Journal
JOURNAL OF PROTEOME RESEARCH
Volume 13, Issue 8, Pages 3679-3684Publisher
AMER CHEMICAL SOC
DOI: 10.1021/pr500202e
Keywords
tandem mass spectrometry; MS/MS; database search algorithm; high-resolution spectra; high mass accuracy; peptide identification; proteomics
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Funding
- Austrian Science Fund (FWF) [TRP 308-N15, P24685-B24, SFB F3402]
- European Community's Seventh Framework Programme [PRIME-XS (262067), MeioSys (222883-2)]
- Austrian Science Fund (FWF) [TRP 308] Funding Source: researchfish
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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.
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