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Cited by 62Glycosylation and Glycoproteins ResearchAdvanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

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What Are We Missing by Using Hydrophilic Enrichment? Improving Bacterial Glycoproteome Coverage Using Total Proteome and FAIMS Analyses

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Ahmad Izaham, Ameera Raudah, Ang, Ching-Seng, Nie, Shuai, Bird, Lauren E., Williamson, Nicholas A., Scott, Nichollas E.·2021·Journal of Proteome Research
DOI 10.1021/acs.jproteome.0c00565

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Abstract

ABSTRACT Hydrophilic Interaction Liquid Chromatography (HILIC) glycopeptide enrichment is an indispensable tool for the high-throughput characterisation of glycoproteomes. Despite its utility, HILIC enrichment is associated with a number of short comings including requiring large amounts of starting material, potentially introducing chemical artefacts such as formylation, and biasing/under-sampling specific classes of glycopeptides. Here we investigate HILIC enrichment independent approaches for the study of bacterial glycoproteomes. Using three Burkholderia species ( B. cenocepacia, B. dolosa and B. ubonensis ) we demonstrate that short aliphatic O -linked glycopeptides are typically absent from HILIC enrichments yet are readily identified in whole proteome samples. Using Field Asymmetric Waveform IMS (FAIMS) fractionation we show that at low compensation voltages (CVs) short aliphatic glycopeptides can be enriched from complex samples providing an alternative means to identify glycopeptides recalcitrant to hydrophilic based enrichment. Combining whole proteome and FAIMS analysis we show that the observable glycoproteome of these Burkholderia species is at least 30% larger than initially thought. Excitingly, the ability to enrich glycopeptides using FAIMS appears generally applicable, with the N -linked glycopeptides of Campylobacter fetus subsp. fetus also enrichable at low FAIMS CVs. Taken together, these results demonstrate that FAIMS provides an alternative means to access glycopeptides and is a valuable tool for glycoproteomic analysis.

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Metadata

Authors
Ahmad Izaham, A. R., Ang, C.-S., Nie, S., Bird, L. E., Williamson, N. A., & Scott, N. E.
Affiliations
  • Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
  • The University of Melbourne (AU)
Corresponding author
Scott, Nichollas E.
ORCID
Venue
Journal of Proteome Research
Publisher
American Chemical Society (ACS)
Published
2020-10-30
Volume
20
Issue
1
Pages
599-612
ISSN
  • 1535-3893 (ISSN-L)
  • 1535-3907
DOI
10.1021/acs.jproteome.0c00565
OpenAlex
W3097160446
Cited by
62
References
2
Citations by year
2026: 2 · 2025: 9 · 2024: 11 · 2023: 8 · 2022: 13 · 2021: 15 · 2020: 3
FWCI
3.17
Type
journal article
Language
en
Open access
Licence
Locations
  • Journal of Proteome Research (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
  • PubMed (publishedVersion)
Funders
National Health and Medical Research Council (APP1100164)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Glycosylation and Glycoproteins Research
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
  • Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
Keywords
glycopeptide enrichment, hydrophilic interaction liquid chromatography, FAIMS, Burkholderia, O-linked glycopeptides, N-glycopeptides, Campylobacter fetus subsp. fetus
MeSH terms
Ion Mobility Spectrometry, Campylobacter, Glycopeptides, Burkholderia, Proteome, Hydrophobic and Hydrophilic Interactions

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