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Comparative Study
. 2004 Sep-Oct;3(5):958-64.
doi: 10.1021/pr0499491.

Open mass spectrometry search algorithm

Lewis Y Geer  1 , Sanford P Markey, Jeffrey A Kowalak, Lukas Wagner, Ming Xu, Dawn M Maynard, Xiaoyu Yang, Wenyao Shi, Stephen H Bryant
Affiliations
Comparative Study

Open mass spectrometry search algorithm

Lewis Y Geer et al. J Proteome Res. 2004 Sep-Oct.

Abstract

Large numbers of MS/MS peptide spectra generated in proteomics experiments require efficient, sensitive and specific algorithms for peptide identification. In the Open Mass Spectrometry Search Algorithm (OMSSA), specificity is calculated by a classic probability score using an explicit model for matching experimental spectra to sequences. At default thresholds, OMSSA matches more spectra from a standard protein cocktail than a comparable algorithm. OMSSA is designed to be faster than published algorithms in searching large MS/MS datasets.

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