First, all the signals in the comparison zone are normalized to 1. Of course, this step is extremely sensitive to noise or other contaminants so we have different options for the comparison method:
Theoretical method: within the comparison zone we start with the theoretical signals. we check if they are present in the experimental spectra if yes the signal in normalized and takes into account for the similarity calculation.
Experimental method: within the comparison zone we start with the experimental signals. We check if the signals are also present in the theoretical spectra, if they are we take into account for the similarity calculation.