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A Statistical Method for Assessing Peptide Identification Confidence in Accurate Mass and Time Tag Proteomics

Citation

Stanley, JR and Adkins, JN and Slysz, GW and Monroe, ME and Purvine, SO and Karpievitch, YV and Anderson, GA and Smith, RD and Dabney, AR, A Statistical Method for Assessing Peptide Identification Confidence in Accurate Mass and Time Tag Proteomics, Analytical Chemistry, 83, (16) pp. 6135-6140. ISSN 0003-2700 (2011) [Refereed Article]

Copyright Statement

Copyright 2011 American Chemical Society

DOI: doi:10.1021/ac2009806

Abstract

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.

Item Details

Item Type:Refereed Article
Research Division:Mathematical Sciences
Research Group:Statistics
Research Field:Biostatistics
Objective Division:Expanding Knowledge
Objective Group:Expanding Knowledge
Objective Field:Expanding Knowledge in the Mathematical Sciences
Author:Karpievitch, YV (Dr Yuliya Karpievitch)
ID Code:80879
Year Published:2011
Web of Science® Times Cited:26
Deposited By:Mathematics and Physics
Deposited On:2012-11-14
Last Modified:2015-01-27
Downloads:0

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