Dynamic proteomic analysis of extracellular matrix in the bleomycin‐induced fibrotic lung

Idiopathic pulmonary fibrosis (IPF) is characterized by excess deposition of extracellular matrix (ECM), and ultimately organ failure. We have developed a “dynamic proteomics” platform which quantifies the synthesis rates of hundreds of proteins via stable isotope labeling and LC/MS. Here we present the first quantitative analysis of lung ECM protein synthesis in a mouse model of IPF. Mice were dosed with bleomycin and labeled with heavy water. Lung tissue was subjected to sequential protein extraction to enrich for ECM. We identified two kinetically distinct pools of ECM proteins in the lung based on guanidine solubility. Fibrillar collagens, basement membrane proteoglycans and microfibrillar proteins were observed in both pools. The turnover rate of ECM proteins in control lungs was generally higher in the guanidine soluble pool suggesting that the insoluble pool reflects older, more cross‐linked matrix components. In bleomycin treated lungs there was a significant increase in the synthesis of soluble and insoluble ECM proteins. These data show the utility of dynamic proteomics in identifying metabolically distinct protein pools and detecting modulations in protein synthesis associated with disease.