Right off the bat, you can run a test with deuterated amino acid, for example an amino acid that has been equilibrated with DCl in D2O, and then lyophilized (freeze-dried). The exchangeable protons with be replaced with deuterium, so when you use it to make the ionic liquid, you should see changes by NMR and IR in the ionic liquid, providing information about where the deuterium went and where the ionizable sites in the ionic liquid are. The exact experimental design depends on the ionic liquid structure and the goals of the project.

Thankyou for the detailed response. I have tried reacting amino acid with pyrazole based cation and i am not sure about the proton transfer has taken place or not given the fact that amino acids exists in zwitter ionic form