The Spectral Setup page contains fields to specify spectral windows, each of which samples a sources's spectrum over a particular range of frequencies. These are defined either manually or with the spectral line selection tool (Section 7.3). All setups should be inspected using the Visual Spectral Editor (Chapter 9).
As mentioned in Section 5.3.2.1, the OT will convert all rest frequencies to their observed equivalent, most obviously using the source velocity. However, if the entered velocity is in the 'lsrk' frame, the entered frequencies are additionally transformed to barycentric. Ideally, the OT would peform a full conversion to topocentric (reference frame of the antenna) but this is not possible as the OT does not know when the observations will take place. The telescope control software then makes the final 'bary' to 'topo' conversion. Single continuum and spectral scan setups are explicitly in topocentric, regardless of the frame specified in the Field Source definition.