Journal
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
Volume 27, Issue 9, Pages 1579-1582Publisher
SPRINGER
DOI: 10.1007/s13361-016-1436-7
Keywords
Proteomics; False discovery rate; X!Tandem; Mascot; Refinement; Target-decoy approach
Funding
- Russian Science Foundation [14-14-00971]
- Russian Science Foundation [14-14-00971] Funding Source: Russian Science Foundation
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A number of proteomic database search engines implement multi-stage strategies aiming at increasing the sensitivity of proteome analysis. These approaches often employ a subset of the original database for the secondary stage of analysis. However, if target-decoy approach (TDA) is used for false discovery rate (FDR) estimation, the multi-stage strategies may violate the underlying assumption of TDA that false matches are distributed uniformly across the target and decoy databases. This violation occurs if the numbers of target and decoy proteins selected for the second search are not equal. Here, we propose a method of decoy database generation based on the previously reported decoy fusion strategy. This method allows unbiased TDA-based FDR estimation in multi-stage searches and can be easily integrated into existing workflows utilizing popular search engines and post-search algorithms.
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