Mass Spectrometric Identification and Molecular Modeling of Glycopeptides Presented by MHC Class I and II Processing Pathways

  • Stacy A. Malaker
  • Michael J. FerracaneEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 2024)


Aberrant glycosylation is a hallmark of cancer that contributes to the disease’s ability to evade the immune system. As the MHC processing pathways communicate cellular health to circulating CD8+ and CD4+ T-cells, MHC-associated glycopeptides are likely a source of neoantigens in cancer. In fact, recent advances in mass spectrometry have allowed for the detection and sequencing of tumor-specific glycopeptides from the MHC class I and class II processing pathways. Here, we describe methods for detecting, sequencing, and modeling these MHC-associated glycopeptides.

Key words

Mass spectrometry MHC-associated glycopeptides Glycopeptide analysis Neoantigens Molecular modeling 



The authors would like to acknowledge Jane V. Aldrich (U Florida), Dina L. Bai, Jeffrey Shabanowitz, and Donald F. Hunt (U Virginia) for their technical and financial support. This work was supported by a research grant from the Melanoma Research Alliance and by an NIH grant AI033993 to D.F.H. S.A.M. is currently funded by an NIH F32 Postdoctoral fellowship.


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© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of ChemistryStanford UniversityStanfordUSA
  2. 2.Department of ChemistryUniversity of RedlandsRedlandsUSA

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