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Thermo Reaches for TOF/TOF Market With ABRF Vacuum MALDI LTQ Release


Thermo Electron will release three new variations on last year’s LTQ and LTQ-FT releases — two this weekend at the Association of Biomolecular Resource Facilities, and one in March at Pittcon, ProteoMonitor has learned. These new variations include a vacuum MALDI ion source fitted especially for the LTQ and later for the LTQ-FT; an integrated proteomics workstation based on the LTQ; and an electron capture dissociation add-on to the LTQ-FT.

The Finnigan vMALDI ion source for the LTQ, to be released this weekend, will be aimed at “anyone who’s doing high-throughput identification,” Ken Miller, product marketing manager for Thermo, told ProteoMonitor. “In essence we’re going after the MALDI TOF/TOF market with this product.”

Although several academic researchers, such as Brian Chait of Rockefeller University in New York, have made their own MALDI ion traps, to date no major instrument company has put a commercial vacuum MALDI ion trap on the market (see PM 1-30-04). “Here it is!” Miller said.

Miller noted that the decision to market a vacuum MALDI source for the LTQ — which replaces an atmospheric pressure MALDI source fitted for the old LCQ, was a response to customer interest. He said the product was developed “in house with some technology licensed from others.”

The MALDI source will not be compatible with any ion trap instruments other than the LTQ, although “later on this year,” a MALDI LTQ-FT combination will be made available as well. The source for the LTQ is available for order immediately, and will ship in April, Miller said.

Thermo expects to break into the TOF/TOF market because “we’ll be able to match it in terms of sensitivity, in terms of throughput, in terms of overall performance,” Miller said. In terms of pricing, he said, “I think it’ll be less expensive, I think it will be more robust.” Miller would not elaborate on exact pricing for any of the new releases. He said that a future MALDI ion trap/TOF combination was also “something we have thought about and considered,” although he would not say when such a hybrid might come out. “Our next step will be to implement this on the FT, so in essence, it will probably provide better [mass resolution and accuracy] than the TOF [option], although unfortunately at a higher price,” Miller said.

Gary Siuzdak, director of the Center for Mass Spectrometry at Scripps Research Institute, who at the end of last year put a linear ion trap/TOF hybrid on his wish list for 2004 (see PM 1-2-04), said that a MALDI ion trap did have some advantages over the MALDI TOF/TOF. “The TOF/TOF has a reasonably large window to isolate the ion you’re interested in, so that can be problematic if you have more than one ion in that region,” Siuzdak said. “For ion traps, their windows are typically smaller, so that means isolation is more effective.” The TOF/TOF, however, has “higher energy collisions, so you get more fragmentation, [and] potentially more information.”

Bruker BioSciences, whose flagship product is a MALDI TOF/TOF, declined to comment on how its product would match up with a vacuum MALDI ion trap.

Markus Kalkum, a former post-doc in Brian Chait’s lab who is working on improvements to Chait’s MALDI ion trap, said that the new instrument “sounds very promising,” and that he would look more closely at the product when he attends ABRF this weekend. “I actually planned to buy an LTQ … and put my own source in front of it,” Kalkum, an assistant professor at the Beckman Research Institute, City of Hope in Duarte, Calif., told ProteoMonitor. “The LTQ is interesting as a MALDI machine in that it is a linear trap, so it has a capacity of storing at least 20-fold more ions than the conventional 3D trap.” Kalkum’s concern is that the LTQ is currently limited to a mass range of 2000, and “for MALDI you would need at least 4000 or, better, 6000, [for] peptide proteomic work.”

Miller said that Thermo was planning to extend the range to 4000, “and I can safely say this will be available in 2004.”

One-Stop Shopping

As part of the company’s push to make Thermo a one-stop shopping proteomics bazaar, Miller said the company this weekend will also release the Finnigan ProteomX LTQ workstation, an update on the previous ProteomX workstation that was fitted with the LCQ. The workstation will come with four different kits, all involving front-end combinations compatible with the LTQ. The first kit, entitled Maximum Sequence Coverage, will be targeted toward researchers looking to get “as much information about the protein as possible,” including post-translational modification identification, Miller said. The set-up involves two peptide traps, one eluting while the researcher loads the other, and a nanospray LC-MS setup.

The second application, entitled High-Throughput Identification, is targeted toward those willing to sacrifice coverage for speed. “We’re using a different trap-column combination to reduce cycle time per sample, so that you can kind of bang the sample through and get your protein identification,” Miller said.

The third application, targeted for MudPIT methods, integrates a strong cation exchanger, peptide traps, and an analytical reverse phase column. The last kit, Phosphorylation Site Mapping, uses a trap-column combination that Miller said does not retain phosphopeptides or phosphoproteins. “If it’s in your sample, it will make it to the mass spec,” he said.

Miller said that while he had expected pharma customers who were inexperienced in proteomics to be the primary customers, interest so far had come equally from pharma and academics. All of the kits will ship in April, Miller said.

This multi-application release comes as part of Thermo’s strategy to “be a single source provider,” as Clive Higgins, marketing director for life and laboratory sciences at Thermo, told ProteoMonitor during a visit to the company’s Woburn, Mass., site in November. At the time he said that there was a lot of demand for a mass spec supplier that can “produce the entire portfolio for drug discovery” — in part, because a pipeline using products made from the same company lends itself better to producing the consistency needed for FDA approval.

Miller said that successes of the LTQ and LTQ-FT have given Thermo the confidence that it can be this provider for proteomics discovery. “If you contrast [now] with where we were 12 months ago I don’t think this was the case,” he said.

All the Bells and Whistles

Thermo has something on the plate for Pittcon as well: The company will announce at that meeting the planned release of an ECD add-on to the LTQ-FT. The enhancement, which will be made available in the third quarter of this year, will be targeted toward scientists taking a top-down approach to proteomics research. “I think this is the first of many enhancements [for the LTQ-FT] that you’ll see this year,” he said. “ASMS is coming after all: We’ll have more to tell you then.” Miller wouldn’t comment, however, on whether Thermo would release an entirely new mass spec this year.



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