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Vendors to Adopt mzData as Standard Format

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Following efforts by the Human Proteome Organization to standardize mass spectrometer data output formats, a slew of mass spec and mass spec data analysis vendors are planning to adopt an open-data format called mzData designed to allow users to share data more easily by standardizing peak lists in one data format.

“It’s a good step forward,” says John Chakel, a product manager for proteomics and metabolomics software at Agilent, which, along with Bruker Daltonics, Matrix Science, Kratos, ABI, and Waters, is planning to adopt the new format. “[It] allows individuals to share data more easily, though to some degree it still puts the burden on the instruments that have generated the data in terms of how well they perform at peak picking and generating peak lists.”

Chris Taylor, a software engineer at the European Bioinformatics Institute who helped organize the collaborative effort between companies and academic institutions to produce mzData, says the new data format was first “put to keyboard” at 2003’s American Society for Mass Spectrometry meeting in Montreal.

Last year, about 10 mass-spec vendors met again to hammer out more details of the format. After final editing, many of the companies are now ready to release products with the new format by spring 2005.

Chakel says Agilent will incorporate mzData into its next release of SpectraMill by mid-2005, while David Creasy, the technical director of Matrix Science, says that mzData would be incorporated into Mascot 2.1 beginning this year.

Following the development of mzData, EBI is now working on developing mz-Ident, another XML format that will unify results from different search engines, such as Mascot and Sequest, facilitating cross-comparisons.

— Tien-Shun Lee

 

PATENT WATCH

US Patent No. 6,822,230 Matrix-assisted laser desorption/ionization sample holders and methods of using the same. Inventors: Arthur Schleifer, Viorica Lopez-Avila, Magdalena Anna Ostrowski, Jean Luc Truche, Jian Bai. Assignee: Agilent Technologies. Issued: November 23, 2004.

The patent describes MALDI sample holders and methods of using and making them. The MALDI sample holders are configured for use in matrix assisted laser desorption/ionization and include a planar substrate having a surface and at least one fluid-retaining structure present on the surface. The fluid-retaining structure includes a material that changes from a fluid state to a solid state in response to a stimulus. Also provided are methods of using the subject MALDI sample holders in a matrix-assisted laser desorption/ionization protocol, as well as methods of producing the subject MALDI sample holders.

 

US Patent No. 6,818,411. Retentate chromatography and protein chip arrays with applications in biology and medicine. Inventors: William Hutchens, Tai-Tung Yip. Assignee: Ciphergen Biosystems. Issued: November 16, 2004.

This invention provides methods of retentate chromatography for resolving analytes in a sample. The methods involve adsorbing the analytes to a substrate under a plurality of different selectivity conditions, and detecting the analytes retained on the substrate by desorption spectrometry. The methods are useful in biology and medicine, including clinical diagnostics and drug discovery.

 

Datapoint

80%

In the process of rebranding itself as a proteomics, molecular diagnostics, and medical devices services company, Zyomyx laid off more than 40 employees, or 80 percent of its staff, and sold about $50 million worth of equipment in October.

 

Proteome Systems implements a cost-management program expected to result in an annualized savings of AU$6 million ($4.7 million) that includes job cuts in its Boston and Sydney, Australia, facilities. The exact number of jobs that will be eliminated was not immediately clear.

 

The National Cancer Institute awards $9.8 million to 17 Biomarkers Developmental Laboratories to examine the human genome, proteome, epitome, and metabolome to identify biomarkers that can potentially serve as early detection biomarkers and markers of progression of the disease.

 

Genomics One acquires from Solidarity Fund QFL a secured debt of CA$175,000 ($147,717) against Dephy Technologies, a Montreal-based proteomics company that recently filed for bankruptcy protection and ceased its activities. Genomics One intends to acquire all of Dephy’s tangible and intangible assets.

 

The Australian Proteome Analysis Facility will partner with LumiCyte to develop LCI’s STS biochip platform technology and to accelerate APAF’s proteomic biomarker discovery efforts.

 

Shamrock Structures will provide integrated structural proteomics services for Trubion Pharmaceuticals, including crystallizing protein samples, collecting synchrotron data, and determining the structure of proteins developed by Trubion.

 

 

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