Probability-based validation of protein identifications using a modified SEQUEST algorithm
Probability-based validation of protein identifications using a modified SEQUEST algorithm
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DOI：
10.1021/ac025826t
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发表时间：
2002-11-01
影响因子：
7.4
通讯作者：
Yates, JR
中科院分区：
文献类型：
--
作者：
MacCoss, MJ;Wu, CC;Yates, JR
与鸟枪法蛋白质组学兼容的数据库搜索算法将肽串联质谱与数据库中氨基酸序列的预测质谱相匹配。SEQUEST是用于肽串联质谱分析的最常见软件算法之一，其通过使用交叉相关（XCorr）评分程序将串联质谱与源自肽序列的模型谱进行匹配。为了评估匹配，SEQUEST使用第一和第二排名序列之间的差异（DeltaCn）。该值取决于数据库大小、搜索参数和序列同源性。在这份报告中，我们证明了使用的评分程序（SEQUEST-NORM），规范化XCorr值是独立的肽大小和数据库用于执行搜索。这种新的评分程序用于仅基于XCorr值客观地计算蛋白质鉴定和翻译后修饰的置信度百分比。
Database-searching algorithms compatible with shotgun proteomics match a peptide tandem mass spectrum to a predicted mass spectrum for an amino acid sequence within a database. SEQUEST is one of the most common software algorithms used for the analysis of peptide tandem mass spectra by using across-correlation (XCorr) scoring routine to match tandem mass spectra to model spectra derived from peptide sequences.. To assess a match, SEQUEST uses the difference between the first- and second-ranked sequences (DeltaCn). This, value is dependent on the database size, search parameters, and sequence homologies. In this report, we demonstrate the use of a scoring routine (SEQUEST-NORM) that normalizes XCorr values to be independent of peptide size and the database used to perform the search. This new scoring routine is used to objectively calculate the percent confidence of protein identifications and posttranslational modifications based solely on the XCorr value.