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ABI Launches New Mass Specs as It Tries To Turn MS Biz Around and Stay On Top

After months of hints and wide anticipation, Applied Biosystems and its MS joint-venture partner MDS last week launched two mass spectrometry systems, putting an end to a technology drought that dragged down ABI’s mass spec business for the past 18 months.
The two new tools, the AB Sciex Triple Quad 5500 and the AB Sciex QTrap 5500, represent the most advanced mass specs ever, according to the partners.
The announcement also happens to mark the firms’ most significant mass-spec introduction in more than three years. In a segment driven by new products, the launches may provide the spark needed to revive ABI’s mass spec business, which has been on the decline recently.
In a webcast announcing the introductions, ABI and MDS officials said that the tools are “next-generation” systems built on new platforms that were designed from the ground up.
To wit, rather than replacing pre-existing instruments, the Triple Quad 5500 and QTrap 5500 are “a true expansion” of the companies’ portfolio, said Andy Boorn, president of MDS Analytical Technologies, the division within MDS that develops and manufactures mass specs.
The companies were short on specific data backing up their claims but according to Laura Lauman, president of ABI’s proteomics and small-molecules division, “These next-generation mass-spec systems represent a significant milestone for the joint venture and Applied Biosystems in providing innovative solutions for our customers. … With this launch we are once again setting new standards for performance in mass spectrometry.”
In the Triple Quad 5500 instrument a new pulse-counting detector, AcQuRate, “effectively” detects ions to increase quantitative accuracy and precision. Compared to other triple quads, the 5500 is up to five times more sensitive, according to ABI/MDS.
New components such as the Qurved LINAC Collision Cell and eQ Electronics increase analysis speed and scanning speeds, according to Boorn, though he did not provide details.
The instrument, he added, enables researchers to ID “the greatest number of target analytes at the lowest concentrations in complex samples … [and] enables a great amount of data to be acquired from a single experiment [resulting in] greater quantitative accuracy and lower limits of detection.”
No specific figures were provided.
Meanwhile, the QTrap 5500 takes the features of the Triple Quad 5500 and combines them with a new Linear Accelerator Trap technology, which is “designed to set a new standard in the linear ion trap-based qualitative mode,” the companies said in a statement.
Another new technology built into the machine, Triple Trap Scanning, allows scientists to migrate from “sensitive, very specific triple quadrupole scan model to highly sensitive full scan ion trap mode in less than 1 millisecond,” Boorn said, enabling workflow data-driven acquisition that cannot be achieved on other systems.
For proteomics research, the QTrap 5500 allows researchers to quantify and confirm an “increasing number of proteins and peptides with greater sensitivity, reproducibility, and precision than any other available system,” said Lauman, though no specific figures were given.
Dominic Gostick, director of new technology business for proteomics and small molecules at ABI, said that as proteomics takes on an increasingly targeted approach to biomarker discovery, the new instruments will give researchers greater capability to find relevant biomarkers.
“People have now discovered fairly long lists of potential biomarkers, and that’s not actually proving to be that useful for them today,” he said. “And I think this technology in both small molecules and proteomics offers a whole new capability because they can take these lists of putative biomarkers and shift those into verification [and] validation.
“And that really is compelling to people because they need to home in on what are the clinically relevant biomarkers against what has just been an artifact of the experimentation,” he said.

“It’s definitely necessary to keep them in line with the herd, so to speak, and maintain their market leadership position.”

Researchers at the Samuel Lunenfeld Research Institute of Mt. Sinai Hospital in Toronto were allowed access to an early iteration of the instruments. For them the higher MRM sensitivity and faster speed of the QTrap 5500 is especially appealing.  
“Even with … moderately complex samples, we have noticed routinely [that] MRM by itself can lead you astray. It can give a lot of false positive information,” said Lorne Taylor, mass spectrometry specialist at the institute. With the QTrap 5500, “we can do an MRM measurement in 1 millisecond in this new box, then we can flip and do an MS/MS in 2 milliseconds, so we have incredible speed. … We want to be very, very sure that we’re measuring what we think we’re measuring.”
In addition, the faster speeds allow for more assays per time unit which in turn will allow researchers to embed controls into the experiments.
“We take these proteins in complexes and we rip them apart to pieces with trypsin. We measure the pieces and then we infer biology back from that,” Taylor said. “There [are] a lot of [moving parts] going from peptide back to protein. Embedded controls are crucial here, so with the ability of the new machine to do so much more at a higher sensitivity allows us to be able to not only look for things that we couldn’t before, but to control for them.”
The new platforms are compatible with ABI’s reagents and workflow technologies including MRMPiolot and MultiQuant software for targeted quantitative proteomics and mTRAQ reagents. 
The systems sell for between $450,000 and $490,000. ABI has orders for them already, Lauman said, and the company is shipping the instruments now.
‘In Line with the Herd’
The launch of the instruments comes after months of speculation about ABI’s mass-spec business, and promises from company officials that major new instruments would be hitting the market by the end of the year. While ABI is still regarded as the industry leader, there was at least the perception that it, and by extension MDS, was becoming complacent as a technology innovator.
The last major mass spec introduction from ABI was in 2005 when it launched the API 5000 for small-molecule analysis in January, followed up four months later with the launch of the 4800 MALDI TOF/TOF for protein biomarker study.
Since then ABI has put out new systems, but rather than being revolutionary the new introductions were seen as incremental improvements on existing platforms.
In the meantime, competitors such as Thermo Fisher Scientific and Waters took advantage of ABI’s technology lull by launching new Orbitrap and Synapt instruments, respectively, which they pushed as transformative technology. Simultaneously, Agilent Technologies, once seen as a marginal player in the mass-spec space, broadened its presence in the market.  
Peter McDonald, an analyst at research and investment firm Wall Street Access, called last week’s launches an important step for ABI to beat back the competition. “It’s definitely necessary to keep them in line with the herd, so to speak, and maintain their market leadership position,” he said. “I don’t know that it’s a dramatic reshaping of the landscape but it definitely adds another wrinkle and it may force people to … delay purchases a little bit longer if they need to take a look at the new systems.
“Overall, it’s probably good for the space as it continues to drive uptake and expand the whole market potential for this,” he said.
Lauman acknowledged that the development cycle for the Triple Quad 5500 and QTrap 5500 took longer than ABI had anticipated but because of the innovations incorporated into the design of the instruments “allows us to create derivative platforms very rapidly.”
Boorn said that the two launches represent only the third time in the 25 years that MDS has been in the LC-MS business that it has created a new platform from the ground up.
“Our research and engineering team examined every component in the system and basically changed them all, and then in very tight iterative loops with our customers around the world, asked them if this was truly going to address their questions,” he said.
Some of the questions and requests coming from customers “were very difficult to solve,” he added, including the need for smaller instruments. The new systems have a 44-percent smaller footprint than previous systems.
In addition, increasing the speed of the systems was a very “challenging part of the development task and required the complete redesign of the electronics and the invention of new scanning modes and designs of the ion optics [to] address those really, really, really fast scanning requirements,” Boorn said.
For ABI, the launches come at an especially challenging time for its mass-spec business. While its competitors have been citing healthy growth in their mass-spec sales in recent quarters — albeit without giving specific numbers — ABI’s year-over-year mass-spec sales have been trending down. For six straight quarters, its mass-spec sales have steadily declined year-over-year from 14 percent in the three months ended Dec. 31, 2006, to less than 1 percent for the quarter ended March 31, 2008.
For the three months ended June 30, the most recent quarter for which figures are available, sales of ABI’s mass specs rose 4 percent year-over-year. The company will release its fiscal 2009 second-quarter results on Oct. 22.
Both Tony White, the former CEO of Applera, ABI’s parent company before it split ABI and Celera into two independent firms, and Mark Stevenson, president and COO of ABI, have acknowledged that the delay in new instrument platforms has put a dent in the company’s mass-spec sales [See PM 01/31/08 and 07/31/08].
When ABI and Invitrogen announced its $6.7 billion merger during the summer, speculation immediately arose that ABI’s mass spec business could be sold because it didn’t fit into the combined company’s business model [See PM 06/19/08]. While ABI and Invitrogen officials have steadfastly said that they have every intention of keeping the mass spec business, MDS’ CEO Stephen DeFalco, sounded a more equivocal note at a recent analyst conference, saying the company was evaluating its joint-venture agreement with ABI and had not ruled out buying the mass spec business from its partner [See PM 09/25/08].
ABI and Invitrogen, however, recently announced that mass spectrometry will make up one of four divisions in the newly combined company. Last week Stevenson called this “a very exciting time for the mass spectrometry market,” as uses for the instruments continue to evolve for a growing number of applications. The launch of the systems “demonstrates our continued commitment to this important market,” he said.
As the ABI/Invitrogen merger closes in on an anticipated November closing, the mass spec launch as well as the introduction of its SOLiD 3.0 next-generation sequencing platform indicates that ABI remains aggressive about technology development, said McDonald, the Wall Street analyst.
“I think it’s a good indication that the merger itself is not distracting them from their new product momentum, which is a good sign for once the deal closes that each of these business can be integrated pretty well,” he said.

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