The use of HRMS in metabolite identification studies provides valuable structural information for compound structural elucidation and identification. Advanced processing tools are required to facilitate the interpretation of this comprehensive data, such as UNIFI Scientific Information System (Waters) or Mass-MetaSite (MMS) and WebMetabase (WMB) from Molecular Discovery. Here, we have demonstrated the coupling of HRMS with an additional, ion mobility-based, gas-phase separation for the determination of metabolic profiles of tienilic acid (TA) and its 3-thiophene isomer. Determination of common and differential metabolites for both compounds in a single processing step was made possible through the coupling of the Vion IMS QTof UNIFI data with MMS and WMB. Additionally, the advantages of IMS were realized through the ability of MMS and WMB to show drift aligned spectra and CCS values when interpreting data. In the case of two glucuronide metabolites of TA, CCS provided an additional separation parameter for these closely eluting compounds.