title: Numerical compression schemes for proteomics mass spectrometry data.
abstract: 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. 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 naïve 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%. It is envisaged that these improvements will be beneficial for data handling within the MS community.
authors.affiliation: From the ‡Department of Immunotechnology, Lund University, Medicon Village building 406, 223 81 Lund Sweden;
authors.forename: Johan
authors.initials: J
authors.lastname: Teleman
authors.affiliation: §Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, United Kingdom; ¶Centre for Advanced Discovery and Experimental Therapeutics (CADET), University of Manchester and Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Oxford Road, Manchester M13 9WL, United Kingdom;
authors.forename: Andrew W
authors.initials: AW
authors.lastname: Dowsey
authors.affiliation: ‖Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom;
authors.forename: Faviel F
authors.initials: FF
authors.lastname: Gonzalez-Galarza
authors.affiliation: ‖Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom;
authors.forename: Simon
authors.initials: S
authors.lastname: Perkins
authors.affiliation: **Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, 98195, USA;
authors.forename: Brian
authors.initials: B
authors.lastname: Pratt
authors.affiliation: ‡‡Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, Wolfgang-Pauli Strasse 16, 8093 Zurich, Switzerland;
authors.forename: Hannes L
authors.initials: HL
authors.lastname: Röst
authors.affiliation: ‡‡Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, Wolfgang-Pauli Strasse 16, 8093 Zurich, Switzerland;
authors.forename: Lars
authors.initials: L
authors.lastname: Malmström
authors.affiliation: §§Department of Clinical Sciences, Faculty of Medicine, Lund University, SE-221 84 Lund, Sweden;
authors.forename: Johan
authors.initials: J
authors.lastname: Malmström
authors.affiliation: ‖Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom;
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Jones
authors.affiliation: ¶¶Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, USA; edeutsch@systemsbiology.org.
authors.forename: Eric W
authors.initials: EW
authors.lastname: Deutsch
authors.affiliation: From the ‡Department of Immunotechnology, Lund University, Medicon Village building 406, 223 81 Lund Sweden; ‖‖Bioinformatics Infrastructure for Life Sciences, Lund University, Sweden.
authors.forename: Fredrik
authors.initials: F
authors.lastname: Levander
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D013058:Mass Spectrometry; D009716:Numerical Analysis, Computer-Assisted; D040901:Proteomics; D012984:Software