Isopropylthioxanthone (ITX), usually applied as a mixture of 2- and 4-isomers, is a common photo-initiator in UV inks used in paper- or plastic-based packaging materials. In this work a pentafluorophenylpropyl column (HS F5) has been used to achieve the chromatographic separation of the two isomers. A gradient elution with acetonitrile and a 25mM formic acid-ammonium formate at pH 3.75 are required to provide an Rs of 1.3 between the two compounds. The fragmentation pattern of ITX was studied using two mass analyzers, an ion trap (IT) (multi-stage fragmentation) and a triple quadrupole mass analyzer of hyperbolic rods (accurate mass (AM) measurement). The protonated molecule [M+H](+) observed in the mass spectrometry (MS) spectrum lost an isopropyl group, [M+H-C(3)H(6)](+). Later, this ion fragmented, yielding the radical ion [M+H-C(3)H(6)-CHO](+). The elemental composition of these product ions was confirmed by AM measurement. Electrospray ionization (ESI) was used as an ionization source to couple liquid chromatography (LC) to MS. Instrumental quality parameters of three acquisition modes provided by the triple quadrupole mass analyzer were studied and good run-to-run precision (relative standard deviation, RSD, lower than 10%) and limits of detection (LODs) down to 0.8pg injected in the LC-MS/MS system were obtained. Finally the LC-MS/MS method using H-SRM Q1 acquisition mode was used to analyze 2- and 4-ITX in a range of food samples. The use of highly selective selected reaction monitoring (H-SRM on Q1) resulted in improved selectivity without sensitivity loss.