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Bioinformatics Advance Access published online on March 31, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp181
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

StatQuant: A post quantification analysis toolbox for improving quantitative mass spectrometry

Bas van Breukelen 1,2,3,4,*, Henk W.P. van den Toorn 1,2,3,4, Madalina M. Drugan 1,2,3,4 and Albert J.R. Heck 1,2,3,4

1Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
2Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
3Netherlands Proteomics Centre, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands.
4Netherlands Bioinformatics Centre, Geert Grooteplein 28, 6525 GA Nijmegen

*To whom correspondence should be addressed. Dr. Bas van Breukelen, E-mail: b.vanbreukelen{at}uu.nl


  Abstract

Motivation: Mass spectrometric protein quantitation has emerged as a high-throughput tool to yield large amounts of data on peptide and protein abundances. Currently differential abundance data can be calculated from peptide intensity ratios by several automated quantitation software packages available. There is, however, still a great need for additional processing to validate and refine the quantitation results. Here, we present a software tool, termed StatQuant, that offers a set of statistical tools to process, filter, compare and represent data from several quantitative proteomics software packages such as MSQuant. StatQuant offers the researcher post processing methods to achieve improved confidence on the obtained protein ratios.

Availability: StatQuant can be downloaded from: https://gforge.nbic.nl/projects/statquant/ (binary and source code).

Contact: b.vanbreukelen{at}uu.nl

Associate Editor: Dr. Jonathan Wren

Received on January 28, 2009; revised on March 13, 2009; accepted on March 26, 2009

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