With an aging population, there has been significant progress in the discovery and measurement of bone turnover biomarkers since the 2000s, especially for monitoring skeletal diseases like osteoporosis. Multiple markers derived from type I collagen, such as CTX, NTX, PINP, and ICTP, have been developed. Extensive efforts have been devoted to characterizing these molecules; however, their complex crosslinked structures have posed significant analytical challenges, and to date, these biomarkers remain poorly characterized. Previous attempts at characterization involved gel-based separation methods and MALDI-TOF analysis on collagen peptides directly extracted from bone. However, using bone powder, while rich in collagen, does not represent the true structure of the peptides in the biofluids. In this study, our goal was to characterize plasma and serum CTX for subsequent LC-MS/MS method development. We extracted and characterized type I collagen peptides directly from human plasma and serum using a proteomics workflow that integrates preparative liquid chromatography, affinity chromatography, and high-resolution mass spectrometry. Subsequently, we successfully identified numerous CTX species, providing valuable insights into the characterization of these crucial biomarkers.