Journal
NATURE METHODS
Volume 18, Issue 12, Pages 1515-+Publisher
NATURE PORTFOLIO
DOI: 10.1038/s41592-021-01306-0
Keywords
-
Categories
Funding
- Max Planck Society
Ask authors/readers for more resources
The study introduces a new glycan-first glycopeptide search engine, pGlyco3, which can comprehensively analyze intact N- and O-glycopeptides, including glycopeptides with modified saccharide units, in a fast and accurate manner.
Great advances have been made in mass spectrometric data interpretation for intact glycopeptide analysis. However, accurate identification of intact glycopeptides and modified saccharide units at the site-specific level and with fast speed remains challenging. Here, we present a glycan-first glycopeptide search engine, pGlyco3, to comprehensively analyze intact N- and O-glycopeptides, including glycopeptides with modified saccharide units. A glycan ion-indexing algorithm developed for glycan-first search makes pGlyco3 5-40 times faster than other glycoproteomic search engines without decreasing accuracy or sensitivity. By combining electron-based dissociation spectra, pGlyco3 integrates a dynamic programming-based algorithm termed pGlycoSite for site-specific glycan localization. Our evaluation shows that the site-specific glycan localization probabilities estimated by pGlycoSite are suitable to localize site-specific glycans. With pGlyco3, we confidently identified N-glycopeptides and O-mannose glycopeptides that were extensively modified by ammonia adducts in yeast samples. The freely available pGlyco3 is an accurate and flexible tool that can be used to identify glycopeptides and modified saccharide units. pGlyco3 is a glycan-first glycopeptide search engine for the identification and localization of site-specific N- and O-glycopeptides, including glycopeptides with modified glycans.
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