Target-small decoy search strategy for false discovery rate estimation.

ABSTRACT:

Background

One of the most important steps in peptide identification is to estimate the false discovery rate (FDR). The most commonly used method for estimating FDR is the target-decoy search strategy (TDS). While this method is simple and effective, it is time/space-inefficient because it searches a database that is twice as large as the original protein database. This inefficiency problem becomes more evident as protein databases get bigger and bigger. We propose a target-small decoy search strategy and present a rigorous verification that it reduces the database size and search time while retaining the accuracy of target-decoy search strategy (TDS).

Results

We show that peptide spectrum matches (PSMs) obtained at 1% FDR in TDS overlap ~ 99% with those in our method. (Cons

SUBMITTER: Kim H 

PROVIDER: S-EPMC6708216 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature