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

Research output: Contribution to journalReview article

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.

Details

Authors
  • 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
  • Daniel Kolarich
  • Pauline M Rudd
  • Manfred Wuhrer
  • Carsten Kettner
  • Nicolle H Packer
  • Kiyoko F Aoki-Kinoshita
  • Frédérique Lisacek
  • Niclas G Karlsson
Organisations
External organisations
  • SparqLite LLC.
  • University of Oxford
  • A*Star, Bioprocessing Technology Institute (BTI)
  • Beilstein Institute for the Advancement of Chemical Sciences
  • Soka University
  • National Bioinformatics Infrastructure Sweden, NBIS
  • University of Gothenburg
  • University of Geneva
  • Medical College of Wisconsin
  • Leiden University
  • University of Copenhagen
  • Swiss Institute of Bioinformatics
  • Niigata University
  • ARC Centre of Excellence for Nanoscale BioPhotonics
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Biomedical Laboratory Science/Technology
Original languageEnglish
Article number3275
JournalNature Communications
Volume10
Issue number1
Publication statusPublished - 2019 Jul 22
Publication categoryResearch
Peer-reviewedYes