Proteomics: Promising Research/Potential Applications/and New Developments

Table of Contents

1. Executive Summary

• 1. Genes and Proteins
  • 1. Genomics and Proteomics
  • 2. Bioinformatics Analysis of Proteomics Data
  • 3. Pharmaceutical Applications
• 2. Proteomics Techniques
  • 1. Proteomics Analysis
  • 2. 2-D Gel Electrophoresis
  • 3. Spectrometry
  • 4. Phage Display
  • 5. Yeast 2-Hybrid System
  • 6. Lab on a Chip (LOC) Technologies
  • 7. Microfluidic LOCs
  • 8. Biochips and Microarrays
  • 9. Additional Proteomics Technologies: Bioinformatics; Functional Genomics; and Structural Genomics

2. Introduction

• 1. Introduction
  • 1. Introduction
  • 2. Proteomic Methods
• 2. Bioinformatics Analysis of Proteomics Data
  • 1. Bioinformatics Analysis of Proteomics Data
  • 2. Studying Proteins Versus Studying Genes
• 3. Pharmaceutical Applications
  • 1. Identifying Novel Therapeutics
  • 2. Drug Discovery
• 4. Proteomics Techniques
  • 1. Proteomics Techniques
  • 2. 2-D Gel Electrophoresis
  • 3. Spectrometry
• 5. Phage Display; Yeast 2-Hybrid System
  • 1. Phage Display
  • 2. Yeast 2-Hybrid System
• 6. Lab-on-a-Chip (LOC) Technologies
  • 1. Lab on a Chip (LOC) Technologies
  • 2. Microfluidic LOCs
  • 3. Biochips and Microarrays

3. New Enabling Technologies

• 1. Cal Tech's Beckman Institute: MRI Shows Gene Expression Anywhere in Organism
  • 1. Cal Tech's Beckman Institute: MRI Shows Gene Expression Anywhere in Organism
• 2. GeneProt: New Method Automates Mass Spec
  • 1. GeneProt: New Method Automates Mass Spec
• 3. University of Michigan: New Protein Separation Faster Than 2-D Gels
  • 1. University of Michigan: New Protein Separation Faster Than 2-D Gels
• 4. Cytogen: Ligand Target Cloning
  • 1. Cytogen: Ligand Target Cloning
• 5. Hybrigenics
  • 1. With Institut Pasteur: Hybrigenics Named Exclusive Licensee To Protein-Interactions Patent
  • 2. Bacterial Two-Hybrid System Better Than Yeast
  • 3. Protein Interactions Mapped out in H. pylori
  • 4. Map of Protein Interactions Between HIV and Host Cells
  • 5. With Lynx Therapeutics: Obesity
  • 6. With XTL: Hepatitis C Virus (HCV) Therapeutics
• 6. Lexicon: Gene-Trapping Technique Detects Rare Proteins
  • 1. Lexicon: Gene-Trapping Technique Detects Rare Proteins
• 7. RheoGene: Multiplexed Gene -Regulation Technology for Studying Complex Gene Interactions
  • 1. RheoGene: Multiplexed Gene -Regulation Technology for Studying Complex Gene Interactions
• 8. HTS Biosystems: Surface Plasmon Resonance
  • 1. HTS Biosystems: Surface Plasmon Resonance
  • 2. With Dyax Corp: Phage Display for Antibody Chips
  • 3. With Boston Probes and Applied Biosystems: Peptide Nucleic Acid (PNA) Technology
  • 4. Mitsubishi Chemical: Purchase and Distribution Agreement
• 9. Rosemount: Mass Spectrometer on a Chip
  • 1. Rosemount: Mass Spectrometer on a Chip
• 10. Caliper Technologies: Microfluidics and Lab on a Chip
  • 1. With Structural Genomix: High-Throughput Protein Analysis
  • 2. Conflict with Aclara Resolved
• 11. Johns Hopkins; NYU; Mount Sinai: Bisubstrates Squelch Errant Enzymes
  • 1. Johns Hopkins; NYU; Mount Sinai: Bisubstrates Squelch Errant Enzymes
• 12. SUNY and University of Tokyo: Making Novel Proteins Using a 21st-Century Amino Acid
  • 1. SUNY and University of Tokyo: Making Novel Proteins Using a 21st-Century Amino Acid
• 13. Vanderbilt University: New Technology Expands Molecular Photography Options
  • 1. Vanderbilt University: New Technology Expands Molecular Photography Options
• 14. Virginia Tech: Dried Cells; Tissues Could Solve Biological Materials Storage; Transport Problems
  • 1. Virginia Tech: Dried Cells; Tissues Could Solve Biological Materials Storage; Transport Problems
• 15. Whitehead Institute and Mass General: Interaction Sequence Tags
  • 1. Whitehead Institute and Mass General: Interaction Sequence Tags
• 16. Phylos
  • 1. Alternative to Phage Display
  • 2. Protein-Expression Chip
  • 3. Antibody-Like Protein Scaffolds for Cancer Treatment
• 17. Harvard University: Protein Chips Probe Protein Function
  • 1. Harvard University: Protein Chips Probe Protein Function
• 18. University of Pennsylvania: IDAT Detects Proteins at Unprecedented Resolution
  • 1. University of Pennsylvania: IDAT Detects Proteins at Unprecedented Resolution
• 19. Caliper and Structural Genomix High Throughput Proteomics Labchip
  • 1. Caliper and Structural Genomix High Throughput Proteomics Labchip
• 20. Detection on a Chip: Microphotonics
  • 1. Detection on a Chip: Microphotonics
  • 2. Northwestern University: Microphotonic Resonator
  • 3. Nanogen: Photonic Energy Transfer
  • 4. Illumina: Fiberoptic Arrays House 250000 Discrete Sensors on Pinhead-Sized Probe
• 21. Hoffman-La Roche: Bacteria Chips to Study Antibiotics
  • 1. Hoffman-La Roche: Bacteria Chips to Study Antibiotics
• 22. EMBL Begets Cellzome: TAP Method Yields Low-Abundance Proteins and Multicomponent Complexes
  • 1. EMBL Begets Cellzome: TAP Method Yields Low-Abundance Proteins and Multicomponent Complexes
• 23. NEN Life Science: Analyzing Gene Expression or Copy Number on a Chip
  • 1. NEN Life Science: Analyzing Gene Expression or Copy Number on a Chip

4. Functional Genomics

• 1. Functional Genomics
  • 1. Functional Genomics
• 2. Human Genome Sciences Wins AIDS-Receptor Drug Target Patent
  • 1. Human Genome Sciences Wins AIDS-Receptor Drug Target Patent
• 3. Agritope: Functional Genomics for Plants
  • 1. Agritope: Functional Genomics for Plants
• 4. Devgen NV: Belgian Firm Focuses on Functional Genomics
  • 1. Devgen NV: Belgian Firm Focuses on Functional Genomics
• 5. Paradigm Genetics: 150 Plant Gene Functions per Week
  • 1. Paradigm Genetics: 150 Plant Gene Functions per Week
• 6. CuraGen: Functional Genomics for Therapeutics
  • 1. CuraGen: Functional Genomics for Therapeutics
  • 2. Protein Interaction Map of Yeast; Fruit Fly
  • 3. With Cor Tx: Cardiovascular Drugs
• 7. Rigel and Pfizer: Allergies
  • 1. Rigel and Pfizer: Allergies
• 8. DOE Grants Focus on Microbial Waste Remediation; Carbon Management; Energy Production; Biotech
  • 1. DOE Grants Focus on Microbial Waste Remediation; Carbon Management; Energy Production; Biotech
• 9. Genset: Protein Takes Fat off Obese Mice
  • 1. Genset: Protein Takes Fat off Obese Mice
• 10. MDS Proteomics Links with Zyomyx; IBM
  • 1. MDS Proteomics Links with Zyomyx; IBM
• 11. Arqule and Acadia: G-Protein-Receptors as Drug Targets
  • 1. Arqule and Acadia: G-Protein-Receptors as Drug Targets
• 12. Neotherapeutics: Therapies for Neurodegenerative Disease
  • 1. Neotherapeutics: Therapies for Neurodegenerative Disease
• 13. Neogene Technologies: G-Protein-Coupled Receptors
  • 1. Neogene Technologies: G-Protein-Coupled Receptors
• 14. Cereon Genomics: Arabidopsis Data Released through Public-Private Partnership
  • 1. Cereon Genomics: Arabidopsis Data Released through Public-Private Partnership
• 15. Exelixis: Functional Genomics in Drosophila
  • 1. Exelixis: Functional Genomics in Drosophila
• 16. Aurora Patents Gene Tagging System
  • 1. Aurora Patents Gene Tagging System
• 17. Upenn: Pure-Blood Microchips
  • 1. Upenn: Pure-Blood Microchips
• 18. Cadus Pharmaceutical: Orphan Receptors and G-Protein
  • 1. Cadus Pharmaceutical: Orphan Receptors and G-Protein
• 19. Mycota Biosciences: Functional Genomics in Fungus to Find Drug Targets
  • 1. Mycota Biosciences: Functional Genomics in Fungus to Find Drug Targets
• 20. Mendel Biotech: Technology Makes Plants More Weatherproof
  • 1. Mendel Biotech: Technology Makes Plants More Weatherproof
• 21. Hyseq Protein May Reduce Blood Clotting
  • 1. Hyseq Protein May Reduce Blood Clotting

5. Structural Genomics

• 1. Structural Genomics
  • 1. Structural Genomics
• 2. Protein Folding
  • 1. Protein Folding
• 3. NIGMS: $150 Million for Multicenter Protein Structure Initiative
  • 1. NIGMS: $150 Million for Multicenter Protein Structure Initiative
  • 2. New York Structural Genomics Research Consortium
  • 3. Northeast Structural Genomics Consortium
  • 4. The Midwest Center for Structural Genomics
  • 5. The Structural Genomic Center
  • 6. Northeast Structural Genomics Consortium
  • 7. TB Structural Genomics Consortium
  • 8. Southeast Collaboratory for Structural Genomics
  • 9. Joint Center for Structural Genomics
• 4. University of Washington: Computational Method may Hold Key to Predicting Protein Folding
  • 1. University of Washington: Computational Method may Hold Key to Predicting Protein Folding
• 5. Berkeley Lab's Advanced Light Source Accelerates X-Ray Crystallography
  • 1. Berkeley Lab's Advanced Light Source Accelerates X-Ray Crystallography
• 6. University of California-Santa Cruz: New Images Reveal the Workings of Cellular Protein Factories
  • 1. University of California-Santa Cruz: New Images Reveal the Workings of Cellular Protein Factories
• 7. Keio University; Teikyo University Biotechnology Center: Snapshots of a Molecular Motor
  • 1. Keio University; Teikyo University Biotechnology Center: Snapshots of a Molecular Motor
• 8. Integrative Proteomics: X-Ray; NMR; Mass Spec for Target ID
  • 1. Integrative Proteomics: X-Ray; NMR; Mass Spec for Target ID
• 9. Wistar Institute: X-Ray Structure Reveals Similarities in Molecules Linked to Cancers
  • 1. Wistar Institute: X-Ray Structure Reveals Similarities in Molecules Linked to Cancers
• 10. NIAID; St. Jude's; St. Andrews: Advance in Tackling Common Viral Respiratory Disease
  • 1. Structure of Respiratory Virus Yields Clues for Drug Design
• 11. Structural Bioinformatics Patents NMR 3-D Structure Technology
  • 1. Structural Bioinformatics Patents NMR 3-D Structure Technology

6. Bioinformatics and Computational Proteomics

• 1. Bioinformatics and Computational Proteomics
  • 1. Bioinformatics and Computational Proteomics
• 2. Incyte Genomics
  • 1. Incyte Genomics
  • 2. With Oxford GlycoSciences: Protein Profiles of Health and Disease
  • 3. Genicon Sciences: Measuring Minute Protein Levels
  • 4. With IBM: Genomics Knowledge Platform Allows Integration of Genomic; Proteomic Data
  • 5. With Galapagos: Overexpression of Human Genes in Adenovirus
  • 6. Conflict with Gene Logic; Affymetrix
• 3. Turbogenomics: Turbo-Charged Blast Sequence Comparison
  • 1. Turbogenomics: Turbo-Charged Blast Sequence Comparison
• 4. Celera Genomics: Now Proteomics
  • 1. Celera Moves into Billion-Dollar Proteomics Program
  • 2. Celera; Compaq; DOE Build Big Supercomputer
• 5. Entigen Provides Services to Smaller Research Groups
  • 1. Entigen Provides Services to Smaller Research Groups
• 6. GeneData AG: Collaboration Targets Antibacterials
  • 1. GeneData AG: Collaboration Targets Antibacterials
• 7. Alphagene Identifies 264 New Genes
  • 1. Alphagene Identifies 264 New Genes
• 8. Lion Bioscience Provides System to Nestle and Bayer
  • 1. Lion Bioscience Provides System to Nestle and Bayer
• 9. Geneformatics: Protein Structure Prediction
  • 1. Schering-Plough: Drug Targets
  • 2. NMR Spectroscopy with Rutgers
• 10. Proteome and Spotfire: Databases and Analytic Software
  • 1. Proteome and Spotfire: Databases and Analytic Software
• 11. Netgenics
  • 1. Netgenics
• 12. Shanghai Genecore: Complicated Genealogy
  • 1. Shanghai Genecore: Complicated Genealogy
• 13. Norwegian Radium Hospital: Mining the Biobibliome
  • 1. Norwegian Radium Hospital: Mining the Biobibliome
• 14. National Center for Genome Resources: ISYS Integrates Bioinformatics Tools; Databases
  • 1. National Center for Genome Resources: ISYS Integrates Bioinformatics Tools; Databases
• 15. McGill University Launches Centre for Bioinformatics
  • 1. McGill University Launches Centre for Bioinformatics
• 16. Compugen and UCSF: New Chemokine Binds HIV Co-Receptors
  • 1. Compugen and UCSF: New Chemokine Binds HIV Co-Receptors

7. More Proteomics Companies and Research Groups

• 1. Millennium Pharmaceuticals
  • 1. Bayer: Proteomics-Derived Drug Candidate
  • 2. Phase II Clinical Trials Underway for Proteasome Inhibitor in Cancer
• 2. ZymoGenetics Runs the Gamut of Protein R&D
  • 1. ZymoGenetics Runs the Gamut of Protein R&D
  • 2. Set Free by Novo Norkisk
  • 3. Zymogenetics Researchers Discover Novel Protein with Potential Role in Psoriasis
• 3. Proteome Systems: Australians Build Proteomics Capabilities
  • 1. Proteome Systems: Australians Build Proteomics Capabilities
• 4. Gemini Genomics and Large Scale Biology Corp. Isolate 70 Disease Proteins
  • 1. Gemini Genomics and Large Scale Biology Corp. Isolate 70 Disease Proteins
• 5. Myriad Genetics
  • 1. Myriad Genetics
  • 2. Myriad; Hitachi; Oracle; Friedli Join Forces to Map Human Proteome
  • 3. Schering AG: Therapeutics
  • 4. Myriad and Cancer
  • 5. Myriad Database: Internet Access by DoubleTwist
• 6. Eos Uses Morphosys Combinatorial Antibody Library
  • 1. Eos Uses Morphosys Combinatorial Antibody Library
• 7. MitoKor: Alzheimer's Disease
  • 1. MitoKor: Alzheimer's Disease
• 8. Oxford Glycosciences
  • 1. Oxford Glycosciences
  • 2. Incyte: Drug Efficacy and Safety
  • 3. Early Access to Applied Biosystems' New Spectroscopy System
  • 4. Pioneer: Plants
  • 5. Packard: Biochips
• 9. Sunesis Pharmaceuticals
  • 1. Sunesis Pharmaceuticals
• 10. Morphochem AG
  • 1. Morphochem AG
• 11. Scriptgen Becomes Anadys and Expands
  • 1. Scriptgen Becomes Anadys and Expands
• 12. Fraunhofer Institute Pinpoints Candida Pathogenicity Proteins
  • 1. Fraunhofer Institute Pinpoints Candida Pathogenicity Proteins
• 13. Genetrace Systems Acquires Strata Biosciences
  • 1. Genetrace Systems Acquires Strata Biosciences
• 14. Axcell Maps Interactions Of WW Domain Proteins
  • 1. Axcell Maps Interactions Of WW Domain Proteins
• 15. Large Scale Biology Corp.; Navy; NIH Look for Stem-Cell Factors
  • 1. Large Scale Biology Corp.; Navy; NIH Look for Stem-Cell Factors
• 16. Syngenta and Myriad: Rice Proteomics May Mean Better Cereal Crops
  • 1. Syngenta and Myriad: Rice Proteomics May Mean Better Cereal Crops
• 17. Ciphergen Biosystems: Biomarkers
  • 1. Ciphergen Biosystems: Biomarkers
• 18. Beyond Proteomics: Glycomics
  • 1. Beyond Proteomics: Glycomics
  • 2. Glycominds
  • 3. Glygen Develops Glycoconjugates For Gene Therapy
• 19. Upenn Scientists Show How Chaperonins Catch Protein-Folding Errors
  • 1. Upenn Scientists Show How Chaperonins Catch Protein-Folding Errors
• 20. Newcastle University: Fragments of Dinosaur Protein can Survive in Bone Fossils
  • 1. Newcastle University: Fragments of Dinosaur Protein can Survive in Bone Fossils
• 21. Scripps: Expanding E. Coli's Amino Acid Repertoire Paves Way for Engineered Proteins
  • 1. Scripps: Expanding E. Coli's Amino Acid Repertoire Paves Way for Engineered Proteins
• 22. Gladstone Institute; UCSF: HIV Viral Protein Plays Offense and Defense Against Immune System
  • 1. Gladstone Institute; UCSF: HIV Viral Protein Plays Offense and Defense Against Immune System
• 23. UCSD: Protein Responsible for Failing Heart
  • 1. UCSD: Protein Responsible for Failing Heart
• 24. Ceres Pharmaceuticals: Powerful New Vaccines from Yeast
  • 1. Ceres Pharmaceuticals: Powerful New Vaccines from Yeast
• 25. Cellular Signaling Alliance Unites Researchers Via Internet
  • 1. Cellular Signaling Alliance Unites Researchers Via Internet
• 26. University of Illinois: New Mechanism for Cell Signaling
  • 1. University of Illinois: New Mechanism for Cell Signaling
• 27. NCI Intensifies Informatics
  • 1. NCI Intensifies Informatics
• 28. Xenometrix Wins US Gene-Profiling Patent
  • 1. Xenometrix Wins US Gene-Profiling Patent
• 29. PNNL: Top Role in Biological Sciences Initiative
  • 1. PNNL: Top Role in Biological Sciences Initiative
• 30. Dana-Farber Cancer Institute: Molecular Gateways to Death
  • 1. Dana-Farber Cancer Institute: Molecular Gateways to Death

8. Markets and Barriers to Commercialization

• 1. Markets
  • 1. Markets
  • 2. Sectors and Opportunities
  • 3. Small Companies Can Compete
  • 4. International Competition
  • 5. Technology Fusion
  • 6. Synergy: New Directions/Partnership Collaborations
  • 7. Software
  • 8. Hardware
  • 9. Bioinformatics
  • 10. Other Markets
• 2. Barriers to Commercialization
  • 1. Barriers to Commercialization
  • 2. Introduction
  • 3. Bioinformatics
  • 4. Labs on Chips (LOCs) and Microarrays

9. Appendices

• 1. Appendix A: Contacts
  • 1. Contacts
  • 2. Council Members; Human Proteomics Organization (HUPO)
• 2. Appendix B: Recent Patents in Proteomics and Bioinformatics
  • 1. General Proteomics
  • 2. Bioinformatics
• 3. Appendix C and D: Website URLs and Publications
  • 1. Website URLs
  • 2. Publications