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Proteome Systems Turns to IBM to Provide Final Link for Integrated Proteomics Platform

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Proteome Systems has chosen IBM to provide the hardware and middleware for its proteomics discovery platform, Proteome Systems CEO Keith Williams said last week. An official announcement of the partnership is expected on November 20, he said.

As part of its strategy to provide customers with an integrated package of instruments for separating, identifying, and quantifying proteins in biological samples, Sydney-based Proteome Systems has brought together a wide spectrum of instrument manufacturers, including Shimadzu Biotech, Millipore, and Sigma-Aldrich, to provide the component pieces of its 2D gel electrophoresis-based platform.

Proteome Systems has said the platform, called ProteomIQ, would hit the market sometime before the end of the year.

The latest partner, IBM, which recently began supplying Proteome Systems’ in-house hardware and database technology, will now provide the computing power to run the software components of the ProteomIQ, which include a laboratory information management system and bioinformatics tools for searching protein databases and data visualization.

“There’s a lot of work that has gone into making sure all of the different elements of the platform integrate, and we haven’t established this on any platform other than the IBM platform and we probably won’t,” Williams said. “I guess what we’ll say is that this is a solution that is going to sit on IBM technology.”

Williams added that partnering with IBM doesn’t mean Proteome Systems won’t incorporate computing technology from other providers, and that the company is planning other informatics offerings that Proteome Systems will announce before the end of the month.

“It’s evolving quite fast at the moment,” Williams said. “The informatics was really the last step in this chain of developing technologies and we were keen to build the offering and get clear on what that offering was before we got down to working out how we wanted to configure it.”

For its standard three-mass-spectrometer ProteomIQ offering, Proteome Systems currently employs an IBM pSeries server, but is considering whether to integrate more powerful IBM servers, such as the Regatta, when users require a larger set of mass spectrometers.

The bioinformatics package, called Bioinformatique, tracks bar-coded samples through the 2D gel electrophoresis separation steps, performs image analysis of the gels, and includes software for matching protein fragments with patterns of known protein fragments that are stored in public databases. In addition, the software automatically updates the local search engine with new protein sequence data from public databases, and curates the sequence data to eliminate redundancies and add search capabilities.

The software should also help make proteomics experiments compliant with laboratory regulations mandated by the US Food and Drug Administration, Williams said.

Proteome Systems’ other equipment partners are Sigma-Aldrich, Alpha Innotech, Millipore, Kratos Analytical, a subsidiary of Shimadzu Biotech, and Thermo Finnigan.

Rather than build its own sales and distribution networks, Proteome Systems chose to work with manufacturing partners with these resources already in place, said Bill Skea, the general manager of Proteome Systems’ US facility in Woburn, Mass. “We’re up against Bio-Rad,” he said. “We’re small, but we had to develop a lot of equipment and we don’t want to have to develop a large sales force. [Our partners] bring us a lot of credibility, and we can help them get into proteomics, which they all want to do.”

— JSM

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