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Thermo s Impending LTQ-Adapted ETD Platform Will Become First Real Rival Against Bruker s ETD Tool

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The market for post-translational modification-friendly ion traps is poised to heat up after Thermo Electron last week promised to release an electron transfer dissociation module for its LTQ linear ion trap next month that will become the first real competitor to Bruker's ETD/ion trap play.

ETD is a special method of fragmenting peptides or proteins that enables researchers to study post-translational modifications, such as phosphorylation (see ProteoMonitor 3/16/2006). With ETD, amino acids are broken apart without affecting post-translational modifications, which allows scientists to identify modification sites.

ETD is of interest to most proteomics researchers who do detailed protein analysis, said Michael Schubert, executive vice president of Bruker Daltonics. According to Schubert, about half of Bruker's ion traps are sold to proteomics researchers in both academia and industry, while the other half are sold to small molecule and metabolomics researchers.

"A substantial part of that half that uses ion traps to do proteomics is certainly interested in ETD," said Schubert.


"The difference between [Thermo's and Bruker's instruments] is night and day. The LTQ [on Thermo's platform] can store a much, much larger number of charges than a 3D trap [found on Bruker's instrument]. Our expectation is that we'll be far more sensitive, we will scan much more quickly, and we will identify many more proteins than is possible with our competitor's device."

Bruker Daltonics became a pioneer in the ETD field in June 2005 when it released the first commercially available ETD module, designed to be used with its high-end HCTultra ion trap (see ProteoMonitor 6/3/2005). And at last month's Pittcon conference in Orlando, Fla., the company released PTMscan, a special mode in which the HCTultra ion trap can switch "on the fly" from MS/MS mode to ETD mode.

But Thermo has also set its sights on this market. The company recently finalized an agreement to exclusively license ETD technology from the University of Virginia, where Donald Hunt pioneered ETD use for protein characterization.

Using ETD, Hunt studied the biochemical basis of histone protein action in the regulation of DNA transcription. He showed that the pattern of histone phosphorylation, methylation, and acetylation is critical to DNA expression.

Ken Miller, proteomics product marketing manager at Thermo, said that the major difference between Thermo and Bruker's ETD units is that Thermo's is implemented on a linear ion trap, while Bruker's is implemented on a 3D ion trap.

"The difference between those products is night and day," said Miller. "The LTQ can store a much, much larger number of charges than a 3D trap. Our expectation is that we'll be far more sensitive, we will scan much more quickly, and we will identify many more proteins than is possible with our competitor's device."

Schubert disagreed with Miller on the difference between linear traps and 3D traps. Bruker's high-capacity 3D ion traps, such as the HCTultra, achieve all the charge capacity that a linear trap has, while scanning at about twice the speed, he said.

"Of course Thermo positions linear traps as being superior to 3D traps, but they don't make the distinction between high-capacity 3D traps and regular 3D traps," said Schubert. "In fact, an HCT has the same charge capacity as a linear trap, and scans much faster, which is a key advantage in any system."

Miller said Thermo plans to introduce its ETD unit at the American Society for Mass Spectrometry conference, will will take place in Seattle May 28-June 1. The unit will be retrofittable to all LTQs present in the field, and it will also be sold as an option with all new LTQs. Pricing has not yet been established on the unit, according to Miller.


"Of course Thermo positions linear traps as being superior to 3D traps, but they don't make the distinction between high-capacity 3D traps and regular 3D traps. In fact, an HCT has the same charge capacity as a linear trap, and scans much faster, which is a key advantage in any system."

Bruker's PTM Discovery System, which consists of the automated ETD module attached to the HCTultra ion trap, costs about $200,000.

In addition to performing ETD, Thermo's unit will also be able to perform pulsed-Q dissociation — a different type of fragmentation technique that Thermo introduced for its ion traps towards the end of 2005.

According to Shubert, while both ETD and PQD eliminate the low mass cut-off for ion traps, ETD is advantageous over PQD in that it preserves information about where post-translational modifications are on a molecule.

"With collision induced dissociation techniques [like PQD], the modification breaks off the molecule in the fragmentation process," he explained. "ETD fragments in a different way such that the modification stays linked to the peptide chain."

However, Miller said that having the option to use PQD could be useful because some customers are accustomed to using PQD for quantitation with iTRAQ labeling reagents.

"I haven't tried to do iTRAQ with ETD," said Miller. "Proteomics is such a diverse field. I find that different fragmentation methods are useful for different types of analyses, and having a box that can do all of [the methods] is ultimately going to prove to be very useful."

— Tien-Shun Lee ([email protected])

Agilent Also in Play, But Partner Bruker Unworried

Though Thermo's plan to start playing in the market for post-translational modification-friendly ion traps means Bruker will no longer be alone in the space, Agilent also sells an ion trap with ETD capabilities. Its instrument, the 6300 Series ion trap, began shipping March 1.

However, that instrument is not a real competitor to Bruker because Bruker manufactures all of Agilent's ion traps as part of a decade-long alliance, according to Michael Schubert, executive vice president of Bruker Daltonics.

"Agilent and Bruker have a collaboration agreement, so all the ion traps that Agilent sells are actually manufactured by Bruker," said Schubert. "But [the ion traps] are not identical. Agilent's ion traps are more limited in mass range than Bruker's."

With a mass range of around 3,000, Bruker's ion traps are able to analyze higher molecular weight peptides than Agilent's ion traps, which have a mass range of about 2,200, Schubert said.

Agilent spokesman Stuart Matlow confirmed that Bruker manufactures Agilent's ion traps.

"I can't say that we don't compete, but we work closely together," said Matlow. "The collaboration with Bruker on ion traps goes back more than 10 years. It's a very close working relationship. With the ETD module, Bruker originated it, and Agilent has worked closely with [Bruker] to commercialize the module."

Agilent's 6300 Series ion trap costs between $190,000 and $260,000.

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