This study investigated the effects of palmitoylethanolamide (PEA) and ibuprofen (IBU) treatment on the dynamic regulation of the skeletal muscle proteome using a C2C12 myotube model. Differentiated myotubes were treated for 36 hours with vehicle control (VC), PEA (10 µM), or IBU (100 µM). Dynamic proteome profiling was performed using deuterium oxide (D₂O) metabolic labelling combined with high-resolution LC–MS/MS analysis on an Orbitrap Q-Exactive (QE) instrument. Samples were collected at 0 h, 12 h, 24 h, and 36 h, with n = 3 biological replicates per timepoint and condition. Protein-specific fractional synthesis rates (FSR) were derived from the 12–36 h labelling period, and relative protein abundance was quantified at 36 h.