A hierarchical MS2/MS3 database search algorithm for automated analysis of phosphopeptide tandem mass spectra
A hierarchical MS2/MS3 database search algorithm for automated analysis of phosphopeptide tandem mass spectra
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DOI：
10.1002/pmic.200800282
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发表时间：
2009-04-01
期刊：
影响因子：
3.4
通讯作者：
Freitas, Michael A.
中科院分区：
文献类型：
--
作者：
Xu, Hua;Wang, Liwen;Freitas, Michael A.
提出了一种新的MS2/MS3数据库分层搜索算法，用于分析MS2/MS3磷酸化肽的蛋白质组学数据。该算法被集成到一个自动数据库搜索程序MassMatrix中。该算法将实验MS2光谱与提供的蛋白质数据库进行匹配，以确定候选肽匹配。然后将相应的实验MS3光谱与候选肽匹配。MS2和MS3光谱协同使用，以达到具有更高置信度的肽匹配，而不是单独搜索MS2和MS3数据。接受者工作特征分析表明，使用MassMatrix进行分层次MS2/MS3数据库搜索比使用MassMatrix、MASCOT和X！串联。对于LCQ和LTQ-FTICR质谱仪收集的数据，使用这种新算法可以在给定的假率下识别出更多的真肽匹配。额外的MS3光谱数据也提高了总体可靠性和真阳性（TPs）的数量，因为MS2/MS3搜索结果的TPs得分高于MS2。
A novel hierarchical MS2/MS3 database search algorithm has been developed to analyze MS2/MS3 phosphopeptides proteomic data. The algorithm is incorporated in an automated database search program, MassMatrix. The algorithm matches experimental MS2 spectra against a supplied protein database to determine candidate peptide matches. It then matches the corresponding experimental MS3 spectra against those candidate peptide matches. The MS2 and MS3 spectra are used in concert to arrive at peptide matches with overall higher confidence rather than combining MS2 and MS3 data searched separately. Receiver operating characteristic analysis showed that hierarchical MS2/MS3 database searches with MassMatrix had better sensitivity and specificity than the two-stage MS2/MS3 database searches obtained with MassMatrix, MASCOT, and X!Tandem. A greater number of true peptide matches at a given false rate were identified by use of this new algorithm for data collected on both LCQ and LTQ-FTICR mass spectrometers. The additional MS3 spectral data also improved the overall reliability and the number of true positives (TPs) due to the fact that the TPs of the MS2/MS3 search results had higher scores than those of the MS2.