We have identified four AP2 proteins that specifically target the mitochondrial matrix in Toxoplasma gondii. To understand the functional significance of these mtAP2 proteins, we performed a comprehensive label-free quantitative proteomic analysis to assess the impact of their deletion on the protein level. Additionally, the effects of deleting two selected mitoribosomal proteins, TguL4m (a known mitoribosomal protein) and TgRAP13 (a newly identified mitoribosomal protein), were investigated as controls.