These cases were used to assess the influence of the CNL mass tolerance and score CN L threshold on the model performance, using the TP, false positive (FP ), and false discovery (FD) rates (Equation , 5, and 6, respectively). Both FP and FD rates were calculated, since they represent different information about the performance assessment and to be able to compare the results of the database fragment with the real data (i.e. measured matrix containing predominantly pesticide standards). The FP rate represents the percentage of TN fragment that are wrongly accepted as a true fragment and requires the number of TN fragments, which can be generated for the database spectra but are difficult to assess for the real data. Whereas the FD rate represents the probability of an accepted fragment actually being a false positive case, which is calculated without using the number of TNs. These rates were calculated for CNL mass tolerances of 0.001, 0.005, 0.010, 0.020, 0.050, 0.100, and 0.200 Da and score CN L thresholds ranging from -1 to 1 with steps of 0.01. Here, the TP and false negative (FN) cases correspond to TP CNLs that had a score CN L above and below the score CN L threshold, respectively. On the other hand, the FP and TN cases correspond to the TN CNLs that have a score CN L above and below the score CN L threshold, respectively.