Exploring patterns of diagenesis in ancient proteins

Palaeoproteomics is a rapidly growing field of research that involves applying mass spectrometry to objects of archaeological and palaeontological interest in order to gain insight into the past. However, due to a lack of clear authentication criteria and understanding of the biomolecular characteristics of ancient proteins, there are suspicions about many remarkable results. This is of particular importance, as many samples are derived from museum collections, which may have been exposed to contamination, or had contaminants added as part of past conservation treatments. This thesis aims to (a) investigate the diagenetic forces acting on ancient proteins by quantifying the patterns of degradation in truly ancient proteins, and (b) use this knowledge in order to develop tools to authenticate results. This thesis develops a novel tool, deamiDATE 1.0, for the authentication of ancient proteins using site-specific deamidation. This is relatively effective in broadly differentiating between modern and ancient proteins (with a focus on structural (collagen) and dietary (milk) proteins). Analysis of site-specific deamidation in ancient milk proteins reveals that although there is a modest trend of increasing deamidation over time, the deamidation of milk proteomes in the archaeological record is hugely variable. Therefore, other lines of evidence are recommended in order to assess the authenticity of low abundance proteins. Lastly, the patterns of collagen degradation in parchment are elucidated, showing that there is a region of the collagen structure that is a hotspot for hydrolysis. Taken together, the results of this thesis represent a novel contribution to the understanding of the diagenetic forces that act on proteins through time, and how to reliably authenticate proteomics data.