The ligation of the analyte to the ligation probe makes the method specific for the 3'-end of the analyte, ligation by T4 DNA ligase being much less efficient over a bulge loop, which would happen for a 3' metabolite N-1 version of the analyte, for example.
One limitation of the method is that it requires a free 3'-end hydroxyl which may not be available when targeting moieties are attached to the 3'-end, for example.