With the introduction of its new Orbitrap Elite mass spectrometer at last month's annual meeting of the American Society of Mass Spectrometry (PM 06/10/2011), Thermo Fisher Scientific has positioned itself to more aggressively pursue the market for top-down proteomics research.
In particular, said Northwestern University professor Neil Kelleher – a leading top-down researcher and the developer of ProSight PC, an informatics package for top-down analysis sold by Thermo Fisher – the new machine represents a challenge to the Fourier transform ion cyclotron resonance mass specs typically used for intact protein work, a category of instrument that has traditionally been dominated by Bruker.
Proteomics over the years has focused primarily on peptide-based research, but recently an increased appreciation of the importance of protein isoforms and post-translational modifications has led to rising interest in top-down, intact protein work. For instance, a PubMed search of co-occurrences of "top-down" and "proteomics" reveals no citations in 2001, two in 2002, 19 in 2005, and 50 in 2010.
Given this increase in interest, top-down is, as Andreas Huhmer, Thermo Fisher's proteomics marketing director, told ProteoMonitor in April, "absolutely a growth area for proteomics and for the vendors that sell into that space" (PM 04/08/2011).
Historically, Orbitrap machines have been relatively weak performers with regard to intact protein work, Kelleher said, but, he noted, with the release of the Elite, "that [limitation] seems to have been remedied."
The Orbitrap Elite, which combines the Velos Pro ion trap with a new high-field Orbitrap, represents a roughly four-fold improvement in resolution compared to previous Orbitrap hybrid machines, featuring a maximum resolving power at 1 Hz of 240,000 FWHM – a level previously obtainable only with FT-ICR machines.
More important for top-down work than the machine's resolving power, though, is its speed, Kelleher told ProteoMonitor. Because of the trade-off in mass spectrometry between speed and resolution, running the Elite at lower than its maximum resolution allows for a dramatic jump in scan speed.
Obtaining an MS-MS spectrum for one protein on Thermo Fisher's LTQ FT FT-ICR machine typically takes his lab around seven to eight seconds, Kelleher said. By comparison, working with the Elite prior to its release at ASMS, his team found they could get MS-MS spectra for three different proteins in 1.5 seconds.
"That [jump in speed] is a big deal when you're talking about intensities and building up signals for top-down [proteomics] on a chromatographic timescale," he said. "It completely erases in my mind the deficit of Orbitraps in top-down."
Another potential edge of the Orbitrap for intact protein work, Kelleher noted, is that its resolving power scales with mass-to-charge ratios more favorably than in FT-ICR machines. In both types of instruments, resolving power decreases as the mass-to-charge of the ions being investigated increases. However, the decline is steeper for FT-ICR machines.
"The practical observable [of this effect] is that if you get out to 2,000 m/z, the FT-ICR has fallen off in resolving power quite substantially, whereas with the Orbitrap the [resolving power] remains," Kelleher said.
"This effect kicks in even in the meat of the spectra," he added. "Even in the range of 1,000 m/z to 2,000 m/z it makes a difference, and that's the meat of the top-down range. I hadn't fully appreciated it before, but it makes a big difference if you do a comparison between FT-ICR and the Orbitrap."
Such advantages, Kelleher suggested, could enable Thermo Fisher to increase its presence in the growing top-down space, carving into the FT-ICR market, which he said Bruker has "taken a fairly aggressive approach to" with its SolariX line of mass spectrometers.
Bruker, Kelleher said, "has done a great job getting [FT-ICR] where it is [currently]" and remains "the dominant [vendor] in top-down." However, "the Orbitrap has made a big statement, and I think clearly ICR [technology] needs to respond aggressively."
"I think that FT-ICR and Orbitrap will continue to battle," he said. "The race is on, and clearly both [technologies] have headroom. Now the question is, 'What will the next two years look like with this new [Orbitrap Elite] instrument?'"
Even with the release of the Elite, FT-ICR machines still maintain a significant advantage in resolving power — indeed, a presentation at ASMS discussed improvements in ICR cells that would increase the resolving power to as high as 22 million FWHM. The question for top-down proteomics researchers, though, is how relevant this power is to their work, Kelleher said.
"If you want the ultimate performance, if you have a protein target and you want to get the most spectacular data, and you want to get the highest resolving power and do an internal calibration and get 500 parts-per-billion mass accuracy, there is a role for FT-ICR," he said. "If you're talking about these heroic kinds of experiments – like a three-minute-long data acquisition, and you want to tweak and get this incredible spectrum, that's still the domain of FT-ICR."
"But that's not my mode," Kelleher said. "My mode is top-down proteomics, not top-down mass spectrometry."
Have topics you'd like to see covered in ProteoMonitor? Contact the editor at abonislawski [at] genomeweb [.] com.