Abstract. Atmospheric methane measurements are important for evaluating high resolution methane inventories and monitoring emissions reductions. Despite recent international efforts to harmonize measurement methodologies and techniques, currently there are no standardized or internationally accepted techniques for estimating emissions from mobile in situ concentration measurements. We present measurements from two different mobile in situ methane laboratories, and compare emission rates calculated from four Gaussian plume Bayesian optimal estimation strategies and a statistical algorithm. For mobile transects from the slower flow-rate instrument, we find a significant asymmetric smoothing artifact. The effect of this asymmetry is most significant for short transects of small (0–50 kg CH4 day−1), nearby methane sources, where the plume crossing time is comparable to the mean residence time of the instrument. We develop a model of this effect, demonstrate how this model can be applied to Gaussian plume inversions, and describe its limitations. We use these results to compute emissions rate estimates for two methane sources from Toronto’s wastewater management system to demonstrate the use and limitations of Gaussian plume inversions to quantify methane emissions in an urban environment. Overall, we highlight the importance of using observed plume enhancement areas rather than the more commonly used enhancement heights for determining comparable emissions estimates between different mobile laboratories.