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HUPO Investigating Standard Mixture Analysis Problems


With results in from the first set of samples in its effort to create a protein-standard mixture, the Human Proteome Organization now faces the task of figuring out why some laboratories had trouble properly identifying the proteins.

The effort is the next step in HUPO’s initiative to create the protein-standard mixture, which began a year ago. In December, the organization sent out its first sample set of 20 proteins in equimolar amounts to 24 laboratories worldwide for analysis. The proteins were created by Invitrogen at a purity level of between 95 and 99 percent.

The objective of the initiative, according to John Bergeron, immediate past president of HUPO, is “to assure the community that proteomics is 100 percent successful.
“The idea was to put together a high-quality set of samples, not just to benchmark the community, but also to educate the community in order to assure it can get 100 percent success characterizing these proteins in test samples,” he says.

But as HUPO began receiving results, coordinators discovered that while some labs were able to identify all of the proteins, others missed some and/or identified some that weren’t there. HUPO contacted those labs and guided them in redoing their analysis until they were able to achieve 100 percent accuracy, but the organization wants to pinpoint exactly what the issues were, Bergeron says.

Currently, HUPO is depositing the raw data from the laboratories’ analyses into the Tranche database so that investigators can try to figure out where the laboratories that had trouble went wrong.

“Through that, we’re going to … figure out why it is that some of the groups characterized proteins which are not there … and missed several proteins that are definitely there,” Bergeron says, adding that details of the results will be presented at HUPO’s annual conference in October.

Tony Fong

Short Reads

Applied Biosystems has three new services: a maintenance program for Agilent Technologies’ high-performance liquid chromatography systems sold with ABI/Sciex mass specs, a software validation consulting service, and a Web-based service, called Smart Center Online, for remote system monitoring and diagnosis. Under this agreement, Agilent will provide training, parts, and documentation to ABI engineers who will maintain and repair Agilent’s 1100 and 1200 Series HPLC instruments.

Denmark’s Proxeon will be integrating and marketing its ProteinCenter software with Matrix Science’s Mascot software. The ProteinCenter application helps researchers understand the biology of mass spec-detected proteins, and Mascot is a search engine. This move, Proxeon says, will help proteomics researchers analyze their data more easily.

Vermillion received a second letter from Nasdaq saying that it is not fulfilling the minimum rules to be listed on the exchange. Vermillion violates the rule that a company has to have at least $2.5 million in stock-holders’ equity, market capitalization of $35 million, or $500,000 of net income from continuing operations during the last fiscal year or during two out of the last three fiscal years.

Bruker BioSciences’ Daltonics division, which includes its proteomics instrument, saw revenues climb to $40.6 million during the second quarter, compared to $39.8 million last year. Company-wide, Bruker’s earnings grew by 21.1 percent.


US Patent 7,265,348. Apparatus for dispensing a sample in electrospray mass spectrometers. Inventors: Joee Rossier and Free Reymond. Assignee: Diagnoswiss. Issued: September 4, 2007.
This patent covers a device that dispenses electrospray ionization mass spectrometry samples, a way to build the device, and how it applies to biological and chemical analysis. The device is made from an electrically non-conductive substrate and one of its substructures holds the sample and the other holds the sheath liquid or sheath gas. The sample and sheath liquid or gas come into contact and/or are mixed in the Taylor cone of the spray.

US Patent 7,265,368. Ion optical mounting assemblies. Inventor: Roy Martin. Assignees: Applera and MDS. Issued: September 4, 2007.
According to this patent, the system contains an ion optical assembly and a system to mount and align the ion optic components. The ion optical elements are aligned and assembled by compressing them with front and back securing members, made of a threaded surface and a contact face, and without a torque pattern.

Data Point

$36 million

Inverness Medical Innovations plans to buy Matritech for $36 million in common stock and up to $2 million in cash or stock. Matritech develops protein-based diagnostic tests, and its leading product is the bladder cancer test NMP22 BladderChek.

The Scan

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