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ASMS 2011 Highlights TOF Technology, Continued Emphasis on Qual-Quant Workflows

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By Adam Bonislawski

Time-of-flight mass spectrometry took center stage at this week's American Society of Mass Spectrometry annual meeting in Denver with vendors including Waters, Agilent, and Bruker releasing new TOF machines and Thermo Fisher Scientific launching its Q Exactive instrument – a quadrupole-Orbitrap hybrid aimed at the Q-TOF market.

The prevalence of new TOF machines demonstrates the technology's progression in recent years, as the release of high-end machines like Bruker's Maxis in 2008 and AB Sciex's TripleTOF 5600 and Water's Xevo G2 QTof in 2010 have made it a more viable platform for high-level proteomics work.

"Historically, in the context of a proteomics lab, everyone followed suit with the thought leaders and placed an Orbitrap in their laboratory," Gus Salem, vice president and general manager of Agilent's Biological Systems division, told ProteoMonitor. "And that was unquestionably the right call at the time. It was the right performance; it was the right instrument; it had the right capability and the right support."

In the last five years, though, "Q-TOF improvements have become so significant that there's a different conversation when you walk into a lab today," Salem said. "While the Orbitrap still exists and provides good data, it's not the answer to every question. The proteomics customer is clearly a lot more accepting of the Q-TOF for a lot of the work they need to do. It's easier to run; it's a less expensive instrument; there are a lot of benefits to working with it."

Agilent launched at ASMS its new 6550 iFunnel Q-TOF machine, which includes the iFunnel technology the company introduced at last year's meeting as part of its 6490 triple quadrupole. The new Q-TOF features 50 Hz acquisition rates, up to five orders of intra-scan dynamic range, and 10 times the sensitivity of its previous Q-TOF models.

Waters also introduced a new TOF machine at the conference: – its Synapt G2-S, which incorporates both the company's Triwave ion mobility technology and its StepWave ion transfer optics, providing a 30-fold jump in signal intensity for mass spectral peaks, a five-fold improvement in signal-to-noise ratio, and a 10-fold leap in limits of quantitation compared to the original Synapt.

Bruker released its new maXis 4G UHR-QTOF at this year's Pittcon meeting in March. That machine, said CEO Frank Laukien at the time, offers so-called "full sensitivity resolution" of greater than 60,000 FWHM and mass accuracy better than 600 ppb at acquisition rates of up to 30 full spectra per second along with four-plus orders of quantitative dynamic range (PM 03/18/2011).

This week the company launched a benchtop version of that device, the maXis Impact, which it said offers 40,000 FSR and 1 ppm mass accuracy along with acquisition rates of up to 50 full spectra per second. Retailing for $380,000, the Impact is positioned as a less expensive alternative to the 4G, which sells for $500,000.

Like Agilent's Salem, Bruker executive vice president Ian Sanders also noted the evolution of TOF technology, asserting that the company's 2008 release of its Maxis system offered the "first real high-resolution Q-TOF the market had ever seen" and was "the first instrument, frankly, to give the Orbitrap a real run for its money."

Thermo Fisher's new Q Exactive machine, which couples a quadrupole to an Orbitrap mass analyzer, is designed perhaps with such competition in mind. With the launch of the instrument this week, the company is "going directly after the Q-TOF market," Ian Jardine, vice president of global R&D, told ProteoMonitor (see story this issue).

While not a traditional Q-TOF in that it uses an Orbitrap instead of a time-of-flight device for mass analysis, the Q Exactive is "fundamentally conceptually equivalent to a Q-TOF," Jardine said, noting that the company plans to market the device to proteomics researchers for applications like peptide sequencing commonly done on Q-TOF machines.

"People buy Q-TOFs for both small-molecule work like drug metabolism, as well as for peptide and protein work, so we're targeting both of those” [applications]," he said. He added that "the price on the instrument will be extremely competitive compared to Q-TOFs."

Providing 140,000 FWHM in full-scan mode and maximum scan speed, the Q Exactive offers roughly three times the resolution of the typical Q-TOF. However, its scan speed of 2 Hz, while double that of the original Exactive instrument, is significantly slower than a typical Q-TOF.

This trade-off between speed and resolution has traditionally been a key point in debates regarding the relative merits of Orbitrap and Q-TOF systems. Jardine asserted that TOF's perceived advantage in this regard is "a little bit smoke and mirrors," saying that because the quality of the data on such instruments tends to be lower, researchers need to average together a larger number of scans to get the same information, somewhat negating the higher speed.

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But David Chiang, CEO of proteomics software firm Sage-N Research, told ProteoMonitor that he thought faster scan speeds, as opposed to improved resolution, would be what pushed proteomics research forward.

"I believe there's more to be gained from speed than resolution," he said. "If you can already do .01 AMU [resolution], most of what you need is there. I believe that going broad, which means going deep into the proteome through speed, is going to be much more useful and powerful in terms of expanding the usability and sensitivity of mass spectrometers than resolution."

"If [a mass spectrometer] isn't fast enough, you do a first-stage scan, but you only get to pick three peaks to look at," Chiang added. "But all the interesting ones are the little [peaks that look like noise]. [Several years ago] researchers were able to pick 10 peaks and now you can pick 30 or 40 peaks per second to analyze. What if in two years you double that and then double that and then double that? That's really where the instrumentation is moving, and we're happy to see that."

Qual-Quant Marches On

Last year's ASMS catchphrase – qual-quant (PM 5/28/2010) – was also in the air this year as vendors touted the capability of their instruments to perform simultaneous qualitative and quantitative workflows.

Steve Smith, senior director of MS product management for Waters, highlighted the Synapt G2-S's MSE acquisition method, which he said "catalogs complex samples in a single analysis, capturing molecular and fragment ion data" and providing "an accurate qualitative and quantitative profile of all the components" in a sample.

Salem similarly noted the demand for qual-quant capabilities, noting that "we get a large request from our customers to be able to do this qual-quant workflow – the ability to get a good understanding of what's present [in a sample] and the ability to get positive confirmation of the target analytes, as well."

Thermo Fisher highlighted what it called the Q Exactive's "quanfirmation" capabilities, which, the company said, allowed the instrument to identify, quantify, and confirm analytes like peptides and proteins in complex mixtures in one analytical run. "It basically means that you can do a single run of LC-MS with MS/MS and the data is so good that you can go into it and identify the components of interest and you can also go back and quantify the components of interest," Jardine said.

Preliminary results from early users suggest that the Q Exactive could, in fact, approach the quantitative capabilities of a high-end triple-quad, Jardine added. "What we're seeing with customers is that you can actually get to the same level of limits of quantitation with the Q Exactive as a triple quad," he said, noting that confirmation of these results would take "three to six months until we get data back from customers. But we're quietly confident that's where we'll be."

AB Sciex, meanwhile, which helped launch the qual-quant trend last year with the release of its TripleTOF 5600, introduced its new SWATH acquisition method that, said Dave Hicks, vice president and general manager of the company's pharmaceutical and proteomics business, allows for "comprehensive coverage of the proteome" by using the SRMAtlas developed by the Institute of Systems Biology and the Swiss Federal Institute of Technology for interpreting mass spectral data captured on the machine (PM 09/24/2010).

According ETH Zurich's Ruedi Aebersold – co-leader of the SRMAtlas project with ISB researcher Rob Moritz – the combination of the 5600's speed, sensitivity, and dynamic range, along with the SRMAtlas database, enables the new SWATH targeted data acquisition strategy.

"The SWATH acquisition data can't be interpreted with conventional database search engines," he said. "To do this targeted analysis we needed reference spectra for the whole proteome, and these reference spectra are contained in the SRMAtlas."

His team had tried to develop the device on other Q-TOF machines, Aebersold told ProteoMonitor, but, he said, thus far only the 5600 has shown high enough performance for it to be effective.

"We need very good sensitivity, large dynamic range, fast scan speed," he said. "It's a complicated relationship between all these things, and when you tweak somewhere it affects the other things. Right now, the 5600 has the optimal combination."


Have topics you'd like to see covered in ProteoMonitor? Contact the editor at abonislawski [at] genomeweb [.] com.

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