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

Publikation: Bidrag til tidsskrift › Review › Forskning › fagfællebedømt

Standard

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.

I: Nature Communications, Bind 10, Nr. 1, 3275, 2019.

Publikation: Bidrag til tidsskrift › Review › Forskning › fagfællebedømt

Harvard

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, bind 10, nr. 1, 3275. https://doi.org/10.1038/s41467-019-11131-x

APA

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

Vancouver

Rojas-Macias MA, Mariethoz J, Andersson P, Jin C, Venkatakrishnan V, Aoki NP o.a. Towards a standardized bioinformatics infrastructure for N- and O-glycomics. Nature Communications. 2019;10(1). 3275. https://doi.org/10.1038/s41467-019-11131-x

Author

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. I: Nature Communications. 2019 ; Bind 10, Nr. 1.

Bibtex

@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",

}

RIS

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 -

ID: 226358079