I think you probably want to use the adduct description "[M+H2O+H]".

What have you tried so far? I'm guessing you were trying "[M+H3O]", which Skyline doesn't currently recognize (yours is the first request for oxonium that I'm aware of). If this is the case I should add it to Skyline's list of predefined adduct descriptions for the convenience of others.

Thanks for using the Skyline support board,

Brian Pratt

Hi Brian,

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.
Thanks,
Giulia

I was thinking in terms of small molecules but of course you're dealing with peptides, so yes, Special Ions is the right approach. If they're showing up in the Targets tree with the proper m/z values then it sounds like you've cracked it, well done!

Best,

Brian