Shotgun proteomics for archaeological bone material - in solution protocol for bone samples from tropical sites

The analysis of bone ancient proteins (palaeoproteomics) is revolutionising the design of research strategies for zooarchaeological assemblages worldwide. By providing means to identify species presence in sites from samples that are not identifiable macroscopically through traditional methods, palaeoproteomics is offering a new exciting approach to understand people’s past interactions with their environments.
Nevertheless, this technique is not depleted of challenges.  Proteins preserved in ancient bones have undergone several modifications, most of which we do not know yet how they change the organic bone component. As a relatively new technique, much progress is needed in the optimization and development of
laboratory protocols tailored to different taphonomic histories.
With a focus in European context, they are currently just few examples of the application of this technique in non-temperate contexts.
This protocol presents a modified version of a common pipeline to prepare bone samples documented in tropical archaeological or palaeontological sites for LC MS/MS analysis. The main differences with other laboratory protocols consist of reducing washings steps, avoiding reduction/alkylation processes, optimizing protein digestion and concentrating eluted samples.
This protocol has been successfully tested at the Australian National University, obtaining positive results for archaeological bone samples from Northwest Australia, Timor-Leste, PNG and Indonesia.