Advances in ancient DNA and palaeoproteomics research have transformed our capacity to reconstruct the human past. It is now increasingly common to extract biomolecular information from archaeological bones to investigate ancient diet, population turnover, and evolutionary processes at unprecedented detail. Yet, it remains unclear why biomolecules are preserved in some contexts and not others, even under seemingly similar conditions. To fill crucial knowledge gaps in our evolutionary history, we need a better understanding of the depositional and taphonomic processes governing biomolecular preservation. This project, therefore, has two related objectives: first, to investigate the differential preservation of proteins at Quinçay Cave (France), a Late Pleistocene site with a Middle to Upper Palaeolithic sequence. Second, to obtain microstratigraphic-scale taxonomic identifications, particularly for the archaeological bones in the Châtelperronian deposits at Quinçay – a key period related to the replacement of Neanderthals by early anatomically modern humans in Europe.