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Bruker vs. Thermo FT-MS, Biomarkers Lead Pittcon Product Release Bonanza

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Top-down proteomics gurus and small-scale biologists were the targets of a slew of mass spec releases at Pittcon 2004, held this week at the McCormick Place convention center in Chicago.

Bruker Daltonics led the charge as it rolled out five new proteomics-focused mass specs. The company turned up the competitive heat in the FT-MS, biomarker discovery, and ion trap arenas by making direct comparisons between its new instruments and competing products from other companies.

Meanwhile, Thermo Electron countered with two new mass spec-related releases in proteomics — while showcasing its two ABRF releases as well (see PM 2-27-04) — and Agilent released an upgraded version of its XCT ion trap.

Bruker and Thermo, which had each released hybrid FT-MS instruments for proteomics applications at last year’s Pittcon (see PM 3-17-03), both came back this year with variations on their original offerings. Bruker, whose original Apex-Q Q-q-FT-MS, fitted with 9.4- or 12-Tesla magnets, was prohibitively expensive for academics in all but the largest core labs at $1.2 million $2 million per instrument, introduced the Apex-QE, a 7-Tesla version of the original with an integrated electron capture dissociation mode for top-down applications, priced at $750,000. ECD is a popular method for top-down approaches, particularly in the search for PTMs. Although Bruker offered a 7-Tesla option on its original machine for around $850,000, as well as an ECD add-on, the newer version is cheaper and more user-friendly, according to Bruker BioSciences president and CEO Frank Laukien. “If you can run an ion trap, you can run our FT-MS — it’s not any harder,” he said during a press conference this week. Also, the instrument gains from having the ECD built right in, Bruker Daltonics vice president John Wronka told ProteoMonitor. “Everyone buys the ECD, so why not make it a standard?” Wronka said.

Cheaper and user-friendly were also two of the features that Thermo, whose LTQ-FT is also priced at $750,000, advertised last year as major advantages for its initial release. At the time, Thermo didn’t offer the option of using ECD or infrared multi-photon dissociation on its machines, both of which Bruker offered as add-ons. This week Thermo changed that by offering both ECD and IRMPD as add-ons, although neither is integrated as a standard feature. Thermo’s other mass spec release this week was a triple-quad with an expanded mass range of 3000, which it is now marketing for proteomics applications.

With the Apex-QE, Bruker has made no secret of its intent to capture some of Thermo’s share in the market for lower-end hybrid FT-MS. Its Apex QE’s “sensitivity, resolution, and mass accuracy greatly surpasses alternative hybrid ion trap-FT-MS combinations that mostly just operate as an ion trap in MS/MS mode without fully using the benefits of ultra-high resolution and superb mass accuracy in FT-MS/MS,” the company claimed in an official statement. “We always take high resolution FT mass spectra,” Wronka added. Thermo, on the other hand, “does a lot of its [LTQ-FT] experiments as a trap, so the FT is just an add-on,” Wronka said. In contrast, he said, even the new lower-end Bruker instrument always operates in FT mode.

Lester Taylor, director of global product marketing for life sciences mass spec at Thermo, declined to comment on Bruker’s statements except to say that “clearly the success of our instrument is having an impact on the market” and “philosophically and scientifically, we think this is the right way to go.”

The competition will no doubt continue, as Thermo has already said that it will continue adding bells and whistles to the LTQ-FT over the next year, and Wronka indicated that Bruker will likely continue to add as well. “As our customers demand more, we give them more,” he said.

Regardless of who wins a larger share of the market in the end, it is clear, at least, that the market for user-friendly and affordable FT-MS hybrids is there — and growing. “FT has more to say in proteomics than ever before, and the new commercial developments are remarkable,” Neil Kelleher of the University of Illinois at Urbana-Champaign said during a presentation on top-down proteomics. Kelleher helped invent the ECD technique as a student of Fred McLafferty in the ‘90s. “This year is a watershed — there’s not only a new wave of great commercial instruments, but also a new wave of FT-ICR experts,” he said.

In Biomarker Discovery, It’s Identification, Identification, Identification

Bruker also took the opportun-ity at Pittcon to actively woo another part of the small-scale biologist market that competitor Ciphergen has so far tried to dominate: those interested in diving into biomarker discovery in their own labs without spending a lot of money. To this end, Bruker released the microflex, a medium-throughput benchtop MALDI-TOF that Wronka said has “higher performance than any other benchtop” MALDI; as well as the autoflex II line of MALDI-TOF and TOF/TOF, which is a high-throughput but less expensive and smaller version of its autoflex I line of MALDI-TOFs (see PM 2-20-04).

“This is a theme,” Laukien said. “We’re taking more and more high-end systems and putting them into benchtop packages to make them more accessible.”

Bruker is marketing both re-leases for use with its ClinProt biomarker discovery system. The microflex is targeted toward open-access, walk-up type of facilities and labs “looking at 20 or 40 samples,” that know what peaks they are looking for and therefore might not need the TOF/TOF function, Wronka said.

With the autoflex II, on the other hand, Bruker is going directly for clinical proteomics researchers looking for mass spec-based biomarker patterns. “By putting the [TOF/TOF] in that [inexpensive] price range, we are opening up biomarker discovery,” Wronka said, noting that the most expensive autoflex II system will go for about $375,000.

Ciphergen’s SELDI system — which the company has aggressively marketed to exactly this segment of biomarker discovery researchers — is already offered at a low price and with a user-friendly interface. But Laukien and Wronka argued that the TOF/TOF function on the auto-flex gives the company a big advantage in the increasingly demanding biomarker field. “I think that the field is changing,” Laukien said, noting that one could no longer look at “25 samples, find a pattern, and get a paper in Nature.” In this “tougher field,” he said, the ability of the TOF/TOF to both produce a pattern and identify the components on the same machine would give Bruker an advantage. SELDI-TOF is not available in a TOF/TOF version.

Wronka cited the oft-noted example of a researcher finding a pattern capable of distinguishing cancer samples from healthy ones, but consisting entirely of non-specific inflammation markers. “A pattern can help you know what to look for, but in the end you need to know what the pattern means,” he said.

Still a Place for Traps

As much as Bruker may not like ion traps inside its FT-MS, the company still hopes to dominate in the ion trap market. The company released three new ion traps at Pittcon, including an upgrade on last year’s HCT release. The new HCTPlus, according to Laukien, now can be considered the “highest performance ion trap out there,” in terms of dynamic range, sensitivity, and sequence coverage capabilities. The upgrade is four times more sensitive than the HCT, Laukien said. Bruker co-developed the original instrument as well as the upgrade in collaboration with Agilent, which also released its own upgrade, the XCTPlus, this week as well. The upgrade resulted mostly from small refinements on the original instrument, Laukien said.

Bruker also released upgrades on its esquire series of traps, releasing traps with 4000 and 6000 m/z ranges. Thermo’s LTQ has a mass range of 2000 (see PM 2-27-04).

Signaling Bruker’s determination not be ignored in the ion trap arena , Laukien said during Bruker’s quarterly earnings conference call last week, “we believe we may together [with Agilent] be at or very close to a co-market leader position in the LC ion trap mass spectrometry market.

In any case, regardless of whether it is old school ion traps or new FT-MS, the round of Pittcon product releases demonstrates the fierce level of competition in proteomics instrumentation.

— KAM

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