We represent each MS/MS spectrum as a vector in which each bit corresponds to a specific mass-over-charge (m/z) value, representing the m/z value of the recorded fragments, while the value of each bit corresponds to the intensity, or otherwise frequency, of the fragments that have been recorded with that specific mass-over-charge value. For that representation, we need to specify the resolution of the mass as well as the minimum and maximum allowed mass values. More specifically, the minimum mass is set to 50 Da while the maximum mass is set to 500 Da. The resolution for the mass values is 0.01 Da. Given that our dataset is of higher resolution, that is more than 4 decimal points are available, the intensity of each bit corresponds to an aggregation of all fragments that have been recorded and have the same mass when considering two decimal points. Finally, the intensity values are normalized by dividing with the maximum intensity over all the vector bits of a given spectrum. The minimum and maximum allowed mass values were selected based on the statistics of the dataset. More specifically, the minimum allowed mass corresponds to the minimum fragment mass that has been recorded over all data. Regarding the maximum allowed mass, although there are molecules in the dataset with larger recorded fragments, the percentage of molecules with fragments larger than 500 Da is very small. In general, a smaller maximum allowed mass, as well as a lower resolution, will result in a more compact and less sparse vector representation which is essential for preventing over-fitting when training the DL model.