The traditional method for performing metabolite identification and structural elucidation through LC-MS is through time-consuming manual interpretation of mass spectral data. Mass shifts of signature fragment ions can be diagnostic of structural soft spots. However, when a complex or unusual biotransformation occurs, the assignment of the fragment ion structures can be challenging. Additional fragmentation of the mass-shifted fragments may be necessary to elucidate and confirm the putativestructural assignments. The metabolite identification and structural elucidation workflow often requires a strong background in gas-phase fragmentation mechanisms. Furthermore, literature searching may be required toconfirm the proposed fragmentation pathways. Discussed is an experiment where multi-stage fragmentation information from an LC-MSn raw data file is interpreted by chemically intelligent structural elucidation software. The program utilizes the fragment ions generated from the parent structure to identify metabolites and localize the site of biotransformation, thus facilitating the process of structural elucidation.