Here, we present a protocol for the purification of MHC class I and class II peptide complexes from mouse and human cell lines providing high-quality immunopeptidomics data. The protocol focuses on sample preparation using commercially available antibodies.
Sirois, I., Isabelle, M., Duquette, J. D., Saab, F., Caron, E. Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis. J. Vis. Exp. (176), e63052, doi:10.3791/63052 (2021).