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

Glycomics Program

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

73 Citations (Scopus)

105 Downloads (Pure)

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
Journal	Nature Communications
Volume	10
Issue number	1
Number of pages	10
ISSN	2041-1723
DOIs	https://doi.org/10.1038/s41467-019-11131-x
Publication status	Published - 2019

Access to Document

10.1038/s41467-019-11131-xLicence: CC BY

Towards a standardized bioinformatics infrastructure for N- and O-glycomicsFinal published version, 1.07 MBLicence: CC BY

Cite this

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), [3275]. https://doi.org/10.1038/s41467-019-11131-x

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; 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, Frédérique; Karlsson, Niclas G.

In: Nature Communications, Vol. 10, No. 1, 3275, 2019.

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

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, no. 1, 3275. https://doi.org/10.1038/s41467-019-11131-x

Rojas-Macias, Miguel A. ; 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, Frédérique ; Karlsson, Niclas G. / Towards a standardized bioinformatics infrastructure for N- and O-glycomics. In: Nature Communications. 2019 ; Vol. 10, No. 1.

@article{7e83cd5cd5094d38b12577c0a2d554c9,

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.}",

year = "2019",

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

language = "English",

volume = "10",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "nature publishing group",

number = "1",

}

TY - JOUR

T1 - Towards a standardized bioinformatics infrastructure for N- and O-glycomics

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.

PY - 2019

Y1 - 2019

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.

U2 - 10.1038/s41467-019-11131-x

DO - 10.1038/s41467-019-11131-x

M3 - Review

C2 - 31332201

AN - SCOPUS:85070249334

VL - 10

JO - Nature Communications

JF - Nature Communications

SN - 2041-1723

IS - 1

M1 - 3275

ER -