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A turn-key approach for large-scale identification of complex posttranslational modifications.
- Source :
-
Journal of proteome research [J Proteome Res] 2014 Mar 07; Vol. 13 (3), pp. 1190-9. Date of Electronic Publication: 2014 Jan 29. - Publication Year :
- 2014
-
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.
- Subjects :
- Amino Acid Sequence
Arabidopsis chemistry
Arabidopsis metabolism
Benchmarking
Combinatorial Chemistry Techniques
Databases, Protein
Humans
Jurkat Cells
Molecular Sequence Data
Peptide Library
Sumoylation
Tandem Mass Spectrometry
Algorithms
Peptide Fragments analysis
Protein Processing, Post-Translational
Proteome metabolism
Software
Subjects
Details
- Language :
- English
- ISSN :
- 1535-3907
- Volume :
- 13
- Issue :
- 3
- Database :
- MEDLINE
- Journal :
- Journal of proteome research
- Publication Type :
- Academic Journal
- Accession number :
- 24437954
- Full Text :
- https://doi.org/10.1021/pr400368u