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Proteomics Software Vendors Align with Mass Spectrometer Suppliers in Push for Market Share

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As proteomics emerges as the next high-growth life sciences area, a number of software vendors have found that alliances with mass spectrometer suppliers are the shortest route to securing a piece of a market recently forecast by Front Line Strategic Management Consulting to reach $2.8 billion by 2005.

Most recently, London-based Matrix Science signed a non-exclusive distribution deal with Applied Biosystems for its Mascot online database search software for protein identification.

Mascot comprises a search engine and a web-browser interface to match data from mass spectrometers against protein and nucleic acid databases. Search results can also be imported into a database for data mining processes. The software can accept data from all major types of mass spectrometers and has the ability to run on Tru64 Unix, Irix, Linux, Solaris, and Microsoft Windows.

Matrix Science also has Mascot distribution deals with Bruker Daltonics, Shimadzu, and Agilent. The company has sold Mascot to over 100 customers. The entry price for the software is around $10,000.

David Creasy, director of Matrix Science, said the company splits its sales efforts between direct sales and distribution deals. The company tends to focus its direct sales on large pharmaceutical companies while the distributors reach “smaller labs and universities that we wouldn’t be able to reach directly.”

Matrix Science will work with Applied Biosystems/MDS Sciex to integrate Mascot with the Analyst and BioAnalyst software packages used for the API Qstar Pulsar system.

While BioAnalyst is an interactive program for data processing one spectrum at a time and Analyst is used for instrument control, Mascot “automates the process of database searching for rapid protein identification,” according to Mark Allen, director of proteomics for LC/MS products for the Applied Biosystems/MDS Sciex joint venture.

“[Mascot] has an excellent reputation in the field. We have many requests for Mascot integration with our software instru-ments,” Allen said.

Applied Biosystems does not have proteomics software deals with any other venders at this time.

Other mass spec vendors have found that partnering with software vendors is the most direct way to meet their customers’ data analysis needs. Amersham Pharmacia Biotech, which offers no protein analysis software of its own, bundles Prowl and ProFound protein database search tools from ProteoMetrics with its Ettan Maldi-TOF system.

ProteoMetrics, based in New York, collaborated for a year and a half with Amersham on the software’s development, but is free to license it to other distributors.

David Fenyö, president of ProteoMetrics, said the company plans to stop selling Prowl and ProFound on its own. “We don’t want to build up a big sales force,” Fenyö said. “It makes more sense to have instrument manufacturers that have a large sales force and can sell it.”

Fenyö added that ProteoMetrics intends to continue selling its Radars system for protein data storage and analysis. Amersham is the company’s first distributor for Prowl and ProFound and ProteoMetrics has not yet signed further distribution deals for the products.

In addition to Matrix Science and ProteoMetrics, Swedish startup BioBridge recently entered the market and said it intends to align itself with mass spec vendors in addition to marketing directly to end users.

But software vendors aren’t going it alone as they attempt to meet the growing demand for protein analysis tools. Applied Biosystems/MDS Sciex are gearing up to launch their own database search engine for the Qstar, the Pro ID software application for automated protein identification.

The launch shouldn’t conflict with the Matrix Science partnership, however. “In our experience many customers want to use more than one database search engine or will have their particular preference,” said Allen. “It’s okay if they use Mascot or Pro ID software for automated data base searching, or PepSea for tag searching, whatever solves their problem.”

— BT

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