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

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; Fredrik Levander; Daniel Kolarich; Pauline M. Rudd; Manfred Wuhrer; Carsten Kettner; Nicolle H. Packer; Kiyoko F. Aoki-Kinoshita; Frédérique Lisacek; Niclas G. Karlsson

doi:10.1038/s41467-019-11131-x

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

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, Fredrik Levander, Daniel Kolarich, Pauline M. Rudd, Manfred Wuhrer, Carsten KettnerNicolle H. Packer, Kiyoko F. Aoki-Kinoshita, Frédérique Lisacek, Niclas G. Karlsson^*

^*Corresponding author for this work

ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP)

Research output: Contribution to journal › Review article › peer-review

73 Citations (Scopus)

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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.

Original language	English
Article number	3275
Pages (from-to)	1-10
Number of pages	10
Journal	Nature Communications
Volume	10
DOIs	https://doi.org/10.1038/s41467-019-11131-x
Publication status	Published - 22 Jul 2019

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Copyright the Author(s) 2019. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

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Rojas-Macias, M. A., Mariethoz, J., Andersson, P., Jin, C., Venkatakrishnan, V., Aoki, N. P., Shinmachi, D., Ashwood, C., Madunic, K., Zhang, T., Miller, R. L., Horlacher, O., Struwe, W. B., Watanabe, Y., Okuda, S., Levander, F., Kolarich, D., Rudd, P. M., Wuhrer, M., ... Karlsson, N. G. (2019). Towards a standardized bioinformatics infrastructure for N- and O-glycomics. Nature Communications, 10, 1-10. Article 3275. https://doi.org/10.1038/s41467-019-11131-x

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title = "Towards a standardized bioinformatics infrastructure for N- and O-glycomics",

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.",

author = "Rojas-Macias, {Miguel A.} and Julien Mariethoz and Peter Andersson and Chunsheng Jin and Vignesh Venkatakrishnan and Aoki, {Nobuyuki P.} and Daisuke Shinmachi and Christopher Ashwood and Katarina Madunic and Tao Zhang and Miller, {Rebecca L.} and Oliver Horlacher and Struwe, {Weston B.} and Yu Watanabe and Shujiro Okuda and Fredrik Levander and Daniel Kolarich and Rudd, {Pauline M.} and Manfred Wuhrer and Carsten Kettner and Packer, {Nicolle H.} and Aoki-Kinoshita, {Kiyoko F.} and Fr{\'e}d{\'e}rique Lisacek and Karlsson, {Niclas G.}",

note = "Copyright the Author(s) 2019. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.",

year = "2019",

month = jul,

day = "22",

doi = "10.1038/s41467-019-11131-x",

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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 2019, 'Towards a standardized bioinformatics infrastructure for N- and O-glycomics', Nature Communications, vol. 10, 3275, pp. 1-10. https://doi.org/10.1038/s41467-019-11131-x

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AU - Rojas-Macias, Miguel A.

AU - Mariethoz, Julien

AU - Andersson, Peter

AU - Jin, Chunsheng

AU - Venkatakrishnan, Vignesh

AU - Aoki, Nobuyuki P.

AU - Shinmachi, Daisuke

AU - Ashwood, Christopher

AU - Madunic, Katarina

AU - Zhang, Tao

AU - Miller, Rebecca L.

AU - Horlacher, Oliver

AU - Struwe, Weston B.

AU - Watanabe, Yu

AU - Okuda, Shujiro

AU - Levander, Fredrik

AU - Kolarich, Daniel

AU - Rudd, Pauline M.

AU - Wuhrer, Manfred

AU - Kettner, Carsten

AU - Packer, Nicolle H.

AU - Aoki-Kinoshita, Kiyoko F.

AU - Lisacek, Frédérique

AU - Karlsson, Niclas G.

N1 - Copyright the Author(s) 2019. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

PY - 2019/7/22

Y1 - 2019/7/22

N2 - 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.

AB - 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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M3 - Review article

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SN - 2041-1723

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SP - 1

EP - 10

JO - Nature Communications

JF - Nature Communications

M1 - 3275

ER -

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

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