Comparing the Use of Magnetic Beads with Ultrafiltration for Ancient Dental Calculus Proteomics

Over the past two decades, proteomic analysis has greatly developed in application to field of biomolecular archaeology, coinciding with advancements LC–MS/MS instrumentation sensitivity and improvements sample preparation methods. Recently, human dental calculus received much attention for its well-preserved proteomes locked mineralized plaque which stores information on diets oral microbiome otherwise invisible other approaches. Maximizing proteome recovery ancient calculus, available only minute quantities irreplaceable after destructive analysis, is paramount importance. Here, we compare more traditional ultrafiltration-based acetone precipitation approaches newer paramagnetic bead approach order test influence demineralization acid recovered complexity obtained from specimens as well sequence coverages matched significant proteins. We found that a protocol utilizing EDTA combined beads increased complexity, some cases doubling number unique peptides proteins matched, compared protocols involving use HCl either or ultrafiltration. Although increase was almost exclusively bacterial origin, development implications study diseases within these populations, an peptide dairy ?-lactoglobulin casein also observed reflecting coverage dietary interest. consider structural explanations discrepancies between key preserved archaeological calculus.