Covalent chemical probes form a covalent bond with a target protein of interest to elicit an effect and methods to identify and characterise them are needed. We developed a native mass spectrometry (nMS) method to screen an electrophilic covalent fragment library and identified specific novel binders for the surface exposed cysteine residues of carbonic anhydrase III (CA III). The nMS method was extended to determine the site of protein modification and measure simultaneous binding of an active site noncovalent inhibitor and covalent fragment hit, which is not possible with intact denaturing MS. This study demonstrates the utility of using nMS and the advantages when compared to intact denaturing MS for the discovery and characterisation of new covalent ligands.