Shell palaeoproteomics: First application of peptide mass fingerprinting for the rapid identification of mollusc shells in archaeology

Abstract Molluscs were one of the most widely-used natural resources in the past, and their shells are abundant among archaeological findings. However, our knowledge of the variety of shells that were circulating in prehistoric times (and thus their socio-economic and cultural value) is scarce due to the difficulty of achieving taxonomic determination of fragmented and/or worked remains. This study aims to obtain molecular barcodes based on peptide mass fingerprints, (PMFs) of intracrystalline proteins, in order to obtain shell identification. Palaeoproteomic applications on shells are challenging, due to low concentration of molluscan proteins and an incomplete understanding of their sequences. We explore different approaches for protein extraction from small-size samples ( Significance We characterise for the first time peptide mass fingerprints (PMFs, by MALDI-TOF mass spectrometry) obtained on the intracrystalline shell protein fraction isolated from different molluscan taxa. We demonstrate that intracrystalline shell proteins yield distinctive PMFs, despite similar shell microstructures or phylogenetic relatedness. Furthermore, we extend the range of sample preparation approaches for “shellomics” by testing the single-pot, solid-phase extraction (SP3), which proved to be well-suited to shell protein extraction from small-size and protein-poor samples. This work thus lays the foundations for future large-scale applications for the identification of mollusc shells and other invertebrate remains from the archaeological and palaeontological records.