title: A simple workflow to increase MS2 identification rate by subsequent spectral library search.
abstract: Searching a spectral library for the identification of protein MS/MS data has proven to be a fast and accurate method, while yielding a high identification rate. We investigated the potential to increase peptide discovery rate, with little increase in computational time, by constructing a workflow based on a sequence search with Phenyx followed by a library search with SpectraST. Searching a consensus library compiled from the search results of the prior Phenyx search increased the number of confidently matched spectra by up to 156%. Additionally matched spectra by SpectraST included noisy spectra, spectra representing missed cleaved peptides as well as spectra from post-translationally modified peptides.
authors.affiliation: Swiss Institute of Bioinformatics, Proteome Informatics Group, Geneva, Switzerland. erik.ahrne@isb-sib.ch
authors.forename: Erik
authors.initials: E
authors.lastname: Ahrné
authors.forename: Alexandre
authors.initials: A
authors.lastname: Masselot
authors.forename: Pierre-Alain
authors.initials: PA
authors.lastname: Binz
authors.forename: Markus
authors.initials: M
authors.lastname: Müller
authors.forename: Frederique
authors.initials: F
authors.lastname: Lisacek
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D008969:Molecular Sequence Data; D019151:Peptide Library; D011506:Proteins / Q000032:analysis* / Q000737:chemistry; D012984:Software
chemical_list: D019151:Peptide Library; D011506:Proteins