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Open Access Research article

A mass accuracy sensitive probability based scoring algorithm for database searching of tandem mass spectrometry data

Hua Xu1 and Michael A Freitas2*

Author Affiliations

1 Department of Chemistry, the Ohio State University, Columbus 43210, OH, USA

2 Department of Molecular Immunology Virology and Medical Genetics, the Ohio State University, Columbus 43210, OH, USA

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BMC Bioinformatics 2007, 8:133  doi:10.1186/1471-2105-8-133

Published: 20 April 2007



Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) has become one of the most used tools in mass spectrometry based proteomics. Various algorithms have since been developed to automate the process for modern high-throughput LC-MS/MS experiments.


A probability based statistical scoring model for assessing peptide and protein matches in tandem MS database search was derived. The statistical scores in the model represent the probability that a peptide match is a random occurrence based on the number or the total abundance of matched product ions in the experimental spectrum. The model also calculates probability based scores to assess protein matches. Thus the protein scores in the model reflect the significance of protein matches and can be used to differentiate true from random protein matches.


The model is sensitive to high mass accuracy and implicitly takes mass accuracy into account during scoring. High mass accuracy will not only reduce false positives, but also improves the scores of true positive matches. The algorithm is incorporated in an automated database search program MassMatrix.