Thermal proteome profiling (TPP) has been widely applied in the identification of drug targets for several years, and TMTpro-16plex has recently been evaluated for TPP of vehicle and drug treated samples in a single labeling process to reduce missing values and save instrument time. A novel isobaric labeling reagent, IBT-16plex, was just developed with slightly better performance in protein identification and quantification than the commercially available TMTpro-16plex. In this study, we applied the newly developed IBT-16plex into the target identification of methotrexate and panobinostat using TPP. The known targets of these two drugs were successfully identified with elevated melting temperatures, and some known off-targets and potential new off-targets were also identified. It indicates that IBT-16plex can be a cost-effective replacement of TMTpro-16plex for TPP applications.