Just as a quick note on "modifications":
In Ursgal 1, we had kept "Modifications" and "Assigned Modifications" (translated as "Mass Difference Annotations" in Ursgal 1) separate, for two reasons:
They are conceptually different. The former refers to modifications that were included in the search, while the latter comes from mass differences mapped to modifications after the search.
The mapped modifications are not necessarily unimod names, i.e. the names can be different from what is stored in the unimod.xml and/or userdefined_unimod.xml.
I'd of course be open to dealing with this in a different way in Ursgal 2, but just wanted to give a heads up on potential issues for the unify/pyprotista/pyiohat step.
Just as a quick note on "modifications": In Ursgal 1, we had kept "Modifications" and "Assigned Modifications" (translated as "Mass Difference Annotations" in Ursgal 1) separate, for two reasons:
I'd of course be open to dealing with this in a different way in Ursgal 2, but just wanted to give a heads up on potential issues for the unify/pyprotista/pyiohat step.