PROTEOMICS PROJECTS
Toward a single MS data format What began as two separate data formats for MS proteomics data will soon become one, possibly later this year. The new format will allow researchers to store spectral data and a description of the parameters used by the mass spectrometer to capture those data. According to Patrick Pedrioli of the Institute for Systems Biology (ISB), merging the existing mzData and mzXML formats should reduce confusion among researchers about which one should be the standard. Randy Julian, who is at Indigo BioSystems and is a leader of the HUPO Proteomics Standards Initiative (PSI)MS working group, says that the two formats were initially developed with different goals in mind. A group led by ISB researchers created mzXML as a data model that could be used with any commercial mass spectrometer. The PSI-MS group, however, was “working on the problem of data interchange so
that instrument vendors could provide export utilities and the format could remain useful over time despite rapid technology advancements in MS,” explains Julian. The groups “were working independently on two different facets of the problem, and we’ve been keeping in close communication,” he adds. Pedrioli says that the goal has been to keep the data models similar to each other, but the idea of unifying the two formats came during a break between sessions at a joint meeting of the mzXML Associated Standard Solutions committee and PSI-MS researchers held last August at ISB in Seattle. Julian says that one of the main differences between mzData and mzXML is the way in which the formats can be extended to accommodate new types of experiments. “While working on the new HUPO results format [called AnalysisXML], we realized it was possible to use the same extension method for both mzData and mzXML,” he says.
“With this difference eliminated, the remaining parts are so similar that it no longer made sense to address pipeline and interchange problems with two different formats.” Pedrioli and Julian are also addressing the technical aspects of the merger. “The harder problem is how fast to push forward a significant change,” says Julian. He says that they must decide whether to implement a single format all at once, even though it might not be compatible with the existing versions, or to announce several small changes. Pedrioli says, “The community-supported mzXML tools could be adapted to export the new format. [The tools] are not bound by the release cycles of instrument vendors and will provide a faster way to [enact] significant changes during the transition.” Julian and Pedrioli plan to ask other researchers for i nput on how to proceed, at the PSI Spring Workshop, to be held April 21–23 in San Francisco. —Katie Cottingham
PEOPLE
New Editorial Advisory Board members R. Graham Cooks, Henry Bohn Hass Distinguished Professor of Chemistry at Purdue University, was educated at the University of Natal (South Africa) and Cambridge University (U.K.). He has made significant contributions to the development of desorption ionization and tandem MS as methods for analyzing complex mixtures. In addition, he has worked on the kinetic method for measuring thermochemical quantities and inelastic and reactive ion collisions with surfaces. Thomas E. Fehniger is employed by AstraZeneca R&D (Sweden) in the Translational Sciences section, the bridge between preclinical drug discovery and
principle testing in clinical trials. He received his doctoral degree in medical microbiology and immunology from the University of California, Los Angeles. Fehniger manages clinical sample collection study design and provides unique facets of project support that i nclude the linkage of proteomics data with clinical presentation measurements and outcomes, guidance on bioethics issues, and disease segmentation based upon pathology. He coedited the March/April 2004 JPR special thematic issue on Proteomics and Disease. Robert F. Murphy, professor of biological sciences and biomedical engineering and director of the Center for Bioimage Informatics at Car negie Mellon University (CMU), codeveloped the Flow Cytometry Standard data file format used throughout the cytometry industry and is chair of the Cytometry Development Workshop held each year in Asilomar, Calif. His research group at CMU
has pioneered the application of machine learning methods to systematically categorize the subcellular location of proteins reflected in fluorescence microscope images. He is interested in automated analysis of protein location and is chair of the Biodata Management and Analysis Study Section of the National Institutes of Health. Scot R. Weinberger, president of GenNext Technologies, received a B.S. in cellular biology from the University of Nevada, Reno. His graduate studies included medical training at the University of Nevada School of Medicine and Ph.D. studies in physical biochemistry at the University of Nevada, Reno. His research interests are in the fields of protein biochip technology, SELDI and MALDI technologies, TOFMS, and microscale separation techniques. Weinberger was one of the pioneering instrument developers for microscale HPLC, CE, and MALDI TOFMS technologies.
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