论文标题

具有挑战性的目标还是描述不匹配的目标?对Madej等人的共同诱饵分布的评论

Challenging targets or describing mismatches? A comment on Common Decoy Distribution by Madej et al

论文作者

Etourneau, Lucas, Burger, Thomas

论文摘要

在最近的文章中,Madej等人。 1提出了一种原始方法,以解决肽 - 光谱匹配(PSM)验证中错误发现率(FDR)的经常性问题。简而言之,他们提议得出称为公共诱饵分布(CDD)的诱饵匹配的单个精确分布,并在仅目标搜索过程中使用它来控制FDR。从概念上讲,这种方法很有吸引力,因为它采取了两个世界的最佳状态,即基于诱饵的方法(利用大规模的经验不匹配收集)和无诱饵的方法(这不受诱饵生成的随机性,同时避免了额外的数据库搜索)。有趣的是,CDD还对应于FDR控制程序的两个主要家族的统计方法中的中间方法:尽管从历史上讲,基于估计虚假阳性分布,但由于原始变量(在蛋白质组学,目标序列,蛋白质组学,目标序列中)及其小说对手(在蛋白质组中,在蛋白质组学中),最近已经证明了FDR控制是可能的。区分这两个理论趋势对于计算蛋白质组学至关重要。除了强调为什么蛋白质组学是理论生物统计学的灵感来源之外,它还对可以对蛋白质组学(包括CDD)中使用的FDR控制方法进行的改进提供了实用的见解。

In their recent article, Madej et al. 1 proposed an original way to solve the recurrent issue of controlling for the false discovery rate (FDR) in peptide-spectrum-match (PSM) validation. Briefly, they proposed to derive a single precise distribution of decoy matches termed the Common Decoy Distribution (CDD) and to use it to control for FDR during a target-only search. Conceptually, this approach is appealing as it takes the best of two worlds, i.e., decoy-based approaches (which leverage a large-scale collection of empirical mismatches) and decoy-free approaches (which are not subject to the randomness of decoy generation while sparing an additional database search). Interestingly, CDD also corresponds to a middle-of-the-road approach in statistics with respect to the two main families of FDR control procedures: Although historically based on estimating the falsepositive distribution, FDR control has recently been demonstrated to be possible thanks to competition between the original variables (in proteomics, target sequences) and their fictional counterparts (in proteomics, decoys). Discriminating between these two theoretical trends is of prime importance for computational proteomics. In addition to highlighting why proteomics was a source of inspiration for theoretical biostatistics, it provides practical insights into the improvements that can be made to FDR control methods used in proteomics, including CDD.

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