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Cerno Adds ECD Feature to MassWorks to Improve Molecular ID on Low-End Mass Specs

Cerno Bioscience, a software startup that specializes in mass-spectrometry data analysis, is launching a new capability for its flagship MassWorks analysis package that it claims can dramatically improve the way relatively low-priced mass specs identify molecular components.
The company will unveil the new feature, called CLIPS (Calibrate Lineshape Isotope Profile Search), at next week’s Pittcon conference in Chicago.
Cerno officials said that CLIPS will enable researchers to perform accurate elemental composition determination — essentially, identifying molecular components at the atomic scale — on single or triple quadrupole mass spectrometers.
While higher-end instruments like quadrupole time-of-flight and Fourier transform mass specs currently offer ECD capability, these instruments can run into the six-figure price range. Cerno claims that its approach can now put the same ability in the hands of researchers using instruments that cost in the hundreds of thousands of dollars.
This philosophy builds on the strategy behind the company’s MassWorks software, which uses a mathematical calibration method to improve the mass accuracy of lower-resolution mass specs [BioInform 03-10-06].
“We’ve had cases where people have held off on buying high-resolution machines because they feel that for what their needs are, this brings that capability,” Don Kuehl, vice president of marketing and product development for Cerno, told BioInform this week.
Kuehl stressed that the company doesn’t claim that its software replaces high-resolution machines, but noted that the firm has seen interest from pharmaceutical firms that run both low-end and high-end instruments.
“Their workhorses are the low-end machines, and what’s exciting to them is they can improve the quality of the information they obtain on a day-to-day basis,” he said. “The majority of experiments get run on the single quads, the triple quads, the trap instruments, and then when they run into problems or they need to identify something, then they’ll move it up to the high-resolution machines and they’ll have to re-run the experiment.
“So I think they’re intrigued because, first of all, the quality of the results they get right off the bat is higher, so they have more confidence in every run that they do,” he said.
MassWorks was officially launched at the end of 2006 — a bit later than its expected mid-year launch date, Kuehl acknowledged. The company has signed several customers for the software, but Kuehl said the firm is still in the early stages of marketing the product.
“The response has been very positive. It’s got people thinking because it’s a very different approach to what people have done in the past and how they’ve done it,” he said. “To be honest, our largest barrier right now is educating people.”
Calibration Improves Accuracy, Formula ID
CLIPS builds on the mass calibration methodology used in MassWorks, which the company claims can improve the mass accuracy on low-resolution mass specs by 100-fold.
Researchers first run a known sample on their instrument as a calibration standard, and then use a standard MS software package to analyze the spectra. MassWorks then uses mathematical modeling to compare the results of the analysis with the expected result to create a correction function that it applies to all the sample data from the instrument.
Because MassWorks “calibrates the actual instrument line shape to a known mathematical function,” it can accurately calculate the “theoretical isotope profile for each formula candidate using the same line shape as the calibrated line shape,” according to company literature.
CLIPS then matches each formula candidate to spectra for the unknown sample and calculates a statistic with less than 1 percent relative error, which is “a level of profile accuracy necessary to differentiate candidate formulas and arrive at unambiguous formula determination,” the company said.
“We’ve realized that because of the way we do our calibration, not only can we use the mass position information, but we can actually model the whole shape of the isotope profile, which is like a fingerprint for a given compound, and if you change the elemental composition of a protein or a peptide or a small organic, it basically changes that pattern,” Kuehl said.

“To be honest, our largest barrier right now is educating people.”

Yongdong Wang, founder and president of the company, said that CLIPS should be of interest to proteomics researchers because it will enable them to identify post-translational modifications — a particular challenge in the field today. Researchers can use the software to analyze proteins and peptides with a low-resolution mass spec “and see if you have a sulfur added or a phosphor added to your protein or peptide by determining the elemental composition of the formula.”
“That’s where we hope to be able to enter into the proteomics area,” he said. 
At least one customer agrees that the method performs as promised. Robert Strife, a senior scientist in consumer products research, said that his analytical chemistry lab is successfully using CLIPS for small-molecule identification on lower-cost mass specs.
Strife, who could not identify his employer due to company policy, said that while his lab has “just gotten started” with the software, “we’re impressed with the early results” — particularly on very low-end instruments, where they have seen “drastic increases” in performance.
“This looks like a very attractive option for getting more bang for your buck,” he said.
In January, Cerno signed a distribution agreement with Lumiere Technology under which Lumiere will distribute Cerno’s MassWorks mass spectrometry analysis software in China [BioInform 01-05-07].
The company is planning on expanding its distribution channels in Asia, and has signed an agreement with an undisclosed distribution partner in Japan.
Kuehl said that the firm will likely start looking for European distributors by the end of the year.
The company also has ongoing discussions with several mass spec vendors, but Kuehl noted that those are “long-term opportunities.” Instrumentation vendors are “primarily hardware oriented,” he said, and have little incentive to sell customers a lower-end system with MassWorks software if they can sell a million-dollar box.
“Until you can go out and create market pressure, [a co-marketing agreement] is just extra work for them,” he said.

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