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Bioinformatics Advance Access originally published online on November 22, 2006
Bioinformatics 2007 23(2):262-263; doi:10.1093/bioinformatics/btl573
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

ProteomeCommons.org IO Framework: reading and writing multiple proteomics data formats

J. A. Falkner *, J. W. Falkner and P. C. Andrews

Department of Biochemistry, Program in Bioinformatics Ann Arbor, MI, 48109, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Effective use of proteomics data, specifically mass spectrometry data, relies on the ability to read and write the many mass spectrometer file formats. Even with mass spectrometer vendor-specific libraries and vendor-neutral file formats, such as mzXML and mzData it can be difficult to extract raw data files in a form suitable for batch processing and basic research. Introduced here are the ProteomeCommons.org Input and Output Framework, abbreviated to IO Framework, which is designed to abstractly represent mass spectrometry data. This project is a public, open-source, free-to-use framework that supports most of the mass spectrometry data formats, including current formats, legacy formats and proprietary formats that require a vendor-specific library in order to operate. The IO Framework includes an on-line tool for non-programmers and a set of libraries that developers may use to convert between various proteomics file formats.

Availability: The current source-code and documentation for the ProteomeCommons.org IO Framework is freely available at http://www.proteomecommons.org/current/531/

Contact: jfalkner{at}umich.edu

Associate Editor: Alfonso Valencia

Received on September 21, 2006; revised on November 10, 2006; accepted on November 11, 2006

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