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

Miguel A Rojas-Macias; Julien Mariethoz; Peter Andersson; Chunsheng Jin; Vignesh Venkatakrishnan; Nobuyuki P Aoki; Daisuke Shinmachi; Christopher Ashwood; Katarina Madunic; Tao Zhang; Rebecca L Miller; Oliver Horlacher; Weston B Struwe; Yu Watanabe; Shujiro Okuda; Fredrik Levander; Daniel Kolarich; Pauline M Rudd; Manfred Wuhrer; Carsten Kettner; Nicolle H Packer; Kiyoko F Aoki-Kinoshita; Frédérique Lisacek; Niclas G Karlsson

doi:10.1038/s41467-019-11131-x

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

Nat Commun. 2019 Jul 22;10(1):3275. doi: 10.1038/s41467-019-11131-x.

Authors

Miguel A Rojas-Macias¹, Julien Mariethoz^{2

3}, Peter Andersson¹, Chunsheng Jin¹, Vignesh Venkatakrishnan¹, Nobuyuki P Aoki^{4

5}, Daisuke Shinmachi^{4

5}, Christopher Ashwood^{6

7}, Katarina Madunic⁸, Tao Zhang⁸, Rebecca L Miller⁹, Oliver Horlacher², Weston B Struwe¹⁰, Yu Watanabe¹¹, Shujiro Okuda¹¹, Fredrik Levander¹², Daniel Kolarich^{13

14}, Pauline M Rudd¹⁵, Manfred Wuhrer⁸, Carsten Kettner¹⁶, Nicolle H Packer^{6

13

14}, Kiyoko F Aoki-Kinoshita⁴, Frédérique Lisacek^{2

3

17}, Niclas G Karlsson¹⁸

Affiliations

¹ Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530, Sweden.
² Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, 1211, Switzerland.
³ Computer Science Department, University of Geneva, Geneva, 1227, Switzerland.
⁴ Soka University, Hachioji, 192-8577, Tokyo, Japan.
⁵ SparqLite LLC., Hachioji, 192-0032, Tokyo, Japan.
⁶ Department of Molecular Sciences, Macquarie University, Sydney, 2109, Australia.
⁷ Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
⁸ Leiden University Medical Center, Leiden, 2333ZA, Netherlands.
⁹ Copenhagen Centre for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, København, DK-2200, Denmark.
¹⁰ Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK.
¹¹ Graduate School of Medical and Dental Sciences, Niigata University, 950-2181, Niigata, Japan.
¹² National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Department of Immunotechnology, Lund University, Lund, 22387, Sweden.
¹³ Institute for Glycomics, Gold Coast Campus, Griffith University, Gold Coast, QLD, QLD 4222, Australia.
¹⁴ ARC Centre for Nanoscale BioPhotonics, Macquarie University and Griffith University, North Ryde and Gold Coast, NSW and QLD, NSW 2109 and QLD 4222, Australia.
¹⁵ Bioprocessing Technology Institute, AStar, Singapore, 138668, Singapore.
¹⁶ Beilstein-Institut, Frankfurt am Main, 60487, Germany.
¹⁷ Section of Biology, University of Geneva, Geneva, 1211, Switzerland.
¹⁸ Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530, Sweden. niclas.karlsson@medkem.gu.se.

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.

Publication types

Research Support, Non-U.S. Gov't
Review

MeSH terms

Animals
Computational Biology / methods*
Computational Biology / standards
Databases, Factual / standards
Databases, Factual / statistics & numerical data
Glycomics / methods*
Glycoproteins / metabolism*
Humans
Mass Spectrometry / methods
Polysaccharides / metabolism*
Reference Standards

Substances

Glycoproteins
Polysaccharides