Towards a standardized bioinformatics infrastructure for N- and O-glycomics.
Miguel A Rojas-MaciasJulien MariethozPeter AnderssonChunsheng JinVignesh VenkatakrishnanNobuyuki P AokiDaisuke ShinmachiChristopher AshwoodKatarina MadunicTao ZhangRebecca L MillerOliver HorlacherWeston B StruweYu WatanabeShujiro OkudaFredrik LevanderDaniel KolarichPauline M RuddManfred WuhrerCarsten KettnerNicolle H PackerKiyoko F Aoki-KinoshitaFrederique LisacekNiclas G KarlssonPublished in: Nature communications (2019)
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.
Keyphrases
- mass spectrometry
- cell surface
- electronic health record
- liquid chromatography
- multiple sclerosis
- ms ms
- big data
- gas chromatography
- high performance liquid chromatography
- capillary electrophoresis
- adverse drug
- high resolution
- traumatic brain injury
- mental health
- clinical practice
- artificial intelligence
- emergency department
- protein protein
- fatty acid
- health information
- amino acid
- deep learning