The rate of deamidation of asparagine and glutamine observed in a protein sample can be used as an index of degradation, and is often considered a ‘molecular clock’ for protein analysis [1]. This analysis method is often applied to the relative dating of archaeologically relevant proteinaceous material (such as bone and other ancient biological remains), particularly in Zooarchaeology by Mass Spectrometry (ZooMS) studies. However, the overall reliability of the correlation between observed deamidation and the age of the materials is yet to be fully understood.
We analysed modern bone reference samples (<50 years old) of seven common animal species, prepared with three established collagen extraction approaches - ammonium bicarbonate gelatinisation, and acid demineralisation in 0.6M HCl followed by separation into acid soluble and acid insoluble fractions using 30kDa ultra centrifuge spin filters [2]. The aim was to assess whether these methods result in variations in deamidation ratios within individual samples. Small amounts of bone powder (~10mg) from each species were prepared using the above-mentioned protocols, trypsin digested, and then analysed on a Thermo Q-Exactive Mass Spectrometer coupled with a Thermo Easy-nLC1000 HPLC system. Peptide to spectrum matching was conducted using the X!Tandem algorithm in GPM against the curated SwissProt database supplement with additional collagen sequences for species of interest. Deamidation ratios for asparagine and glutamine residues identified were assessed using an in-house script written in RStudio. This approach will subsequently be applied to the analysis of a set of early Colonial Australian (c. 1830) bone knife handles, for comparison against the deamidation ratios of the more modern samples. Data will be presented on the utility of deamidation ratios as an index for age and degradation of modern and ancient bone samples.