Palaeoproteomics
The research field dedicated to the study of ancient proteinaceous material is referred to as palaeoproteomics. Proteins are known to survive in the archaeological record often for much longer than other biomolecules, making their extraction and analysis an attractive alternative to ancient DNA.
A suite of analytical tools and protocols have been developed in the last decade and the field is currently blooming with exciting new research.
Peptide Mass Fingerprinting (ZooMS)
Peptide Mass Fingerprinting (also known as ZooMS, standing for Zooarchaeology by Mass Spectrometry) is one of the two main techniques in the analysis of ancient proteins. The other one is shotgun proteomics. ZooMS is a fantastic tool for the taxonomic identification of collagenous material, in particularly bone, teeth, ivory and leather.
In 2017, I co-established and led a new ZooMS facility at the Department of Archaeology, Max Planck Institute for the Science of Human History (now Max Planck Institute for Geoanthropology) in Jena, Germany. This was the first dedicated ZooMS laboratory outside the UK where the method was developed a decade earlier.
My commitment to democratize the method and make it available to all interesting users (from early career researchers to established professionals) and my move to University of Vienna in 2021, led to the establishment of the first palaeoproteomics facility in Austria. The Douka Lab is housed in brand new space at the Biology Building (UBB) of the Life Sciences Faculty, in the Department of Evolutionary Anthropology of the University of Vienna.
We have analysed over 25,000 bone samples from most corners of the planet, from the Pacific islands to northern Europe, and from East Africa to southern Siberia.
We are always looking for new and exciting projects and collaborations!
ERC-funded Projects
Idea
It all began in 2013 when working at Denisova Cave in southern Siberia. Intrigued by the sheer number of tiny, unidentifiable bones uncovered at the site, we wanted to know whether some human bones were hidden amongst the volumes of broken animal bones.
In the first bag we analysed, we found Denny (DC11), the tiny bone of a girl who lived ~100,000 years ago, and had a Neanderthal mother and a Denisovan father.
Funding
In 2016, I was awarded a €2M-worth ERC Starting Grant for the implementation of FINDER (2017-2024). In 2025, I launched a new ERC (Consolidator) project, called RIFT-to-RIM. The projects centre around the application of ZooMS on Pleistocene sites from around the world.
This funding has allowed me to establish a research team of PhD students, postdoctoral researchers, and several volunteers who work closely with the large number of international collaborators.
Implementation
FINDER processed over 15,000 bone fragments from 30 sites across Eurasia. Among the thousands of animal bones, we have discovered 35 new human fossils, and have helped establishing two new ZooMS laboratories in China (Jilin University) and Russia (Novosibirsk). This allowed us and our colleagues to process samples locally, while transferring knowledge to local scientists.
RIFT-to-RIM is currently working on new screening methodologies and analytical tools that did not exist 10 years ago.