hierarchical MS²/MS³ database search algorithm for automated analysis of phosphopeptide tandem mass spectra

• Published in: Proteomics (Weinheim) Vol. 9; no. 7; pp. 1763 - 1770
• Main Authors: Xu, Hua, Wang, Liwen, Sallans, Larry, Freitas, Michael A
• Format: Journal Article
• Language: English
• Published: Weinheim Wiley-VCH Verlag 01.04.2009; WILEY‐VCH Verlag; Wiley-VCH
• Subjects: Algorithms; Analytical, structural and metabolic biochemistry; Animals; Biological and medical sciences; Caseins - chemistry; Cattle; Data Interpretation, Statistical; Fundamental and applied biological sciences. Psychology; Hierarchical MS2; Miscellaneous; MS3 database search; Phosphopeptides - chemistry; Phosphoproteomics; Proteins; Proteomics - methods; ROC Curve; Sensitivity and Specificity; Software; Tandem Mass Spectrometry; Hierarchical MS2; Tandem mass spectrometry; Phosphoproteomics; Mass spectrometry MS/MS; Proteomics; Database; MS3 database search; Method; Algorithm
• ISSN: 1615-9853; 1615-9861; 1615-9861
• DOI: 10.1002/pmic.200800282

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.