The completion of the Human Genome Project last year marked a milestone in medicine. The detailed mapping of the entire set of human genes was a decade-long project worked on by some of the best minds in biology. But in many ways it was only the beginning of the real medical challenge: understanding the million or so proteins that are the molecular workhorses of the human body. Genes are really just the programming code that tells cells how to synthesize proteins; almost all the biological action occurs among these large, complex molecules.

When proteins misbehave they can destroy our health in myriad ways, from the amyloid proteins that gum up the brains of Alzheimer's patients to the proteins that cause runaway cancer-cell growth. Battling disease more effectively means getting a better grip on how proteins work and interact-and fail. The most important emerging tools in reading the vast protein library are micro-arrays, small chips containing thousands of protein samples that can be analyzed quickly and cheaply. "This is where people will get answers about how disease develops, how drugs work, and how to find new drugs," says Peter Wagner, chief technical officer of Zyomyx, a Hayward, CA-based protein-chip startup.

Zyomyx has nearly a dozen competitors, including Large Scale Proteomics, Ciphergen Biosystems, Packard BioScience and Phylos. The industry's first products are expected on the market in a year, and while technologies vary, the new biochips are generally two-dimensional grids of proteins or protein fragments attached to a solid support.

When the protein microarray is exposed to biochemicals or solutions of other proteins, some of those molecules will stick and some will wash off; the ones that stick can be identified by various markers, such as fluorescent tags. Molecules that adhere strongly to specific proteins are valuable leads in the search for new drugs, because that binding ability is what makes pharmaceuticals effective. And for diagnostics, measuring abnormally high amounts of telltale proteins in a blood sample using these biochips could be a fast method for early detection of heart attacks and cancer.