Fig. 3

Identification of CQ target proteins through MS-CETSA. a General workflow of MS-CETSA used to identify CQ interacting protein. Parasite lysates were incubated with CQ at various concentrations, followed by heating under different temperature conditions. The remaining soluble proteins were collected for LysC/Trypsin digestion. The digested peptides are labeled by TMT10plex reagent and quantified by mass spectrometry. The profile of protein thermal stability along the CQ concentration gradient was generated. The proteins with significant thermal shifts were identified as the potential CQ-targeting proteins. b A R²-AUC plot showing the protein thermal stability shift of the whole Plasmodium falciparum proteome after incubation with 0–300 µmol/L CQ from the lysate ITDR MS-CETSA experiment. The potential hit proteins are in orange color, with the highlighted ones in dark blue color. c Venn diagram showing the overlap of target proteins identified in ABPP and MS-CETSA. d Thermal shift profile of the 8 overlap target proteins. CQ chloroquine, MDT minimum dose threshold, AUC area under the curve, ABPP activity-based protein profiling, MS-CETSA mass spectrometry-coupled cell thermal shift analysis, ITDR isothermal dose–response