Atmospheric pressure ionisation quadrupole/ time-of-flight mass spectrometry was used to perform accurate mass measurements on the product ion fragments of moclobemide and remikiren. The low energy collision induced dissociation fragmentation pathways of the two compounds could be established using accurate mass, MSn data and MS interpretation software (Mass Frontier). An atypical fragmentation corresponding to the loss of neutral dimethylvinyl could be clearly identified. The knowledge gained from these experiments was used to demonstrate the application of data dependent experiments on a triple quadrupole instrument for the screening of metabolites. Data dependent experiments were performed using either Q3 single scan or precursor ion scan mode as the survey scan, and product ion scan as the dependent scan.