Can airborne observations from infrequent flights be used to infer the budget of ozone in the upper troposphere with any degree of certainty or representativeness? Fluctuations in ozone mixing ratio observed along flights are dominated by flying between air masses with distinct origins, rather than the recent chemical transformation that has occurred within those air masses. Reverse domain filling trajectories arriving on a high-resolution three-dimensional grid (RDF3D) can simulate air mass structure accurately by coloring arrival grid points with specific humidity (q) from the origin of each trajectory. Typical displacement errors in tracer filaments are only about 30 km, but the associated phase errors greatly reduce the correlations between airborne observations of long-lived chemicals and their model simulations. However, the comparison can be vastly improved if equivalent potential temperature (θe) and specific humidity are used as coordinates to label air masses. Both properties are approximately conserved following unsaturated air and serve as good markers of air masses even if the air is saturated or mixing takes place. Ozone simulations from a Lagrangian model are evaluated against observations in thermodynamic coordinates, factoring out many of the transport phase errors. The proportion of the atmosphere occupied by different chemical air masses is estimated by using RDF3D trajectories to simulate the distributions of q and θe and then assuming that chemical composition is homogeneous within air masses, each with characteristic (q, θe). Mass density in thermodynamic coordinates is used to weight the modeled ozone transformation and error in concentration (calculated along flight tracks) to estimate photochemically produced ozone throughout a volume encompassing the flights.