By Randall Osborne

First, there was genomics. Then, proteomics. Now comes ¿phenomics,¿ an area of research named by Ciphergen Biosystems Inc., which uses a protein-chip, phenotype-discovery tool for biomarkers.

¿When you look at proteomics, what you¿re looking at is a very good tool for doing protein analysis, but what people really want to look at is [protein] functions, after they analyze them,¿ said William Rich, the company¿s president and CEO. ¿That¿s the real game.¿

Most protein technologies, he said, are ¿characterized either by a deficiency in sample preparation or in the detection part, where you might have an elegant separation, like [on] a lab chip, but you have to derivatize everything, and proteins don¿t like to be derivatized.¿

Earlier this month, Palo Alto, Calif.-based Ciphergen launched its ProteinChip system, Series PBS II, which ¿integrates separation, purification and detection on the same chip,¿ Rich said.

PBS II is aimed at the research community. Ciphergen expects to introduce a new system next year, designed more specifically for luring pharmaceutical companies to take advantage of biomarker discovery, characterization and assay services.

¿You can start with a very crude biological sample ¿ serum, tissue, spinal fluid ¿ and, in a very short period of time, you can rapidly purify it,¿ Rich said. ¿When you¿ve discovered the proteins of interest, you can characterize them by doing secondary processing on the same chip.

In April, researchers disclosed results of a cancer study using the company¿s ProteinChip technology at the annual meeting of the American Association for Cancer Research.

The study team used laser capture microdissection to extract cells from prostate, breast and colon cancers, and went on to capture and characterize the proteins associated with various forms of cancer, from benign to pre-invasive to invasive types.

Rich said the company hopes to develop the proteins as diagnostic markers of disease progression, and as targets for therapeutic drugs. ¿We think this will be a breakout¿ application for us,¿ he said.

Genomics-driven strategies, Rich said, are ¿necessary, but not sufficient.¿

¿The noise level is very high¿ in genomics and proteomics, he added, so describing Ciphergen¿s technology properly has been critical.

¿Positioning this as a protein lab on a chip is not the best positioning,¿ Rich said, as the company found during its two years of testing a prototype system in various laboratories to ¿find out where the value proposition was maximized. We¿ve done a lot of work to get ready for this.¿

Founded in 1995, the company has 60 employees and has raised $25 million. n