The MS/MS predictions for DrugBank 6.0 were performed by the latest version of the competitive fragment modeling tool called CFM-ID version 4.0 (10). The performance of CFM-ID 4.0 is approximately 30% better than previous versions of CFM-ID. CFM-ID 4.0 was used to predict both the positive ion and negative ion mode MS/MS spectra (at collision energies 10, 20 and 40 eV) for ∼10 000 small molecule drug compounds in DrugBank 6.0. This led to the generation of 59 721 MS/MS predicted spectra for drug compounds and 15 144 predicted MS/MS spectra for 3132 drug metabolites. These MS/MS data have also been incorporated into DrugBank's new MS/MS search functions.
