Currently, proton-transfer reaction mass spectrometry (PTR-MS) allows for quantitative determination of volatile organic compounds in real time at concentrations in the low ppt range, but cannot differentiate isomers or isobaric molecules, using the conventional quadrupole mass filter. Here we pursue the application of linear quadrupole ion trap (LIT) mass spectrometry in combination with proton-transfer reaction chemical ionization to provide the advantages of specificity from MS/MS. A commercial PTR-MS platform composed of a quadrupole mass filter with the addition of end cap electrodes enabled the mass filter to operate as a linear ion trap. The utility of the PTR-LIT was demonstrated by distinguishing between the isomeric isoprene oxidation pair, methyl vinyl ketone (MVK) and methacrolein (MACR) in a photochemical reactor and in ambient forest conditions with 100 ppt LOD. The PTR-LIT method was compared to an established GC/MS method by quantifying MVK and MACR and with a QqQ-MS for distinguishing several monoterpenes and sesquiterpenes. The role of isoprene and its oxidation products, monoterpenes, sesquiterpenes, hydrocarbons, and aromatics was determined in terms of aerosol production and growth, and the formation of organic nitrates from the reaction of VOC with OH or NO3.