MS/MS-Based Bone CHIP Species Identification

ESR7 Dorothea Mylopotamitaki

I am a chemist from Greece who picked research in ancient biomolecules as my main topic. My main research interest is in developing new methodologies applied to ancient human DNA, pathogens, and proteins. My BSc and MSc theses were both focused on testing and modifying methods for the recovery of ancient DNA from human bones and teeth.

In 2017, I moved to Copenhagen originally as an Erasmus+ trainee. Moreover, I worked as a student assistant at the University of Copenhagen and the University of Crete. Lately, in 2019-2020, I was employed as a research assistant on the ERC “The Fall of 1200 BC” project at the GLOBE Institute, Denmark.

My PhD Project

Palaeoanthropology uses peptide mass fingerprinting to screen sample sets encompassing thousands of bone specimens from archaeological sites known to be occupied by anatomically modern humans, Neanderthals and Denisovans to identify hominin remains and further characterize them through deep palaeogenomic sequencing. Despite being cheap and robust, peptide mass fingerprinting has some clear limitations, because it commonly uses MALDI-TOF-MS instruments that are less sensitive and have lower resolution compared to what is now the state-of-the-art proteomics technology, i.e. Orbitrap (commercialized by partner organization Thermo).

My PhD project will apply data-independent acquisition (DIA) and data-dependent acquisition (DDA) tandem MS and the ultra-fast peptide separation technology (~8 mins/run) the PUSHH partner organization EvoSEP patented. The outcome will be to develop and apply a novel proteomic approach to identify the biological species of archaeological bone specimens by screening with Orbitrap technology up to 200 samples per day. The advantages over peptide mass fingerprinting will be represented by the acquisition of a much richer dataset per sample, higher sensitivity, higher automation, and the ability to use off-the-shelf spectral identification software.

During this PhD, my main goals are to acquire a deeper understanding of experimental proteomics techniques and to improve my skills in computational analysis. Finally, I believe that participating in this project seems a great opportunity to collaborate and exchange opinions with different people, learn and discuss new ideas and methodologies in a multidisciplinary environment.

Planned secondments

Secondment period of 4 months, during PhD year 2, at University of Copenhagen under Jesper V. Olsen’s supervision to receive training on how to use DIA MS and EvoSEP technology, in collaboration with ESR9 and 11.



Research assistant, GLOBE Institute, University of Copenhagen, Denmark

2018- 2019

Awarded Erasmus+ scholarship, State Scholarships Foundation, Greece, University of Copenhagen, Denmark


MSc in Chemistry (Biochemistry), Department of Chemistry, University of Crete, Greece

MSc Thesis: "Optimizing methods for the recovery of ancient DNA sequence data." University of Copenhagen, Denmark.


BSc in Chemistry, Department of Chemistry, University of Crete, Greece.

BSc Thesis: "Basic studies for processing archaeological samples and the recovery of ancient DNA for further analysis." Institute of Molecular Biology and Biotechnology (IMBB), Crete


Anna K. Fotakis, Dorothea Mylopotamitaki, Enrico Cappellini, Thomas P. Gilbert. Multi-omic detection of Mycobacterium leprae in archaeological human dental calculus. Phil. Trans. R. Soc. B 20190584.

Nägele Kathrin, Mylopotamitaki Dorothea, Schroeder Hannes (2020) Genomic Insights into the Early Peopling of the Caribbean. Science. eaba8697.

Moreno-Mayar JV, Mylopotamitaki D, Willerslev Eske (2018) Early Human Dispersals within the Americas. Science 362 (6419).

Host Institution

Germany 🇩🇪



Frido Welker 🇳🇱