The ideal drug discovery program would quickly pinpoint the proteins that are responsible for, or defective in, a given disease. Genomics has dominated recent drug discovery efforts, but now several companies are touting proteomics as a more relevant technology, raising the question of which is the better starting point for target identification, genes or proteins?

Proteomics is to protein biochemistry what genomics is to molecular biology: just as genomics seeks to profile the identity and amount of every gene expressed in a given cell, proteomics seeks to profile the identity, amount, and post-translational modifications of every protein synthesized in a cell.

In theory, proteins should more closely reflect the physiology of a normal or diseased tissue and thus provide a faster route to drug discovery than a focus on genes. In practice, however, the primary technology used for proteomic analysis is technically demanding and genomics still is much more amenable to high-throughput research approaches.

That difference means that genomics is better suited to a comprehensive, broad base for discovery while proteomics may provide more detail across a more limited scope. Thus rather than the alternative to genomics that advocates of the technology sometimes imply, proteomics forms a bridge between structural genomics, which provides gene sequence information, and functional genomics, which seeks to relate gene and protein expression to phenotype and disease.

In this context, the products and services being offered by proteomics companies will complement rather than replace the more established genomics platform, and the practical issues will not be the choice between genomics and proteomics, but rather how best to use each tool.

The proteomics niche

The perceived need for proteomics stems from the fact that in a given tissue, the profile (amount and composition) of total protein cannot be predicted based on levels of gene expression. In 1997, researchers from Incyte Pharmaceuticals Inc. (INCY) and Large Scale Biology Corp., a proteomics company, published in Electrophoresis the relative abundance of 19 proteins found in liver compared to the abundance of those proteins' mRNA transcripts.