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Bottom-upproteomics database search algorithms used for peptideidentification cannot comprehensively identify post-translationalmodifications (PTMs) in a single-pass because of high false discoveryrates (FDRs). A new approach to database searching enables globalPTM (G-PTM) identification by exclusively looking for curated PTMs,thereby avoiding the FDR penalty experienced during conventional variablemodification searches. We identified over 2200 unique, high-confidencemodified peptides comprising 26 different PTM types in a single-passdatabase search. IntroductionProtein post-translationalmodifications (PTMs) play essential rolesin protein signaling, localization, function, degradation, and other important biologicalprocesses. Despite the considerable success of protein identificationvia liquid chromatography–mass spectrometry (LC–MS),most studies do not provide information regarding PTMs on the identifiedproteins. This is because identifying even a single type of PTM requiresspecialized procedures and introduces problems with the increaseddatabase size required for the search.
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