Towards a standardized bioinformatics infrastructure for N- and O-glycomics
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Mariethoz, Julien
Andersson, Peter
Jin, Chunsheng
Venkatakrishnan, Vignesh
Aoki, Nobuyuki P
Shinmachi, Daisuke
Ashwood, Christopher
Madunic, Katarina
Zhang, Tao
Miller, Rebecca L
Horlacher, Oliver
Struwe, Weston B
Watanabe, Yu
Okuda, Shujiro
Levander, Fredrik
Kolarich, Daniel
Rudd, Pauline M
Wuhrer, Manfred
Kettner, Carsten
Packer, Nicolle H
Aoki-Kinoshita, Kiyoko F
Lisacek, Frederique
Karlsson, Niclas G
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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.
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Nature Communications
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10
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1
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© The Author(s). 2019. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
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Biological sciences
Glycobiology
Glycoconjugates
Proteomics and intermolecular interactions (excl. medical proteomics)
Science & Technology
Multidisciplinary Sciences
Science & Technology - Other Topics
MASS-SPECTROMETRY
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Rojas-Macias, MA; Mariethoz, J; Andersson, P; Jin, C; Venkatakrishnan, V; Aoki, NP; Shinmachi, D; Ashwood, C; Madunic, K; Zhang, T; Miller, RL; Horlacher, O; Struwe, WB; Watanabe, Y; Okuda, S; Levander, F; Kolarich, D; Rudd, PM; Wuhrer, M; Kettner, C; Packer, NH; Aoki-Kinoshita, KF; Lisacek, F; Karlsson, NG, Towards a standardized bioinformatics infrastructure for N- and O-glycomics, Nature Communications, 2019, 10 (1)