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Open Mass Spectrometry Search Algorithm

Lewis Y. Geer·Sanford P. Markey·Jeffrey A. Kowalak·Lukas Wagner·Ming Xu·Dawn M. Maynard·Xiaoyu Yang·Wenyao Shi·Stephen H. Bryant
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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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Lewis Y. Geer, Sanford P. Markey, Jeffrey A. Kowalak, Lukas Wagner, Ming Xu, Dawn M. Maynard, Xiaoyu Yang, Wenyao Shi, Stephen H. Bryant. 2004-06-01. Open Mass Spectrometry Search Algorithm. https://arxiv.org/abs/q-bio/0406002

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