Open AccessA Turn-Key Approach for Large-Scale Identification of Complex Posttranslational Modifications
Author(s) -
Jian Wang,
Veronica G. Anania,
Jeff Knott,
A. John Rush,
Jennie R. Lill,
Philip E. Bourne,
Nuno Bandeira
Publication year - 2014
Publication title -
journal of proteome research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.644
H-Index - 161
eISSN - 1535-3907
pISSN - 1535-3893
DOI - 10.1021/pr400368u
Subject(s) - identification (biology) , posttranslational modification , key (lock) , computational biology , turn (biochemistry) , biology , biochemistry , ecology , enzyme
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.