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. 2019 Sep;16(9):902-910.
doi: 10.1038/s41592-019-0504-x. Epub 2019 Aug 5.

Glyco-DIA: a method for quantitative O-glycoproteomics with in silico-boosted glycopeptide libraries

Zilu Ye  1 , Yang Mao  1   2 , Henrik Clausen  1 , Sergey Y Vakhrushev  3
Affiliations

Glyco-DIA: a method for quantitative O-glycoproteomics with in silico-boosted glycopeptide libraries

Zilu Ye et al. Nat Methods. 2019 Sep.

Abstract

We report a liquid chromatography coupled to tandem mass spectrometry O-glycoproteomics strategy using data-independent acquisition (DIA) mode for direct analysis of O-glycoproteins. This approach enables characterization of glycopeptides and structures of O-glycans on a proteome-wide scale with quantification of stoichiometries (though it does not allow for direct unambiguous glycosite identification). The method relies on a spectral library of O-glycopeptides; the Glyco-DIA library contains sublibraries obtained from human cell lines and human serum, and it currently covers 2,076 O-glycoproteins (11,452 unique glycopeptide sequences) and the 5 most common core1 O-glycan structures. Applying the Glyco-DIA library to human serum without enrichment for glycopeptides enabled us to identify and quantify 269 distinct glycopeptide sequences bearing up to 5 different core1 O-glycans from 159 glycoproteins in a SingleShot analysis.

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