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Life (and Building HTP Platforms) is a Race

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For a busy fellow like Robin Offord, president of Geneva Proteomics, Australia seems an awfully long way to go for a 60-minute speaking engagement. Then again, Australian life scientists might wonder why Offord built his company so far away from the birthplace of proteomics.

Offord and Compaq, his host at a bioinformatics and biocomputing meeting down under in May, make a strong case for GeneProt as the world leader in proteome research. With a cluster of 1,420 Alpha processors, GeneProt says it possesses the most powerful civilian supercomputer of the moment. And deep-pocketed backers lend the company an air of invincibility: Compaq, Bruker, and Novartis have all taken equity stakes, and a research deal with Novartis is expected to reap $41 million over the next three years.

Even so, some folks in Australia beg to differ with GeneProt’s claim that it has been first to industrialize proteomics research.

Brad Walsh, who directs the Australian Proteome Analysis Facility (APAF) situated just outside Sydney on Macquarie University’s sprawling research campus, where leaves were falling in early May, says his operation was established five years ago. Which would make it, not GeneProt, the world’s first proteomics factory.

With an annual operating budget of $2 million, APAF can’t match GeneProt on muscle. But its assembly-line-like setup that shuttles proteins from 2D gel through mass spectrometry and in silico analysis would seem to qualify it as an industrial-scale operation. Walsh says he is close to being capable of characterizing the proteome of an entire sequenced microorganism — up to 4,000 proteins — in one week. In fact, APAF’s partnership with BioRad and Micromass has resulted in the development of a platform of integrated technologies for high-throughput proteome analysis that are now commercially available to others who aspire to such projects in the form of the ProteomeWorks System.

APAF’s ties to several of the field’s forefathers — Ian Humphery-Smith, now a professor in the department of pharmaceutical proteomics at the University of Utrecht and the organizer of the Human Proteome Organization, helped establish the facility, and Denis Hochstrasser, a GeneProt founder and 2D-gel guru, spent a year at the lab in its early stages and remains an advisor — give credence to its claim to first place.

Marc Wilkins, known far and wide for having coined the term proteome, was also an APAF founder. But he has since defected to an office park down the street. Wilkins was among a group of APAFers who followed the facility’s former director, the elfin and energetic Keith Williams, in a mass exodus in 1999 to pursue a parallel plan with a more capitalist bent. Having teamed up with Shimadzu Biotech, Sigma-Aldrich, and Millipore to develop their own proteome analysis platform, Wilkins and Williams now say that Proteome Systems has created “the world’s first integrated, high-throughput platform for proteome analysis.” Williams observes, “Life’s a race.” Which explains why everyone wants to be first.

— Adrienne Burke

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