Journal
JOURNAL OF PROTEOME RESEARCH
Volume 13, Issue 3, Pages 1190-1199Publisher
AMER CHEMICAL SOC
DOI: 10.1021/pr400368u
Keywords
small ubiquitin-like modification (SUMOylation); posttranslational modification (PTM); combinatorial peptide library; peptide fragmentation patterns; algorithms; database search method; linked peptides
Categories
Funding
- National Institutes of Health [GM078596]
- National Institute of General Medical Sciences [3-P41-GM103484]
Ask authors/readers for more resources
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.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available