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A critical step in satellite retrievals of trace gas columns is the calculation of the air mass factor (AMF) used to convert observed slant columns to vertical columns. This calculation requires a priori information on the shape of the vertical profile. As a result, comparisons between satellite-retrieved and model-simulated column abundances are influenced by the a priori profile shape. We examine how differences between the shape of the simulated and a priori profiles can impact the interpretation of satellite retrievals by performing an adjoint-based four-dimensional variational (4D-Var) assimilation of synthetic NO₂ observations for constraining NO_x emissions. We use the GEOS-Chem adjoint model to perform assimilations using a variety of AMFs to examine how a posteriori emission estimates are affected if the AMF is calculated using an a priori shape factor that is inconsistent with the simulated profile. In these tests, an inconsistent a priori shape factor increased root mean square errors in a posteriori emission estimates by up to 30 % for realistic conditions over polluted regions. As the difference between the simulated profile shape and the a priori profile shape increases, so do the corresponding assimilated emission errors. This reveals the importance of using simulated profile information for AMF calculations when comparing that simulated output to satellite-retrieved columns.