Abstract. Thermal infrared (IR) radiances measured near 8 microns contain information about the vertical distribution of water vapor (H₂O), the water isotopologue HDO, and methane (CH₄), key gases in the water and carbon cycles. Previous versions (Version 4 or less) of the TES profile retrieval algorithm used a "spectral-window" approach to minimize uncertainty from interfering species at the expense of reduced vertical resolution and sensitivity. In this manuscript we document changes to the vertical resolution and uncertainties of the TES version 5 retrieval algorithm. In this version (Version 5), joint estimates of H₂O, HDO, CH₄ and nitrous oxide (N₂O) are made using radiances from almost the entire spectral region between 1100 cm⁻¹ and 1330 cm⁻¹. The TES retrieval constraints are also modified in order to better use this information. The new H₂O estimates show improved vertical resolution in the lower troposphere and boundary layer, while the new HDO/H₂O estimates can now profile the HDO/H₂O ratio between 925 hPa and 450 hPa in the tropics and during summertime at high latitudes. The new retrievals are now sensitive to methane in the free troposphere between 800 and 150 mb with peak sensitivity near 500 hPa; whereas in previous versions the sensitivity peaked at 200 hPa. However, the upper troposphere methane concentrations are biased high relative to the lower troposphere by approximately 4% on average. This bias is likely related to temperature, calibration, and/or methane spectroscopy errors. This bias can be mitigated by normalizing the CH₄ estimate by the ratio of the N₂O estimate relative to the N₂O prior, under the assumption that the same systematic error affects both the N₂O and CH₄ estimates. We demonstrate that applying this ratio theoretically reduces the CH₄ estimate for non-retrieved parameters that jointly affect both the N₂O and CH₄ estimates. The relative upper troposphere to lower troposphere bias is approximately 2.8% after this bias correction. Quality flags based upon the vertical variability of the methane and N₂O estimates can be used to reduce this bias further. While these new CH₄, HDO/H₂O, and H₂O estimates are consistent with previous TES retrievals in the altitude regions where the sensitivities overlap, future comparisons with independent profile measurement will be required to characterize the biases of these new retrievals and determine if the calculated uncertainties using the new constraints are consistent with actual uncertainties.