We investigate flux tube emergence in the solar photosphere using a diagnostic procedure based on analyzing Stokes signals from different spectral lines calculated in 3-D radiation-MHD simulations. The simulations include the effects of radiative transport and partial ionization and cover layers both above and below the solar surface. The simulations consider the emergence of a twisted magnetic flux tube through the solar surface. We consider different stages in the emergence process, starting from the early appearance of the flux tube at the solar surface, and following the emergence process until the emerged flux looks similar to a normal bipolar region. At every stage we compute line profiles by numerically solving the Unno-Rachkovsky equations at every horizontal grid point. Then, following observational practice, we apply Milne-Eddington-type inversions to the synthetic spectra in order to retrieve different atmospheric parameters. We include the influence of spatial smearing on the deduced atmospheric parameters to identify signatures of different stages of flux emergence in the solar photosphere.