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Proton-transfer-reaction mass spectrometry (PTR-MS) is a technique that is widely used to detect volatile organic compounds (VOCs) with proton affinities higher than water. However, <i>n</i>-alkanes generally have a lower proton affinity than water and therefore proton transfer (PT) by reaction with H₃O⁺ is not an effective mechanism for their detection. In this study, we developed a method using a conventional PTR-MS to detect <i>n</i>-alkanes by optimizing ion source and drift tube conditions to vary the relative amounts of different primary ions (H₃O⁺, O₂⁺, NO⁺) in the reaction chamber (drift tube). There are very few studies on O₂⁺ detection of alkanes and the mixed mode has never been proposed before. We determined the optimum conditions and the resulting reaction mechanisms, allowing detection of <i>n</i>-alkanes from <i>n</i>-pentane to <i>n</i>-tridecane. These compounds are mostly emitted by evaporative/combustion process from fossil fuel use. The charge transfer (CT) mechanism observed with O₂⁺ was the main reaction channel for <i>n</i>-heptane and longer <i>n</i>-alkanes, while for <i>n</i>-pentane and <i>n</i>-hexane the main reaction channel was hydride abstraction (HA). Maximum sensitivities were obtained at low <i>E</i>&thinsp;∕&thinsp;<i>N</i> ratios (83 Td), low water flow (2 sccm) and high O₂⁺ ∕ NO⁺ ratios (<i>U</i>_so =  180 V). Isotopic ¹³C contribution was taken into account by subtracting fractions of the preceding ¹²C ion signal based on the number of carbon atoms and the natural abundance of ¹³C (i.e., 5.6 % for <i>n</i>-pentane and 14.5 % for <i>n</i>-tridecane). After accounting for isotopic distributions, we found that PT cannot be observed for <i>n</i>-alkanes smaller than <i>n</i>-decane. Instead, protonated water clusters of <i>n</i>-alkanes (M  ⋅  H₃O⁺) species were observed with higher abundance using lower O₂⁺ and higher water cluster fractions. M  ⋅  H₃O⁺ species are probably the source for the M + H⁺ species observed from <i>n</i>-decane to <i>n</i>-tridecane. Normalized sensitivities to O₂⁺ or to the sum of O₂⁺+ NO⁺ were determined to be a good metric with which to compare sensitivities for <i>n</i>-alkane detection between experiments. Double hydride abstraction was observed from the reaction with O₂⁺. Sensitivity to CT increased with carbon chain length from <i>n</i>-pentane to <i>n</i>-dodecane, sensitivity to HA increased from <i>n</i>-heptane to <i>n</i>-dodecane and sensitivity to PT increased from <i>n</i>-decane to <i>n</i>-tridecane. Sensitivity to CT exponentially decreased with molecular ionization energy, which is inversely related to the carbon chain length. We introduce a calibrated fragmentation algorithm as a method to determine the concentrations of <i>n</i>-alkanes and demonstrate its effectiveness using a custom <i>n</i>-alkane mixture and a much more complex oil example representing perhaps the most difficult mixture available for application of the method. We define optimum conditions for using the mixed ionization mode to measure <i>n</i>-alkanes in conventional PTR-MS instruments regardless of whether they are equipped with switchable reagent ion (SRI) capabilities.