Mass spectrometry–based glycomics and proteomics profiling of on-slide digested tissue from complex biological samples

Sayantani Chatterjee, Joseph Zaia, Manveen K. Sethi

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

Abstract

Mass spectrometry–based investigation of the heterogeneous glycoproteome from complex biological specimens is a robust approach to mapping the structure, function, and dynamics of the glycome and proteome. Sampling whole wet tissues often provides a large amount of starting material; however, there is a reasonable variability in tissue handling prior to downstream processing steps, and it is difficult to capture all the different biomolecules from a specific region. The on-slide tissue digestion approach, outlined in this protocol chapter, is a simple and cost-effective method that allows comprehensive mapping of the glycoproteome from a single spot of tissue of 1 mm or greater diameter. It provides a selection of target areas on tissue slides appropriate for tissue volumes of 10 nL or greater, corresponding to a 1 μL droplet of enzyme solution applied to a 1-mm diameter target on a 10-μm-thick tissue slice. Sequential enzymatic digestions and desalting of the biomolecules without any prior derivatization from the surface of fresh frozen or formalin-fixed paraffin-embedded tissue slides enable the simultaneous identification of glycosaminoglycan disaccharides such as hyaluronan, chondroitin sulfate and heparan sulfate, asparagine or N-linked glycans, and intact (glyco)peptides using liquid chromatography-tandem mass spectrometry. The in-depth information obtained from this method including the disaccharide compositions, glycan structures, peptide abundances, and site-specific glycan occupancies provides a detailed profiling of a single spot of tissue which has the potential to be disseminated to biomedical laboratories.
Original languageEnglish
Title of host publicationTissue Proteomics
Subtitle of host publicationMethods and Protocols
EditorsTaufika Islam Williams
PublisherSpringer, Springer Nature
Chapter18
Pages279-303
Number of pages25
ISBN (Print)9781071642979, 9781071642986
DOIs
Publication statusPublished - 2025
Externally publishedYes

Publication series

NameMethods in Molecular Biology
PublisherSpringer
Volume2884
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Keywords

  • Formalin-fixed paraffin-embedded tissue
  • Fresh frozen tissue
  • Glycomics
  • Glycoproteomics
  • Liquid chromatography
  • Mass spectrometry
  • On-slide tissue digestion
  • Proteomics

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