Updated publication reference for PubMed record(s): 31390575. To identify malaria protein interactions systematically we combined blue native polyacrylamide electrophoresis fractionation with quantitative mass spectrometry and machine learning. Our integrative approach identified over twenty thousand protein interactions in Plasmodium schizonts, organized into 600 complexes, the majority of which are novel, and generated a high-confidence Plasmodium protein interaction network.