  With a scheduled launch in October 2018, the James Webb Space Telescope
(JWST) is expected to revolutionise the field of atmospheric characterization
of exoplanets. The broad wavelength coverage and high sensitivity of its
instruments will allow us to extract far more information from exoplanet
spectra than what has been possible with current observations. In this paper,
we investigate whether current retrieval methods will still be valid in the era
of JWST, exploring common approximations used when retrieving transmission
spectra of hot Jupiters. To assess biases, we use 1D photochemical models to
simulate typical hot Jupiter cloud-free atmospheres and generate synthetic
observations for a range of carbon-to-oxygen ratios. Then, we retrieve these
spectra using TauREx, a Bayesian retrieval tool, using two methodologies: one
assuming an isothermal atmosphere, and one assuming a parametrized temperature
profile. Both methods assume constant-with-altitude abundances. We found that
the isothermal approximation biases the retrieved parameters considerably,
overestimating the abundances by about one order of magnitude. The retrieved
abundances using the parametrized profile are usually within one sigma of the
true state, and we found the retrieved uncertainties to be generally larger
compared to the isothermal approximation. Interestingly, we found that using
the parametrized temperature profile we could place tight constraints on the
temperature structure. This opens the possibility to characterize the
temperature profile of the terminator region of hot Jupiters. Lastly, we found
that assuming a constant-with-altitude mixing ratio profile is a good
approximation for most of the atmospheres under study.
