title: MS Amanda, a universal identification algorithm optimized for high accuracy tandem mass spectra.
abstract: 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.
authors.affiliation: Bioinformatics Research Group, University of Applied Sciences Upper Austria , Softwarepark 11, 4232 Hagenberg, Austria.
authors.forename: Viktoria
authors.initials: V
authors.lastname: Dorfer
authors.forename: Peter
authors.initials: P
authors.lastname: Pichler
authors.forename: Thomas
authors.initials: T
authors.lastname: Stranzl
authors.forename: Johannes
authors.initials: J
authors.lastname: Stadlmann
authors.forename: Thomas
authors.initials: T
authors.lastname: Taus
authors.forename: Stephan
authors.initials: S
authors.lastname: Winkler
authors.forename: Karl
authors.initials: K
authors.lastname: Mechtler
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D006367:HeLa Cells; D006801:Humans; D010455:Peptides / Q000302:isolation & purification*; D040901:Proteomics / Q000379:methods*; D057386:Search Engine; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D010455:Peptides