Absolute quantification of tumor antigens using embedded MHC-I isotopologue calibrants

Proc Natl Acad Sci U S A. 2021 Sep 14;118(37):e2111173118. doi: 10.1073/pnas.2111173118.


Absolute quantification measurements (copies per cell) of peptide major histocompatibility complex (pMHC) antigens are necessary to inform targeted immunotherapy drug design; however, existing methods for absolute quantification have critical limitations. Here, we present a platform termed SureQuant-IsoMHC, utilizing a series of pMHC isotopologues and internal standard-triggered targeted mass spectrometry to generate an embedded multipoint calibration curve to determine endogenous pMHC concentrations for a panel of 18 tumor antigens. We apply SureQuant-IsoMHC to measure changes in expression of our target panel in a melanoma cell line treated with a MEK inhibitor and translate this approach to estimate antigen concentrations in melanoma tumor biopsies.

Keywords: MHC class I; antigen presentation; immunopeptidomics.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antigen Presentation / drug effects
  • Antigen Presentation / immunology*
  • Antigens, Neoplasm / analysis*
  • Antigens, Neoplasm / drug effects
  • Antigens, Neoplasm / immunology
  • Benzimidazoles / pharmacology*
  • Histocompatibility Antigens Class I / immunology*
  • Histocompatibility Antigens Class I / metabolism
  • Humans
  • Immunotherapy
  • MAP Kinase Kinase 1 / antagonists & inhibitors*
  • Melanoma / drug therapy
  • Melanoma / immunology*
  • Melanoma / metabolism
  • Tumor Cells, Cultured


  • Antigens, Neoplasm
  • Benzimidazoles
  • Histocompatibility Antigens Class I
  • binimetinib
  • MAP Kinase Kinase 1