Lin Miin S, Cherny Justin J, Fournier Claire T, Roth Samuel J, Krizanc Danny, Weir Michael P
Department of Biology and ‡Department of Mathematics and Computer Science, Wesleyan University Middletown Connecticut 06459, United States.
J Proteome Res. 2014 Apr 4;13(4):1823-32. doi: 10.1021/pr401090d. Epub 2014 Mar 7.
Peptide mass spectrometry relies crucially on algorithms that match peptides to spectra. We describe a method to evaluate the accuracy of these algorithms based on the masses of parent proteins before trypsin endoprotease digestion. Measurement of conformance to parent proteins provides a score for comparison of the performances of different algorithms as well as alternative parameter settings for a given algorithm. Tracking of conformance scores for spectrum matches to proteins with progressively lower expression levels revealed that conformance scores are not uniform within data sets but are significantly lower for less abundant proteins. Similarly peptides with lower algorithm peptide-spectrum match scores have lower conformance. Although peptide mass spectrometry data is typically filtered through decoy analysis to ensure a low false discovery rate, this analysis confirms that the filtered data should not be considered as having a uniform confidence. The analysis suggests that use of different algorithms and multiple standardized parameter settings of these algorithms can increase significantly the numbers of peptides identified. This data set can be used as a resource for future algorithm assessment.
肽质谱分析在很大程度上依赖于将肽与光谱进行匹配的算法。我们描述了一种基于胰蛋白酶内切蛋白酶消化前亲本蛋白质的质量来评估这些算法准确性的方法。对亲本蛋白质一致性的测量提供了一个分数，用于比较不同算法的性能以及给定算法的替代参数设置。对与表达水平逐渐降低的蛋白质的光谱匹配的一致性分数进行跟踪发现，数据集中的一致性分数并不统一，对于丰度较低的蛋白质，一致性分数显著更低。同样，算法肽-谱匹配分数较低的肽具有较低的一致性。尽管肽质谱数据通常通过诱饵分析进行过滤以确保低错误发现率，但该分析证实，过滤后的数据不应被视为具有统一的可信度。该分析表明，使用不同的算法以及这些算法的多个标准化参数设置可以显著增加鉴定出的肽的数量。该数据集可作为未来算法评估的资源。
