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Bruker Daltonics Adds ProFound and Sonar to Growing Proteomics Software Portfolio

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Last week, Bruker Daltonics and the Genomic Solutions subsidiary of Harvard Bioscience announced a reseller agreement for Genomic Solutions’ ProFound and Sonar search engines. Under the terms of the non-exclusive deal, ProFound and Sonar will be incorporated with Bruker’s line of mass spectrometry instruments. It will join the Mascot search engine from Matrix Science, which Bruker currently bundles with its mass spec equipment.

For Bruker, the arrangement simply provides more options for its customers — a key component of the company’s strategy in bioinformatics, according to Herbert Thiele, director of bioinformatics.

David Green, president of Harvard Bioscience, said the OEM deal is typical for the company, but that it intends to continue marketing the programs as standalone packages as well. ProteoMetrics, the company that originally developed ProFound and Sonar, relied on reseller agreements to sell its software because it had a relatively small sales force. That sales force has grown exponentially via ProteoMetrics’ acquisition by Genomic Solutions, which Harvard Bioscience subsequently acquired, but Green said Harvard would continue to rely on specialty distribution channels in certain niche areas, such as mass spec.

“It’s a very common product marketing strategy for us to partner up with people who have distribution reach into places we’ll never get to by ourselves,” said Green.

Under the agreement, Bruker will add the ProFound and Sonar search engines to Mascot as the recommended third-party solutions for proteomics database searching.

These offerings, according to Thiele, make up only a small part of the company’s broad bioinformatics portfolio.

Bruker’s bioinformatics team has developed software solutions to meet three primary levels of bioinformatics associated with mass spectrometry, Thiele explained: hardware-related bioinformatics, data-mining-related bioinformatics, and problem-related bioinformatics. Hardware-related tools address quality control and quality assurance issues surrounding the company’s MALDI-TOF, TOF/TOF, and electrospray ionization LC-MS/MS technologies. For example, online data evaluation software triggers feedback procedures that help improve identification success rates and minimize analysis time, Thiele said.

Data-mining-related tools include the recommended third-party search engines, which plug into ProteinScape, a data repository that provides access to public and proprietary sources of protein data. Thiele explained that the combination of several search algorithms increases the success rate of protein identification.

While most mass spec vendors offer similar configurations of proprietary and third-party software to meet these requirements, Thiele went on to explain how Bruker has modified its mass spec software portfolio to meet the specific demands of the third level of bioinformatics that he calls “problem-related” or “application-related.” This level is itself split into three areas: expression proteomics, genomics, and metabolomics.

“The raw data generated by mass spec instruments are not sufficient for a meaningful understanding of biological problems. Depending on the analytical question, dedicated problem-related bioinformatics solutions have to be supplied,” said Thiele. With this philosophy in mind, the company offers Proteineer for “pure proteomics” — protein analysis and characterization — along with GenoTools as a component of the GenoLink product line for SNP and genotyping applications, and MetaboliteTools to predict and identify metabolites for metabolomic research.

Each software package acts as a specialized front end for researchers engaged in particular areas of mass spec-related research.

One emerging application area for which the company is currently developing a new software line is clinical proteomics — screening for specific diagnostic biomarkers in blood serum samples. According to Thiele, evaluation of individual protein peaks is not sufficient for diagnostic applications of mass spec technology, so the company is working on algorithms “capable of determining complex biomarker patterns.” Thiele did not disclose further details on this upcoming suite of software products, but said the company expects to introduce it by the end of 2003.

The “key message,” according to Thiele, is that after protein identification, “more information regarding characterization of the protein, especially its functionality, potential underlying genetic polymorphisms, and clinical relevance, is often required.” Bruker’s internal software development and partnering strategy reflect that philosophy. In addition to the upcoming line of clinical proteomics software, Thiele said the company is expanding the capabilities of its ProteinScape database to integrate with a number of new data sources “in the very near future,” and is also evaluating “various web accessible tools as well as third-party software” to add to its expanding software portfolio.

— BT

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