Open mass spectrometry search algorithm

J Proteome Res. 2004 Sep-Oct;3(5):958-64. doi: 10.1021/pr0499491.


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.

Publication types

  • Comparative Study
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

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


  • Peptide Fragments
  • Proteins