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Startups GenoLogics and Proteome Software to Tackle Proteomics Market with Integrated Products

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Two startups in the bourgeoning proteomics software sector are hoping to get a boost in the market by integrating their respective products.

Last week, GenoLogics and Proteome Software said that they would integrate Proteome Software's Scaffold analysis software with GenoLogics' ProteusLIMS data-management platform.

Both companies were founded within the past several years to address the informatics demands of the proteomics research market, and officials from both companies described their offerings as complementary rather than competitive.

"We provide more of the data management and the contextual information around how you got to that protein, whereas they provide the more analytic results around analyzing those proteins," Michael Ball, CEO of GenoLogics, told ProteoMonitor's sister publication BioInform. "So it's a very positive and collaborative relationship, and very symbiotic."

ProteusLIMS is gaining ground among proteomics core facilities as a flexible platform for integrating data from gels, mass spectrometry, and protein searches. Last month, GenoLogics announced that Scripps Florida and St. George's University of London Medical Biomics Center had licensed the technology, joining the University of Pittsburgh Genomics and Proteomics Core Laboratories, the University of Texas Medical Branch Proteomic Center, Oregon Health & Science University, the Genome British Columbia Proteomics Center, and the University of Toronto's Proteomics Research Center as publicly disclosed ProteusLIMS customers.


"We provide more of the data management and the contextual information around how you got to that protein, whereas they provide the more analytic results around analyzing those proteins."

Proteome Software's Scaffold, meanwhile, is emerging as the "best of breed" product for protein analysis, Ball said. Scaffold is a data-visualization and analysis tool that runs on protein lists that have already been generated with the Mascot or Sequest search engines.

Ball said that ProteusLIMS already works with all the major protein search engines, including Mascot, Sequest, X! Tandem, and SpectrumMill, but the partnership with Scaffold "allows more deep analytics across those different platforms."

The integration project is expected to be completed "later this year," Ball said, but he did not provide a more specific timeline.

Mark Pitman, sales and marketing director of Proteome Software, said that the companies "haven't really worked out the details" of the integration process, but he said he expects it to be a smooth one.

Pitman said the collaboration grew out of last year's American Society for Mass Spectroscopy meeting, where Proteome Software officially launched Scaffold. "We talked to GenoLogics initially and we thought that this would be a great partnership. It's just that for a year, nothing really occurred because we were both going our separate ways."

Things came together at another conference, this year's Association of Biomedical Research Facilities meeting. "We talked about it again," Pitman said, "and we said not only do we have customers that want to look at us both, and use both of our products, but we're going after the same marketplace, so why don't we get this put together quickly?"

So far, the companies have two customers in common: OHSU and Scripps.

Though the two companies are both relatively young — Proteome Software was founded in 2004 and GenoLogics in 2002 — Proteome Software is much smaller and is therefore likely to benefit more from the partnership. The Portland, Ore.-based company employs three people, while GenoLogics, based in Victoria, BC, Canada, just passed the 45-employee mark last week.

GenoLogics also has a stronger cash position. The company raised $5 million in VC funding last February (see BioInform 02-07-05), while Proteome Software is self-funded.

But GenoLogics' Ball said that the smaller firm already has a strong presence in the market. "What we're seeing in the marketplace is that there's strong desire among researchers to compare protein search results, and as we work through our customer base and do prospects, we continue to run into Proteome Software, because that appears to be the best-of-breed product in that space for the analysis of proteins."

In addition to the integration with ProteusLIMS, Proteome Software is planning to release a version of its software that will enable researchers to submit their proteomics data to peer-reviewed journals. "There will be an export function in our program that will just at a press of a button compile all your data together and submit it for publication," Pitman said.

The company is hoping to have that capability ready by this year's ASMS meeting in late May, Pitman said.

GenoLogics, meanwhile, plans to expand beyond its foothold in the proteomics informatics market in the year ahead. "We want to move closer to systems biology," Ball said.

The company is developing a version of ProteusLIMS called GeniusLIMS that will be targeted to the microarray-analysis market, and plans to develop similar modules of the product that will enable integration across the various -omics disciplines, Ball said.

While he conceded that the data-management market is more crowded in the genomics sector than it is in proteomics, he said that GenoLogics should have an advantage because "no one is providing a platform to integrate data across all these different platforms."

Ball did not provide a release date for GeniusLIMS or further details of the company's product-development plans.

— Bernadette Toner ([email protected])

A version of this article originally appeared in BioInform.