I think this would be a good place to employ Tobi when he first starts on the project. Get him to work on expanding the options for ion annotation in the Library Match view, first to include reporter ions and then all small molecule transitions in the document, and finally small molecule annotations in .blib files, assuming you can get that done in time.
But start him with just the "Special Ions" that can be added in the Transition Settings - Filter tab.
There is another related issue (34) from a very long time ago requesting that we show immonium ions. So, I expect this could be an are of focus for Tobi for a few weeks at least.