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By Mark D. Uehling

Sept 11, 2003 | If a company calls itself "The ProteinChip Company" and trademarks the phrase "ProteinChip," one would predict it is in the business of selling protein chips.

But does Ciphergen Biosystems make such chips? Not everyone thinks so. "What they do is not a protein microarray," Yale's Michael Snyder says. "I would define a protein microarray as putting down individual proteins in an addressable format. Their protein microarray is a substrate of a bunch of affinity resins."

Another way to describe Ciphergen's approach might be to say it provides a user-friendly way to do SELDI — a mass spectroscopy technique formally known as surface-enhanced laser desorption-ionization. The advantages of the Ciphergen system include detecting unknown proteins and minimal sample preparation.

Despite Snyder's jibe, Ciphergen occupies a central position in the protein microarray market. Key customers include Pfizer, seeking pulmonary disease biomarkers; and Novartis, for oncology biomarkers. Part of Ciphergen's success can be traced to a few high-profile papers — the company's technology helped to identify a protein that protects some HIV-infected patients from developing AIDS (see "Chipping Away at AIDS Mystery," Nov. 2002 Bio·IT World, page 20).

Kate Gilbert, who manages Ciphergen's protein chip business unit, says that much of the demand for the technology has been for biomarker discovery — identifying and measuring proteins that exist in very small quantities. "It's been steady, but we are seeing ramp-up of demand," she says.

Early on, Gilbert says, customers wanted to see every protein in a sample. "Now people are realizing that when you do that, you get the same old proteins, again and again."

A more useful approach, she suggests, may be to look "for techniques that can enrich low-abundance proteins and find some of the things that are not apparent when you try to see everything. Then you're actually finding things that may be of more interest, things that may be unique."

Ciphergen is already selling tools to answer obvious questions once a biomarker is confirmed: "Where does it sit in the pathway? What other proteins does it bind? You might think about what they mean, what their function is, where they might sit in a pathway, or how you might develop an assay for them. That will be the next logical step."

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