To evaluate the performance of the classification model with that of the existing mass difference method, the performance for the in-house mass difference method was evaluated for a mass tolerance of 0.0001 Da. The mass tolerance was selected based on the assumption that there is no error present in the theoretical mono-iso pairs and the full receiver operator curve can be found in sectionS4. For a mass tolerance of 0.0001 Da, a TP r and FP r of 16.2 and 0.02% was found, respectively. Compared to the results of the classification model (i.e., TP r of 99.0% and FP r of 1.8%), both methods performed well with regard to the FP r (i.e., ≤ 5%). However, the classification model outperformed the mass difference method for the TP r .