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      Open mass spectrometry search algorithm.

      Journal of Proteome Research

      Algorithms, Computational Biology, methods, Databases, Protein, False Positive Reactions, Mass Spectrometry, Peptide Fragments, analysis, Poisson Distribution, Proteins, Proteomics, ROC Curve, Reproducibility of Results

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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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          Journal
          15473683
          10.1021/pr0499491

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