Journal Article

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

Xiaowen Liu, Yonghua Han, Denis Yuen and Bin Ma

in Bioinformatics

Volume 25, issue 17, pages 2174-2180
Published in print September 2009 | ISSN: 1367-4803
Published online June 2009 | e-ISSN: 1460-2059 | DOI:
Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy

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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


Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  5934 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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