Photoageing in skin is commonly recognised by architectural remodelling of dermal extracellular matrix components. Mass spectrometry was previously used to identify tissue-specific patterns of fibrillin-1 and collagen VI peptide spectrum matches (PXD008450). This study aimed to determine if the same mass spectrometry-based approach could detect peptide spectrum match patterns and significantly differences in relative abundance of peptide sequences characteristic of damage following exposure to UVR of co-purified suspensions of fibrillin and collagen VI microfibrils. Human dermal fibroblast-derived suspensions of microfibrils were irradiated with either broadband UVB or solar simulated radiation (SSR). UVR-induced molecular damage was characterised by proteolytic peptide generation with elastase followed by liquid chromatography tandem mass spectrometry (LC-MS/MS). This allowed the molecular scale identification of UV-induced structural changes within two skin matrix assemblies. The proteomic approaches used have the potential to facilitate the rapid, protein-specific identification of differential molecular fingerprints of damage in key extracellular matrix proteins.