Proteogenomic Analysis of <i>CDPK1</i> Mutant in <i>Plasmodium falciparum</i>

Malaria caused by Plasmodium falciparum remains a health burden worldwide due to drug resistance and limited treatment options. Calcium-dependent protein kinase 1 ( CDPK1 ) plays a central role in parasite development and invasion, but the downstream molecular alterations that occur upon its disruption remain poorly understood. We present a proteogenomic-based data analysis pipeline for the reanalysis of the publicly available P. falciparum CDPK1 mutant dataset (PRIDE: PXD005207), integrating proteomic and phosphoproteomic data with six-frame genome translation. This led to the discovery of 24 new protein-coding genes, including 17 exonic and 7 intronic peptides, thereby enriching the current genome annotation. Several peptides, such as NILLTFDK, THNNNPQPNPQQK, and EVTSNFGNIR, mapped to previously unannotated genomic regions, which showed orthologous evidence in other Plasmodium species. The reanalysis of phosphoproteomics data identified 37 novel peptides that imply changes in phosphorylation signaling upon CDPK1 knockdown. The identification of conserved peptides like those associated with metacaspase and HSP70, indicates their potential roles in the survival and adaptation of parasites. Overall, this study highlights the potential of proteogenomics to improve genome annotation and reveal hidden coding regions of the P. falciparum genome. This provides new insights into kinase-regulated pathways and potential molecular targets for malaria control.