Proteomics: A Key Enabling Tool for Genomics?


1. Introduction: Why Proteomics?

Gene expression information is often insufficient to determine the ultimate cause of a condition or disease.


2. Scientific Background: The Challenge of Greater Complexity

The differences between proteomics and genomics far outweigh the similarities, but the two fields can be highly complementary.

2.1 Comparing Proteomics with Genomics



2.2 Using Proteomics and Genomics in a Complementary Fashion


3. The Current and Emerging Technologies: The Search for High Throughput

The major goal for proteomics leaders is to accelerate high-throughput capacity, but as the field enters the next level of analysis—further elucidation of protein function—there will be an increasing need for better systems of data capture and analysis, as well as models capable of representing complex networks.

3.1 The First Level of Analysis: Protein Separation, Identification, and Characterization

Sample Preparation

2-D Gel Electrophoresis


Image Analysis

Mass Spectrometry

Protein Chips



3.2 The Next Level of Analysis: Tools And Approaches for Protein Function Studies


High-Throughput Expression

Protein-Protein Interactions

Protein Function

What’s Next?


4. Business and Strategic Considerations: The Leaders Are Far Ahead

A handful of companies have taken the lead in this field’s various markets—for services, specialized products, and supplies—and despite the growing demand in these markets, proteomics newcomers face a challenge in catching the leaders.

4.1 Industry Leaders

4.2 Selected Tool and Service Providers

4.3 Bench-Top Platform Technology Providers


5. Applications: Early Signs of Valuable Potential

Proteomics is already showing substantial promise in key areas of drug development—

toxicology and the identification of surrogate markers of drug response—as well as in studies of pathogens and other primitive organisms.

5.1 Basic Research

5.2 Diagnostics and Prognostic Indicators

5.3 Drug Discovery and Development

Target Identification snd Validation

Pathway Elucidation

Mode of Action


Surrogate Markers of Drug Response

Drug Resistance

5.4 Pathogen Studies

5.5 Agriculture and Other Areas


6. Outlook: New Tools and a Context for Managing Data

As genomic sequence information becomes a commodity, a new set of criteria— expertise in bioinformatics, protein function, and modeling complex systems— will determine this field’s leaders.

6.1 Key Remaining Issues

Is 2-D Gel Electrophoresis Replaceable?

Access to Genetic Sequence Information

Plain Skepticism

6.2 The Future of Proteomics

6.3 Commentaries from Editorial Board Members


Appendix A: Table of Companies with Proteomics Related Activities


Appendix B: Company Profiles