Matt is adding a new Peptide Settings section and will change what is currently "Document Settings" to "Transition Settings" to better align with the UI.
We should also:
1) Change the order of the transition settings to align with the tab order in the Transition Settings UI (Prediction, Filter, Library, Instrument, Full-Scan, Ion Mobility) - It is currently (Filter, Prediction, Library, Full-Scan, Ion Mobility, Instrument)
2) Deprecate the "Create an ion mobility library" section and its arguments (i.e. undocumented but still working), and move that functionality to the following arguments to cover the Transition Settings - Ion Mobility tab in the UI:
--ims-library-name=<name>
--ims-library-file=<path/to/file.imsdb>
--ims-library-create
To make them fit more seamlessly with the way our other arguments work and the existing:
--ims-library-res=<resolving power>
When --ims-library-create is not present, then --ims-library-name and --ims-library-file would simply add an existing IMDB library to the document and use it.
CONSIDER: Should we make it possible to add to an existing IMSDB file or only create a new one?