In this study, we compare different antibodies to mouse MHC class I complexes for their efficiency of associated peptide recovery. Input was murine EL-4 cells, which are T lymphoblast cells derived from a C57BL/6 background. We performed immunoprecipitation (IP) with different antibodies either singly or sequentially to enrich MHC class I, followed by gentle elution of associated peptides, and finally peptide analysis by mass spectrometry. Each IP workflow yielded a different (but overlapping) cohort of peptides, suggesting optimal methodologies for analyses of immunopeptidomes from common laboratory mouse strains.

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