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Cerno Improves 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 comparatively lower-priced mass specs identify molecular components.

The company unveiled the new feature, called CLIPS (Calibrate Lineshape Isotope Profile Search), this week at the Pittsburgh Conference in Chicago.

Cerno officials say that CLIPS allows 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, they can run into the six-figure price range. Cerno says 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.

“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,” says Don Kuehl, vice president of marketing and product development for Cerno.

Kuehl stresses that the company doesn’t claim that its software replaces high-
resolution machines, but notes 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 says. “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.”

Bernadette Toner

Short Reads

Oxford University has a new Synapt HDMS. The chemistry department will be using this mass spectrometer to study oxygen-sensing by cells.

Nanosys and Bruker Daltonics entered into an R&D and distribution agreement that will couple Nanosys’ NALDI target plates with Bruker’s mass spectrometers. Under the agreement, Nanosys will supply Bruker with its nanotechnology-enabled matrix-free target plates, called NALDI chips, which Bruker will market with its laser desorption ionization time-of-flight mass spectrometers.

Shimadzu and Waters say they plan to co-develop software that will allow Waters’ Empower chromatography software to control Shimadzu’s Prominence liquid chromatographer.

The US Food and Drug Administration has approved the first phase of a BG Medicine and National Center for Toxicological Research project to develop biomarkers for liver toxicity, in which BG Medicine says it will use mass spectrometry technology from Applied Biosystems.

Potomac Affinity Proteins and the University of Maryland Biotechnology Institute received $105,000 as part of $5.2 million given to private companies and researchers from the University of Maryland to develop high-tech commercial products.


US Patent 7,183,118. Methods for quantitative proteome analysis of glycoproteins. Inventors: Rudolf Aebersold and Hui Zhang. Assignee: Institute for Systems Biology. Issued: February 27, 2007.

This patent describes a technique to identify and quantify glycoproteins by “immobilizing glycopolypeptides to a solid support; cleaving the immobilized glycopolypeptides, thereby releasing non-glycosylated peptides and retaining immobilized glycopeptides; releasing the glycopeptides from the solid support; and analyzing the released glycopeptides.”

US Patent 7,179,592. Size-exclusion-based extraction of affinity ligands and active compounds from natural samples. Inventors: Yuriy Dunayevskiy, Dallas Hughes, Andrew Weiskopf. Assignee: Cetek. Issued: February 20, 2007.

“The invention encompasses an improved, rapid, size-exclusive method for screening for small molecular weight ligands that bind specifically to a protein target, using size-exclusion separation, ultrafiltration, and mass spectrometry,” says the patent abstract.

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