A novel deep eutectic solvent-based protein extraction method for pottery residues and archaeological implications

Proteomic analysis of absorbed residues are increasingly used to identify the foodstuffs processed in ancient ceramic vessels, but detailed methodological investigations in this field remain rare. Here, we present three interlined methodological developments with important consequences in palaeoproteomics— the comparative absorption and identification of various food proteins, the application of a deep eutectic solvent (DES) for extracting ceramic bound
proteins, and the role of database choice in taxonomic identification. Our experiments with modern and ethnoarchaeological ceramics show that DES is generally more effective at extracting ceramic-bound proteins than GuHCl, and cereal proteins are absorbed and subsequently extracted and determined at least as readily as meat proteins. We also highlight some of the challenges in cross-species proteomics, whereby species that are less well-represented in databases can be attributed an incorrect species-level taxonomic assignment due to inter-species similarities in protein sequence. This is particularly problematic potentially mixed samples such as cooking generated organic residues deposited in pottery. Our work demonstrates possible proteomic separation of fishes and birds, the latter of which have so far eluded detection through lipodomic analyses of organic residues deposits pottery, which has important implications for tracking the exploitation of avain species in various ancient
communities around the globe.

KEYWORDS: Deep Eutectic Solvent (DES), Archaeological pottery, Residue analysis, Protein extraction, Cross-species proteomics