For the performance assessment of the CNL model and the conventional methods, TP and FD rates were calculated (Equations 4 and 6, respectively). Each of the three methods has a different threshold requirement for accepting or rejecting an m/z value as a fragment ion of the precursor ion. For the CNL model, the score CN L needs to be above the score CN L threshold, the correlation need to be above a correlation threshold, and the peak apex time difference needs to be below a maximum t r difference. To calculate the detection rates (Equation 4 and 6), the TP and FN cases are the true fragments (i.e., found in the suspect screening list) that were accepted and rejected by a fragment deconvolution method, respectively. As for FP cases, these were fragments that were not present in the suspect screening list and were accepted as fragments. Finally, the MS1 feature lists, the extracted MS2 signals for the reference compounds, the suspect screening results and the suspect list can be found on Figshare.