Proteomics - Technologies, Markets and Companies -





Published: July 2014 | Pages: 644 | Format: PDF

 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. Important areas of application include cancer (oncoproteomics) and neurological disorders (neuroproteomics). The text is supplemented with 44 tables, 27 figures and over 500 selected references from the literature. 

 The number of companies involved in proteomics has increased remarkably during the past few years. More than 300 companies have been identified to be involved in proteomics and 222 of these are profiled in the report with 460 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 2013 and are projected to years 2018 and 2023. The largest expansion will be in bioinformatics and protein biochip technologies. Important areas of application are cancer and neurological disorders 

 Part I: Technologies & Markets  

  

 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 

 Golgi complex 

 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 

 Impact of the genetic factors on the human proteome 

 Proteomics and systems biology 

 Functional synthetic proteins  

  

 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 (MS) 

 Electrospray ionization 

 Desorption electrospray ionization 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 

 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 

 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 

 Nanowire transistor for the detection of protein-protein interactions 

 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 

 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 

 Phage display 

 Protein affinity chromatography 

 Protein-fragment complementation system 

 Yeast 2-hybrid system 

 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 

 Tag-Mass IMS 

 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 

 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 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 

 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 

 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 

 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 

 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 

 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 

 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 

 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 

 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 

 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 

 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 

 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 

 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 

 BAMF? Technology 

 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 

 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 

 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 

 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 

 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 

 Removal of altered cellular proteins in aging 

 Study of the role of Parkin in modulating aging 

 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 

 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 

 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 

 Diseases due to pathological prion protein 

 Transmissible spongiform encephalopathies 

 Creutzfeld-Jakob disease 

 Bovine spongiform encephalopathy 

 Variant Creutzfeldt-Jakob disease 

 Protein misfolding and neurodegenerative disorders 

 Ion channel link for protein-misfolding disease 

 Detection of misfolded proteins 

 Neurodegenerative disorders with protein abnormalities 

 Alzheimer disease 

 Common denominators of Alzheimer and prion diseases 

 Parkinson disease 

 Amyotrophic lateral sclerosis 

 Proteomics and glutamate repeat disorders 

 Proteomics and Huntington's disease 

 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 

 Proteomics of CNS aging 

 Protein aggregation as a bimarker of aging 

 Neuroproteomics of psychiatric disorders 

 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 

 Proteomics of BBB 

 Future prospects 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 

 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 

 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: 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 2013-2023 

 Table 10-2: 2013 revenues of major companies from protein separation technologies 

 Table 10-3: Geographical distribution of markets for proteomic technologies 2013-2023 

 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 with controls. 

 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: Matrix-Assisted Laser Desorption/Ionization (MALDI) 

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

 Figure 2-6: A diagrammatic presentation of yeast 2-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 8-1: Relation of oncoproteomics to other technologies 

 Figure 9-1: 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 

  

 11. Companies involved in developing proteomics 

 Introduction 

 Profiles of selected companies 

 Collaborations 

 Tables 

  

 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