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GeneProt Returns to Bruker Daltonics For Seven Next-Generation MALDI-TOF/TOFs


Breaking its silence on plans for its New Jersey facility, GeneProt said last week that it has purchased six Bruker Daltonics Ultraflex MALDI-TOF/TOF mass spectrometers for its new facility in North Brunswick, NJ, and an additional system for its Geneva laboratory.

For weeks, the company had refused to discuss how the new proteomics discovery workshop would differ from its flagship facility in Geneva. That facility, opened in April, contains both 2D gel electrophoresis- and liquid chromatography-based separation schemes, and 45 ion trap and 6 MALDI-TOF mass spectrometers supplied exclusively by Bruker.

But GeneProt has said that the technology for analyzing proteins is evolving too rapidly to build an identical platform in New Jersey, and the purchase of the TOF/TOF instruments, priced at $575,000 each, represents a significant investment in next-generation technology.

“Clearly [the TOF/TOF] gives extra information,” said Keith Rose, GeneProt’s chief scientific officer. “Now there’s the possibility with MALDI of getting MS/MS information, and we’ve gone for the TOF/TOF platform from Bruker to give us this extra dimension to the information.”

Rose added that Bruker’s TOF/TOF has several advantages over the Reflex IV, not to mention the Reflex III, an older MALDI-TOF instrument that GeneProt has installed in Geneva. In addition to its MS/MS capability, the TOF/TOF can also be run as a simple TOF, Rose said, with performance that exceeds the Reflex IV, and at a higher sample throughput, and faster laser repetition rate. “This extra capacity, which comes at extra expense, is useful to us,” Rose said.

GeneProt has purchased an additional Bruker TOF/TOF instrument for its Geneva R&D lab, Rose said, but does not plan to integrate the TOF/TOF instrument into its Geneva production facility.

Bruker announced in July that it would enter the market for MALDI TOF/TOF mass spectrometers, joining rival Applied Biosystems. Rose said GeneProt had considered purchasing the ABI instrument, and even visited ABI’s Framingham, Mass., Proteomics Research Center in January, but ultimately went with Bruker because of the two companies’ strong relationship.

“It’s not just a price issue,” Rose said about GeneProt’s decision to buy Bruker’s less expensive TOF/TOF instrument. In May, an ABI salesperson quoted a price of $750,000 for its TOF/TOF system. “Bruker is our partner for the Geneva site, so they are people we have worked with over this past year. That helps,” Rose added.

Rose also indicated that there are technical differences between the two companies’ instruments, making the distinction that Bruker’s system employs its patented LIFT technology for performing MS/MS analysis on small amounts of sample.

In addition to the TOF/TOF instruments, GeneProt has plans to purchase electrospray mass spectrometry equipment, although Rose would not reveal the supplier. GeneProt will also purchase additional computing power for the US laboratory, Rose said, because the company does not have the cross-Atlantic bandwidth to shuttle the data back to Geneva for analysis. Compaq currently powers GeneProt’s Geneva facility.

Rose said the company will continue to use both 2D gel electrophoresis and liquid chromatography to separate proteins. “The small [proteins] are better separated by multidimensional chromatography whereas today, the large ones are still best separated by gels.”

GeneProt has already begun hiring employees for the New Jersey facility, Rose said, and is looking to hire an additional 100 scientists and bioinformaticists. Rose himself will move to the US to supervise the new facility’s ramp-up, he said, leaving Diana Wetmore, the company’s chief technical officer, in charge of the Geneva facility.

“We will have just as many annotators [in New Jersey] because that [number] depends on the number of proteins you find,” but there may be fewer code writers, he said.

The facility is slated to come online by the second quarter of 2002.


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