Food and its associated material culture offer an important window into past social worlds, but difficulties in inferring vessel function from and the degradation of organic residues on pottery can hinder archaeological investigations of culinary practices. To overcome these limitations, we applied indirect ELISA assays using both polyclonal antibodies and synthetic aptamers to detect specific proteins and a cereal polysaccharide in ceramic sherds from two hilltop sites in north-eastern Slovenia: an early medieval settlement beneath Ptuj Castle (7th-9th centuries CE) and a Late Roman–early medieval fortified site at Ančnikovo Gradišče (4–5th, 7–10th centuries CE). Sherds bearing charred cooking residues were powder-extracted and assayed on MaxiSorp microtiter plates for six protein targets (ovalbumin, lysozyme, gluten, casein, collagen, and myosin) and for (1→3)-β-d-glucan target using matching primary antibodies and biotinylated DNA aptamers, with detection achieved by adding alkaline phosphatase–conjugated secondary antibodies to label primary antibody binding or alkaline phosphatase–conjugated streptavidin to label aptamer binding. At Ptuj, both formats identified egg proteins, bone collagen, myosin and gluten on individual sherds, with aptamers consistently yielding larger ΔOD margins than antibodies. At Ančnikovo Gradišče, meat residues dominated: myosin and collagen were detected on most Late Roman sherds, while sherd 402 (early medieval) uniquely registered cereal markers—gliadin and β-d-glucan—alongside meat and egg proteins. Casein appeared in only one Late Roman vessel. Co-occurrence of animal and plant residues implies composite dishes such as stews or porridges. Our findings demonstrate that aptamer‐based ELISAs offer enhanced sensitivity for archaeological proteins, and that protein and polysaccharide residue analysis can reconstruct nuanced dietary patterns. This approach holds promise for broad application in contexts lacking textual records. Caution should be taken when attempting to extrapolate broader patterns from this limited dataset.
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