Proteomics: Promising Research, Potential Applications, And New Developments (Technical Insights)

Published by: Frost & Sullivan

Published: Oct. 1, 2001

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

Abstract

Proteomics research is growing at a rapid rate and has become one of the most important areas of investigation in biotechnology. There are proteomics programs in nearly every major biotechnology and pharmaceutical firm, and critical developments are virtually impossible to track. Technical Insights report separates the good news from the mundane by providing the following:

• A detailed overview of technological advances in development laboratories
• Identification of key companies and developers and provision of estimates of timelines for commercializing technology
• Definitions of key markets and applications
• Reporting on technology drivers as well as obstacles in the way of commercial success
• A detailed list of key contacts in the field, including names, titles, addresses, phone numbers, e-mail addresses, and URLs

Proteomics is not the study of proteins one by one, as has traditionally been done, but a highly automated endeavor operating on a massive scale. High-throughput is the operative phrase, with increasingly sensitive assay techniques, the integration of multiple techniques into a single platform, and robotics and computers taking the place of lab technicians. A great challenge lies ahead, therefore, for scientists to develop effective systems with high-throughput, suitably sensitive arrays, and a complicated level of integration.

Proteins are the building blocks of tissues and cells, circulate in the blood to eliminate disease, regulate body temperature, digest food, synthesize other proteins and small molecules, and in general perform all the work necessary to keep an organism working. Under- or overproduction of proteins is implicated in many human diseases. Thus, knowing which genes are responsible for which proteins gives medical science a point of attack for potentially curing many illnesses.

In the 1980s, when working with DNA and characterizing genes became easy, vast numbers of researchers in biology abandoned whatever they were studying to pursue the glamorous field of molecular genetics. Newspapers and magazines extolled the medical miracles that would come from identifying the gene for this disorder or that form of cancer. Investors made millions in genomic biotech. But a group of scientists stayed behind to study proteins. They were content to labor quietly behind the scenes, out of the limelight, for one reason. They believed proteins were the key to everything---that if you didn't understand what was happening in a cell beyond the DNA sequence of a given gene, you didn't understand anything. Now everyone has realized these guys were right all along. Proteins are the next new thing. The endeavor of characterizing the human proteome is an order of magnitude more complex than genomics. Additional new technologies and refinements of standard techniques are needed urgently, and considerable effort is being devoted to the development of novel tools for the pro-teomics trade.

Proteomics is an intensely more difficult field of study. One paramount reason for this is that the one-gene, one-protein hypothesis is disproved. Many genes produce multiple proteins via alternative splicing of mRNA transcripts, proving that there are many more proteins in human cells than there are genes in the human genome.

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