Introduction: With the advent of high-perfomance liquid chromatography (HPLC)-tandem mass spectrometry (MS) using ion trap mass analysers it is possible to acquire unambigious structural information in particular with respect to aspects of regiochemistry and stereochemistry of organic compounds present in complex mixtures such as coffee extracts. However, HPLC–MS methods are resource extensive, laborious and lacking user friendliness. Objective: To introduce a simple parameter – the energy threshhold for fragmentation – determined using energy resolved MS and demonstrate its value for the complete structural characterisation and even relative quantification of individual isomeric chlrogenic acids in direct infusion experiments. Methodology: Monocaffeoyl and dicaffeoyl quinic acids were investigated by direct infusion energy resolved mass spectrometry (ER-MS) in negative in mode, using a quadrupole ion trap and quadrupole time-of-flight (Q-TOF) mass spectrometer. Methanolic coffee extracts were quantitatively investigated by HPLC–MS and direct infusion ER-MS. Results: Fragmentation occurs with retention of regiochemistry and regiochemistry of fragment ions can be determined using ER-MS. Analysis of breakdown graphs allows extraction of a single numerical parameter that allows assignment of regiochemistry. Analysis of monocaffeoyl and dicaffeoyl quinic acids revealed that regiosiomers could be distinguished and assigned based on their dissociation energies in collisional induced activation. Furthermore relative quantification of regioisomers by direct infusion ER-MS is possible within an error range of ±10% if compared with a conventional quantitative LC–MS method. Conclusion: ER-MS can be exploited in determining relative isomers quantities of chlorogenic acids (CGAs) in crude plant extracts by direct infusion tandem MS omitting time and resource intensive chromatographic separation.