Numerical compression schemes for proteomics mass spectrometry data.

Research output: Contribution to journalArticle

Abstract

The open XML format mzML, used for representation of mass spectrometry (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. 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 4-fold or even up to 18-fold larger compared to 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%. It is envisaged that these improvements will be beneficial for data handling within the MS community.

Details

Authors
  • Johan Teleman
  • Andrew W Dowsey
  • Faviel F Gonzalez-Galarza
  • Simon Perkins
  • Brian Pratt
  • Hannes Rost
  • Lars Malmstrom
  • Johan Malmström
  • Andrew R Jones
  • Eric W Deutsch
  • Fredrik Levander
Organisations
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Infectious Medicine
Original languageEnglish
Pages (from-to)1537-1542
JournalMolecular & Cellular Proteomics
Volume13
Issue number6
Publication statusPublished - 2014
Publication categoryResearch
Peer-reviewedYes

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