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Towards a standardized bioinformatics infrastructure for N- and O-glycomics

Journal article
Authors Miguel A. Rojas-Macias
J. Mariethoz
Peter Andersson
Chunsheng Jin
Vignes Venkatakrishnan
N. P. Aoki
D. Shinmachi
C. Ashwood
K. Madunic
T. Zhang
R. L. Miller
O. Horlacher
W. B. Struwe
Y. Watanabe
S. Okuda
F. Levander
D. Kolarich
P. M. Rudd
M. Wuhrer
C. Kettner
N. H. Packer
K. F. Aoki-Kinoshita
F. Lisacek
N. G. Karlsson
Published in Nature Communications
Volume 10
ISSN 2041-1723
Publication year 2019
Published at Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology
Language en
Links dx.doi.org/10.1038/s41467-019-11131...
Keywords mass-spectrometry, minimum information, quantitative glycomics, unicarb-db, proteomics, database, glycosylation, glycans, disease, platform, Science & Technology - Other Topics
Subject categories Biochemistry and Molecular Biology

Abstract

The mass spectrometry (MS)-based analysis of free polysaccharides and glycans released from proteins, lipids and proteoglycans increasingly relies on databases and software. Here, we review progress in the bioinformatics analysis of protein-released N- and O-linked glycans (N-and O-glycomics) and propose an e-infrastructure to overcome current deficits in data and experimental transparency. This workflow enables the standardized submission of MS-based glycomics information into the public repository UniCarb-DR. It implements the MIRAGE (Minimum Requirement for A Glycomics Experiment) reporting guidelines, storage of unprocessed MS data in the GlycoPOST repository and glycan structure registration using the GlyTouCan registry, thereby supporting the development and extension of a glycan structure knowledgebase.

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