Journal
ANALYTICAL CHEMISTRY
Volume 83, Issue 16, Pages 6135-6140Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ac2009806
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Funding
- NIH National Center for Research Resources [RR18522]
- National Institute of Allergy and Infectious Diseases NIH/DHHS [Y1-AI-8401, U54AI081680]
- U.S. Department of Energy's Office of Biological and Environmental Research
- U.S. Department of Energy [DE-AC05-76RL0 1830]
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Current algorithms for quantifying peptide identification confidence in the accurate mass and time (AMT) tag approach assume that the AMT tags themselves have been correctly identified. However, there is uncertainty in the identification of AMT tags, because this is based on matching LC-MS/MS fragmentation spectra to peptide sequences. In this paper, we incorporate confidence measures for the AMT tag identifications into the calculation of probabilities for correct matches to an AMT tag database, resulting in a more accurate overall measure of identification confidence for the AMT tag approach. The method is referenced as Statistical Tools for AMT Tag Confidence (STAC). STAC additionally provides a uniqueness probability (UP) to help distinguish between multiple matches to an AMT tag and a method to calculate an overall false discovery rate (FDR). STAC is freely available for download, as both a command line and a Windows graphical application.
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