Journal article

Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis

Rebeca Kawahara, Anastasia Chernykh, Kathirvel Alagesan, Marshall Bern, Weiqian Cao, Robert J Chalkley, Kai Cheng, Matthew S Choo, Nathan Edwards, Radoslav Goldman, Marcus Hoffmann, Yingwei Hu, Yifan Huang, Jin Young Kim, Doron Kletter, Benoit Liquet, Mingqi Liu, Yehia Mechref, Bo Meng, Sriram Neelamegham Show all

NATURE METHODS | NATURE PORTFOLIO | Published : 2021

Abstract

Glycoproteomics is a powerful yet analytically challenging research tool. Software packages aiding the interpretation of complex glycopeptide tandem mass spectra have appeared, but their relative performance remains untested. Conducted through the HUPO Human Glycoproteomics Initiative, this community study, comprising both developers and users of glycoproteomics software, evaluates solutions for system-wide glycopeptide analysis. The same mass spectrometrybased glycoproteomics datasets from human serum were shared with participants and the relative team performance for N- and O-glycopeptide data analysis was comprehensively established by orthogonal performance tests. Although the results w..

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Grants

Awarded by Early Career Fellowship (Cancer Institute)


Awarded by Australian Research Council


Awarded by FAPESP


Awarded by Australian Research Council Centre of Excellence in Nanoscale Biophotonics


Funding Acknowledgements

Rosa Viner and Sergei Snovida (Thermo Fisher Scientific) are thanked for providing high-quality LC-MS/MS data. Krishnatej Nishtala is thanked for aiding the data analysis. Catherine Hayes, Julien Mariethoz and Frederique Lisacek are thanked for informatics assistance. RK was supported by an Early Career Fellowship (Cancer Institute NSW ECF181259). DK was supported by an Australian Research Council Future Fellowship (FT160100344). GP was funded by FAPESP (no 2018/15549-1). MT-A was supported by a Macquarie University Safety Net Grant. DK and NHP were supported by the Australian Research Council Centre of Excellence in Nanoscale Biophotonics (CE140100003).