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Bioinformatics Advance Access published online on October 16, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn513
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

mspire: Mass spectrometry proteomics in Ruby

John T. Prince 1,2 and Edward M. Marcotte 1–3,*

1Institute for Cellular and Molecular Biology, 2Center for Systems and Synthetic Biology and 3Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712, USA

*To whom correspondence should be addressed. Dr. Edward M. Marcotte, E-mail: marcotte{at}icmb.utexas.edu


  Abstract

Summary: Mass spectrometry based proteomics stands to gain from additional analysis of its data, but its large, complex data sets make demands on speed and memory usage requiring special consideration from scripting languages. The software library ‘mspire’—developed in the Ruby programming language—offers quick and memory-efficient readers for standard xml proteomics formats, converters for intermediate file types in typical proteomics spectral-identification work flows (including the Bioworks .srf format), and modules for the calculation of peptide false identification rates.

Availability: Freely available at http://mspire.rubyforge.org

Contact: marcotte{at}icmb.utexas.edu

Supplementary information: Additional data models, usage information, and methods available at http://bioinformatics.icmb.utexas.edu/mspire

Associate Editor: Prof. John Quackenbush

Received on May 15, 2008; revised on September 26, 2008; accepted on October 1, 2008

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