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New Standards Afoot with Organizers HUPO, ABRF

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The Human Proteome Organization and Invitrogen plan to co-develop two sets of experimental protein standards — mixes of proteins — for proteomics platforms. Separately, Sigma-Aldrich plans to launch a standard it co-developed last year with the Association of Biomolecular Resource Facilities’ Proteomics Standards Research Group.

Invitrogen’s and HUPO’s standards, which the company also plans to commercialize, will join other efforts in the field to create standardized mixtures of proteins or peptides for benchmarking proteomics platforms, a dynamic that underscores the need among scientists to test their platforms before comparing data.

“You need to know the limitations of what you do and how you do it. Without those [standards], it’s very difficult to do,” says Eugene Kolker, president and director of the Biatech Institute, a nonprofit research organization that has developed and distributed two standard mixes for proteome studies in the past.

The first standard from HUPO and Invitrogen will comprise 20 proteins in equimolar amounts selected from a list of 100 for their “extremely high purity, quality, stability, and robustness,” according to John Bergeron, HUPO president. These proteins, whose identity will be kept under wraps for now, “cover various criteria which the committee put together,” he says. The second standard will contain 20 proteins in four different samples at varying concentrations spanning either three or four logs, with some kept constant at high abundance, some at low abundance, and others mixed in.

Meanwhile, Sigma aims to sell a protein mix that came out of the ABRF proteomics standards group. Earlier this year, the group presented results from its 2006 study, which involved the analysis of a mixture of 49 human proteins in equimolar amounts by participating laboratories. The group developed this protein standard in collaboration with Sigma-Aldrich, which plans to launch the mix commercially this fall, according to Dale Peluso, the company’s market segment manager for quantitative proteomics.

— Julia Karow

PATENT WATCH

US Patent 7,081,618. Use of conductive glass tubes to create electric fields in ion mobility spectrometers. Inventor: Bruce Laprade. Assignee: Burle Technologies. Issued: July 25, 2006.

The patent covers an ion mobility spectrometer “in which the reaction-ionization chamber and/or the ion drift chamber are constructed with one or more single-piece glass tubes,” according to the abstract. “The use of the glass tube(s) provides a significant reduction in the number of parts used in such spectrometers, simplification in their manufacture, and improvements in their performance and reliability.”

US Patent 7,078,684. High-resolution Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry methods and apparatus. Inventors: Steven Beu, Greg Blakney, John Quinn, Christopher Hendrickson, and Alan Marshall. Assignee: Florida State University. Issued: July 18, 2006.

The patent covers a high-resolution FT-ICR mass spec system with “excitation circuitry including an excitation amplifier for generating an electrical excitation signal and excitation electrodes for applying an oscillating electric field to excite ions in the system.”

SHORT READS

PerkinElmer will work with Johns Hopkins University and the University of Birmingham, UK, to establish tools and technologies to discover diagnostic and therapeutic biomarkers in undisclosed indications using the company’s protein-based biomarker enrichment technology.

BioMachines teamed up with the University of Massachusetts Proteomic Fractionation Group to form a new division offering protein analysis services. The agreement is significant for BioMachines, marking a new business model incorporating a revenue source other than equipment design and manufacturing. And for UMass, the deal could enable it to attract a new breed of customer for its year-old Proteomics Consortium.

Mount Sinai School of Medicine will use a peptide-microarray platform from JPT Peptide Technologies as part of a biomarker discovery collaboration looking at B-cell epitopes for vaccines and diagnostics in food allergies.

The Swiss Institute of Bioinformatics will use the e-Proxemis bioinformatics software from Geneva Bioinformatics for its proteomic research.

Proteomics company CS-Keys received seed funding from Midwest venture capital firm Triathlon Medical Ventures. The company called the investment “significant” but did not disclose details. Based in Indianapolis, CS-Keys will use the investment to continue researching and developing cancer-specific biomarkers.

DATAPOINT

$21 million

Amount for which Thermo Electron acquired GV Instruments, a Manchester, UK-based mass spec company. GV manufactures isotope-ratio mass spectrometers.

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