RT Journal Article
SR Electronic
T1 Mass spectrometrists should search for all peptides, but assess only the ones they care about
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 094581
DO 10.1101/094581
A1 Adriaan Sticker
A1 Lennart Martens
A1 Lieven Clement
YR 2017
UL http://biorxiv.org/content/early/2017/02/21/094581.abstract
AB In shotgun proteomics identified mass spectra that are deemed irrelevant to the scientific hypothesis are often discarded. Noble (2015)1 therefore urged researchers to remove irrelevant peptides from the database prior to searching to improve statistical power. We here however, argue that both the classical as well as Noble’s revised method produce suboptimal peptide identifications and have problems in controlling the false discovery rate (FDR). Instead, we show that searching for all expected peptides, and removing irrelevant peptides prior to FDR calculation results in more reliable identifications at controlled FDR level than the classical strategy that discards irrelevant peptides post FDR calculation, or than Noble’s strategy that discards irrelevant peptides prior to searching.