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

doi:10.1021/pr0499491

PubMed · 15473683

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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Algorithms Computational Biology Databases, Protein False Positive Reactions Mass Spectrometry Peptide Fragments Poisson Distribution Proteins Proteomics ROC Curve Reproducibility of Results Comparative Study Journal Article Research Support, U.S. Gov't, P.H.S.

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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. Open mass spectrometry search algorithm.. https://doi.org/10.1021/pr0499491

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