We performed MS/MS investigations of biogenic volatile organic compounds (BVOC) using a triple quadrupole tandem mass spectrometer (QqQ-MS) equipped with a Townsend Discharge ion source and a Proton Transfer Reaction Linear Ion Trap (PTR-LIT) mass spectrometer. Both instruments use H2O chemical ionization to produce protonated molecular ions. Here we report a study of the application of these instruments to determine methyl vinyl ketone (MVK) and methacrolein (MACR) and a series of monoterpenes (α-pinene, β-pinene, 3-carene, limonene, myrcene, ocimene) and sesquiterpenes (humulene and farnesene). Both instruments achieved sub-ppb detection limits in the single MS mode and in the MS/MS mode for differentiating MVK and MACR. Collision induced dissociation (CID) of protonated monoterpenes and sesquiterpenes was studied under the high-energy, single-to-few collision conditions of the QqQ-MS instrument and under the low-energy, multiple collision conditions of the PTR-LIT. Differences and similarities in the breakdown curves obtained are discussed. In addition, we performed MS4 of protonated limonene to illustrate the analytical power of the PTR-LIT. In spite of the progress we have made, the selective on-line mass-spectrometric detection of individual monoterpenes or sesquiterpenes in complex mixtures currently does not yet seem to be possible.