Peptides play an indispensable role in various biological functions and show therapeutic potential. The forest musk deer, an important source of musk, is a focal species in traditional medicine. While cell culture techniques offer a sustainable alternative for musk production, the complexity of peptide components produced by these methods remains poorly understood. To bridge this knowledge gap, we compared the peptidomic profiles of secretions from cultured musk gland cells with those of natural musk cells using the EASY-nLC 1000 UHPLC (Ultra-High Performance Liquid Chromatography) system. Our analysis revealed similarities and notable differences between the peptide profiles of cultured cell secretions and those of natural musk, with significant implications for the biosynthesis and chemical composition of musk. This study provides critical insights into the peptidomic differences between cultured cell secretions and natural musk, highlighting the challenges and potential of using cell culture techniques for the sustainable production of musk components. Future research should focus on refining conditions to more closely emulate the natural biosynthetic pathways of musk peptides.