of protein structure75

Protein tomography76

X-ray scattering-based method for determining the structure of proteins77

Prediction of protein function77

Three-dimensional proteomics for determination of function77

An algorithm for genome-wide prediction of protein function78

Monitoring protein function by expression profiling78

Isotope-coded affinity tag peptide labeling78

Differential Proteomic Panning79

Cell map proteomics79

Topological proteomics80

Organelle or subcellular proteomics81

Nucleolar proteomics81

Glycoproteomic technologies81

High-sensitivity glycoprotein analysis82

Fluorescent in vivo imaging of glycoproteins82

Integrated approaches for protein characterization82

Imaging mass spectrometry83

IMS technologies83

Applications of IMS83

The protein microscope84

Automation and robotics in proteomics84

Laser capture microdissection85

Microdissection techniques used for proteomics85

Uses of LCM in combination with proteomic technologies85

Concluding remarks about applications of proteomic technologies86

Precision proteomics86

3.Protein biochip technology89


Types of protein biochips90


Applications and advantages of ProteinChip91

ProteinChip Biomarker System91

Matrix-free ProteinChip Array92

Aptamer-based protein biochip92

Fluorescence planar wave guide technology-based protein biochips93

Lab-on-a-chip for protein analysis93

Microfluidic biochips for proteomics94

Protein biochips for high-throughput expression95

Nucleic Acid-Programmable Protein Array95

High-density protein microarrays95

HPLC-Chip for protein identification95

Antibody microarrays96

Integration of protein array and image analysis96

Tissue microarray technology for proteomics96

Protein biochips in molecular diagnostics97

A force-based protein biochip98

L1 chip and lipid immobilization98

Multiplexed Protein Profiling on Microarrays98

Live cell microarrays99

ProteinArray Workstation99

Proteome arrays100

The Yeast ProtoArray100

ProtoArray Human Protein Microarray100

TRINECTIN proteome chip101

Peptide arrays101

Surface plasmon resonance technology102

Biacore's SPR102


Combination of surface plasmon resonance and MALDI-TOF103

Protein chips/microarrays using nanotechnology103

Nanoparticle protein chip103

Protein nanobiochip103

Protein nanoarrays104

Self-assembling protein nanoarrays104

Companies involved in protein biochip/microarray technology105

4.Bioinformatics in Relation to Proteomics109


Bioinformatic tools for proteomics109

Testing of SELDI-TOF MS Proteomic Data109

BioImagine's ProteinMine110

Bioinformatics for pharmaceutical applications of proteomics110

In silico search of drug targets by Biopendium110

Compugen's LEADS111


Proteochemometric modeling111

Integration of genomic and proteomic data112

Proteomic databases: creation and analysis113


Proteomic databases113


Human Protein Atlas114

Human Proteomics Initiative115

International Protein Index115

Proteome maps116

Protein Structure Initiative ? Structural Genomics Knowledgebase116

Protein Warehouse Database116

Protein Data Bank116

Universal Protein Resource117

Protein interaction databases117

Biomolecular Interaction Network Database118


Functional Genomics Consortium119

Human Proteinpedia119


Databases of the National Center for Biotechnology Information120

Bioinformatics for protein identification120

Application of bioinformatics in functional proteomics120

Use of bioinformatics in protein sequencing120

Bottom-up protein sequencing121

Top-down protein sequencing122

Protein structural database approach to drug design122

Bioinformatics for high-throughput proteomics122

Companies with bioinformatic tools for proteomics123

5.Research in Proteomics125


Applications of proteomics in biological research125

Identification of novel human genes by comparative proteomics125

Study of relationship between genes and proteins126

Characterization of histone codes126

Structural genomics or structural proteomics127

Protein Structure Factory128

Protein Structure Initiative128

Studies on protein structure at Argonne National Laboratory129

Structural Genomics Consortium129

Protein knockout130

Antisense approach and proteomics130

RNAi and protein knockout130

Total knockout of cellular proteins130

Ribozymes and proteomics131

Single molecule proteomics131

Single-molecule photon stamping spectroscopy131

Single nucleotide polymorphism determination by TOF-MS132

Application of proteomic technologies in systems biology132

Signaling pathways and proteomics132


Combinatorial RNAi for quantitative protein network analysis133

Proteomics in neuroscience research133

Stem cell proteomics134

hESC phosphoproteome134

Proteomic studies of mesenchymal stem cells135

Proteomics of neural stem cells135

Proteome Biology of Stem Cells Initiative136

Proteomic analysis of the cell cycle137

Nitric oxide and proteomics137

A proteomic method for identification of cysteine S-nitrosylation sites137

Study of the nitroproteome137

Study of the phosphoproteome138

Study of the mitochondrial proteome138

Proteomic technologies for study of mitochondrial proteomics139


Study of protein transport in health and disease139

Proteomics research in the academic sector140

Vanderbilt University's Center for Proteomics and Drug Actions142

ProteomeBinders initiative142

6.Pharmaceutical Applications of Proteomics143


Current drug discovery process and its limitations143

Role of omics in drug discovery144

Genomics-based drug discovery144

Metabolomics technologies for drug discovery145

Role of metabonomics in drug discovery145

Basis of proteomics approach to drug discovery146

Proteins and drug action146

Transcription-aided drug design147

Role of proteomic technologies in drug discovery147

Liquid chromatography-based drug discovery148

Capture compound mass spectrometry149

Protein-expression mapping by 2DGE149

Role of MALDI mass spectrometry in drug discovery149

Tissue imaging mass spectrometry149

Companies using MALDI for drug discovery151

Oxford Genome Anatomy Project151

Proteins as drug targets152

Ligands to capture the purine binding proteome152

Chemical probes to interrogate key protein families for drug discovery152

Global proteomics for pharmacodynamics153

CellCarta® proteomics platform153

ZeptoMARK protein profiling system154

Role of proteomics in targeting disease pathways154

Identification of protein kinases as drug targets154

Mechanisms of action of kinase inhibitors155

G-protein coupled receptors as drug targets155

Methods of study of GPCRs156

Cell-based assays for GPCR156

Companies involved in GPCR-based drug discovery157

GPCR localization database158

Matrix metalloproteases as drug targets158

PDZ proteins as drug targets159

Proteasome as drug target159

Serine hydrolases as drug targets160

Targeting mTOR signaling pathway160

Targeting caspase-8 for anticancer therapeutics161

Bioinformatic analysis of proteomics data for drug discovery162

Drug design based on structural proteomics162

Protein crystallography for determining 3D structure of proteins162

Automated 3D protein modeling163

Drug targeting of flexible dynamic proteins163

Companies involved in structure-based drug-design163

Integration of genomics and proteomics for drug discovery164

Ligand-receptor binding165

Role of proteomics in study of ligand-receptor binding165

Aptamer protein binding166

Systematic Evolution of Ligands by Exponential Enrichment166

Aptamers and high-throughput screening166

Nucleic Acid Biotools167

Aptamer beacons167

Peptide aptamers168

Riboreporters for drug discovery168

Target identification and validation168

Application of mass spectrometry for target identification169

Gene knockout and gene suppression for validating protein targets169

Laser-mediated protein knockout for target validation169

Integrated proteomics for drug discovery170

High-throughput proteomics170

Companies involved in high-throughput proteomics171

Drug discovery through protein-protein interaction studies171

Protein-protein interaction as basis for drug target identification172

Protein-PCNA interaction as basis for drug design172

Two-hybrid protein interaction technology for target identification173

Biosensors for detection of small molecule-protein interactions173

Protein-protein interaction maps174

ProNet (Myriad Genetics)174

Hybrigenics' maps of protein-protein interactions174

CellZome's functional map of protein-protein interactions175

Mapping of protein-protein interactions by mass spectrometry175

Protein interaction map of Drosophila melanogaster176

Protein-interaction map of Wellcome Trust Sanger Institute176

Protein-protein interactions as targets for therapeutic intervention176

Inhibition of protein-protein interactions by peptide aptamers177

Selective disruption of proteins by small molecules177

Post-genomic combinatorial biology approach177

Differential proteomics178

Shotgun proteomics178

Chemogenomics/chemoproteomics for drug discovery179

Chemoproteomics-based drug discovery180

Companies involved in chemogenomics/chemoproteomics181

Activity-based proteomics182

Locus Discovery technology182

Automated ligand identification system183

Expression proteomics: protein level quantification183

Role of phage antibody libraries in target discovery184

Analysis of posttranslational modification of proteins by MS184

Phosphoproteomics for drug discovery185

Application of glycoproteomics for drug discovery185

Role of carbohydrates in proteomics185

Challenges of glycoproteomics186

Companies involved in glycoproteomics186

Role of protein microarrays/ biochips for drug discovery187

Protein microarrays vs DNA microarrays for high-throughput screening187

BIA-MS biochip for protein-protein interactions187

ProteinChip with Surface Enhanced Neat Desorption188

Protein-domains microarrays188

Some limitations of protein biochips188

Concluding remarks about role of proteomics in drug discovery189

RNA versus protein profiling as guide to drug development189

RNA as drug target189

Combination of RNA and protein profiling190

RNA binding proteins191






Protein/peptide therapeutics193

Peptide-based drugs193

Phylomer® peptides194

Cryptein-based therapeutics194

Synthetic proteins and peptides as pharmaceuticals195

Genetic immunization and proteomics195

Proteomics and gene therapy196

Role of proteomics in clinical drug development196


Role of proteomics in clinical drug safety197

7.Application of Proteomics in Human Healthcare199

Clinical proteomics200

Definition and standards200

Vermillion's Clinical Proteomics Program200

Pathophysiology of human diseases201

Diseases due to misfolding of proteins201

Mechanism of protein folding202

Nanoproteomics for study of misfolded proteins203

Therapies for protein misfolding203

Intermediate filament proteins204

Significance of mitochondrial proteome in human disease205

Proteome of Saccharomyces cerevisiae mitochondria205

Rat mitochondrial proteome205

Proteomic approaches to biomarker identification206

The ideal biomarker206

Proteomic technologies for biomarker discovery206

MALDI mass spectrometry for biomarker discovery207

BAMF Technology207

Protein biochips/microarrays and biomarkers208

Antibody-based biomarker discovery208

Tumor-specific serum peptidome patterns208

Search for protein biomarkers in body fluids209

Challenges and strategies for discovey of protein biomarkers in plasma209

3-D structure of CD38 as a biomarker210

BD™ Free Flow Electrophoresis System210

Isotope tags for relative and absolute quantification211

N-terminal peptide isolation from human plasma211

Plasma protein microparticles as biomarkers211

Proteome partitioning212

SISCAPA method for quantitating proteins and peptides in plasma212

Stable isotope tagging methods212

Technology to measure both the identity and size of the biomarker213

Biomarkers in the urinary proteome213

Application of proteomics in molecular diagnosis214

Proximity ligation assay215

Protein patterns215

Proteomic tests on body fluids215

Cyclical amplification of proteins217

Applications of proteomics in infections217

Role of proteomics in virology217

Study of interaction of proteins with viruses218

Role of proteomics in bacteriology218

Epidemiology of bacterial infections218

Proteomic approach to bacterial pathogenesis219

Vaccines for bacterial infections219

Protein profiles associated with bacterial drug resistance220

Analyses of the parasite proteome220

Application of proteomics in cystic fibrosis220


Application of CellCarta technology for oncology223

Accentuation of differentially expressed proteins using phage technology223

Identification of oncogenic tyrosine kinases using phosphoproteomics223

Single-cell protein expression analysis by microfluidic techniques224

Dynamic cell proteomics in response to a drug224

Desorption electrospray ionization for cancer diagnosis224

Proteomic analysis of cancer cell mitochondria224

Mass spectrometry for identification of oncogenic chimeric proteins225

Id proteins as targets for cancer therapy225

Proteomic study of p53226

Human Tumor Gene Index226

Integration of cancer genomics and proteomics226

Laser capture microdissection technology and cancer proteomics227

Cancer tissue proteomics227

Use of proteomics in cancers of various organ systems228

Proteomics of brain tumors228

Proteomics of breast cancer229

Proteomics of colorectal cancer230

Proteomics of esophageal cancer230

Proteomics of hepatic cancer231

Proteomics of leukemia231

Proteomics of lung cancer232

Proteomics of pancreatic cancer232

Proteomics of prostate cancer233

Diagnostic use of cancer biomarkers233

NCI's Network of Clinical Proteomic Technology Centers for Cancer Research235

Proteomics and tumor immunology236

Proteomics and study of tumor invasiveness237

Anticancer drug discovery and development237

Kinase-targeted drug discovery in oncology237

Anticancer drug targeting: functional proteomics screen of proteases238

Small molecule inhibitors of cancer-related proteins238

Role of proteomics in studying drug resistance in cancer239

Future prospects of oncoproteomics239

Companies involved in application of proteomics to oncology239

Application of proteomics in neurological disorders240


Proteomics of prion diseases241

Transmissible spongiform encephalopathies242

Protein misfolding and neurodegenerative disorders243

Ion channel link for protein-misfolding disease243

Detection of misfolded proteins243

Neurodegenerative disorders with protein abnormalities243

Alzheimer disease245

Common denominators of Alzheimer and prion diseases246

Parkinson disease246

Amyotrophic lateral sclerosis247

Proteomics and glutamate repeat disorders247

Proteomics and Huntington's disease248

Proteomics and demyelinating diseases248

Proteomics of neurogenetic disorders249

Fabry disease249

GM1 gangliosidosis249

Quantitative proteomics and familial hemiplegic migraine250

Spinal muscular atrophy250

Proteomics of CNS trauma250

Proteomics of traumatic brain injury250

Chronic traumatic encephalopathy and ALS251

Proteomics of CNS aging252

Protein aggregation as a bimarker of aging252

Neuroproteomics of psychiatric disorders252

Neuroproteomic of cocaine addiction253

Neurodiagnostics based on proteomics253

Disease-specific proteins in the cerebrospinal fluid253

Tau proteins254

CNS tissue proteomics255

Diagnosis of CNS disorders by examination of proteins in urine256

Diagnosis of CNS disorders by examination of proteins in the blood257

Serum pNF-H as biomarker of CNS damage258

Proteomics of BBB258

Future prospects of neuroproteomics in neurology258

HUPO's Pilot Brain Proteome Project260

Proteomics of cardiac disorders260

Study of cardiac mitochondrial proteome in myocardial ischemia261

Cardiac protein databases261

Proteomics of dilated cardiomyopathy and heart failure261

Role of proteomics in heart transplantation262

Future of application of proteomics in cardiology262

Proteomic technologies for research in pulmonary disorders262

Application for proteomics in renal disorders264

Diagnosis of renal disorders264

Proteomic biomarkers of acute kidney injury264

Cystatin C as biomarker of glomerular filtration rate264

Protein biomarkers of nephritis265

Proteomics and kidney stones265

Proteomics of eye disorders265

Retinal dystrophies266

Use of proteomics in inner ear disorders266

Use of proteomics in aging research266

Removal of altered cellular proteins in aging267

Proteomics and nutrition268

8.Commercial Aspects of Proteomics269


Potential markets for proteomic technologies269

Geographical distribution of proteomics technologies markets270

Markets for protein separation technologies270

Markets for 2D gel electrophoresis271

Trends in protein separation technologies and effect on market271

Protein biochip markets271

Mass spectrometry markets272

Markets for MALDI for drug discovery272

Markets for nuclear magnetic resonance spectroscopy272

Market for structure-based drug design273

Bioinformatics markets for proteomics273

Markets for protein biomarkers273

Markets for cell-based protein assays273

Business and strategic considerations274

Cost of protein structure determination274

Opinion surveys of the scientist consumers of proteomic technologies274

Opinions on mass spectrometry274

Opinions on bioinformatics and proteomic databases274

Systems for in vivo study of protein-protein interactions275

Perceptions of the value of protein biochip/microfluidic systems275

Small versus big companies275

Expansion in proteomics according to area of application275

Growth trends in cell-based protein assay market276

Challenges for development of cell-based protein assays276

Future trends and prospects of cell-based protein assays276

Strategic collaborations277

Analysis of proteomics collaborations according to types of companies277

Types of proteomic collaborations278

Proteomics collaborations according to application areas278

Analysis of proteomics collaborations: types of technologies278

Collaborations based on protein biochip technology279

Concluding remarks about proteomic collaborations279

Proteomic patents280

Market drivers in proteomics280

Needs of the pharmaceutical industry280

Need for outsourcing proteomic technologies281

Funding of proteomic companies and research281

Technical advances in proteomics281

Changing trends in healthcare in future282

Challenges facing proteomics282

Magnitude and complexity of the task282

Technical challenges282

Limitations of proteomics283

Limitations of 2DGE283

Limitations of mass spectrometry techniques283

Complexity of the pharmaceutical proteomics283

Unmet needs in proteomics284

9.Future of Proteomics285

Genomics to proteomics285

Faster technologies285

FLEXGene repository285

Need for new proteomic technologies286

Emerging proteomic technologies287

Detection of alternative protein isoforms287

Direct protein identification in large genomes by mass spectrometry287

Proteome identification kits with stacked membranes287

Vacuum deposition interface288

In vitro protein biosynthesis288

Proteome mining with adenosine triphosphate288

Proteome-scale purification of human proteins from bacteria288

Proteostasis network289


Subcellular proteomics289

Individual cell proteomics290

Live cell proteomics290

Fluorescent proteins for live-cell imaging291

Membrane proteomics291

Identification of membrane proteins by tandem MS of protein ions291

Solid state NMR for study of nanocrystalline membrane proteins292

Multiplex proteomics292

High-throughput for proteomics292

Future directions for protein biochip application293

Bioinformatics for proteomics293

High-Throughput Crystallography Consortium293

Study of protein folding by IBM's Blue Gene294

Study of proteins by atomic force microscopy294

Population proteomics294

Comparative proteome analysis295

Human Proteome Organization295

Human Salivary Proteome296

Academic-commercial collaborations in proteomics296

Indiana Centers for Applied Protein Sciences296

Role of proteomics in the healthcare of the future297

Proteomics and molecular medicine297


Proteomics and personalized medicine298

Targeting the ubiquitin pathway for personalized therapy of cancer298

Protein patterns and personalized medicine298

Personalizing interferon therapy of hepatitis C virus300

Protein biochips and personalized medicine300

Combination of diagnostics and therapeutics301

Future prospects301


TablesTable 1 1: Landmarks in the evolution of proteomics17

Table 1 2: Comparison of DNA and protein25

Table 1 3: Comparison of mRNA and protein25

Table 1 4: Methods of analysis at various levels of functional genomics31

Table 2 1: Proteomics technologies35

Table 2 2: Protein separation technologies of selected companies40

Table 2 3: Companies supplying mass spectrometry instruments42

Table 2 4: Companies involved in cell-based protein assays64

Table 2 5: Methods used for the study of protein-protein interactions66

Table 2 6: A selection of companies involved in protein-protein interaction studies72

Table 2 7: Proteomic technologies used with laser capture microdissection85

Table 3 1: Applications of protein biochip technology89

Table 3 2: Selected companies involved in protein biochip/microarray technology105

Table 4 1: Proteomic databases and other Internet sources of proteomics information113

Table 4 2: Protein interaction databases available on the Internet117

Table 4 3: Bioinformatic tools for proteomics from academic sources123

Table 4 4: Selected companies involved in bioinformatics for proteomics124

Table 5 1: Applications of proteomics in basic biological research125

Table 5 2: A sampling of proteomics research projects in academic institutions140

Table 6 1: Pharmaceutical applications of proteomics143

Table 6 2: Selected companies relevant to MALDI-MS for drug discovery151

Table 6 3: Selected companies involved in GPCR-based drug discovery157

Table 6 4: Companies involved in drug design based on structural proteomics164

Table 6 5: Proteomic companies with high-throughput protein expression technologies171

Table 6 6: Selected companies involved in chemogenomics/chemoproteomics181

Table 6 7: Companies involved in glycoproteomic technologies186

Table 7 1: Applications of proteomics in human healthcare199

Table 7 2: Companies involved in applications of proteomics to oncology239

Table 7 3: Neurodegenerative diseases with underlying protein abnormality244

Table 7 4: Disease-specific proteins in the cerebrospinal fluid of patients253

Table 7 5: Eye disorders and proteomic approaches265

Table 8 1: Potential markets for proteomic technologies 2009-2019269

Table 8 2: Geographical distribution of markets for proteomic technologies 2009-2019270

Table 8 3: 2009 revenues of major companies from protein separation technologies270

Table 9 1: Role of proteomics in personalizing strategies for cancer therapy298

FiguresFigure 1 1: A schematic miRNA pathway20

Figure 1 2: Relationship of DNA, RNA and protein in the cell26

Figure 1 3: Protein production pathway from gene expression to functional protein with controls.28

Figure 1 4: Parallels between functional genomics and proteomics29

Figure 2 1: Proteomics: flow from sample preparation to characterization36

Figure 2 2: The central role of spectrometry in proteomics42

Figure 2 3: Electrospray ionization (ESI)43

Figure 2 4: Matrix-Assisted Laser Desorption/Ionization (MALDI)44

Figure 2 5: Scheme of bio-bar-code assay59

Figure 2 6: A diagrammatic presentation of yeast two-hybrid system67

Figure 3 1: ProteinChip System91

Figure 3 2: Surface plasma resonance (SPR)102

Figure 4 1: Role of bioinformatics in integrating genomic/proteomic-based drug discovery112

Figure 4 2: Bottom-up and top-down approaches for protein sequencing121

Figure 6 1: Drug discovery process144

Figure 6 2: Regulatory changes induced by drugs and implemented at the proteins level.147

Figure 6 3: Relation of proteome to genome, diseases and drugs148

Figure 6 4: The mTOR pathways161

Figure 6 5: Steps in shotgun proteomics179

Figure 6 6: Chemogenomic approach to drug discovery (3-Dimensional Pharmaceuticals)180

Figure 7 1: Relation of oncoproteomics to other technologies222

Figure 7 2: A scheme of proteomics applications in CNS drug discovery and development260

Figure 8 1: Types of companies involved in proteomics collaborations277

Figure 8 2: Types of collaborations: R & D, licensing or marketing278

Figure 8 3: Proteomics collaborations according to application areas278

Figure 8 4: Proteomics collaborations according to technologies279

Figure 8 5: Unmet needs in proteomics284

Figure 9 1: A scheme of the role of proteomics in personalized management of cancer300

To order this report:Drug Discovery and Development Industry: Proteomics - Technologies, Markets and Companies

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