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Assignment of Saccharide Identities through Analysis of Oxonium Ion Fragmentation Profiles in LC-MS/MS of Glycopeptides.

Journal article
Authors Adnan Halim
Ulrika Westerlind
Christian Pett
Manuel Schorlemer
Ulla Rüetschi
Gunnar Brinkmalm
Carina Sihlbom
Johan Lengqvist
Göran Larson
Jonas Nilsson
Published in Journal of proteome research
Volume 13
Issue 12
Pages 6024-32
ISSN 1535-3907
Publication year 2014
Published at Institute of Biomedicine, Department of Clinical Chemistry and Transfusion Medicine
Core Facilities, Proteomics
Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry
Pages 6024-32
Language en
Keywords glycobiology, mass spectrometry, oxonium ions
Subject categories Analytical Chemistry, Bioorganic chemistry, Chemistry, Clinical Laboratory Medicine


Protein glycosylation plays critical roles in the regulation of diverse biological processes, and determination of glycan structure-function relationships is important to better understand these events. However, characterization of glycan and glycopeptide structural isomers remains challenging and often relies on biosynthetic pathways being conserved. In glycoproteomic analysis with liquid chromatography-tandem mass spectrometry (LC-MS/MS) using collision-induced dissociation (CID), saccharide oxonium ions containing N-acetylhexosamine (HexNAc) residues are prominent. Through analysis of beam-type CID spectra and ion trap CID spectra of synthetic and natively derived N- and O-glycopeptides, we found that the fragmentation patterns of oxonium ions characteristically differ between glycopeptides terminally substituted with GalNAcα1-O-, GlcNAcβ1-O-, Galβ3GalNAcα1-O-, Galβ4GlcNAcβ-O-, and Galβ3GlcNAcβ-O- structures. The difference in the oxonium ion fragmentation profiles of such glycopeptides may thus be used to distinguish among these glycan structures and could be of importance in LC-MS/MS-based glycoproteomic studies.

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