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

Author

Listed:
  • Miguel A. Rojas-Macias

    (University of Gothenburg)

  • Julien Mariethoz

    (SIB Swiss Institute of Bioinformatics
    University of Geneva)

  • Peter Andersson

    (University of Gothenburg)

  • Chunsheng Jin

    (University of Gothenburg)

  • Vignesh Venkatakrishnan

    (University of Gothenburg)

  • Nobuyuki P. Aoki

    (Soka University, Hachioji
    SparqLite LLC., Hachioji)

  • Daisuke Shinmachi

    (Soka University, Hachioji
    SparqLite LLC., Hachioji)

  • Christopher Ashwood

    (Macquarie University
    Medical College of Wisconsin)

  • 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
    Macquarie University and Griffith University)

  • Pauline M. Rudd

    (Bioprocessing Technology Institute, AStar)

  • Manfred Wuhrer

    (Leiden University Medical Center)

  • Carsten Kettner

    (Beilstein-Institut)

  • Nicolle H. Packer

    (Macquarie University
    Griffith University
    Macquarie University and Griffith University)

  • Kiyoko F. Aoki-Kinoshita

    (Soka University, Hachioji)

  • Frédérique Lisacek

    (SIB Swiss Institute of Bioinformatics
    University of Geneva
    Section of Biology, University of Geneva)

  • Niclas G. Karlsson

    (University of Gothenburg)

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.

Suggested Citation

  • Miguel A. Rojas-Macias & Julien Mariethoz & Peter Andersson & Chunsheng Jin & Vignesh Venkatakrishnan & Nobuyuki P. Aoki & Daisuke Shinmachi & Christopher Ashwood & Katarina Madunic & Tao Zhang & Rebe, 2019. "Towards a standardized bioinformatics infrastructure for N- and O-glycomics," Nature Communications, Nature, vol. 10(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-11131-x
    DOI: 10.1038/s41467-019-11131-x
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