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Seeing Demand for FPGA-Enabled Proteomics, Sage-N Snags Sequest Sublicense from Thermo

While tight-lipped about its rationale, Thermo Fisher Scientific has granted Sage-N Research the first sublicense to market and distribute the Sequest proteomic search engine for which it holds an exclusive license from the University of Washington.
Thermo and Sage-N joined forces two years ago to develop a system based on field-programmable gate array technology to accelerate Thermo’s Sequest protein identification software. The offspring of their collaboration, called Sequest Sorcerer, speeds Sequest searches up to 50 times over a CPU [BioInform 03-14-05].
Since then, the firms have been co-marketing Sequest Sorcerer, but the new agreement now gives Sage-N the right to market it on its own as well as to develop new versions of the software. Thermo will no longer sell the Sorcerer appliance.
“Thermo continues to sell the Sequest software, but nothing that is developed by Sage-N,” said David Chiang, Sage-N’s CEO. “Sage-N can sell any form of Sequest, including the proprietary version within the Sorcerer. Sage-N can even sell software-only versions, but does not currently do so.”
A spokesperson from Thermo told Bioinform that, “Thermo Fisher Scientific has had an exclusive license with Sequest for the past 10 years and we have the right to sublicense it to others, Sage-N Research is the first company we reserve the right to sublicense to.”
She declined to comment further.
Sage-N plans to capitalize on its existing clients with Thermo while it strikes out to gain new customers and partners. “We are also bringing on additional partners, so Thermo is not our only partner by any means,” said Chiang.
Sage-N Research was founded five years ago with the intention of building so-called integrated data appliances based on FPGA technology to handle the computational demands of proteomics research. Since then, the company has collaborated with Thermo as well as other partners, including Rosetta Biosoftware and Proteome Software.
“We are actually signing on some software additional companies that have not [yet] been disclosed,” Chiang said.
Chiang said the company’s Sorcerer technology also supports the open source X!Tandem proteomics software developed by Beavis Informatics and that it plans to add support for the National Center for Biotechnology Information’s OMSSA (Open Mass Spectrometry Search Algorithm) as well.
Chiang said he’d also like to partner with Matrix Science to add the company’s popular Mascot software to Sage-N’s offering, “and I think the user base would like to see us support Mascot as well, but it takes two to tango. I think it benefits the user base if Mascot works with us.”
John Cottrell, director at Matrix Science, did not comment on whether it had been courted by Sage-N, but acknowledged via e-mail that Matrix Science has been “approached on several occasions by companies and academic groups with proposals to put Mascot into firmware.”  He added that he considers any speed or cost advantages from hardware to be “arguable.”
“The advantages are mainly in power consumption and, possibly, maintenance costs, although it is hard to put a firm figure on the latter,” he said.
Cottrell said that Matrix Science does not plan to partner with other hardware providers or build an accelerated system on its own. While the company does offer a version of Mascot that runs on clusters for customers who require it, he said that commodity hardware offers sufficient performance for most users.
“The latest multi-core processors from Intel and AMD give very impressive performance-to-cost ratios,” he said. “The PC industry has gigantic resources, so it is tough for proprietary hardware to keep pace with the performance of standard PCs unless a company is prepared to support a continuous and expensive hardware development program.”
Cottrell said another concern is flexibility. “Proteomics is a fast-moving field with lots of new ideas and new requirements. Software updates can be developed, released, and distributed to users much faster than firmware updates. So, we don't see a compelling business or technical argument for a hardware accelerator.”
Furthermore, he said, the company doesn’t see the need to expand its current distribution channels. “We have good market coverage through a combination of direct sales and partnerships with a number of leading [mass spectrometry] vendors,” he said.
Building on a Known Brand
Sage-N, meanwhile, is burgeoning on the world market, with systems in place from Tokyo to Sydney to Seoul. “Our main focus [though] will be North America and Europe. About half the market is in the US,” Chiang said, noting that he plans to add additional sales staff to his current team of 10 in order to support the company’s marketing efforts for Sequest Sorcerer.
Chiang described Thermo as “more of a technology-based company, in that they sell Sequest  to whoever wants to buy it, our focus will be more in the pharmaceuticals space, more in drug discovery, related to products. We will be much more application-specific than I see they are trying to be.”

“If this means that Sage-N will be putting development resources into Sequest, that has to be a good thing for the user community. There are a very large number of search engines out there, and it requires a real commitment to stay competitive.”

Sage-N said it has redesigned Sorcerer Sequest to incorporate several improvements, including the ability to search variable modifications. The company also plans to build “application-optimized” versions of Sequest for biomarker discovery, phosphorylation site localization, and real-time protein identification.

The redesigned Sequest Sorcerer 2 still measures approximately 24 x 24 x 8 inches, including 1.5 TB of storage.
Need for Speed?
Chiang anticipates great demand for the product as a result of recent improvements in the sensitivity of mass specs. “The extra sensitivity and the large amounts of spectral data generated has given new challenges to the proteomics industry, in terms of more information, but needing more compute power,” he said.
Chiang said the company has 40 systems in place around the world and that demand in the past six months in particular has been very high.
“We’ve probably seen a tripling of customer interest compared to a year ago,” he said. He attributed this spike to several papers that were published last year by Sage-N scientific advisory board members in Nature Biotechnology and Nature Methods. “They’ve been driving a lot of demand,” he said.
Sage-N also stands to benefit from a resurgence of interest in FPGAs in the bioinformatics community, where the technology has been used since the mid-1990s to analyze DNA sequence data.
“We have plans to move beyond proteomics, though not necessarily DNA sequencing,” he said, noting that the market for DNA sequence analysis is not likely to grow as quickly as proteomics analysis.
“We see compute-intensive proteomics analysis as an expanding market, but not DNA sequencing as it stands today,” he said. In the sequence analysis arena, “the technology was successful, but the market was not. There were simply not enough sequencing analysis dollars to support the effort, at least beyond the height of the human genome effort,” Chiang said.
Cottrell, said he just doesn’t see strong demand among Matrix Science customers for additional compute power. “I see no evidence for this … and most labs find that a relatively small system, usually between one and four processors, is adequate for their needs,” he said. “Relatively few groups have large-scale requirements of more than 12 processors.”
Cottrell said that the computational requirements for proteomics software do not appear to be hampering research in the field.
“We estimate labs spend between 10 and 20 times as much on MS hardware as on MS application software. If software throughput was a real bottleneck, I think we'd see a shift in this balance,” he said.
Will the new deal help bioinformatics as a whole? Cottrell was hopeful.
“If this means that Sage-N will be putting development resources into Sequest, that has to be a good thing for the user community. There are a very large number of search engines out there, and it requires a real commitment to stay competitive,” he said.

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