Proton-Transfer-Reaction Mass Spectrometry (PTR-MS) is a very useful tool for high frequency detection and quantification of gas-phase volatile organic compounds (VOCs) but the soft ionization means it is difficult to discriminate structural isomers. For example, to date it has only been possible to measure the sum of monoterpene concentrations, which have been monitored most commonly at m/z 81 and 137 at a constant drift voltage and pressure. We show here that PTR-MS is capable of discriminating individual monoterpenes when operating in the alternating drift voltage (AD) mode. The approach is based on the principle that slightly different energies are required for the fragmentation/clustering of a given monoterpene, so in AD mode each monoterpene has different time points for fragmentation. Therefore from a fragmentation analysis of background-subtracted standards it is possible to calculate the percentage of each monoterpene in an absolute concentration of their sum. Although monoterpenes have been chosen as an example, the method is likely to be effective for other structural isomeric species such as the sesquiterpenes or methyl vinyl ketone/methacrolein (MVK/MACR).