In practice, compound identification often relies on a specific threshold for similarity scores. A similarity score equal to or higher than this threshold indicates a correct identification; otherwise, it is deemed incorrect. To reflect this practice, we also evaluated the similarity measures using receiver operating characteristic (ROC) curves based on the thresholds of similarity scores. Suppose there are m query mass spectra (I 1 , I 2 , . . . , I m ) and n reference mass spectra (J 1 , J 2 , . . . , J n ). Each query mass spectrum is matched against the reference spectra, producing the highest similarity scores, s i (for i = 1 to m), with s i being the highest score for the ith query spectrum I i . Assuming t query spectra match correctly to the reference spectra and the remaining query spectra are mismatches, we identify R query spectra as discoveries based on the similarity score threshold, among which V are incorrect and S are correct identifications, with R = V + S. We then define the True Positive Rate (T P R; also known as (aka) sensitivity), as follows: