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

BMC Bioinformatics

Research

Lei Xin¹  Baozhen Shan¹  Xiaowen Liu²  Bin Ma² 

[1] Bioinformatics Solutions, Inc., Waterloo, Canada;Department of Computer Science, University of Western Ontario, Canada;David R. Cheriton School of Computer Science, University of Waterloo, Canada;

关键词: Score Function;    Collision Induce Dissociation;    Electron Capture Dissociation;    Electron Transfer Dissociation;    Global Rank;   

DOI  :  10.1186/1471-2105-11-S1-S4

来源: Springer

【 摘 要 】

BackgroundTandem 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.ResultsTo 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.ConclusionA 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.

【 授权许可】

Unknown   
© Liu et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.