Ian Engels, Tristan Dedrie, Synnøve K Mo, Simon Van de Vyver, Thijs R A Vandenbroucke, Kévin Di Modíca, Jan Decher, Alice Toso, Dieter Deforce, Simon Daled, Alexandra Burnett, Grégory Abrams, Maarten Dhaenens
Species identification in palaeoproteomics relies on genome-derived protein sequences which are often poor-quality, and lacks tools to cope with multi-species samples. Here, we address both challenges through the analysis of "physical and genetic mixtures". Species that are absent from our database are considered a "genetic mixture", i.e. a patchwork of peptides from closely related species. Inversely, various overlapping peptide stretches allow us to resolve complex "physical mixtures". This is benchmarked by analysing physical mixtures of modern bone fragments, including genetic mixtures. We illustrate the impact of our approach via a rapid and high-throughput analysis of >2500 bone fragments, revealing the Eemian-era faunal environment around Scladina Cave, including the first Palaeoloxodon antiquus identified at this site.