期刊
JOURNAL OF PROTEOME RESEARCH
卷 18, 期 2, 页码 585-593出版社
AMER CHEMICAL SOC
DOI: 10.1021/acs.jproteome.8b00802
关键词
spectrum identification; false discovery rate; mass spectrometry
Decoy database search with target-decoy competition (TDC) provides an intuitive, easy-to-implement method for estimating the false discovery rate (FDR) associated with spectrum identifications from shotgun proteomics data. However, the procedure can yield different results for a fixed data set analyzed with different decoy databases, and this decoy-induced variability is particularly problematic for smaller FDR thresholds, data sets, or databases. The average TDC (aTDC) protocol combats this problem by exploiting multiple independently shuffled decoy databases to provide an FDR estimate with reduced variability. We provide a tutorial introduction to aTDC, describe an improved variant of the protocol that offers increased statistical power, and discuss how to deploy aTDC in practice using the Crux software toolkit.
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