Rationale Thermal proteome profiling (TPP) has been widely used for 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 developed with slightly better performance in protein identification and quantification than the commercially available TMTpro‐16plex. Methods In this study, we applied the newly developed IBT‐16plex for target identification of methotrexate and panobinostat using TPP. Results 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. Conclusions IBT‐16plex can be a cost‐effective replacement for TMTpro‐16plex for TPP applications.