Plasmodium falciparum is the causative agent of severe human malaria, responsible for over 2 million deaths annually. Of the 5,300 polypeptides predicted to control the parasite life cycle in mosquitoes and humans, 60% are of unknown function. A major challenge of malaria postgenomic biology is to understand how the 5,300 predicted proteins coexist and interact to perform the essential tasks that define the complex life cycle of the parasite. One approach to assign function to these proteins is by identifying their physiological partners. Here we describe the use of tandem affinity purification (TAP) and mass spectrometry for identification of native protein interactions and purification of protein complexes in P. falciparum. Transgenic parasites were generated which express the translation elongation factor PfEF-1 harboring a C-terminal PTP tag which consists of the protein C epitope, a tobacco etch virus protease cleavage site, and two protein A domains. Purification of PfEF-1-PTP from crude extracts followed by mass spectrometric analysis revealed, in addition to the tagged protein itself, the presence of the native PfEF-1, the G-protein PfEF-1␣, and two new proteins that we named PfEF-1␥ and PfEF-1␦ based on their homology to other eukaryotic ␥ and ␦ translation elongation factor subunits. These data, which constitute the first application of TAP for purification of a protein complex under native conditions in P. falciparum, revealed that the translation elongation complex in this organism contains at least two subunits of PfEF-1. The success of this approach will set the stage for a systematic analysis of protein interactions in this important human pathogen.Plasmodium falciparum is the causative agent of the most severe form of human malaria. Over 2 million deaths caused by this parasite are reported annually worldwide (34). The alarming rate of appearance of drug-resistant parasites and mosquitoes, the limited effective antimalarial therapeutic arsenal, and the lack of an effective malaria vaccine have severely hampered international efforts to control the spread of the disease and limit the morbidity and mortality associated with it. The development of new effective malaria eradication strategies requires a better understanding of the parasite cellular biology and advanced knowledge of the metabolic discrepancies that exist between the parasite and the host.P. falciparum has a nuclear genome size of ϳ23 MB distributed among 14 chromosomes varying in size from 0.643 to 3.29 MB (11). This nuclear genome is predicted to encode about 5,300 polypeptides (9). An approximate 60% (3,208 hypothetical proteins) of the predicted open reading frames in the P. falciparum genome encode proteins with no significant homology to proteins in other organisms, and another 5% of the predicted proteins share significant homology to hypothetical proteins of other organisms. The difficulty to genetically manipulate the genome of this parasite has resulted in a very limited analysis of the function of its proteome, with less...