This dataset contains the raw mass spectrometry data of Menin immunoprecipitation-mass spectrometry (IP-MS) performed in mouse cortex tissue. The study aims to identify Menin-interacting proteins in the cerebral cortex. Menin-associated protein complexes were immunoprecipitated using anti-Menin antibodies, separated by SDS-PAGE, and subjected to in-gel trypsin digestion. The resulting peptides were analyzed by nano-flow liquid chromatography coupled to a timsTOF Pro mass spectrometer (Bruker) operated in PASEF mode. Protein identification was performed using PEAKS Studio X against the UniProt mouse protein database. This dataset provides the raw MS files and protein identification results for Menin-associated protein profiling in mouse cortex.