Users of Waters' ProteinLynx Global Server software will now have the option to use either Matrix's Mascot or Waters' ProteinLynx search engine to identify and characterize proteins following mass spec analysis, according to terms of a collaboration between the two companies.
The collaboration will also enable Matrix to improve its Distiller product, which reads raw data from different mass spec brands. "Now that we have an arrangement with Waters, we'll be able to get more information from Waters data files," David Creasy, a director at London-based Matrix Science, told ProteoMonitor this week.
The alliance makes Waters the latest of the big mass spec tool vendors to offer customers the Mascot option. Bruker, Applied Biosystems, and Shimadzu already had similar collaborations with Matrix, which leaves Thermo Electron as the only big mass spec vendor that does not offer Mascot as an option.
Creasy and Tim Riley, vice president of proteomics business development at Waters, said the agreement came about mainly in response to the needs of customers.
"What happened is many of [Waters'] customers wanted a choice of running the searches either with ProteinLynx Global Server or with Mascot, so it was in their interest and in ours to get Mascot incorporated into the software suite," said Creasy.
Financial terms of the collaboration were not revealed.
The newest version of ProteinLynx, which offers users the choice between Mascot and ProteinLynx search engines, is currently being shipped to Waters customers, Waters spokeswoman Ann McDonough said this week. The version is named ProteinLynx Global Server 2.2.
Riley said users of Waters' older versions of ProteinLynx Global Server, which is compatible only with Waters' instruments, were able to access Mascot, but it was "quite challenging" to do so. "With the new version, we've made it really much more transparent to the end user as to how to access Mascot," Riley said.
Matrix is an old hand with mass spec vendors, having penned collaborations with various large companies to directly link Mascot to the firms' in-house software. In fact, Matrix CEO John Cottrell told ProteoMonitor in 2003 that Matrix regards itself as "vendor-independent" (see ProteoMonitor 3/17/2003). "We aim to offer a solution which is applicable to all the different mass spectrometry products which are popular for protein work," Cottrell said.
Aside from offering Waters' users the choice of Mascot, an ancillary goal of the alliance is to improve Matrix's Distiller product, which takes raw mass spec data and creates high-quality peak lists. Matrix's Distiller product has improved with each collaboration between a major mass spec vendor, Creasy noted, because the alliances allow Distiller to better read the vendors' raw mass spec data.
"The alliance is "a two-way thing, really," said Creasy. "We'd always been keen to work with [Waters], and it just finally came about."
When asked what the difference is between the ProteinLynx search engine and the Mascot search engine, Riley said the differences are very subtle and technical. "Frankly, they both produce somewhat similar results," he said. Many users of Waters' ProteinLynx Global Server probably prefer to use the Mascot search engine because they became accustomed to using it while working with other mass spec brands, Riley said.
Asked to comment on Mascot, and Matrix's latest collaboration, Ken Miller, a proteomics product marketing manager at Thermo Electron, said his company invites users to process their data using whatever software they prefer. Thermo currently offers customers its own Sequest software.
While Miller did not specifically rule out a collaboration with Matrix, he suggested that Waters and other mass spec companies are offering Mascot to their users because they do not have "credible" search engines of their own.
"It appears that Waters has joined Bruker, Applied Biosystems, and other companies who do not have a credible searching solution of their own by now offering Mascot to their customers," Miller said.
Peptide probability scoring has recently been added to Thermo's Sequest software.