This dataset corresponds to an intact mass spectrometry study focusing on the covalent binding interaction between purified FGFR2 V564F protein and compound LC-F2-1. The purified FGFR2 V564F was adjusted to 28 μM, then incubated with LC-F2-1 at molar ratios of 1:2 or 1:5 for 4 hours at room temperature. Preliminary LC-MS analysis confirmed that all FGFR2 V564F molecules formed covalent adducts with LC-F2-1 after incubation. Subsequently, intact mass analysis was conducted using an Agilent 6230 time-of-flight LC/MS system (equipped with Dual AJS ESI), and protein samples were desalted via an Agilent 1290 Infinity II instrument prior to mass spectrometry detection. BioConfirm software was applied to deconvolute the protein spectra, aiming to characterize the covalent binding product of FGFR2 V564F and LC-F2-1.