These datasets contain mass spectrometry-based proteomics results from affinity-purification/pulldown assays designed to identify proteins associated with the autophagy regulator EGFP::ATG16L1 and the RAC1-specific GTPase-activating protein ARHGAP15::MYC. Experiments were performed using mouse embryonic fibroblasts expressing tagged EGFP::ATG16L1 or ARHGAP15::MYC, followed by immunoprecipitation using GFP-Trap or Myc-Trap/anti-tag magnetic agarose beads and LC–MS/MS analysis. The datasets were generated to investigate protein interaction networks linking ARHGAP15, RAC1 signalling, ATG16L1-dependent autophagy and centrosome regulation.