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.

诱饵数据库搜索（decoy database searches）常被用于过滤搜索引擎所得到的假阳性蛋白质鉴定结果，但目前学界尚未就何种诱饵方案为“最佳”达成统一共识。本研究借助已知组分样本的公开数据集，对九种不同的诱饵设计方案进行了系统性评估。结果显示，不同诱饵方案的性能存在统计学意义上的显著差异，但没有任何一款诱饵方案能在最优表现者中脱颖而出。最终，本研究推荐采用独立于靶标数据库开展搜索的肽水平反向诱饵（peptide level reverse decoys）方案。