title: Large-scale unrestricted identification of post-translation modifications using tandem mass spectrometry.
abstract: TwinPeaks, a close variant of the SEQUEST protein identification algorithm, is capable of unrestricted, large-scale, identification of post-translation modifications (PTMs). TwinPeaks is applied on a sample of 100441 tandem mass spectra from the HUPO Plasma Proteome Project data set, with full non-redundant human as a reference protein database. With a 3.5% error rate, TwinPeaks identifies a collection of 539 spectra that were not identified by the usual PTM-restricted identification algorithm. At this error rate, TwinPeaks increases the rate of spectra identifications by at least 17.6%, making unrestricted PTM identification an integral part of proteomics.
authors.affiliation: Notal Vision Limited, 5 Droyanov Street, Tel Aviv, 63143 Israel. moshe@notalvision.com
authors.forename: Moshe
authors.initials: M
authors.lastname: Havilio
authors.forename: Assaf
authors.initials: A
authors.lastname: Wool
mesh_terms: D000465:Algorithms; D000818:Animals; D001798:Blood Proteins / Q000032:analysis* / Q000378:metabolism*; D002417:Cattle; D030562:Databases, Protein; D006801:Humans; D011499:Protein Processing, Post-Translational; D012680:Sensitivity and Specificity; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D001798:Blood Proteins