Thanks for your response.
Actually, I have just worked it out - I think - however, I am not sure it is the right way to do it.
To insert the oxonium ions for HexNac (204, 138, 168, 186) Neu5ac(274, 292) and HexHexNac (366) I did the following:
Go to settings>transition settings> Special ions/Edit list>Add: here insert name of modification, select custom product ion and insert the molecular formula (e.g. HexNac = C8H13N1O5+1H) then insert charge = 1.
The ions are found in pick-children of the precusor ions.
This paper helped too https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5116676/
Please, let me know if this sounds reasonable.