We present a detailed investigation of the factors governing the quantification of formic acid (FA), acetic acid (AA), and their relevant mass analogues by proton-transfer-reaction mass spectrometry (PTR-MS), assess the underlying fragmentation pathways and humidity dependencies, and present a new method for separating FA and AA from their main isobaric interferences. PTR-MS sensitivities towards glycolaldehyde, ethyl acetate, and peroxyacetic acid at m/z 61 are comparable to that for AA; when present, these species will interfere with ambient AA measurements by PTR-MS. Likewise, when it is present, dimethyl ether can interfere with FA measurements. For a reduced electric field (E/N) of 125 Townsend (Td), the PTR-MS sensitivity towards ethanol at m/z 47 is 5-20 times lower than for FA; ethanol will then only be an important interference when present in much higher abundance than FA. Sensitivity towards 2-propanol is <1% of that for AA, so that propanols will not in general represent a significant interference for AA. Hydrated product ions of AA, glycolaldehyde, and propanols occur at m/z 79, which is also commonly used to measure benzene. However, the resulting interference for benzene is only significant when E/N is low (≲100 Td). Addition of water vapor affects the PTR-MS response to a given compound by (i) changing the yield for fragmentation reactions and (ii) increasing the importance of ligand switching reactions. In the case of AA, sensitivity to the molecular ion increases with humidity at low E/N but decreases with humidity at high E/N due to water-driven fragmentation. Sensitivity towards FA decreases with humidity throughout the full range of E/N. For glycolaldehyde and the alcohols, the sensitivity increases with humidity due to ligand switching reactions (at low E/N) and reduced fragmentation in the presence of water (at high E/N). Their role as interferences will typically be greatest at high humidity. For compounds such as AA where the humidity effect depends strongly on the collisional energy in the drift tube, simple humidity correction factors (XR) will only be relevant for a specific instrumental configuration. We recommend E/N ∼ 125 Td as an effective condition for AA and FA measurements by PTR-MS, as it optimizes between the competing E/N-dependent mechanisms controlling their sensitivities and those of the interfering species. Finally, we present the design and evaluation of an online acid trap for separating AA and FA from their interfering species at m/z 61 and 47, and we demonstrate its performance during a field deployment to St. Louis, USA, during August-September of 2013.