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Investigators from Lund University Report New Data on Proteomics (Numerical Compression Schemes for Proteomics Mass Spectrometry Data)

July 14, 2014

By a News Reporter-Staff News Editor at Proteomics Weekly -- A new study on Proteomics is now available. According to news reporting out of Lund, Sweden, by NewsRx editors, research stated, "The open XML format mzML, used for representation of MS data, is pivotal for the development of platform-independent MS analysis software. Although conversion from vendor formats to mzML must take place on a platform on which the vendor libraries are available (i.e."

Our news journalists obtained a quote from the research from Lund University, "Windows), once mzML files have been generated, they can be used on any platform. However, the mzML format has turned out to be less efficient than vendor formats. In many cases, the naive mzML representation is fourfold or even up to 18-fold larger compared with the original vendor file. In disk I/O limited setups, a larger data file also leads to longer processing times, which is a problem given the data production rates of modern mass spectrometers. In an attempt to reduce this problem, we here present a family of numerical compression algorithms called MS-Numpress, intended for efficient compression of MS data. To facilitate ease of adoption, the algorithms target the binary data in the mzML standard, and support in main proteomics tools is already available. Using a test set of 10 representative MS data files we demonstrate typical file size decreases of 90% when combined with traditional compression, as well as read time decreases of up to 50%."

According to the news editors, the research concluded: "It is envisaged that these improvements will be beneficial for data handling within the MS community."

For more information on this research see: Numerical Compression Schemes for Proteomics Mass Spectrometry Data. Molecular & Cellular Proteomics, 2014;13(6):1537-1542. Molecular & Cellular Proteomics can be contacted at: Amer Soc Biochemistry Molecular Biology Inc, 9650 Rockville Pike, Bethesda, MD 20814-3996, USA. (American Society for Biochemistry and Molecular Biology -; Molecular & Cellular Proteomics -

Our news journalists report that additional information may be obtained by contacting J. Teleman, Lund University, S-22100 Lund, Sweden. Additional authors for this research include A.W. Dowsey, F.F. Gonzalez-Galarza, S. Perkins, B. Pratt, H.L. Rost, L. Malmstrom, J. Malmstrom, A.R. Jones, E.W. Deutsch and F. Levander (see also Proteomics).

Keywords for this news article include: Lund, Sweden, Europe, Proteomics

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Source: Proteomics Weekly

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