Encyclopedia of Systems Biology

2013 Edition
| Editors: Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho, Hiroki Yokota

Proteomics Data Formats

  • Lars Malmström
  • Andreas Quandt
  • Ela Pustulka-Hunt
Reference work entry
DOI: https://doi.org/10.1007/978-1-4419-9863-7_1007



Proteomics data formats are standardized file formats defined by the Human Proteomics Standards Initiative (PSI 2011) and based on XML Schema (XML 2011). The standards are part of larger-scale standardization efforts which aim to facilitate data exchange and mediate between various types of software, databases, and file systems (BioSharing 2011; MIBBI 2011; OBO 2011; ISA-TAB 2011). The standards evolve in response to new technological developments. In most cases, a standard is associated with a document type definition which software can use to check if a file conforms to the standard, and tools for conversion into other formats. The reference to the XML schema of the data format used is found at the top of each XML file.

Examples (PSI 2011) are as follows:
  • mzML: The data measured by MS is normally stored as a collection of spectra or ion chromatograms in a format called mzML. Each spectrum has some metadata associated with...

This is a preview of subscription content, log in to check access.


  1. BioSharing (2011) http://biosharing.org. Accessed 24 May 2011
  2. ISA (2011) Investigation/Study/Assay Infrastructure. http://isatab.sourceforge.net. Accessed 24 May 2011
  3. MIBBI (2011) Minimum Information for biological and biomedical investigations. http://mibbi.org. Accessed 24 May 2011
  4. OBO (2011) Open biomedical ontologies. http://www.obofoundry.org. Accessed 24 May 2011
  5. PSI (2011) Human Proteomics Standards Initiative. http://www.psidev.info. Accessed 24 May 2011
  6. XML (2011) XML Schema. http://www.w3.org/2001/XMLSchema-instance. Accessed 24 May 2011

Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  • Lars Malmström
    • 1
  • Andreas Quandt
    • 1
  • Ela Pustulka-Hunt
    • 2
  1. 1.Institute of Molecular Systems Biology IMSBETH ZurichZurichSwitzerland
  2. 2.GS SystemsXETH ZurichZurichSwitzerland