MS Amanda, a Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra

被引:326
作者
Dorfer, Viktoria [1 ]
Pichler, Peter [2 ,4 ]
Stranzl, Thomas [2 ]
Stadlmann, Johannes [2 ]
Taus, Thomas [2 ]
Winkler, Stephan [1 ]
Mechtler, Karl [2 ,3 ]
机构
[1] Univ Appl Sci Upper Austria, Bioinformat Res Grp, A-4232 Hagenberg, Austria
[2] Res Inst Mol Pathol, Prot Chem Facil, IMP, A-1030 Vienna, Austria
[3] Austrian Acad Sci, Inst Mol Biotechnol, Prot Chem Facil, IMBA, A-1030 Vienna, Austria
[4] Wiener Krankenanstaltenverbund, A-1030 Vienna, Austria
基金
奥地利科学基金会;
关键词
tandem mass spectrometry; MS/MS; database search algorithm; high-resolution spectra; high mass accuracy; peptide identification; proteomics; SPECTROMETRY-BASED PROTEOMICS; PEPTIDE IDENTIFICATION; PROTEIN MIXTURES; SEARCH ALGORITHM; HIGH-RESOLUTION; CELL-LINE; C-TRAP; DATABASE;
D O I
10.1021/pr500202e
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Today's highly accurate spectra provided by modern tandem mass spectrometers offer considerable advantages for the analysis of proteomic samples of increased complexity. Among other factors, the quantity of reliably identified peptides is considerably influenced by the peptide identification algorithm. While most widely used search engines were developed when high-resolution mass spectrometry data were not readily available for fragment ion masses, we have designed a scoring algorithm particularly suitable for high mass accuracy. Our algorithm, MS Amanda, is generally applicable to HCD, ETD, and CID fragmentation type data. The algorithm confidently explains more spectra at the same false discovery rate than Mascot or SEQUEST on examined high mass accuracy data sets, with excellent overlap and identical peptide sequence identification for most spectra also explained by Mascot or SEQUEST. MS Amanda, available at http://ms.imp.ac.at/?goto=msamanda, is provided free of charge both as standalone version for integration into custom workflows and as a plugin for the Proteome Discoverer platform.
引用
收藏
页码:3679 / 3684
页数:6
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