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By Malorye Branca

September 9, 2002 | Foster City, Calif.-based Applied Biosystems, an operating group of Applera Corp., and Somerville, Mass.-based Spotfire have signed an agreement that will knit one of the most popular genomics visualization tools with a cutting-edge proteomics platform.

The two companies will integrate ABI/MDS Sciex’ Pro ICAT software with Spotfire’s DecisionSite for Functional Genomics. ABI’s ICAT system is used with mass spectrometry to compare the relative amounts and kinds of proteins in two samples.

“It makes good sense for them to do this. Being able to visualize your results is key,” says Andrew Link, Ingram assistant professor of cancer research at Vanderbilt Medical Center, and a pioneer in mass spectrometry for proteomics.

“This is our first proteomics software,” says Spotfire’s director of market applications, Kristen Stoop. “ABI was getting ready to release the ICAT system, and it saw our software as a great way to extend its analysis capacities with visualization and clustering.” Spotfire has developed a special configuration of the DecisionSite software for the ICAT system. Spotfire will distribute the new software for ICAT and will not pay royalties to ABI.

The ICAT (isotope-coded affinity tag) reagents were first developed by Ruedi Aebersold, now at the Institute for Systems Biology, and Michael Gelb of the University of Washington, while Aebersold was on the faculty there. ABI has an exclusive license for the technology. The Pro ICAT software for the atmospheric pressure ionization QSTAR Pulsar Hybrid LC/MS/MS system was released by ABI in February of this year.

The deal is significant, not just because it involves lead players in two highly competitive fields (mass spectrometry instrumentation and visualization software), but because proteomics is a growing field. There are not nearly as many commercial analysis programs for proteomics as there are for gene expression analysis. “Many labs design their own software,” says Link. “Proteomics software essentially mimicks the DNA microarray software packages—different molecules, but the same idea.”

The ICAT appears to be successful for ABI. “We are seeing sales of QSTAR’s that are specifically related to ICAT,” says Senttineri (who’s this?). She won’t give specifics, but says, “Demand is progressing, and that’s one reason we are glad to have this arrangement with Spotfire.”

How much this deal means to either company will depend partly on how good the software is, and partly on how the field and the competition progresses. “Proteomics is still focused in relatively few labs,” says Link. Having Spotfire on their ABI/MDS Sciex instruments doesn’t mean all of a group’s protein informatics needs will be met. “Most people tend to use a mix of mass spectrometry instruments,” he says.

Spotfire also recently signed a licensing deal with Agilent, which is licensing the DecisionSite Analytics Platform. In another recent deal, Rosetta Biosoftware and Spotfire agreed to integrate their products. “These deals are part of an established strategy to expand our market base,” says Stoops. “It helps that we are now well established in the marketplace.”

ABI has traditionally concentrated more strongly on instruments and supplies than informatics. This deal was orchestrated by the proteomics unit, which is angling for more like it. “We are working on a similar arrangement for the 4700 [Proteomics Analyzer] as well as the QTrap [LC/MS/MS System],” says Tina Senttineri, proteomics technical marketing specialist at Applied Biosystems. “ICAT on the 4700 will be released any day.” 

ABI recently took over marketing and further development of the Celera Discovery System, and established a new Knowledge Business division headed by Deborah Smeltzer, vice president.


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