Here are some ideas though…

In LC-MS/MS you have to balance both sensitivity (which is often where sodiated precursor ions are used, for isoprostanes for instance) against selectivity.

If you perform MS/MS (product ion scans) do you get the same spectral information (i.e. high energy product ions to use as selective transitions?) If so, the next step would be to test the sensitivity of each transition (protonated vs sodiated) in real samples, often in sodium adduct work, you will need to add sodium acetate into the mobile phase for reproducibility if sodiation within the source. If you wish to add more details I can definately help you resolve these questions.

regards
russ