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 and Niclas G. Karlsson ()
Additional contact information
Miguel A. Rojas-Macias: University of Gothenburg
Julien Mariethoz: SIB Swiss Institute of Bioinformatics
Peter Andersson: University of Gothenburg
Chunsheng Jin: University of Gothenburg
Vignesh Venkatakrishnan: University of Gothenburg
Nobuyuki P. Aoki: Soka University, Hachioji
Daisuke Shinmachi: Soka University, Hachioji
Christopher Ashwood: Macquarie University
Katarina Madunic: Leiden University Medical Center
Tao Zhang: Leiden University Medical Center
Rebecca L. Miller: University of Copenhagen
Oliver Horlacher: SIB Swiss Institute of Bioinformatics
Weston B. Struwe: University of Oxford
Yu Watanabe: Niigata University
Shujiro Okuda: Niigata University
Fredrik Levander: Lund University
Daniel Kolarich: Griffith University
Pauline M. Rudd: Bioprocessing Technology Institute, AStar
Manfred Wuhrer: Leiden University Medical Center
Carsten Kettner: Beilstein-Institut
Nicolle H. Packer: Macquarie University
Kiyoko F. Aoki-Kinoshita: Soka University, Hachioji
Frédérique Lisacek: SIB Swiss Institute of Bioinformatics
Niclas G. Karlsson: University of Gothenburg

Nature Communications, 2019, vol. 10, issue 1, 1-10

Abstract: 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.

Date: 2019
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DOI: 10.1038/s41467-019-11131-x

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