Comparison of novel decoy database designs for optimizing protein identification searches using ABRF sPRG2006 standard MS/MS data sets.

Decoy database searches are used to filter out false positive protein identifications derived from search engines, but there is no consensus about which decoy is "the best". We evaluate nine different decoy designs using public data sets from samples of known composition. Statistically significant performance differences were found, but no single decoy stood out among the best performers. Ultimately, we recommend peptide level reverse decoys searched independently from the target.