Glycomics-assisted glycoproteomics enables deep and unbiased n-glycoproteome profiling of complex biological specimens

The Huong Chau, Anastasia Chernykh, Julian Ugonotti, Benjamin L. Parker, Rebeca Kawahara, Morten Thaysen-Andersen*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

7 Citations (Scopus)


Mass spectrometry-driven glycomics and glycoproteomics, the system-wide profiling of detached glycans and intact glycopeptides from biological samples, respectively, are powerful approaches to interrogate the heterogenous glycoproteome. Efforts to develop integrated workflows employing both glycomics and glycoproteomics have been invested since the concerted application of these complementary approaches enables a deeper exploration of the glycoproteome. This protocol paper outlines, step-by-step, an integrated -omics technology, the "glycomics-assisted glycoproteomics" method, that first establishes the N-glycan fine structures and their quantitative distribution pattern of protein extracts via porous graphitized carbon-LC-MS/MS. The N-glycome information is then used to augment and guide the challenging reversed-phase LC-MS/MS-based profiling of intact N-glycopeptides from the same protein samples. Experimental details and considerations relating to the sample preparation and the N-glycomics and N-glycoproteomics data collection, analysis, and integration are discussed. Benefits of the glycomics-assisted glycoproteomics method, which can be readily applied to both simple and complex biological specimens such as protein extracts from cells, tissues, and bodily fluids (e.g., serum), include quantitative information of the protein carriers and site(s) of glycosylation, site occupancy, and the site-specific glycan structures directly from biological samples. The glycomics-assisted glycoproteomics method therefore facilitates a comprehensive view of the complexity and dynamics of the heterogenous glycoproteome.

Original languageEnglish
Title of host publicationSerum/Plasma Proteomics
Subtitle of host publicationMethods and Protocols
EditorsDavid W. Greening, Richard J. Simpson
Place of PublicationNew York, NY
PublisherSpringer, Springer Nature
Number of pages29
ISBN (Electronic)9781071629789
ISBN (Print)9781071629772
Publication statusPublished - 2023

Publication series

NameMethods in molecular biology (Clifton, N.J.)
PublisherHumana Press
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • Chromatography, Liquid/methods
  • Glycomics/methods
  • Tandem Mass Spectrometry/methods
  • Glycopeptides/chemistry
  • Proteome
  • Polysaccharides/chemistry
  • Glycomics
  • Glycoproteomics
  • Glycoproteome
  • Glycomics-assisted glycoproteomics
  • Glycopeptide
  • Mass spectrometry
  • N-Glycan


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