Skip Navigation



Bioinformatics Advance Access published online on November 22, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl573
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
23/2/262    most recent
btl573v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Falkner, J. A.
Right arrow Articles by Andrews, P. C.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Falkner, J. A.
Right arrow Articles by Andrews, P. C.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received September 21, 2006
Revised November 10, 2006
Accepted November 11, 2006

Applications note

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

J. A. Falkner 1 *, J. W. Falkner 1, and P. C. Andrews 1

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


  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 is 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/.

Associate Editor: Alfonso Valencia
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
J. A. Siepen, K. Belhajjame, J. N. Selley, S. M. Embury, N. W. Paton, C. A. Goble, S. G. Oliver, R. Stevens, L. Zamboulis, N. Martin, et al.
ISPIDER Central: an integrated database web-server for proteomics
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W485 - W490.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
A. K. Yocum, T. E. Gratsch, N. Leff, J. R. Strahler, C. L. Hunter, A. K. Walker, G. Michailidis, G. S. Omenn, K. S. O'Shea, and P. C. Andrews
Coupled Global and Targeted Proteomics of Human Embryonic Stem Cells during Induced Differentiation
Mol. Cell. Proteomics, April 1, 2008; 7(4): 750 - 767.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.