This paper studied the deactivation of propionyl shikonin(PS) to tobacco mosaic virus(TMV).After preparation and isolation of TMV coat protein(CP),concentration and purity test were made by SDS-PAGE and MALDI-TOF MS.Bonding of PS and TMV-CP was determined also by MALDI-TOF MS.Peptide mass spectra of trypsin enzymolysis treated by propionyl shikonin were studied.Based on the rate of changes of peptide relative abundance of TMV-CP bonding with PS,the bonding site was computed with SGI workstation,the pKa value was 4.95.