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Title: Benchmarking palaeoproteomics strategies in ceramics

Abstract: Studying the protein contents of archaeological ceramics can give us highly valuable insights into the past, like the transport of goods, diet or cooking practices. However, protein decay and diagenesis and contamination remain a challenge. Moreover, there is not much knowledge on how the proteins and the different mineral ceramic substrates interact that can be used to overcome some of these challenges. On the data analysis front, typically only ~10% of the queried spectra is identified above a given significance level. Nonetheless, practitioners are constantly developing novel protocols and strategies or adapting existing ones from the broader proteomics field. We also require stringent rules on the identification of peptides and proteins and accurate estimation of false discovery rates. But so far there have been limited attempts to justify these standardised approaches in the analyses and interpretation of complex, degraded protein mixtures from different substrates and materials, and in different contexts. I will present the results from systematic analyses of experimental samples and the performance of different software, approaches and strategies. One set of samples comes from artificial degradation experiments on beta-lactoglobulin, one of the most robust and ubiquitous proteins in the archaeological record. The other are cooking experiments on ceramic briquettes made with different clays and tempers.