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This article is part of the supplement: Selected articles from the Eighth Asia-Pacific Bioinformatics Conference (APBC 2010)

Open Access Research

Better score function for peptide identification with ETD MS/MS spectra

Xiaowen Liu1, Baozhen Shan23, Lei Xin23 and Bin Ma1*

Author Affiliations

1 David R. Cheriton School of Computer Science, University of Waterloo, Canada

2 Bioinformatics Solutions, Inc., Waterloo, Canada

3 Department of Computer Science, University of Western Ontario, Canada

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BMC Bioinformatics 2010, 11(Suppl 1):S4  doi:10.1186/1471-2105-11-S1-S4

Published: 18 January 2010



Tandem mass spectrometry (MS/MS) has become the primary way for protein identification in proteomics. A good score function for measuring the match quality between a peptide and an MS/MS spectrum is instrumental for the protein identification. Traditionally the to-be-measured peptides are fragmented with the collision induced dissociation (CID) method. More recently, the electron transfer dissociation (ETD) method was introduced and has proven to produce better fragment ion ladders for larger and more basic peptides. However, the existing software programs that analyze ETD MS/MS data are not as advanced as they are for CID.


To take full advantage of ETD data, in this paper we develop a new score function to evaluate the match between a peptide and an ETD MS/MS spectrum. Experiments on real data demonstrated that this newly developed score function significantly improved the de novo sequencing accuracy of the PEAKS software on ETD data.


A new and better score function for ETD MS/MS peptide identification was developed. The method used to develop our ETD score function can be easily reused to train new score functions for other types of MS/MS data.