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A turn-key approach for large-scale identification of complex posttranslational modifications.


ABSTRACT: The conjugation of complex post-translational modifications (PTMs) such as glycosylation and Small Ubiquitin-like Modification (SUMOylation) to a substrate protein can substantially change the resulting peptide fragmentation pattern compared to its unmodified counterpart, making current database search methods inappropriate for the identification of tandem mass (MS/MS) spectra from such modified peptides. Traditionally it has been difficult to develop new algorithms to identify these atypical peptides because of the lack of a large set of annotated spectra from which to learn the altered fragmentation pattern. Using SUMOylation as an example, we propose a novel approach to generate large MS/MS training data from modified peptides and derive an algorithm that learns properties of PTM-specific fragmentation from such training data. Benchmark tests on data sets of varying complexity show that our method is 80-300% more sensitive than current state-of-the-art approaches. The core concepts of our method are readily applicable to developing algorithms for the identifications of peptides with other complex PTMs.

SUBMITTER: Wang J 

PROVIDER: S-EPMC3993922 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature

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A turn-key approach for large-scale identification of complex posttranslational modifications.

Wang Jian J   Anania Veronica G VG   Knott Jeff J   Rush John J   Lill Jennie R JR   Bourne Philip E PE   Bandeira Nuno N  

Journal of proteome research 20140129 3


The conjugation of complex post-translational modifications (PTMs) such as glycosylation and Small Ubiquitin-like Modification (SUMOylation) to a substrate protein can substantially change the resulting peptide fragmentation pattern compared to its unmodified counterpart, making current database search methods inappropriate for the identification of tandem mass (MS/MS) spectra from such modified peptides. Traditionally it has been difficult to develop new algorithms to identify these atypical pe  ...[more]

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