Department of Data Analysis and Articial Intelligence, Faculty of Computer Science , National Research University Higher School of Economics (HSE) , 3 Kochnovskiy Proezd , Moscow 125319 , Russian Federation.
J Proteome Res. 2019 May 3;18(5):2354-2358. doi: 10.1021/acs.jproteome.8b00991. Epub 2019 Apr 18.
Accurate target-decoy-based false discovery rate (FDR) control of peptide identification from tandem mass-spectrometry data relies on an important but often neglected assumption that incorrect spectrum annotations are equally likely to receive either target or decoy peptides. Here we argue that this assumption is often violated in practice, even by popular methods. Preference can be given to target peptides by biased scoring functions, which result in liberal FDR estimations, or to decoy peptides by correlated spectra, which result in conservative estimations.
准确的基于目标-诱饵的假发现率（FDR）控制肽鉴定串联质谱数据依赖于一个重要但经常被忽视的假设，即不正确的谱注释同样有可能接收目标肽或诱饵肽。在这里，我们认为即使是在流行的方法中，这种假设在实践中也经常被违反。有偏差的评分函数可以优先考虑目标肽，导致宽松的 FDR 估计，或者相关的谱可以优先考虑诱饵肽，导致保守的估计。
