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Distinctive MS/MS Fragmentation Pathways of Glycopeptide-Generated Oxonium Ions Provide Evidence of the Glycan Structure.

Journal article
Authors Jin Yu
Manuel Schorlemer
Alejandro Gomez Toledo
Christian Pett
Carina Sihlbom
Göran Larson
Ulrika Westerlind
Jonas Nilsson
Published in Chemistry (Weinheim an der Bergstrasse, Germany)
Volume 22
Issue 3
Pages 1114–1124
ISSN 1521-3765
Publication year 2016
Published at Institute of Biomedicine, Department of Clinical Chemistry and Transfusion Medicine
Core Facilities, Proteomics
Pages 1114–1124
Language en
Keywords Mass spectrometry, glycopeptide, oxonium ions
Subject categories Chemistry, Clinical Laboratory Medicine


Post-translational glycosylation of proteins play key roles in cellular processes and the site-specific characterisation of glycan structures is critical to understanding these events. Given the challenges regarding identification of glycan isomers, glycoproteomic studies generally rely on the assumption of conserved biosynthetic pathways. However, in a recent study, we found characteristically different HexNAc oxonium ion fragmentation patterns that depend on glycan structure. Such patterns could be used to distinguish between glycopeptide structural isomers. To acquire a mechanistic insight, deuterium-labelled glycopeptides were prepared and analysed. We found that the HexNAc-derived m/z 126 and 144 oxonium ions, differing in mass by H2 O, had completely different structures and that high-mannose N-glycopeptides generated abundant Hex-derived oxonium ions. We describe the oxonium ion decomposition mechanisms and the relative abundance of oxonium ions as a function of collision energy for a number of well-defined glycan structures, which provide important information for future glycoproteomic studies.

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