This project provides comparative proteomic and phosphoproteomic data from mouse tissues collected after immunomodulatory treatment with turnip extract and from untreated control mice. Using proteomics and phosphoproteomics, this study investigated signaling pathways associated with the immune response induced by turnip extract. Data were acquired using a high-resolution mass spectrometry platform and cover the complete workflow from sample preparation and mass spectrometry analysis to database searching. The deposited files include raw mass spectrometry data (.raw) and normalized quantitative analysis results. This dataset was generated to support open and transparent scientific research and to provide a resource for further investigation of proteins involved in the immunomodulatory functions of turnip.