Novel Deep Eutectic Solvent-Based Protein Extraction Method for Pottery Residues and Archeological Implications

Proteomic analysis of absorbed residues is increasingly
used to
identify the foodstuffs processed in ancient ceramic vessels, but
detailed methodological investigations in this field remain rare.
Here, we present three interlinked methodological developments with
important consequences in paleoproteomics: 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 ethnoarcheological ceramics show that DES is generally
more effective at extracting ceramic-bound proteins than guanidine
hydrochloride (GuHCl), and cereal proteins are absorbed and subsequently
extracted and identifiedat 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 interspecies
similarities in protein sequence. This is particularly problematic
in 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 lipidomic analyses of organic residue deposits in pottery,
which has important implications for tracking the exploitation of
avian species in various ancient communities around the globe.