Palaeoproteomic deconvolution of physical and genetic collagen mixtures

Engels, I.; Dedrie, T.; Saugen, S. M.; Van de Vyver, S.; Vandenbroucke, T.; Di Modica, K.; Decher, J.; Toso, A.; Deforce, D.; Daled, S.; Burnett, A.; Abrams, G.; Dhaenens, M.

doi:10.64898/2026.06.17.732552

bioRxiv · 10.64898/2026.06.17.732552

Palaeoproteomic deconvolution of physical and genetic collagen mixtures

Engels, I.·Dedrie, T.·Saugen, S. M.·Van de Vyver, S.·Vandenbroucke, T.·Di Modica, K.·Decher, J.·Toso, A.·Deforce, D.·Daled, S.·Burnett, A.·Abrams, G.·Dhaenens, M.

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Abstract

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. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=182 SRC="FIGDIR/small/732552v1_ufig1.gif" ALT="Figure 1"> View larger version (67K): org.highwire.dtl.DTLVardef@a33296org.highwire.dtl.DTLVardef@4e4b85org.highwire.dtl.DTLVardef@402290org.highwire.dtl.DTLVardef@9d35b6_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Engels, I., Dedrie, T., Saugen, S. M., Van de Vyver, S., Vandenbroucke, T., Di Modica, K., Decher, J., Toso, A., Deforce, D., Daled, S., Burnett, A., Abrams, G., Dhaenens, M.. 2026-06-18. Palaeoproteomic deconvolution of physical and genetic collagen mixtures. https://doi.org/10.64898/2026.06.17.732552

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