A new approach to the detection of 3-chloropropane-1,2-diol (3-MCPD) by “soft” mass spectrometry methods is proposed. The method is based on the chemical modification of a target compound with derivatizing agents, such as 4-bromobutyl- and 3-(bromomethyl) phenylboronic acids, followed by the quaternization of pyridine by the derivatives. The resulting products are organic salts, the cations of which are easily detected by matrix-assisted laser desorption/desorption/ionization ionization (MALDI) and electrospray ionization (ESI) mass spectrometry. The mass spectra of the stimulated fragmentation of such cations mainly contain ion peaks corresponding to protonated pyridine molecules, which makes it possible to use the selected reaction monitoring for the selective detection of 3-MCPD and other diols.