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

Rojas-Macias, Miguel A ; Mariethoz, Julien ; Andersson, Peter ; Jin, Chunsheng ; Venkatakrishnan, Vignesh ; Aoki, Nobuyuki P ; Shinmachi, Daisuke ; Ashwood, Christopher ; Madunic, Katarina and Zhang, Tao , et al. (2019) In Nature Communications 10(1).
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... (More)

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.

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Nature Communications
volume
10
issue
1
article number
3275
publisher
Nature Publishing Group
external identifiers
  • pmid:31332201
  • scopus:85070249334
ISSN
2041-1723
DOI
10.1038/s41467-019-11131-x
language
English
LU publication?
yes
id
93e00fe5-1261-46bc-b7d5-bf1c29fc3a27
date added to LUP
2019-08-27 16:38:14
date last changed
2020-05-26 05:30:25
@article{93e00fe5-1261-46bc-b7d5-bf1c29fc3a27,
  abstract     = {<p>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.</p>},
  author       = {Rojas-Macias, Miguel A and Mariethoz, Julien and Andersson, Peter and Jin, Chunsheng and Venkatakrishnan, Vignesh and Aoki, Nobuyuki P and Shinmachi, Daisuke and Ashwood, Christopher and Madunic, Katarina and Zhang, Tao and Miller, Rebecca L and Horlacher, Oliver and Struwe, Weston B and Watanabe, Yu and Okuda, Shujiro and Levander, Fredrik and Kolarich, Daniel and Rudd, Pauline M and Wuhrer, Manfred and Kettner, Carsten and Packer, Nicolle H and Aoki-Kinoshita, Kiyoko F and Lisacek, Frédérique and Karlsson, Niclas G},
  issn         = {2041-1723},
  language     = {eng},
  month        = {07},
  number       = {1},
  publisher    = {Nature Publishing Group},
  series       = {Nature Communications},
  title        = {Towards a standardized bioinformatics infrastructure for N- and O-glycomics},
  url          = {http://dx.doi.org/10.1038/s41467-019-11131-x},
  doi          = {10.1038/s41467-019-11131-x},
  volume       = {10},
  year         = {2019},
}