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,‡ and Stephen H. Bryant†
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, and the Laboratory of Neurotoxicology, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland 20892
Journal of Proteome Research, 2004, 3 (5), pp 958–964
DOI: 10.1021/pr0499491
Publication Date (Web): July 2, 2004
Copyright © 2004 American Chemical Society
*

 To whom correspondence should be addressed. E-mail:  lewisg@ mail.nih.gov.

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†

 National Center for Biotechnology Information.

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‡

 Laboratory of Neurotoxicology.

Abstract

Abstract Image

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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History

  • Published In Issue October 11, 2004
  • Received February 23, 2004

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