In order to minimize variations in the spectra data, due to differences in the experimental conditions, we chose to keep certain variables in the dataset fixed. In particular, we used only the high resolution MS/MS spectra and more specifically we used the spectra that are obtained through higher-energy collision dissociation (HCD) which was the most common fragmentation method in the NIST dataset and additionally it is known to have high sensitivity and produce more fragments . We did not use MS3 and MS4 spectra as these were provided only for a small percentage of the data. Regarding the precursor ions, we retained only the most common ones, that is [M+H]+ and [M-H]-. For each precursor ion, we used two spectra, one obtained using low collision energy and one with high collision energy. The level for characterizing low collision energy was set to 35% NCE (Normalized Collision Energy) and for high energy it was set to 130% NCE. These values were selected because they were the most common energy levels in the NIST dataset for characterizing low and high energy, respectively. In the cases where a spectrum with energy 35% or 130% NCE was not available, we selected the spectrum that was obtained using collision energy that was closest to that level. Therefore, each instance in the dataset we constructed is characterized by four MS/MS spectra derived from two different precursor ions and two energy levels. It should be highlighted though, that not all molecules in the NIST dataset have experimental data for the specific precursors and energy levels. However, we have allowed cases with missing data in the dataset and the missing spectra are represented as empty spectra, that is spectra with no peaks, in an attempt to develop a model that is robust to missing data. Therefore, the model is being trained and evaluated on cases that may not have available all four spectra.