Hardware for Palaeoproteomics

ESR11 Florian Simon Harking

Driven by my curiosity of natural sciences, I did my Bachelor and Master degrees in Molecular Biotechnology, providing me with a solid background in protein biochemistry, cell biology and biomolecule analysis. During my studies, I caught interest in the analysis of proteins using LC-MS/MS methods, resulting in an internship and my Master Thesis focusing on the establishment of targeted proteomics measurement methods.

After that, I went on to work in a contract-research company, where proteomics is applied for biotech and pharma companies. As this technology is still laborious and requires a lot of training and experience, it is often in the interest of big companies to outsource this specialized analysis to a research contractor. During my time there, I did a plethora of projects, involving targeted proteomics, high-throughput workflows, post-translational modifications, biomarker discovery and characterization, protein profiling and the establishment of experimental workflows for internal use.

In my PHD project, I will optimize and develop methods to analyze ancient proteins using LC-MS/MS, as the main technique. I hope to gain insight into our understanding of ancient proteins and their analysis, but also the information they hold, when it comes to human evolution and craftsmanship

My PhD Project

In the last decade, the employment of confident ancient protein residue sequencing by high-throughput, high resolution tandem mass spectrometry (MS), i.e. paleoproteomics, has proven to be a valuable tool in the analysis of ancient samples.

While ancient DNA (aDNA) has shaped our understanding about paleoanthropology to a great extent, its sample recovery in sub-arctic conditions is limited due to sample degradation processes, making sample analysis challenging. Ancient protein preservation on the other hand, was shown to be much more robust, allowing the detection and analysis of ancient protein residue that can be millions of years old.

This project will focus on the technological optimization of the analysis of ancient proteins from hominin and hominin-related samples via liquid chromatography (LC) coupled MS. Recent advances in LC-MS technology driven by commercial vendors ThermoFisher and EvoSep, enable robust and sensitive measurement of protein samples, in a high-throughput manner. To implement and optimize this technology on the measurement of ancient samples, focusing on those of hominin background, will be the main goal of this project.

Planned secondments

Secondment period of 4 months at Thermo (Bremen) to get hands-on experience with the latest technology in a company environment.

Further secondment period of 2 months, during the second year of PhD , at EVOSEP, to optimize the use of EVOSEP technology on ancient samples.




Research assistant, OmicScouts GmbH, Freising.

Project work for Biotech and Pharma companies, applying proteomics technologies.



Master of Sciences in Molecular Biotechnology, Technical University of Munich.

MSc Thesis : Development of a multiplexed kinase activity assay in complex background using targeted mass spectrometry


Bachelor of Sciences in Molecular Biotechnology, Technical University of Munich.

BSc Thesis: A cell biological analysis of two subunits of the plant TRAPPII tethering complex.

Host Institution

Denmark 🇩🇰