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Bioinformatics Advance Access originally published online on June 17, 2009
Bioinformatics 2009 25(17):2174-2180; doi:10.1093/bioinformatics/btp366
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy

Xiaowen Liu 1, Yonghua Han 2, Denis Yuen 3 and Bin Ma 1,*

1 David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, 2 Department of Computer Science, University of Western Ontario, London and 3 Bioinformatics Solutions, Inc., Waterloo, Canada

* To whom correspondence should be addressed.


  Abstract

Motivation: The bottom-up tandem mass spectrometry (MS/MS) is regularly used in proteomics nowadays for identifying proteins from a sequence database. De novo sequencing software is also available for sequencing novel peptides with relatively short sequence lengths. However, automated sequencing of novel proteins from MS/MS remains a challenging problem.

Results: Very often, although the target protein is novel, it has a homologous protein included in a known database. When this happens, we propose a novel algorithm and automated software tool, named Champs, for sequencing the complete protein from MS/MS data of a few enzymatic digestions of the purified protein. Validation with two standard proteins showed that our automated method yields >99% sequence coverage and 100% sequence accuracy on these two proteins. Our method is useful to sequence novel proteins or ‘re-sequence’ a protein that has mutations comparing with the database protein sequence.

Availability: The software, named Champs (Complete Homology-Assisted Ms/ms Protein Sequencing), and the MS/MS data used in the article, are freely available at http://monod.uwaterloo.ca/champs/.

Contact: binma{at}uwaterloo.ca

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Alex Bateman

Received on March 22, 2009; revised on May 17, 2009; accepted on June 9, 2009

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