Open Mass Spectrometry Search Algorithm
Lewis Y. Geer(National Institute of Mental Health), Sanford P. Markey(National Center for Biotechnology Information), Jeffrey A. Kowalak(National Institutes of Health), Lukas Wagner(National Institutes of Health), Ming Xu(National Institutes of Health), Dawn Maynard(National Institutes of Health), Xiaoyu Yang(National Institutes of Health), Wenyao Shi(National Center for Biotechnology Information), Stephen H. Bryant(National Institutes of Health)
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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. Keywords: protein identification • algorithm • bioinformatics • mass spectrometry • proteomics • significance testing
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