Qscore: An algorithm for evaluating SEQUEST database search results

  • Roger E. Moore
  • Mary K. Young
  • Terry D. LeeEmail author


A scoring procedure is described for measuring the quality of the results for protein identifications obtained from spectral matching of MS/MS data using the Sequest database search program. The scoring system is essentially probabilistic and operates by estimating the probability that a protein identification has come about by chance. The probability is based on the number of identified peptides from the protein, the total number of identified peptides, and the fraction of distinct tryptic peptides from the database that are present in the identified protein. The score is not strictly a probability, as it also incorporates information about the quality of the individual peptide matches. The result of using Qscore on a large test set of data was similar to that achieved using approaches that validate individual spectral matches, with only a narrow overlap in scores between identified proteins and false positive matches. In direct comparison with a published method of evaluating Sequest results, Qscore was able to identify an equivalent number of proteins without any identifiable false positive assignments. Qscore greatly reduces the number of Sequest protein identifications that have to be validated manually.


Peptide Peptide Match Threshold Approach Manual Validation Tryptic Cleavage 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© American Society for Mass Spectrometry 2002

Authors and Affiliations

  • Roger E. Moore
    • 1
  • Mary K. Young
    • 1
  • Terry D. Lee
    • 1
    Email author
  1. 1.Division of ImmunologyBeckman Research Institute of the City of HopeDuarteUSA

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