HiXCorr: a portable high-speed XCorr engine for high-resolution tandem mass spectrometry

Bioinformatics
Hyunwoo KimEunok Paek

Abstract

Peptide identification is an important problem in proteomics. One of the most popular scoring schemes for peptide identification is XCorr (cross-correlation). Since calculating XCorr is computationally intensive, a lot of efforts have been made to develop fast XCorr engines. However, the existing XCorr engines are not suitable for high-resolution MS/MS spectrometry because they are either slow or require a specific type of CPU. We present a portable high-speed XCorr engine for high-resolution tandem mass spectrometry by developing a novel algorithm for calculating XCorr. The algorithm enables XCorr calculation 1.25-49 times faster than previous algorithms for 0.01 Da fragment tolerance. Furthermore, our engine is easily portable to any machine with different types of CPU because it is developed in C language. Hence, our XCorr engine will expedite peptide identification by high-resolution tandem mass spectrometry. Available at http://isa.hanyang.ac.kr/HiXCorr/HiXCorr.html. hjpark@hanyang.ac.kr Supplementary data are available at Bioinformatics online.

References

Sep 2, 2004·Nature Reviews. Molecular Cell Biology·Hanno Steen, Matthias Mann
Sep 9, 2008·Journal of Proteome Research·Jimmy K EngMichael J Maccoss
Jul 19, 2011·Journal of Proteome Research·Benjamin J Diament, William Stafford Noble
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Nov 1, 1994·Journal of the American Society for Mass Spectrometry·J K EngJ R Yates
Jun 5, 2014·Molecular & Cellular Proteomics : MCP·J Jeffry Howbert, William Stafford Noble

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