Seeking answers

Collaboration between Thermo, Matrix combines proteomics search engines.

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SAN JOSE, Calif.—After a nine-month effort, Thermo Fisher Scientific Inc. and London-based Matrix Science have combined Matrix's Mascot search engine for protein identification with Thermo's BioWorks software. This is a significant move, say both companies, as the SEQUEST search algorithm from the University of Washington—which is a component of the BioWorks software—and Mascot are "the two most widely accepted search engines in the field for protein identification and PTM characterization."
"Partnering with Matrix Science and integrating our products enables customers to have the best features of both and to enhance their productivity," says Andreas Hühmer, proteomics marketing director at Thermo Fisher Scientific. "It's become apparent that customers get their best protein identification results when they combine the results from both search engines, and over the last year we started to see more and more technical posters presented at conferences in which customers went through the process of painstakingly combining the results manually to increase their proteome coverage, reduce their false positive rates or increase the confidence in their results."
Because customers saw the search engines as complementary, Hühmer says, the timing seemed right to provide an automated way for them to merge their results.
In addition to being able to consolidate identification results from the two search engines, users will be able to cross-validate the results, taking advantage of the complementary information provided by each, the companies report.
"With an integrated results output, researchers will increase their productivity," he notes. "Finally, because the algorithms used for Mascot and SEQUEST are fundamentally different in the way that they evaluate spectra to find good protein identifications, finding the same hit with each search engine increases the customer's confidence that the hit is real."
This collaboration is important for exposing more people to search engines they might not already have used—whether SEQUEST or Mascot, says Richard Jacob, Matrix's country manager for the United States. For Matrix specifically,  the integration means more sales.
The deal with Thermo also builds on momentum that Matrix has gained in other Mascot integration deals, such as with Denmark-based Proxeon in August 2007; Milford, Mass.-based Waters Corp. in April 2005; and U.K.-based Nonlinear Dynamics in August 2004. DDN
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