The purpose of this study was to establish a collagen determination method based on an isotope-labeled collagen peptide as an internal reference via high-performance liquid chromatography–tandem mass spectrometry (HPLC–MS/MS), and using the established method to evaluate the degradation process of collagen-based implants in vivo. The specific peptide (GPAGPQGPR) of bovine type I collagen was identified with an Orbitrap mass spectrometer. Then, the quantification method based on the peptide detection with HPLC-MS/MS was established and validated, and then further used to analyze the degradation trend of the collagen sponge and acellular matrix (ACM) in vivo at 2, 4, 6, 8, 12, 16, and 18 weeks after implantation. The results indicate that the relative standard deviation (RSD) of the detection precision and repeatability of the peptide-based HPLC-MS/MS quantification method were 3.55% and 0.63%, respectively. The limitations of quantification and detection were 2.05 × 10−3 μg/mL and 1.12 × 10−3 μg/mL, respectively. The collagen sponge and ACM were completely degraded at 10 weeks and 18 weeks, respectively. Conclusion: A specific peptide (GPAGPQGPR) of bovine type I collagen was identified with an Orbitrap mass spectrometer, and a standardized HPLC-MS/MS-based internal reference method for the quantification of bovine type I collagen was established. The method can be used for the analysis of the degradation of collagen-based implants in vivo.
