Proteomics

Technologies, Markets and Companies

Publication Date	October 2009
Publisher	Jain PharmaBiotech
Product Type	Report
Pages	592
ISBN Number	not applicable
Product Code	JAI00039

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Summary

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.The text is supplemented with 42 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 216 of these are profiled in the report with 468 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 2008 and are projected to years 2013 and 2018. The largest expansion will be in bioinformatics and protein biochip technologies. Important areas of application are cancer and neurological disorders.

Content

0 Executive Summary
1 Basics of Proteomics
- Introduction
- History
- Nucleic acids, genes and proteins
  - Genome
  - DNA
  - RNA
    - MicroRNAs
    - Decoding of mRNA by the ribosome
  - Genes
  - Alternative splicing
  - Transcription
  - Gene regulation
  - Gene expression
  - Chromatin
  - Proteins
    - Spliceosome
    - Functions of proteins
    - Inter-relationship of protein, mRNA and DNA
- Proteomics
  - Mitochondrial proteome
    - S-nitrosoproteins in mitochondria
- Proteomics and genomics
  - Classification of proteomics
  - Levels of functional genomics and various "omics"
  - Glycoproteomics
  - Transcriptomics
  - Metabolomics
  - Cytomics
- Phenomics
- Proteomics and systems biology
2 Proteomic Technologies
- Key technologies driving proteomics
- Sample preparation
  - New trends in sample preparation
  - Pressure Cycling Technology
- Protein separation technologies
  - High resolution 2D gel electrophoresis
  - Variations of 2D gel technology
  - Limitations of 2DGE and measures to overcome these
  - 1-D sodium dodecyl sulfate (SDS) PAGE
  - Capillary electrophoresis systems
  - Head column stacking capillary zone electrophoresis
  - Removal of albumin and IgG
  - Companies with protein separation technologies
- Protein detection
- Protein identification and characterization
  - Mass spectrometry (MS)
    - Companies involved in mass spectrometry
    - Electrospray ionization
    - Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry
    - Cryogenic MALDI- Fourier Transform Mass Spectrometry
    - Stable-isotope-dilution tandem mass spectrometry
    - HUPO Gold MS Protein Standard
  - High performance liquid chromatography
  - Multidimensional protein identification technology (MudPIT)
  - Peptide mass fingerprinting
  - Combination of protein separation technologies with mass spectrometry
    - Combining capillary electrophoresis with mass spectrometry
    - 2D PAGE and mass spectrometry
    - Quantification of low abundance proteins
    - SDS-PAGE
  - Antibodies and proteomics
  - Detection of fusion proteins
  - Labeling and detection of proteins
    - Fluorescent labeling of proteins in living cells
    - Combination of microspheres with fluorescence
    - Self-labeling protein tags
  - Analysis of peptides
    - Differential Peptide Display
    - Peptide analyses using NanoLC-MS
- Protein sequencing
- Real-time PCR for protein quantification
- MS-based quantitative proteomics
- Functional proteomics: technologies for studying protein function
  - Functional genomics by mass spectrometry
- RNA-Protein fusions
- Designed repeat proteins
- Application of nanbiotechnology to proteomics
  - Nanoproteomics
    - Protein nanocrystallography
    - Single-molecule mass spectrometry using a nanopore
    - Nanoelectrospray ionization
  - Nanoparticle barcodes
    - Biobarcode assay for proteins
  - Resonance Light Scattering technology
  - Nanoscale protein analysis
  - Nanobiotechnology for discovery of protein biomarkers in the blood
  - Study of single membrane proteins at subnanometer resolution
  - Nanotube-vesicle networks for study of membrane proteins
  - Qdot-nanocrystals
  - Nanotube electronic biosensor
  - A nanoscale mechanism for protein engineering
- Protein expression profiling
- Cell-based protein assays
  - Living cell-based assays for protein function
  - Companies developing cell-based protein assays
- Protein function studies
  - Transcriptionally Active PCR
  - Protein-protein interactions
    - Yeast two-hybrid system
    - Membrane one-hybrid method
    - Protein affinity chromatography
    - Phage display
    - Fluorescence Resonance Energy Transfer
    - Bioluminescence Resonance Energy Transfer
    - Detection Enhanced Ubiquitin Split Protein Sensor technology
    - Protein-fragment complementation system
    - In vivo study of protein-protein interactions
    - Computational prediction of interactions
    - Interactome
    - Protein-protein interactions and drug discovery
    - Companies with technologies for protein-protein interaction studies
  - Protein-DNA interaction
- Determination of protein structure
  - X-Ray crystallography
  - Nuclear magnetic resonance
  - Electron spin resonance
  - Prediction of protein structure
  - Protein tomography
  - X-ray scattering-based method for determining the structure of proteins
- Prediction of protein function
  - Three-dimensional proteomics for determination of function
  - An algorithm for genome-wide prediction of protein function
  - Monitoring protein function by expression profiling
- Isotope-coded affinity tag peptide labeling
- Differential Proteomic Panning
- Cell map proteomics
- Topological proteomics
- Organelle or subcellular proteomics
- Nucleolar proteomics
- Glycoproteomic technologies
  - High-sensitivity glycoprotein analysis
  - Fluorescent in vivo imaging of glycoproteins
- Integrated approaches for protein characterization
- Imaging mass spectrometry
  - IMS technologies
  - Applications of IMS
  - The protein microscope
- Automation and robotics in proteomics
- Laser capture microdissection
  - Microdissection techniques used for proteomics
  - Uses of LCM in combination with proteomic technologies
- Concluding remarks about applications of proteomic technologies
  - Precision proteomics
3 Protein biochip technology
- Introduction
- Types of protein biochips
  - ProteinChip
    - Applications and advantages of ProteinChip
    - ProteinChip Biomarker System
    - Matrix-free ProteinChip Array
  - Aptamer-based protein biochip
  - Fluorescence planar wave guide technology-based protein biochips
  - Lab-on-a-chip for protein analysis
  - Microfluidic biochips for proteomics
  - Protein biochips for high-throughput expression
    - Nucleic Acid-Programmable Protein Array
    - High-density protein microarrays
    - HPLC-Chip for protein identification
    - Antibody microarrays
    - Integration of protein array and image analysis
- Tissue microarray technology for proteomics
- Protein biochips in molecular diagnostics
  - A force-based protein biochip
  - L1 chip and lipid immobilization
  - Multiplexed Protein Profiling on Microarrays
- Live cell microarrays
- ProteinArray Workstation
- Proteome arrays
  - The Yeast ProtoArray
  - ProtoArray™ Human Protein Microarray
  - TRINECTIN proteome chip
- Peptide arrays
- Surface plasmon resonance technology
  - Biacore's SPR
  - FLEX CHIP
  - Combination of surface plasmon resonance and MALDI-TOF
- Protein chips/microarrays using nanotechnology
  - Nanoparticle protein chip
  - Protein nanobiochip
  - Protein nanoarrays
  - Self-assembling protein nanoarrays
- Companies involved in protein biochip/microarray technology
4 Bioinformatics in Relation to Proteomics
- Introduction
- Bioinformatic tools for proteomics
  - Testing of SELDI-TOF MS Proteomic Data
  - BioImagine's ProteinMine
- Bioinformatics for pharmaceutical applications of proteomics
  - Compugen's LEADS
  - DrugScore
  - Proteochemometric modeling
- Integration of genomic and proteomic data
- Proteomic databases: creation and analysis
  - Introduction
  - Proteomic databases
    - GenProtEC
    - Human Protein Atlas
    - Human Proteomics Initiative Index
    - Proteome maps
    - Protein Structure Initiative - Structural Genomics Knowledgebase
    - Protein Warehouse Database
    - Protein Data Bank
    - Universal Protein Resource
  - Protein interaction databases
    - Biomolecular Interaction Network Database
  - ENCODE
    - Functional Genomics Consortium
    - Human Proteinpedia
    - ProteinCenter
    - Databases of the National Center for Biotechnology Information
- Bioinformatics for protein identification
- Application of bioinformatics in functional proteomics
- Use of bioinformatics in protein sequencing
  - Bottom-up protein sequencing
  - Top-down protein sequencing
- Protein structural database approach to drug design
- Bioinformatics for high-throughput proteomics
- Companies with bioinformatic tools for proteomics
5 Research in Proteomics
- Introduction
- Applications of proteomics in biological research
  - Identification of novel human genes by comparative proteomics
  - Study of relationship between genes and proteins
- Structural genomics or structural proteomics
  - Protein Structure Factory
  - Protein Structure Initiative
  - Studies on protein structure at Argonne National Laboratory
  - Structural Genomics Consortium
- Protein knockout
  - Antisense approach and proteomics
  - RNAi and protein knockout
  - Total knockout of cellular proteins
- Ribozymes and proteomics
- Single molecule proteomics
  - Single-molecule photon stamping spectroscopy
  - Single nucleotide polymorphism determination by TOF-MS
- Application of proteomic technologies in systems biology
  - Signaling pathways and proteomics
  - Kinomics
  - Combinatorial RNAi for quantitative protein network analysis
- Proteomics in neuroscience research
- Stem cell proteomics
  - hESC phosphoproteome
  - Proteomic studies of mesenchymal stem cells
  - Proteomics of neural stem cells
  - Proteome Biology of Stem Cells Initiative
- Proteomic analysis of the cell cycle
- Nitric oxide and proteomics
  - A proteomic method for identification of cysteine S-nitrosylation sites
  - Study of the nitroproteome
- Study of the phosphoproteome
- Study of the mitochondrial proteome
  - Proteomic technologies for study of mitochondrial proteomics
- Cryptome
- Study of protein transport in health and disease
- Proteomics research in the academic sector
  - Vanderbilt University's Center for Proteomics and Drug Actions
  - ProteomeBinders initiative
6 Pharmaceutical Applications of Proteomics
- Introduction
- Current drug discovery process and its limitations
- Role of omics in drug discovery
  - Genomics-based drug discovery
  - Metabolomics technologies for drug discovery
  - Role of metabonomics in drug discovery
  - Basis of proteomics approach to drug discovery
    - Proteins and drug action
    - Transcription-aided drug design
  - Role of proteomic technologies in drug discovery
    - Liquid chromatography-based drug discovery
    - Capture compound mass spectrometry
    - Protein-expression mapping by 2DGE
    - Role of MALDI mass spectrometry in drug discovery
    - Tissue imaging mass spectrometry
    - Companies using MALDI for drug discovery
  - Oxford Genome Anatomy Project
  - Proteins as drug targets
  - Ligands to capture the purine binding proteome
  - Chemical probes to interrogate key protein families for drug discovery
  - Global proteomics for pharmacodynamics
  - CellCarta® proteomics platform
  - ZeptoMARK™ protein profiling system
- Role of proteomics in targeting disease pathways
  - Identification of protein kinases as drug targets
    - Mechanisms of action of kinase inhibitors
  - G-protein coupled receptors as drug targets
    - Methods of study of GPCRs
    - Cell-based assays for GPCR
    - Companies involved in GPCR-based drug discovery
    - GPCR localization database
  - Matrix metalloproteases as drug targets
  - PDZ proteins as drug targets
  - Proteasome as drug target
  - Serine hydrolases as drug targets
  - Targeting mTOR signaling pathway
  - Targeting caspase-8 for anticancer therapeutics
- Bioinformatic analysis of proteomics data for drug discovery
- Drug design based on structural proteomics
  - Protein crystallography for determining 3D structure of proteins
  - Automated 3D protein modeling
    - Drug targeting of flexible dynamic proteins
  - Companies involved in structure-based drug-design
- Integration of genomics and proteomics for drug discovery
- Ligand-receptor binding
  - Role of proteomics in study of ligand-receptor binding
  - Aptamer protein binding
    - Systematic Evolution of Ligands by Exponential Enrichment
    - Aptamers and high-throughput screening
    - Nucleic Acid Biotools
    - Aptamer beacons
    - Peptide aptamers
- Riboreporters for drug discovery
- Target identification and validation
  - Application of mass spectrometry for target identification
  - Gene knockout and gene suppression for validating protein targets
  - Laser-mediated protein knockout for target validation
- Integrated proteomics for drug discovery
- High-throughput proteomics
  - Companies involved in high-throughput proteomics
- Drug discovery through protein-protein interaction studies
  - Protein-protein interaction as basis for drug target identification
  - Protein-PCNA interaction as basis for drug design
  - Two-hybrid protein interaction technology for target identification
  - Biosensors for detection of small molecule-protein interactions
  - Protein-protein interaction maps
    - ProNet (Myriad Genetics)
    - Hybrigenics' maps of protein-protein interactions
    - CellZome's functional map of protein-protein interactions
  - Mapping of protein-protein interactions by mass spectrometry
  - Protein interaction map of Drosophila melanogaster
  - Protein-interaction map of Wellcome Trust Sanger Institute
  - Protein-protein interactions as targets for therapeutic intervention
  - Inhibition of protein-protein interactions by peptide aptamers
  - Selective disruption of proteins by small molecules
- Post-genomic combinatorial biology approach
- Differential proteomics
- Shotgun proteomics
- Chemogenomics/chemoproteomics for drug discovery
- Expression proteomics: protein level quantification
- Role of phage antibody libraries in target discovery
- Analysis of posttranslational modification of proteins by MS
- Phosphoproteomics for drug discovery
- Application of glycoproteomics for drug discovery
  - Role of carbohydrates in proteomics
  - Challenges of glycoproteomics
  - Companies involved in glycoproteomics
- Role of protein microarrays/ biochips for drug discovery
  - Protein microarrays vs DNA microarrays for high-throughput screening
  - BIA-MS biochip for protein-protein interactions
  - ProteinChip with Surface Enhanced Neat Desorption
  - Protein-domains microarrays
  - Some limitations of protein biochips
- Concluding remarks about role of proteomics in drug discovery
- RNA versus protein profiling as guide to drug development
  - RNA as drug target
  - Combination of RNA and protein profiling
    - RNA binding proteins
- Toxicoproteomics
  - Hepatotoxicity
  - Nephrotoxicity
  - Cardiotoxicity
  - Neurotoxicity
- Protein/peptide therapeutics
  - Peptide-based drugs
  - Phylomer® peptides
  - Cryptein-based therapeutics
  - Synthetic proteins and peptides as pharmaceuticals
- Genetic immunization and proteomics
- Proteomics and gene therapy
- Role of proteomics in clinical drug development
  - Pharmacoproteomics
  - Role of proteomics in clinical drug safety
7 Application of Proteomics in Human Healthcare
- Clinical proteomics
  - Definition and standards
  - Vermillion's Clinical Proteomics Program
- Pathophysiology of human diseases
  - Diseases due to misfolding of proteins
    - Mechanism of protein folding
    - Nanoproteomics for study of misfolded proteins
    - Therapies for protein misfolding
  - Intermediate filament proteins
  - Significance of mitochondrial proteome in human disease
    - Proteome of Saccharomyces cerevisiae mitochondria
    - Rat mitochondrial proteome
- Proteomic approaches to biomarker identification
  - The ideal biomarker
  - Proteomic technologies for biomarker discovery
    - MALDI mass spectrometry for biomarker discovery
    - BAMF™ Technology
  - Protein biochips/microarrays and biomarkers
  - Antibody-based biomarker discovery
  - Tumor-specific serum peptidome patterns
  - Search for protein biomarkers in body fluids
  - Challenges and strategies for discovey of protein biomarkers in plasma
    - 3-D structure of CD38 as a biomarker
    - BD™ Free Flow Electrophoresis System
    - Isotope tags for relative and absolute quantification
    - Plasma protein microparticles as biomarkers
    - Proteome partitioning
    - Stable isotope tagging methods
    - Technology to measure both the identity and size of the biomarker
    - SISCAPA method for quantitating proteins and peptides in plasma
  - Biomarkers in the urinary proteome
- Application of proteomics in molecular diagnosis
  - Proximity ligation assay
  - Protein patterns
  - Proteomic tests on body fluids
  - Cyclical amplification of proteins
- Applications of proteomics in infections
  - Role of proteomics in virology
    - Study of interaction of proteins with viruses
  - Role of proteomics in bacteriology
    - Epidemiology of bacterial infections
    - Proteomic approach to bacterial pathogenesis
    - Vaccines for bacterial infections
    - Protein profiles associated with bacterial drug resistance
  - Analyses of the parasite proteome
- Application of proteomics in cystic fibrosis
- Oncoproteomics
  - Application of CellCarta technology for oncology
  - Accentuation of differentially expressed proteins using phage technology
  - Identification of oncogenic tyrosine kinases using phosphoproteomics
  - Single-cell protein expression analysis by microfluidic techniques
    - Dynamic cell proteomics in response to a drug
  - Desorption electrospray ionization for cancer diagnosis
  - Proteomic analysis of cancer cell mitochondria
  - Mass spectrometry for identification of oncogenic chimeric proteins
  - Id proteins as targets for cancer therapy
  - Proteomic study of p53 Index
  - Integration of cancer genomics and proteomics
  - Laser capture microdissection technology and cancer proteomics
  - Cancer tissue proteomics
  - Use of proteomics in cancers of various organ systems
    - Proteomics of brain tumors
    - Proteomics of breast cancer
    - Proteomics of colorectal cancer
    - Proteomics of esophageal cancer
    - Proteomics of hepatic cancer
    - Proteomics of leukemia
    - Proteomics of lung cancer
    - Proteomics of pancreatic cancer
    - Proteomics of prostate cancer
  - Diagnostic use of cancer biomarkers
  - NCI's Network of Clinical Proteomic Technology Centers for Cancer Research
  - Proteomics and tumor immunology
  - Proteomics and study of tumor invasiveness
  - Anticancer drug discovery and development
  - Kinase-targeted drug discovery in oncology
    - Anticancer drug targeting: functional proteomics screen of proteases
    - Small molecule inhibitors of cancer-related proteins
  - Role of proteomics in studying drug resistance in cancer
  - Future prospects of oncoproteomics
  - Companies involved in application of proteomics to oncology
- Application of proteomics in neurological disorders
  - Neuroproteomics
    - Prion diseases
    - Proteomics and transmissible spongiform encephalopathies
    - Proteomics and neurodegenerative disorders
    - Detection of misfolded proteins
    - Proteomics and glutamate repeat disorders
    - Proteomics and Huntington's disease
    - Proteomics and Parkinson's disease
    - Proteomics and Alzheimer's disease
    - Common denominators of Alzheimer's and prion diseases
    - Ion channel link for protein-misfolding disease
    - Proteomics and demyelinating diseases
    - Proteomics of amyotrophic lateral sclerosis
    - Proteomics of spinal muscular atrophy
    - Proteomics of Fabry disease
    - Proteomics and GM1 gangliosidosis
    - Proteomics of CNS trauma
    - Proteomics of CNS aging
    - Neuroproteomics of psychiatric disorders
    - Neuroproteomic of cocaine addiction
  - Neurodiagnostics based on proteomics
    - Testing for disease-specific proteins in the cerebrospinal fluid
    - Tau proteins
    - CNS tissue proteomics
    - Diagnosis of CNS disorders by examination of proteins in urine
    - Diagnosis of CNS disorders by examination of proteins in the blood
    - Serum pNF-H as biomarker of CNS damage
    - Proteomics of BBB
  - Future prospects of neuroproteomics in neurology
  - HUPO's Pilot Brain Proteome Project
- Proteomics of cardiac disorders
  - Study of cardiac mitochondrial proteome in myocardial ischemia
  - Cardiac protein databases
  - Proteomics of dilated cardiomyopathy and heart failure
  - Role of proteomics in heart transplantation
  - Future of application of proteomics in cardiology
- Proteomic technologies for research in pulmonary disorders
- Application fo proteomics in renal disorders
  - Diagnosis of renal disorders
  - Proteomic biomarkers of acute kidney injury
  - Cystatin C as biomarker of glomerular filtration rate
  - Protein biomarkers of nephritis
  - Proteomics and kidney stones
- Proteomics of eye disorders
  - Retinal dystrophies
- Use of proteomics in inner ear disorders
- Use of proteomics in aging research
  - Removal of altered cellular proteins in aging
- Proteomics and nutrition
8 Commercial Aspects of Proteomics
- Introduction
- Potential markets for proteomic technologies
  - Geographical distribution of proteomics technologies markets
  - Markets for protein separation technologies
    - Markets for 2D gel electrophoresis
    - Trends in protein separation technolgies and effect on market
  - Protein biochip markets
  - Mass spectrometry markets
  - Markets for MALDI for drug discovery
  - Markets for nuclear magnetic resonance spectroscopy
  - Market for structure-based drug design
  - Bioinformatics markets for proteomics
  - Markets for protein biomarkers
  - Markets for cell-based protein assays
- Business and strategic considerations
  - Cost of protein structure determination
  - Opinion surveys of the scientist consumers of proteomic technologies
    - Opinions on mass spectrometry
    - Opinions on bioinformatics and proteomic databases
    - Systems for in vivo study of protein-protein interactions
    - Perceptions of the value of protein biochip/microfluidic systems
  - Small versus big companies
  - Expansion in proteomics according to area of application
  - Growth trends in cell-based protein assay market
    - Challenges for development of cell-based protein assays
    - Future trends and prospects of cell-based protein assays
  - Strategic collaborations
    - Analysis of proteomics collaborations according to types of companies
    - Types of proteomic collaborations
    - Proteomics collaborations according to application areas
    - Analysis of proteomics collaborations: types of technologies
    - Collaborations based on protein biochip technology
    - Concluding remarks about proteomic collaborations
  - Proteomic patents
- Market drivers in proteomics
  - Needs of the pharmaceutical industry
  - Need for outsourcing proteomic technologies
  - Funding of proteomic companies and research
  - Technical advances in proteomics
  - Changing trends in healthcare in future
- Challenges facing proteomics
  - Magnitude and complexity of the task
  - Technical challenges
  - Limitations of proteomics
    - Limitations of 2DGE
    - Limitations of mass spectrometry techniques
    - Complexity of the pharmaceutical proteomics
  - Unmet needs in proteomics
9 Future of Proteomics
- Genomics to proteomics
  - Faster technologies
  - FLEXGene repository
- Need for new proteomic technologies
- Emerging proteomic technologies
  - Detection of alternative protein isoforms
  - Direct protein identification in large genomes by mass spectrometry
  - Proteome identification kits with stacked membranes
  - Vacuum deposition interface
    - In vitro protein biosynthesis
  - Proteome mining with adenosine triphosphate
  - Proteome-scale purification of human proteins from bacteria
  - Proteostasis network
  - Cytoproteomics
    - Subcellular proteomics
    - Individual cell proteomics
    - Live cell proteomics
    - Fluorescent proteins for live-cell imaging
  - Membrane proteomics
    - Identification of membrane proteins by tandem MS of protein ions
    - Solid state NMR for study of nanocrystalline membrane proteins
  - Multiplex proteomics
  - High-throughput for proteomics
  - Future directions for protein biochip application
  - Bioinformatics for proteomics
  - High-Throughput Crystallography Consortium
  - Study of protein folding by IBM's Blue Gene
  - Study of proteins by atomic force microscopy
- Population proteomics
- Comparative proteome analysis
- Human Proteome Organization
- Human Salivary Proteome
- Academic-commercial collaborations in proteomics
  - Indiana Centers for Applied Protein Sciences
- Role of proteomics in the healthcare of the future
  - Proteomics and molecular medicine
  - Proteodiagnostics
  - Proteomics and personalized medicine
    - Targeting the ubiquitin pathway for personalized therapy of cancer
    - Protein patterns and personalized medicine
    - Personalizing interferon therapy of hepatitis C virus
    - Protein biochips and personalized medicine
    - Combination of diagnostics and therapeutics
    - Future prospects
10 References
11 Companies involved in developing proteomics
- Introduction
- Profiles of selected companies
- Collaborations
Tables
- Table 1-1: Landmarks in the evolution of proteomics
- Table 1-2: Comparison of DNA and protein
- Table 1-3: Comparison of mRNA and protein
- Table 1-4: Methods of analysis at various levels of functional genomics
- Table 2-1: Proteomics technologies
- Table 2-2: Protein separation technologies of selected companies
- Table 2-3: Companies supplying mass spectrometry instruments
- Table 2-4: Companies involved in cell-based protein assays
- Table 2-5: Methods used for the study of protein-protein interactions
- Table 2-6: A selection of companies involved in protein-protein interaction studies
- Table 2-7: Proteomic technologies used with laser capture microdissection
- Table 3-1: Applications of protein biochip technology
- Table 3-2: Selected companies involved in protein biochip/microarray technology
- Table 4-1: Proteomic databases and other Internet sources of proteomics information
- Table 4-2: Protein interaction databases available on the Internet
- Table 4-3: Bioinformatic tools for proteomics from academic sources
- Table 4-4: Selected companies involved in bioinformatics for proteomics
- Table 5-1: Applications of proteomics in basic biological research
- Table 5-2: A sampling of proteomics research projects in academic institutions
- Table 6-1: Pharmaceutical applications of proteomics
- Table 6-2: Selected companies relevant to MALDI-MS for drug discovery
- Table 6-3: Selected companies involved in GPCR-based drug discovery
- Table 6-4: Companies involved in drug design based on structural proteomics
- Table 6-5: Proteomic companies with high-throughput protein expression technologies
- Table 6-6: Selected companies involved in chemogenomics/chemoproteomics
- Table 6-7: Companies involved in glycoproteomic technologies
- Table 7-1: Applications of proteomics in human healthcare
- Table 7-2: Companies involved in applications of proteomics to oncology
- Table 7-3: Neurodegenerative diseases with underlying protein abnormality
- Table 7-4: Disease-specific proteins in the cerebrospinal fluid of patients
- Table 7-5: Eye disorders and proteomic approaches
- Table 8-1: Potential markets for proteomic technologies 2008-2018
- Table 8-2: Geographical distribution of markets for proteomic technologies 2008-2018
- Table 8-3: 2008 revenues of major companies from protein separation technologies
- Table 9-1: Role of proteomics in personalizing strategies for cancer therapy
- Table 11-1: Companies with proteomics as the main activity/service
- Table 11-2: Selected companies with equipment and laboratory services for proteomics
- Table 11-3: Biotechnology and drug discovery companies involved in proteomics
- Table 11-4: Bioinformatics companies involved in proteomics
- Table 11-5: Biopharmaeutical companies with in-house proteomics technology
- Table 11-6: Major players in proteomics
- Table 10-7: Selected collaborations of companies in the area of proteomics
Figures
- Figure 1-1: Relationship of DNA, RNA and protein in the cell
- Figure 1-2: Protein production pathway from gene expression to functional protein with controls
- Figure 1-3: Parallels between functional genomics and proteomics
- Figure 2-1: Proteomics: flow from sample preparation to characterization
- Figure 2-2: The central role of spectrometry in proteomics
- Figure 2-3: Electrospray ionization (ESI)
- Figure 2-4: Matrix-Assisted Laser Desorption/Ionization (MALDI)
- Figure 2-5: Scheme of bio-bar-code assay
- Figure 2-6: A diagrammatic presentation of yeast two-hybrid system
- Figure 3-1: ProteinChip System
- Figure 3-2: Surface plasma resonance (SPR)
- Figure 4-1: Role of bioinformatics in integrating genomic/proteomic-based drug discovery
- Figure 4-2: Bottom-up and top-down approaches for protein sequencing
- Figure 6-1: Drug discovery process
- Figure 6-2: Regulatory changes induced by drugs and implemented at the proteins level
- Figure 6-3: Relation of proteome to genome, diseases and drugs
- Figure 6-4: The mTOR pathways
- Figure 6-5: Steps in shotgun proteomics
- Figure 6-6: Chemogenomic approach to drug discovery (3-Dimensional Pharmaceuticals)
- Figure 7-1: Relation of oncoproteomics to other technologies
- Figure 7-2: A scheme of proteomics applications in CNS drug discovery and development
- Figure 8-1: Types of companies involved in proteomics collaborations
- Figure 8-2: Types of collaborations: R & D, licensing or marketing
- Figure 8-3: Proteomics collaborations according to application areas
- Figure 8-4: Proteomics collaborations according to technologies
- Figure 8-5: Unmet needs in proteomics
- Figure 9-1: A scheme of the role of proteomics in personalized management of cancer