Multiplexed relative quantitation with isobaric tagging mass spectrometry reveals MHC-I ligand dynamics in response to doxorubicin

MHC-I peptides are intracellular-cleaved peptides, usually 8-11 amino acids in length, which are presented on the cell surface and facilitate CD8+ T cell responses. Despite the appreciation of CD8+ T cell anti-tumor immune responses towards improvement in patient outcomes, the MHC-I peptide ligands that facilitate the response are poorly described. Along these same lines, although many therapies have been recognized for their ability to reinvigorate anti-tumor CD8+ T cell responses, whether these therapies alter MHC-I peptide repertoire has not been fully assessed due to the lack of quantitative strategies. We here develop a multiplexing platform for screening therapy-induced MHC-I ligands by employing tandem mass tags (TMT). We applied this approach to measuring responses to doxorubicin, which are known to promote anti-tumor CD8+ T cell responses during their therapeutic administration in cancer patients. Using both in vitro and in vivo systems, we show successful relative quantitation of MHC-I ligands u...