High‐resolution analysis of the murine MHC class II immunopeptidome

The reliable identification of peptides bound to major histocompatibility complex (MHC) class II is fundamental for the study of the host immune response against pathogens and the pathogenesis of autoimmune conditions. Here, we describe an improved methodology combining immuno‐affinity enrichment of MHC class II complexes, optimized elution conditions and quadrupole Orbitrap mass spectrometry‐based characterization of the immunopeptidome. The methodology allowed the identification of over 1000 peptides with 1% false discovery rate from 10⁸ murine A20 lymphoma cells. The study revealed the I‐A^d‐specific motif in high resolution after multisequence alignment. The methodology was generally applied to the purification of MHC class II from cell lines and murine spleens. We identified 2963 peptides from BALB/c and 2712 from C57BL/6 mouse spleens. The identification of peptides bound to MHC class II in vitro and in vivo will facilitate the characterization of T‐cell specificities, as well as the development of biotherapeutics and vaccines.