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A Statistical Method for Assessing Peptide Identification Confidence in Accurate Mass and Time Tag Proteomics
journal contribution
posted on 2023-05-17, 14:19 authored by Stanley, JR, Adkins, JN, Slysz, GW, Monroe, ME, Purvine, SO, Karpievitch, YV, Anderson, GA, Smith, RD, Dabney, ARCurrent 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.
History
Publication title
Analytical ChemistryVolume
83Issue
16Pagination
6135-6140ISSN
0003-2700Department/School
School of Natural SciencesPublisher
Amer Chemical SocPlace of publication
1155 16Th St, Nw, Washington, USA, Dc, 20036Rights statement
Copyright 2011 American Chemical SocietyRepository Status
- Restricted