Proteomics

Proteins are the building blocks of life that contain all information about the phenotype of a living organism. Proteomics can thus enrich the information provided by ancient DNA sequencing, isotope analysis, and anthropology, revealing otherwise opaque details about health, sexes, age, and lifeways.

Methodological Developments

As most proteomic processes for sample preparation and data analysis are geared towards modern samples, we will optimise existing protocols and develop new methods to maximise information gain from ancient organic materials.

With thoroughly validated protocols in place, the impact of sampling strategies will be tested. Protein content may differ between individuals, and in accordance with where on the bone or tooth the sample is taken. By mapping these differences, we aim to create a data archive for more comprehensive understanding of biological and taphonomic variability in ancient organic proteomes, and to use this understanding towards improved data outcomes.
Equally important is the association of certain peptide biomarkers with visual evidence of disease; or animal and plant matter on bones, teeth and tools. For example, a bone may display signs of disease and is subsequently analysed for the presence of peptides to identify both the pathogen as well as the inflammatory response of the individual. Ancient DNA sequences of the pathogen can also be used to match the peptide sequences, either as a confirmatory measure or to generate peptide databases for improved analysis.

Applications

We aim to study protein targets related to diet, health, and sex from human and animal bones, and teeth; and associated stone tools.

Teeth

Proteins in human enamel are used by archaeologists to determine the biological sex of ancient individuals [1]. This is possible because one of the enamel proteins, amelogenin, can be transcribed from both the X and the Y chromosome. As there are some differences between amelogenin-X and amelogenin-Y, and only males have a Y chromosome, males can be identified using this method. We apply this technique as well as carrying out more widespread investigations into protein variability in enamel, including looking at differences between different teeth and at different biological ages.

Bone

Human bone is a rich store of structural, immunological, and 'housekeeping' proteins, even after hundreds or thousands of years. While numerous targeted palaeopathological studies have previously been undertaken, for example into bone cancer [2] and tuberculosis [3], we aim to examine the range of variability in healthy ancient individuals. This will enable more reliable interpretation of potential disease markers, and holds potential for enabling proteomic age and sex estimations based on bone protein.

We are also expanding our capabilities in determining the unknown species of bone fragments, using tailored softwares to expand the conventional suite of collagen targets for shotgun analysis of single-species and metaproteomic samples. This is hoped to contribute to understanding of Mesolithic subsistence patterns and diets.

Lithic-bound residues

It has previously proven to be very challenging to retrieve genuine protein information from stone tools, especially through immunological approaches [4]. It is our hope that with new and highly sensitive instruments and purpose-built analytical tools, LC-MS/MS can be used to concretely identify animal species and/or tissues from visible residues on ancient tools. This work on modern experimental tools is carried out in close association with Dr. Éva Halbrucker, drawing on her observations based on established practices. Eventually, we aim to bring these innovations back to Mesolithic tools.

You can check out our related papers, chapters, lectures, and public outreach in the Publications tab.

[1] Parker, G.J., Yip, J.M., Eerkens, J.W., Salemi, M., Durbin-Johnson, B., Kiesow, C., Haas, R., Buikstra, J.E., Klaus, H., Regan, L.A. and Rocke, D.M., 2019. Sex estimation using sexually dimorphic amelogenin protein fragments in human enamel. Journal of Archaeological Science, 101, pp.169-180.

[2] Bona, A., Papai, Z., Maasz, G., Toth, G.A., Jambor, E., Schmidt, J., Toth, C., Farkas, C. and Mark, L., 2014. Mass spectrometric identification of ancient proteins as potential molecular biomarkers for a 2000-year-old osteogenic sarcoma. PLoS One, 9(1), p.e87215.

[3] Hendy, J., Collins, M., Teoh, K.Y., Ashford, D.A., Thomas-Oates, J., Donoghue, H.D., Pap, I., Minnikin, D.E., Spigelman, M. and Buckley, M., 2016. The challenge of identifying tuberculosis proteins in archaeological tissues. Journal of Archaeological Science, 66, pp.146-153.

[4] Hendy, J., 2021. Ancient protein analysis in archaeology. Science Advances, 7(3), p.eabb9314.