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Error tolerant searching of uninterpreted tandem mass spectrometry data
Author(s) -
Creasy David M.,
Cottrell John S.
Publication year - 2002
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/1615-9861(200210)2:10<1426::aid-prot1426>3.0.co;2-5
Subject(s) - tandem mass spectrometry , mascot , mass spectrometry , tandem , computer science , database search engine , matching (statistics) , chemistry , extension (predicate logic) , selected reaction monitoring , peptide , search engine , chromatography , information retrieval , mathematics , statistics , biochemistry , programming language , materials science , political science , law , composite material
An error tolerant mode for database matching of uninterpreted tandem mass spectrometry data is described. Selected database entries are searched without enzyme specificity, using a comprehensive list of chemical and post‐translational modifications, together with a residue substitution matrix. The modifications are tested serially, to avoid the catastrophic loss of discrimination that would occur if all the permutations of large numbers of modifications in combination were possible. The new mode has been coded as an extension to the Mascot search engine, and tested against a number of Liquid chromatography‐tandem mass spectrometry datasets. The results show a number of additional peptide matches, but require careful interpretation. The most significant limitation of this approach is that it can only reveal new matches to proteins that already have at least one significant peptide match.