Proteomic partnership: Nonlinear Dynamics and Waters team up

MILLFORD, Mass.—In late summer, instrumentation powerhouse Waters Corp. and bioinformatics provider Nonlinear Dynamics announced a co-development and co-marketing agreement that will result in an integrated bioinformatics package for protein identification and quantitative protein profiling using Waters' ProteinLynx Global Server and Nonlinear's Progenesis 2D gel informatics platform.

Development and testing of interoperability are ongoing at both companies now, with an anticipated market arrival of new versions of each company's software set for release in early 2006.

"For us the major driving force behind this agreement was our MALDI micro MX product," says Tim Riley, vice president, proteomics business development for Waters. "Nonlinear Dynamics has developed a lead position in the imaging software for 2D gels which are frequently analyzed using mass spectrometry. So having a better relationship with a market leader like that is a plus for us and a win for them, as well, because they have closer ties into making their software interact with a quality mass spectrometry vendor's software."

For Nonlinear, the agreement is the latest in a long line of partnerships the company has struck in the past couple of years as it looks to rapidly increase its presence in the market. "We know we can't do this alone, hence forming strategic relationships with quality companies such as Waters makes sense," says John Spreadbury, group sales and marketing director of Nonlinear and CEO of Nonlinear USA Inc.  At virtually the same time it announced its agreement with Waters, Nonlinear also announced a distribution deal with Invitrogen Corp. (see sidebar).

The bang for the buck in the Waters deal, however, involves analysis and annotation of 2D gel images produced by Nonlinear's Progenesis software.  "They will send 2D gel images to Waters software and the Waters software will perform a search against a database of known proteins and return the proteins it finds.

This particular level of interoperability between the companies' software may only be the beginning, though officials from both companies cautious in their approach. "I think we need to take this one step at a time and certainly the first step is to get the software introduced early next year," says Riley. "But there are possibilities. We are very interested in quantitative proteomics, an interest Nonlinear shares because a lot of their imaging work is being used to look for the differential expression of proteins."

More immediate possibilities are in adding more interoperability to ProteinLynx and Progenesis.