Yuan Zuo-Fei, Lin Shu, Molden Rosalynn C, Garcia Benjamin A
Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania , 3400 Civic Center, Building 421, Philadelphia, Pennsylvania 19104, United States.
J Proteome Res. 2014 Oct 3;13(10):4470-8. doi: 10.1021/pr5008015. Epub 2014 Sep 7.
Identification of histone post-translational modifications (PTMs) is challenging for proteomics search engines. Including many histone PTMs in one search increases the number of candidate peptides dramatically, leading to low search speed and fewer identified spectra. To evaluate database search engines on identifying histone PTMs, we present a method in which one kind of modification is searched each time, for example, unmodified, individually modified, and multimodified, each search result is filtered with false discovery rate less than 1%, and the identifications of multiple search engines are combined to obtain confident results. We apply this method for eight search engines on histone data sets. We find that two search engines, pFind and Mascot, identify most of the confident results at a reasonable speed, so we recommend using them to identify histone modifications. During the evaluation, we also find some important aspects for the analysis of histone modifications. Our evaluation of different search engines on identifying histone modifications will hopefully help those who are hoping to enter the histone proteomics field. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD001118.
对蛋白质组学搜索引擎而言，鉴定组蛋白翻译后修饰（PTM）颇具挑战性。在一次搜索中纳入多种组蛋白PTM会显著增加候选肽段的数量，导致搜索速度降低且鉴定出的谱图减少。为评估数据库搜索引擎在鉴定组蛋白PTM方面的性能，我们提出了一种方法，即每次搜索一种修饰类型，例如未修饰的、单个修饰的和多重修饰的，每次搜索结果都用错误发现率小于1%进行过滤，并且将多个搜索引擎的鉴定结果合并以获得可靠结果。我们将此方法应用于八个搜索引擎处理组蛋白数据集。我们发现，pFind和Mascot这两个搜索引擎能以合理的速度鉴定出大部分可靠结果，因此我们建议使用它们来鉴定组蛋白修饰。在评估过程中，我们还发现了组蛋白修饰分析的一些重要方面。我们对不同搜索引擎在鉴定组蛋白修饰方面的评估有望帮助那些希望进入组蛋白蛋白质组学领域的人。质谱蛋白质组学数据已通过数据集标识符PXD001118存入蛋白质组交换联盟。
