MS/MS-based bone CHIP species identification

The research presented in this thesis has demonstrated the successful integration of proteomic taxonomic assignments from morphologically unidentifiable skeletal remains through high-throughput proteomic screening. Computational proteomic analysis enhances and speeds up taxonomic identification of unidentified Pleistocene bone assemblages, highlighting the need to tailor proteomic extraction to the preservation state of the bone proteomes. We confirmed that the recent development in computational LC-MS/MS analysis combined with site-specific extraction protocols, enable taxonomic identification of highly degraded bone remains. Furthermore, the proteomic analysis of the bone assemblages provides critical insights into faunal composition and heterogeneity in bone protein preservation and facilitates a direct identification of hominin bones. This identification allows us to perform multidisciplinary analysis in selected specimens of interest, limiting the cost. We identify, through palaeoproteomics, the first hominins related to the Lincombian-Ranisian-Jerzmanowician technocomplex. Further analysis assigns the human bone specimens to Homo sapiens, which makes them the earliest in northwestern Europe dated before 45,000 cal BP. In conclusion, this work demonstrates that palaeoproteomics is an effective tool when exploring human evolution and ancient hominin phylogeny. However, analytical tools, such as computational pipelines, open-source analytical software and updated reference databases need to be advanced for the complete analysis of archaeological skeletal proteomes.