Palmer et al: Dental Method Comparison

The dental calculus proteome from human remains is a considered a valuable archaeological resource for studying the diet, oral microbiome, health/disease of individuals and occupation activities individuals within past societies/civilisations. The combination of advancements in LC/MS instrument sensitivity and sample prepartion methods enables the analysis of these well preserved proteomes otherwise invisible to other biomolecular approaches. Maximizing proteome recovery from this minute and finite resource is paramount to our understanding of these past societies and civilisations in terms of diet and disease. Here we compare the more traditional ultrafiltration-based and acetone precipitation approaches with the newer paramagnetic bead approach (SP3) in a step towards achieving this aim. We specifically evaluate different acids (EDTA and HCl) and proteome extraction methodologies (Ultrafiltration, Acetone Precipitation and SP3)to test the influence of demineralization acid and method of extraction on the recovered proteome complexity (including numbers of peptides recovered) and sequence coverageand observed for these ancient dental calculus specimens.