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