Therapeutic protein discovery study highlights the need for the development of quantitative bioanalytical methods for determining the levels of both the therapeutic protein and the target protein, as well. For the quantitation of BMS-986089, both accuracy (99–103%) and precision (2.4–12%) were obtained for the analysis of the surrogate peptide (ITYGGNSPVQEFTVPGR), in addition to the accuracy (100–108%) and precision (0.7–18%) that were obtained for the analysis of the surrogate peptide (VVSVLTVLHQDWLNGK). For Myostatin, accuracy (94–103%) and precision (2.4–14.9%) were obtained for the analysis of the surrogate peptide (IPAMVVDR). The developed method was applied to the analysis of samples following dosing of BMS-986089 to mice. This method highlights the potential of LC–MS/MS-based methods to eventually assess in vivo drug–target engagement.