A proteomic procedure for analyzing mouse left ventricular collagen by mass spectrometry has been developed. Hearts were extracted from 4-week-old mice and the left ventricles were sectioned and collected. The procedure involves a purification step that removes non-collagenous cellular components from the collagen extracellular matrix, a step that solubilizes the collagen in aqueous solvents before it is proteolytically digested for analysis with ESI-LCMS/MS. Collagen from healthy and lathrytic mice has been positively identified by applying the SEQUEST database search algorithm to spectra from the collagen prepared using this procedure. Analysis shows that the relative percentage of collagen peptides detected in lathrytic tissue is significantly greater than that of the healthy tissue. These preliminary results suggest that the percentage of cross-linked collagen is lower in the lathrytic tissue as indicated by the greater protein sequence coverage obtained for this tissue. These findings were expected, because lathrytic tissues are known to contain fewer cross-links, due to a reduction in the cross-link dependent enzyme, lysyl oxidase. This procedure lays the ground work for future experimentation that has the ability to allow for the identification and quantification of cross-linked peptides, as well as the ability to conclusively identify the regions of cross-linking within the amino acid sequence of the protein.