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ABI Looks to the Stars with Functional Proteomics, i-Science, & Futuristic Applications


After “sticking its toe in” to functional proteomics with the release of its multiplexing SPR chip in September, Applied Biosystems is pushing forward further into the field, com-pany officials told ProteoMonitor during a visit to ABI’s Framingham, Mass., site. The company, they said, is also exploring what it calls “integrated science” as well as future “Star Wars”-type mass spec applications, while continuing to rely on its core competencies like high-end mass specs.

“We’re looking for areas where we can have a fundamental, factor-of-10 impact,” David Hicks, senior director of the proteomics business group at ABI, said in explaining why the company decided to launch the SPR-based 8500 Affinity Chip Anal-yzer, which it is shipping this quarter. “We weren’t interested in replacing Biacore[‘s SPR products] — we wanted to make a jump,” he said. “We’re a large enough company that we have to do that.” Hicks did not say what would be next in functional proteomics for ABI, but he did indicate that it was an area in which the company was looking to get heavily involved.

ABI’s desire to dominate all ends of the proteomics market, while maintaining an aversion to what Hicks termed “me-too products,” is apparent in most areas of its business plan. While the company intends to be “heavily involved with biomarkers,” for example, it is “not going to be opening a biomarker discovery center like Ciphergen,” according to Hicks. Hicks also pointed out that ABI was already involved with Ciphergen via its partnership to interface the ProteinChip with ABI’s Q-STAR. Similarly, while the company intends to try and continue its dominance in high-end mass specs, it will not join Bruker Daltonics and Thermo Electron in developing FT-MS instrumentation. “We are not interested in FT-MS — it’s a niche machine that I don’t think is ever going to be inexpensive enough or easy to use enough to be in wide use,” said Rick Carberry, worldwide marketing and communications director at ABI. “Let Bruker and Thermo duke it out.”

But ABI is jumping on at least two other bandwagons: “integrated science,” which some scientists might call systems biology, and marketing toward less experienced biologists. In the first area, the company hopes to convince customers to combine its various genomics and proteomics offerings into cross-disciplinary integrated science, or “i-science” projects. It is also reaching out to small-time biologists without much experience in the use of proteomics techniques — an approach that Ciphergen pioneered, and that many competing companies have since adopted (see PM 9-26-03).

Much of ABI’s courting of both inexperienced and experienced scientists takes place in its demo labs — which Carberry said host five to seven groups per week at the Framingham site alone. “People bring in samples, they try them on three different platforms, and they generate data to justify a purchase or apply for a grant,” Carberry said. He added that about 20 percent of the customers who came in were new to mass spectrometry.

While ABI is selling its current wares to customers in the demo labs, in its Discovery Proteomics Small Molecule Research Center right down the hall, the company is working on some new applications that Hicks termed “real Star Wars stuff.” The PRC, located only at Framingham, is used as a sort of pre- and post-R&D center, where in-house scientists do preliminary development work with collaborators to look into possible new product lines and applications, as well as test new products and workflows prior to launch.

One project that started here but has recently moved onto R&D, according to Carberry, is the much-anticipated Molecular Scanner created in collaboration with Denis Hochstrasser at the University of Geneva (see PM 4-15-02). The envisioned process would involve simultaneous digestion and transfer of gel spots to a membrane that would then be scanned and the proteins identified by mass spec via peptide fingerprinting — ultimately producing an annotated, multidimensional image of the original gel. Hicks said that ABI is currently working on optimizing the transfer and membrane capture mechanisms and applying the procedure to MS/MS workflows in its R&D facil-ity, but that preliminary results for 1D gels were promising. He would not speculate as to when the product would finally make it to the market.

Another technique that is in studies both at the PRC and in R&D is MALDI-based tissue imaging, which the company is developing in collaboration with Richard Caprioli at Vanderbilt University (see PM 7-1-02). This technique would theoretically allow surgeons to put unprocessed tumor samples straight into a mass spec for spatially sensitive analysis. Since Caprioli published his paper describing the technique in Nature Medicine in 2001, interest has been high, but after nearly two years of work — ABI picked up the project in February 2002 — “there is still R going on; D hasn’t started yet,” according to Carberry. Still, Hicks said that the “preliminary data works,” and that the company is now working on details such as whether to digest the proteins and how thick a tissue section should be used.

But ABI is not “hanging its complete wardrobe on one hook,” according to Hicks. “We are making investments [in futuristic projects] but we are balancing our portfolio” with core products like chromatography and mass specs, he said.



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