All tissues contain an extracellular matrix (ECM) which is constantly and dynamically remodeled, either in physiological or pathological processes, such as fibrosis or cancer. One of the key contributors in the establishment of a fibrotic state is the abnormal deposition of extracellular matrix and cross-linked proteins, in particular collagen, leading to tissue stiffening and disruption of organ function. The precise and sensitive measurement of these cross-links by LC-MS/MS is a very powerful tool for providing a quantitative and qualitative analysis of fibrosis and is a key requirement in the study of this state, as well as in the development of drugs for this unmet clinical need.