一种可用于评估肽质量指纹谱数据的方法--反转错位数据库

Reversed-shift Database:Alternative Method to Evaluate Peptide Mass Fingerprint Results

反转数据库常被用于估算大规模蛋白质组研究中串联质谱搜索数据库结果的可靠性。然而,对于经典的且现在依然在产出的肽质量指纹谱的数据,这种方法并不适用。为解决该问题,构建了另外一种随机数据库,称为反转错位数据库。这种数据库是在反转数据库的基础上,将序列中的K和R及其后的氨基酸交换位置(对于胰蛋白酶切割的结果)获得。这种处理避免了某些肽段因前后胰蛋白酶酶切位点氨基酸相同而在序列反转后质量依然不变,导致肽质量指纹谱法无法区分的问题。通过串联质谱和肽质量指纹谱测试数据的搜索结果,证明了这种方法同时适用于串联质谱和肽质量指纹谱的数据。这种方法扩大了经典反转数据库的适用范围,将对评估和整合串联质谱和肽质量指纹谱的数据具有重要意义。

Reversed database is popularly used to estimate the confidence level of database searching results from tandem MS data in large-scale proteomic research. However, it is not suitable for the evaluation of peptide mass fingerprint（PMF） data, which is a classical protein identification approach and still generously used today. In this study, another kind of database called ＂reversed-shift database＂ is constructed by exchanging the ＂K＂ or ＂R＂ amino acid （for the fully tryptic peptides） with their following amino acids, which was demonstrated to be effective for evaluating both tandem MS and PMF data. Reversed-shift processing could avoid the unchanged mass weight of parent ions in the reversed processing for those peptides with the same cleavage site amino acid occurred in the end of peptide and its leading one, which could not be separated by PMF results. Reversed-shift database presents an efficient approach for the evaluation of the large-scale peptide fragment fingerprint （PFF）, PMF and their combined identified results should be a powerful tool in the integration of PMF and tandem MS data.