CHU Sainte-Justine Research Center 1 article published in JoVE Biochemistry Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis Isabelle Sirois*1, Maxim Isabelle*1, Jérôme D. Duquette1, Frederic Saab1, Etienne Caron1,2 1CHU Sainte-Justine Research Center, 2Department of Pathology and Cellular Biology, Faculty of Medicine, Université de Montréal 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.