Encyclopedia of Systems Biology

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

Proteomics Data Capture

  • Lars Malmström
  • Andreas Quandt
  • Ela Pustulka-Hunt
Reference work entry
DOI: https://doi.org/10.1007/978-1-4419-9863-7_1001

Definition

Proteomics data capture involves gathering data from an instrument, such as a mass spectrometer, and making it available for analysis. Because the data generated by the instrument is often stored in a format that is not supported by the analysis software, data capture often includes conversion from the vendor specific format to a standard proteomics data format.

Characteristics

Data generated by mass spectrometry is organized into data files where data from a single sample injection is stored in a file or a directory of files. Each vendor has one or more proprietary formats that are binary or XML based. As a personal computer (PC) running the Microsoft Windows operating system controls the vast majority of mass spectrometers, the most common storage solution on that PC is a consumer-grade hard drive that can store a few months’ worth of data.

As mass spectrometers are used in various contexts, the analysis software that comes bundled with the acquisition softwareis geared...

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References

  1. Dropbox (2011) Dropbox is a file-hosting service for data sharing. https://www.dropbox.com. Accessed 25 May 2011
  2. Bauch A, Adamczyk I, Buczek P, Elmer F-J, Enimanev K, Glyzewski P, Kohler M, Pylak T, Quandt A, Ramakrishnan C, Beisel C, Malmström L, Aebersold R, Rinn B (2011) OpenBIS: a flexible framework for managing and analyzing complex data in biology research. BMC Bioinformatics 12:468Google Scholar
  3. Kessner D, Chambers M, Burke R, Agus D, Mallick P (2008) ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 24(21):2534–2534PubMedGoogle Scholar
  4. ProteoWizard (2011) http://proteowizard.sourceforge.net/. Accessed 25 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 IMSB, ETH ZurichZurichSwitzerland
  2. 2.GS SystemsXETH ZurichZurichSwitzerland