GlypNirO: An automated workflow for quantitative <i>N</i>- and <i>O</i>-linked glycoproteomic data analysis

Phung, Toan K.; Pegg, Cassandra L.; Schulz, Benjamin L.

doi:10.3762/bjoc.16.180

Cited by 7 publications

(3 citation statements)

References 26 publications

(31 reference statements)

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“…Instrument settings were specific to an ABSCIEX 5600 instrument. The results from the Skyline were converted to a readable format for GlypNirO ( Phung et al. 2020 ).…”

Section: Methodsmentioning

confidence: 99%

The role of N-glycosylation in spike antigenicity for the SARS-CoV-2 gamma variant

Pegg,

Modhiran,

Parry

et al. 2023

Glycobiology

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The emergence of SARS-CoV-2 variants alters the efficacy of existing immunity towards the viral spike protein, whether acquired from infection or vaccination. Mutations that impact N-glycosylation of spike may be particularly important in influencing antigenicity, but their consequences are difficult to predict. Here, we compare the glycosylation profiles and antigenicity of recombinant viral spike of ancestral Wu-1 and the Gamma strain, which has two additional N-glycosylation sites due to amino acid substitutions in the N-terminal domain (NTD). We found that a mutation at residue 20 from threonine to asparagine within the NTD caused the loss of NTD-specific antibody COVA2-17 binding. Glycan site-occupancy analyses revealed that the mutation resulted in N-glycosylation switching to the new sequon at N20 from the native N17 site. Site-specific glycosylation profiles demonstrated distinct glycoform differences between Wu-1, Gamma, and selected NTD variant spike proteins, but these did not affect antibody binding. Finally, we evaluated the specificity of spike proteins against convalescent COVID-19 sera and found reduced cross-reactivity against some mutants, but not Gamma spike compared to Wuhan spike. Our results illustrate the impact of viral divergence on spike glycosylation and SARS-CoV-2 antibody binding profiles.

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“…Instrument settings were specific to an ABSCIEX 5600 instrument. The results from the Skyline were converted to a readable format for GlypNirO ( Phung et al. 2020 ).…”

Section: Methodsmentioning

confidence: 99%

The role of N-glycosylation in spike antigenicity for the SARS-CoV-2 gamma variant

Pegg,

Modhiran,

Parry

et al. 2023

Glycobiology

Self Cite

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“…Instrument settings were specific to an ABSCIEX 5600 instrument. The results from the Skyline were converted to a readable format for GlypNirO 64 . Heatmaps and bar graphs were produced using PRISM v9.1.0 (GraphPad Software, La Jolla California USA).…”

Section: Data Analysis Glycoformsmentioning

confidence: 99%

The role ofN-glycosylation in spike antigenicity for the SARS-CoV-2 Gamma variant

Pegg

Modhiran

Parry

et al. 2023

Preprint

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The emergence of SARS-CoV-2 variants alters the efficacy of existing immunity towards the viral spike protein, whether acquired from infection or vaccination. Mutations that impactN-glycosylation of spike may be particularly important in influencing antigenicity, but their consequences are difficult to predict. Here, we compare the glycosylation profiles and antigenicity of recombinant viral spike of ancestral Wu-1 and the Gamma strain, which has two additionalN-glycosylation sites due to amino acid substitutions in the N-terminal domain (NTD). We found that a mutation at residue 20 from threonine to asparagine within the NTD caused the loss of NTD-specific antibody binding. Glycan site-occupancy analyses revealed that the mutation resulted inN-glycosylation switching to the new sequon at N20 from the native N17 site. Site-specific glycosylation profiles demonstrated distinct glycoform differences between Wu-1, Gamma, and selected NTD variant spike proteins, but these did not affect antibody binding. Finally, we evaluated the specificity of spike proteins against convalescent COVID-19 sera and found reduced cross-reactivity against some mutants, but not Gamma spike compared to Wuhan spike. Our results illustrate the impact of viral divergence on spike glycosylation and SARS-CoV-2 antibody binding profiles.

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“…Most structural data at this stage is generated by analytical approaches, such as mass spectrometry (MS), high-pressure liquid chromatography (HPLC), and capillary electrophoresis (CE). The articles by Phung et al [ 9 ] and by Lippold et al [ 10 ] suggest ways of combining and customising available MS data analysis tools for glycoproteomic characterization and quantification. The article by Walsh et al [ 11 ], on the other hand, addresses the problems of an irreproducible retention time and peak integration in antibody glycomic analysis using CE, thus allowing small quantitative differences to be detected when comparing similar glycomes by this method.…”

mentioning

confidence: 99%

GlycoBioinformatics

Aoki‐Kinoshita¹,

Lisacek²,

Karlsson³

et al. 2021

Beilstein J. Org. Chem.

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GlypNirO: An automated workflow for quantitative N- and O-linked glycoproteomic data analysis

Cited by 7 publications

References 26 publications

The role of N-glycosylation in spike antigenicity for the SARS-CoV-2 gamma variant

The role of N-glycosylation in spike antigenicity for the SARS-CoV-2 gamma variant

The role ofN-glycosylation in spike antigenicity for the SARS-CoV-2 Gamma variant

GlycoBioinformatics

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