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

Nature Methods
Zilu YeSergey Y Vakhrushev

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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Citations

Mar 18, 2020·Nature·Jyoti Madhusoodanan
Sep 18, 2020·International Journal of Molecular Sciences·Xing LiXia Zou
Jan 14, 2021·Biochemical Society Transactions·Anastasia ChernykhMorten Thaysen-Andersen
Dec 30, 2020·Molecular & Cellular Proteomics : MCP·Zilu Ye, Sergey Y Vakhrushev
Sep 5, 2020·Molecular & Cellular Proteomics : MCP·William E Hackett, Joseph Zaia
Sep 18, 2020·Molecular & Cellular Proteomics : MCP·Nicholas M RileySharon J Pitteri
Jul 3, 2020·Molecular & Cellular Proteomics : MCP·Weiqian CaoPengyuan Yang
Oct 23, 2020·Nature Reviews. Molecular Cell Biology·Katrine T SchjoldagerHenrik Clausen
Feb 9, 2021·Frontiers in Immunology·Alex OlveraChristian Brander
Jan 29, 2021·Current Opinion in Structural Biology·Tomislav ČavalSergey Y Vakhrushev
Jun 25, 2020·Molecular & Cellular Proteomics : MCP·Daniel G Delafield, Lingjun Li
Feb 23, 2021·The Journal of Biological Chemistry·Yoshiki NarimatsuHenrik Clausen
Nov 22, 2020·Current Opinion in Chemical Biology·Vahap Canbay, Ulrich Auf dem Keller
Oct 31, 2020·Current Opinion in Chemical Biology·Anna CioceBenjamin Schumann
Feb 9, 2021·Molecular & Cellular Proteomics : MCP·Weiqian CaoPengyuan Yang
Feb 16, 2021·Molecular & Cellular Proteomics : MCP·Nicholas M RileySharon J Pitteri
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Aug 7, 2021·Current Opinion in Biotechnology·Yuanwei Xu, Hui Zhang
Aug 11, 2021·Expert Review of Proteomics·Christopher S SauerLingjun Li
Jun 6, 2020·Journal of Proteome Research·Nicholas M RileyCarolyn R Bertozzi
Sep 24, 2021·Frontiers in Chemistry·Yong ZhangHao Yang
Nov 25, 2021·Journal of Proteome Research·Evan E HubbardRyan R Julian

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Methods Mentioned

BETA
glycosylation

Software Mentioned

Excel
Spectronaut
DIA
Sequest HT
R
Proteome Discoverer
SingleShot
ShapeQualityScore
Percolator Node
mProphet

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