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. The most commonly used technologies are 2D gel electrophoresis for protein separation and analysis of proteins by mass spectrometry. Microanalytical protein characterization with multidimensional 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 the 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 the 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 complementary to genomic approaches. Toxicoproteomics, i.e. the evaluation of protein expression for the understanding of toxic events, is an important application of proteomics in preclinical drug safety. The 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 the 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, 31 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 223 of these are profiled in the report with 444 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 2020 and are projected to years 2024 and 2030. The largest expansion will be in bioinformatics and protein biochip technologies. Important areas of application are cancer and neurological disorders.
The report contains information on the following:
- Basics of Proteomics
- Proteomic Technologies
- Protein Biochip technology
- Bioinformatics in Relation to Proteomics
- Research in Proteomics
- Pharmaceutical Applications of Proteomics
- Application of Proteomics in Healthcare
- Oncoproteomics
- Neuroproteomics
- Commercial Aspects of Proteomics
- Future of Proteomics
- Companies Involved in Developing Proteomics
Table of Contents
Part I: Technologies & Markets
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
- Golgi complex
- Proteins
- Functions of proteins
- Proteasome
- Spliceosome
- Inter-relationship of protein, mRNA and DNA
- Microproteins
- Proteomics
- Endoplasmic reticulum
- Mitochondrial proteome
- S-nitrosoproteins in mitochondria
- Proteomics and genomics
- Classification of proteomics
- Levels of functional genomics and various "omics"
- Glycoproteomics
- Transcriptomics
- Metabolomics
- Cytomics
- Phenomics
- Impact of the genetic factors on the human proteome
- Proteomics and systems biology
- Proteomics and synthetic biology
- Functional synthetic proteins
- Synthetic proteomics for study of apoptosis
2. Proteomic Technologies
- Key technologies driving proteomics
- Sample preparation
- New trends in sample preparation
- Pressure Cycling Technology
- Protein separation technologies
- High resolution 2DGE
- 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
- SeraFILE™ separations platform
- Companies with protein separation technologies
- Protein purification
- Technologies for protein purification
- Applications of protein purification
- Protein detection
- Protein identification and characterization
- Mass spectrometry
- Electrospray ionization
- Desorption electrospray ionization MS
- Ion-mobility spectrometry-MS
- Mirosaic 3500 MiD
- Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry
- Cryogenic MALDI- Fourier Transform Mass Spectrometry
- Stable-isotope-dilution tandem mass spectrometry
- HUPO Gold MS Protein Standard
- Companies involved in mass spectrometry
- High performance liquid chromatography
- Multidimensional protein identification technology (MudPIT)
- Multiple reaction monitoring assays
- Peptide mass fingerprinting
- Current status and future prospects of clinical mass spectrometry
- 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
- Proteomics quantification in complex samples
- Antibodies and proteomics
- Detection of fusion proteins
- Labeling and detection of proteins
- Bioorthogonal non-canonical amino-acid-tagging techniques
- Stable-isotope labeling of amino acids in cell culture
- Fluorescent labeling of proteins in living cells
- Combination of microspheres with fluorescence
- Self-labeling protein tags
- Analysis of peptides
- C-terminal peptide analysis
- Differential Peptide Display
- Peptide analyses using NanoLC-MS
- Protein sequencing
- Real-time PCR for protein quantification
- Quantitative proteomics
- MS-based quantitative proteomics
- MS and cryo-electron tomography
- Selected reaction monitoring MS
- Functional proteomics: technologies for studying protein function
- Functional genomics by mass spectrometry
- LC-MS-based method for annotating the protein-coding genome
- RNA-Protein fusions
- Designed repeat proteins
- Application of nanobiotechnology to proteomics
- Nanoproteomics
- Nanoflow liquid chromatography
- Nanopores for phosphoprotein analysis
- Nanotube electronic biosensor for proteomics
- Protein nanocrystallography
- Single-molecule mass spectrometry using a nanopore
- Nanoelectrospray ionization
- Nanoproteomics for discovery of protein biomarkers in the blood
- QD-protein nanoassembly
- Nanoparticle barcodes
- Biobarcode assay for proteins
- Nanopore-based protein sequencing
- Nanoscale protein analysis
- Nanoscale mechanism for protein engineering
- Nanotube electronic biosensor
- Nanotube-vesicle networks for study of membrane proteins
- Qdot-nanocrystals
- Resonance Light Scattering technology
- Study of single membrane proteins at subnanometer resolution
- Protein expression profiling
- Cell-based protein assays
- Living cell-based assays for protein function
- Companies developing cell-based protein assays
- 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
- Protein function studies
- Transcriptionally Active PCR
- Protein-protein interactions
- Bacterial protein interaction studies for assigning function
- Bioluminescence Resonance Energy Transfer
- Computational prediction of interactions
- Detection Enhanced Ubiquitin Split Protein Sensor technology
- Double Switch technology
- Fluorescence Resonance Energy Transfer
- In vivo study of protein-protein interactions
- In vitro study of protein-protein interactions
- Interactome
- Membrane 1-hybrid method
- Nanowire transistor for the detection of protein-protein interactions
- Phage display
- Protein affinity chromatography
- Protein-fragment complementation system
- Proximity-dependent hybridization chain reaction
- Yeast 2-hybrid system
- Companies with technologies for protein-protein interaction studies
- Protein-DNA interaction
- Monitoring protein function by expression profiling
- Study of microprotein functions
- Isotope-coded affinity tag peptide labeling
- Differential Proteomic Panning
- Cell map proteomics
- Topological proteomics
- Organelle or subcellular proteomics
- SubCellBarCode
- 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
- Tag-Mass IMS
- Quantitative immunofluorescence for proteomics
- Automation and robotics in proteomics
- Western blot
- Limitations of WB
- Innovations in WB
- Capillary electrophoresis and WB
- Chemiluminescent western blotting
- Fluorescent WB
- Microfluidics and WB
- Multiplexing WB
- Applications of Western blot
- Research applications of Western blot
- Molecular diagnostic applications of Western blot
- Companies involved in Western blotting technologies
- Laser capture microdissection
- Microdissection techniques used for proteomics
- Uses of LCM in combination with proteomic technologies
- Concluding remarks about applications of proteomic technologies
- NextGen Proteomics Platform
- 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
- Biochips for peptide arrays
- Microfluidic biochips for proteomics
- Protein biochips and microarrays for high-throughput expression
- Nucleic Acid-Programmable Protein Array
- High-density protein microarrays
- HPLC-Chip for protein identification
- Antibody microarrays
- HuProt™ Human Proteome 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
- SPR Systems
- 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
- In silico search of drug targets by Biopendium
- 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
- Human proteome map
- International Protein Index
- MS-based draft of the human proteome
- Protein Structure Initiative Structural Genomics Knowledgebase
- Protein Warehouse Database
- Protein Data Bank
- Repository for raw data from proteomics MS
- 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
- Application of bioinformatics for protein identification
- Tandem MS for protein identification
- Targeted MS for specific identification of proteins
- Application of bioinformatics in functional proteomics
- Use of bioinformatics in protein sequencing
- Bottom-up protein sequencing
- Top-down protein sequencing
- Integration of next generation proteomics and gene sequencing data
- Protein structural database approach to drug design
- Bioinformatics for high-throughput proteomics
- Bioinformatics for protein-protein interactions
- 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
- Characterization of histone codes
- 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
- Comparative proteomic analysis of somatic cells, iPSCs and ESCs . 159 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
- Ancient proteomics
- Proteomics research in the academic sector
- Netherlands Proteins@Work
- ProteomeBinders initiative
- Rutgers University’s Center for Integrative Proteomics Research
- Vanderbilt University's Center for Proteomics and Drug Actions
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
- In vivo production of therapeutic proteins by mRNA
- Role of proteomic technologies in drug discovery
- Liquid chromatography-based drug discovery
- Capture compound mass spectrometry
- Protein-expression mapping by 2DGE
- Protein-protein interactions and drug discovery
- Role of MALDI mass spectrometry in drug discovery
- Structural proteomics and drug discovery
- Tissue imaging mass spectrometry
- Oxford Genome Anatomy Project
- Proteins as drug targets
- Monitoring drug target binding using the cellular thermal shift assay
- Ligands to capture the purine binding proteome
- Chemical probes to interrogate key protein families for drug discovery
- Global proteomics for pharmacodynamics
- ProteoCarta® proteomics platform
- ZeptoMARK protein profiling system
- Role of proteomics in targeting disease pathways
- Dynamic proteomics
- 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
- Oligodendrocyte proteome as a target for antipsychotics
- PDZ proteins as drug targets
- Proteasome as drug target
- Serine hydrolases as drug targets
- Targeting mTOR signaling pathway
- Targeting caspase-8 for anticancer therapeutics
- 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
- Measuring drug binding of proteins
- 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
- Hyper Reaction Monitoring
- Targeted proteomics
- Chemogenomics/chemoproteomics for drug discovery
- Chemoproteomics-based drug discovery
- Companies involved in chemogenomics/chemoproteomics
- Activity-based proteomics
- Locus Discovery technology
- Automated ligand identification system
- 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
- Microproteins as targets for drug discovery
- 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
- Alphabody technology for improving protein therapeutics
- Peptide-based drugs
- Phylomer® peptides
- Cryptein-based therapeutics
- Synthetic proteins and peptides as pharmaceuticals
- Genetic immunization and proteomics
- Role of proteomics in synthetic antivenoms
- 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
- Introduction
- 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
- Protein biochips/microarrays and biomarkers
- Affinity proteomics for discovery of biomarkers
- Antibody array-based biomarker discovery
- Discovery of biomarkers by MAb microarray profiling
- 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
- N-terminal peptide isolation from human plasma
- Plasma protein microparticles as biomarkers
- Proteome partitioning
- SISCAPA method for quantitating proteins and peptides in plasma
- Stable isotope tagging methods
- Technology to measure both the identity and size of the biomarker
- Biomarkers in the urinary proteome
- Application of proteomics in molecular diagnosis
- MassARRAY
- Proximity ligation assay
- Protein patterns
- Proteomic tests on body fluids
- Cyclical amplification of proteins
- Applications of proteomics in infections
- MALDI-TOF MS for microbial identification
- Recognition of microbial glycans by human lectins
- Role of proteomics in virology
- Interaction of proteins with viruses
- Quantitative temporal viromics
- 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
- Proteomics of cardiovascular diseases
- Pathomechanism of cardiovascular diseases
- Protein misfolding in cardiac dysfunction
- Study of cardiac mitochondrial proteome in myocardial ischemia
- Cardiac protein databases
- Proteomics of dilated cardiomyopathy and heart failure
- Proteomic biomarkers of cardiovascular diseases
- Regulation of cardiac rhythmicity by Purkinje cell protein-4
- Role of proteomics in cardioprotection
- Role of proteomics in heart transplantation
- Future of application of proteomics in cardiology
- Proteomic technologies for research in pulmonary disorders
- Application of 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
- Proteomics of cataract
- Proteomics of diabetic retinopathy
- Retinal dystrophies
- Use of proteomics in inner ear disorders
- Use of proteomics in aging research
- Alteration of glycoproteins during aging
- Carbamylation of proteins with aging
- Proteomics of muscle aging
- Removal of altered cellular proteins in aging
- Role of protein aggregation in aging and degenerative diseases
- Study of the role of Parkin in modulating aging
- Study of proteins that protect against hypoxic injury in age-related disorders
- Proteomics and nutrition
8. Oncoproteomics
- Introduction
- Proteomic technologies for study of cancer
- Application of CellCarta technology for oncology
- Accentuation of differentially expressed proteins using phage technology
- Cancer tissue proteomics
- Dynamic cell proteomics in response to a drug
- Desorption electrospray ionization for cancer diagnosis
- Id proteins as targets for cancer therapy
- Identification of oncogenic tyrosine kinases using phosphoproteomics
- Laser capture microdissection technology and cancer proteomics
- Mass spectrometry for identification of oncogenic chimeric proteins
- Proteomic analysis of cancer cell mitochondria
- Proteomic study of p53
- Human Tumor Gene Index
- Integration of cancer genomics and proteomics
- Role of proteomics in study of cancer stem cell biology
- Single-cell protein expression analysis by microfluidic techniques
- Use of proteomics in cancers of various organ systems
- Proteomics of brain tumors
- Malignant glial tumors
- Meningiomas
- DESI-MS for intraoperative diagnosis of brain tumors
- Proteomics of breast cancer
- Integration of proteomic and genomic data for 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
- Proteomics of renal cancer
- Diagnostic use of cancer biomarkers
- Proteomic technologies for tumor biomarkers
- Nuclear matrix proteins (NMPs)
- Antiannexins as tumor markers in lung cancer
- NCI’s Network of Clinical Proteomic Technology Centers
- Proteomics and tumor immunology
- Proteomics and study of tumor invasiveness
- Anticancer drug discovery and development
- Anticancer drug targeting: functional proteomics screen of proteases
- Kinase-targeted drug discovery in oncology
- Protein-drug interactions in cancer
- Role of proteomics in studying drug resistance in cancer
- Small molecule inhibitors of cancer-related proteins
- Future prospects of oncoproteomics
- International oncoproteomic initiatives
- Clinical Proteomic Tumor Analysis Consortium
- Companies involved in application of proteomics to oncology
9. Neuroproteomics
- Introduction
- Application of proteomics for the study of nervous system
- Proteomics of prion diseases
- Normal function of prions in the brain
- Detection of protein aggregates and prions
- Diseases due to pathological prion protein
- Transmissible spongiform encephalopathies
- Creutzfeld-Jakob disease
- Bovine spongiform encephalopathy
- Variant Creutzfeldt-Jakob disease
- Protein misfolding/aggregation in neurodegenerative disorders
- Alzheimer disease
- Amyotrophic lateral sclerosis
- Common denominators of Alzheimer and prion diseases
- Detection of misfolded proteins in neurodegenerative disorders
- Ion channel link for protein-misfolding disease
- Modulation of proteostasis in neurodegenerative disorders
- Neurodegenerative disorders with protein abnormalities
- Parkinson disease
- Proteomics and glutamate repeat disorders
- Proteomics and Huntington's disease
- Targets to limit protein aggregation in neurodegenerative diseases
- Aggregate contactome
- Clusterin for clearance of aggregating misfoded proteins
- Proteomics and demyelinating diseases
- Proteomics of neurogenetic disorders
- Fabry disease
- GM1 gangliosidosis
- Quantitative proteomics and familial hemiplegic migraine
- Proteomics of spinal muscular atrophy
- Proteomics of CNS trauma
- Proteomics of traumatic brain injury
- Chronic traumatic encephalopathy and ALS
- Proteomics of cerebrovascular disease
- Pathogenesis of cerebral small vessel disease
- Proteomics of CNS aging
- Protein aggregation as a biomarker of aging
- Neuroproteomics of psychiatric disorders
- Schizophrenia
- Anxiety disorders
- Depression ans suicidal behavior
- Neuroproteomic of cocaine addiction
- Neurodiagnostics based on proteomics
- 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
- Intraoperative application of proteomics in surgery of brain tumors
- Proteomics of BBB
- Future of neuroproteomics in neurology
- HUPO’s Pilot Brain Proteome Project
10. Proteomics Markets
- Introduction
- Potential markets for proteomic technologies
- Bioinformatics markets for proteomics
- Markets for protein separation technologies
- Markets for 2D gel electrophoresis
- Market trends in protein separation technolgies
- Protein purification markets
- Mass spectrometry markets
- Markets for MALDI for drug discovery
- Markets for nuclear magnetic resonance spectroscopy
- Market for structure-based drug design
- Markets for protein biomarkers
- Markets for cell-based protein assays
- Protein biochip markets
- Western blot markets
- Geographical distribution of proteomics technologies markets
- 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
11. 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
- Single cell proteomics
- Fluorescent proteins for live-cell imaging
- Live cell proteomics
- Microfluidics for cell proteomics
- Nanoscale study of cell proteomics
- Membrane proteomics
- Identification of membrane proteins by tandem MS of protein ions
- Solid state NMR for study of nanocrystalline membrane proteins
- Subcellular proteomics
- 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
- Cell-based Human Proteome Project
- 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
12. References
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: Companies involved in Western blotting
Table 2-8: 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: Eye disorders and proteomic approaches
Table 8-1: Large scale international oncoproteomic initiatives
Table 8-2: Companies involved in applications of proteomics to oncology
Table 9-1: Neurodegenerative diseases with underlying protein abnormality
Table 9-2: Disease-specific proteins in the cerebrospinal fluid of patients
Table 10-1: Potential markets for proteomic technologies 2020-2030
Table 10-2: Geographical distribution of markets for proteomic technologies 2020-2030
Table 11-1: Role of proteomics in personalizing strategies for cancer therapy
Figures
Figure 1-1: A schematic miRNA pathway
Figure 1-2: Relationship of DNA, RNA and protein in the cell
Figure 1-3: Protein production pathway from gene expression to functional protein
Figure 1-4: 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: Ion-mobility spectrometry-MS
Figure 2-5: Matrix-Assisted Laser Desorption/Ionization (MALDI)
Figure 2-6: Scheme of bio-bar-code assay
Figure 2-7: A diagrammatic presentation of yeast 2-hybrid system
Figure 2-8: A schematic view of SubCellBarCode
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 8-1: Relation of oncoproteomics to other technologies
Figure 9-1: Identification of protein targets in neurodegenerative disorders
Figure 9-2: Clusterin bringing misfolded proteins into cells to be degraded by lysosomes
Figure 9-3: A scheme of proteomics applications in CNS drug discovery and development
Figure 10-1: Types of companies involved in proteomics collaborations
Figure 10-2: Types of collaborations: R & D, licensing or marketing
Figure 10-3: Proteomics collaborations according to application areas
Figure 10-4: Proteomics collaborations according to technologies
Figure 10-5: Unmet needs in proteomics
Figure 11-1: A scheme of the role of proteomics in personalized management of cancer
Part II: Companies
13. Companies involved in developing proteomics
- Introduction
- Profiles of selected companies
- Collaborations
Tables
Table 13-1: Companies with proteomics as the main activity/service
Table 13-2: Selected companies with equipment and laboratory services for proteomics
Table 13-3: Biotechnology and drug discovery companies involved in proteomics
Table 13-4: Bioinformatics companies involved in proteomics
Table 13-5: Biopharmaeutical companies with in-house proteomic technologies
Table 13-6: Major players in proteomics
Table 13-7: Selected collaborations of companies in the area of proteomics
Samples
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