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A hierarchical MS 2 /MS 3 database search algorithm for automated analysis of phosphopeptide tandem mass spectra
Author(s) -
Xu Hua,
Wang Liwen,
Sallans Larry,
Freitas Michael A.
Publication year - 2009
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.200800282
Subject(s) - mascot , tandem mass spectrometry , database search engine , false positive paradox , mass spectrometry , search engine , computer science , mass spectrum , algorithm , chemistry , database , chromatography , artificial intelligence , information retrieval , political science , law
A novel hierarchical MS 2 /MS 3 database search algorithm has been developed to analyze MS 2 /MS 3 phosphopeptides proteomic data. The algorithm is incorporated in an automated database search program, MassMatrix. The algorithm matches experimental MS 2 spectra against a supplied protein database to determine candidate peptide matches. It then matches the corresponding experimental MS 3 spectra against those candidate peptide matches. The MS 2 and MS 3 spectra are used in concert to arrive at peptide matches with overall higher confidence rather than combining MS 2 and MS 3 data searched separately. Receiver operating characteristic analysis showed that hierarchical MS 2 /MS 3 database searches with MassMatrix had better sensitivity and specificity than the two‐stage MS 2 /MS 3 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 MS 3 spectral data also improved the overall reliability and the number of true positives (TPs) due to the fact that the TPs of the MS 2 /MS 3 search results had higher scores than those of the MS 2 .