When a reference compound monoisotopic parent mass was present, all features within a time range of ± 0.1 minutes were extracted. If a feature's mass was higher than the monoisotopic mass and lower than the monoisotopic mass plus 1.0033 × 6 (i.e., isotopologue mass depth of six), it was evaluated as a potential isotopologue with both the classification model and the mass difference method. When a model correctly identifies an isotopologue according to the reference parent isotopologue distribution, it is considered a TP case. Whereas the FP cases are incorrectly identified isotopoloues and the FN cases are the TP cases that were not detected by a model. With these cases, the TP r and FD r were calculated for the classification model and mass difference method (Equation 8 and 10, respectively), which were used to compare the two isotopologue identification methods.