Toxoplasma gondii is a ubiquitous pathogen of warm-blooded animals and belongs to the phylum of apicomplexan parasites. Apicomplexans cause diseases of high mortality, including toxoplasmosis, malaria, and cryptosporidiosis. Cyclic nucleotide-dependent protein kinases in this divergent family of parasites play crucial roles in pathogenesis and spread. Here, we conduct a phosphoproteomics experiment after T. gondii parasites are depleted of the protein kinase A regulatory subunit (PKA R), resulting in up-regulation of the PKA catalytic subunit 1 (PKA C1).