During early drug discovery, the study of metabolism plays an essential role in determining which drug candidates move forward into development and later stages. Current methods for analysis to identify metabolic soft spots are through LC/MSn interpretation. The main challenge in this work has always been the structure elucidation of metabolites, and there have been a number of strategies developed to address these difficulties. Typically, the use of data dependent scanning has been the primary mode of data acquisition for structure elucidation, but in the past several years the use of MSe or All Ions Fragment (AIF) acquisition has become more prominent. Here we present a computational routine that automatically analyzes MSe/AIF data for LC/MSn based drug metabolism studies.