Patrick Rüther (UCPH)

About Patrick

With degrees in `Molecular Biotechnology`, I acquired a broad background in protein biochemistry, cell biology, and organic chemistry. As a student trainee at a pharmaceutical company, I had the opportunity to get hands-on experience in applied research, which set the foundation for my interest in the scientific fields of proteomics and analytical technology. My subsequent Bachelor’s thesis dealt with drug target profiling using chemical proteomics. During my Master’s studies, I spent nine months in the United States, where I did research in proteomics on breast cancer cells at Oklahoma State University and drug product characterization at Genentech. For my Master’s thesis, I went back to chemical proteomics, where I developed and tested an enrichment-tool for proteins involved in epigenetics. In the same research group, I subsequently supported the technology-focused ProteomeTools project, aiming at the optimization of targeted proteomics and providing reference data to improve database searching.

My PhD project aims at the optimization of the technology, used for data-acquisition in palaeoproteomics. Compared to samples produced under laboratory conditions, ancient and degraded proteins bring about new challenges to mass-spectrometry. To overcome these, I will apply and refine existing strategies, such as top-down proteomics and different modes of peptide fragmentation, and benchmark them with modern and artificially aged reference proteins. By providing methods with superior sensitivity and access to a wider range of age-related modifications, I hope to contribute to the field of cultural heritage material analysis.

Patrick's PhD project


The project aims at the optimization of the technology, used for data-acquisition in palaeoproteomics. Compared to modern protein samples, ancient and degraded proteins bring about new challenges and requirements to mass-spectrometry. Our goal is to achieve high peptide sequence coverage, robust identification of degraded and modified protein fragments, and good sensitivity despite the high degree of degradation and low abundance of protein remains.

Expected results

Existing strategies, such as top-down proteomics and different modes of peptide fragmentation, will be applied and refined, and benchmarked with modern and artificially aged reference proteins. To integrate these results with the ones from a traditional bottom-up workflow, new approaches for data analysis and protein sequence assembly will be developed.

My project

The latest generation of high-resolution tandem mass spectrometers can reliably and rapidly detect proteins in complex mixtures, even at the very limited quantities typical of ancient samples. Despite these developments, ancient protein analysis is still in its infancy. Protein extraction and preparation for MS analysis is the first critical phase affecting recovery success. Simplification of sample preparation by integration of different chemical treatments: reduction, alkylation and digestion, into single-steps already proved to improve recovery in the most recalcitrant ancient samples. The recent availability of new high-resolution mass spectrometric instruments offers increased sensitivity in the low attomoles range. The possibility to combine complementary fragmentation methods (HCD + ETD) maximises the possibility to improve peptide identification and analyze ancient protein modifications with unprecedented depth and accuracy. Confident use of these technologies is still limited to very few specialized research units, with direct connections with instrument suppliers.

As an alternative to bottom-up proteomics, the emergence of new ion dissociation methods continues to drive top-down proteomics by offering valuable alternatives to traditional slow-heating methods (e.g., collision-activated dissociation, CAD). Electron transfer dissociation (ETD) leverages electron-driven radical rearrangements to promote cleavage of N–Cα bonds between amino acid residues, preserving labile post-translational modifications (PTMs) and providing extensive sequence-informative fragmentation of peptides and proteins. The complementary of the different types of fragmentation methods significantly increases confidence in peptide and protein identification in particular for PTM analyses. Therefore, top-down analysis allows for the measurement of intact protein masses and provides information on post-translational modifications, as well as the protein sequence via fragmentation of the intact proteins in the mass spectrometer. Application of top-down proteomics to cultural heritage materials will remove many of the limits hampering analysis of this category of samples.


Planned secondments:

  1. Secondment period of 6 months at MPG (co-supervision) to collaborate with Petra Gutenbrunner and Jürgen Cox for automatic interpretation of the data generated using the developed methodologies.

  2. Secondment period of 6 months at Thermo (Bremen) to work on hardware improvement in a company environment.



2014-2017 Master of Science in Molecular Biotechnology, Technical University of Munich

2015 Exchange semester, Faculty of Biochemistry, Oklahoma State University

2011-2014: Bachelor of Science in Molecular Biotechnology, Technical University of Munich

Professional Career

2017 Research assistant, Chair of Proteomics and Bioanalytics, Technical University of Munich

2016 Internship, Dept. Protein Analytical Chemistry, Genentech Inc. San Francisco

2012-2014 Cooperative Studies, Various Depts., Roche Diagnostics GmbH Penzberg

2011 Internship, Dept. Molecular Biology, Institute Dr. Erdmann Rheda


In April and May 2019, ESR 6 completed a secondment at Thermo Fisher Scientific in Bremen, Germany. It involved training with the new Thermo mass spectrometer, training staff at Thermo with the operation of an Evosep LC, measuring proteomes of woolly mammoth samples brought from Copenhagen, and optimizing data-independent acquisition on short gradients for high-throughput palaeoproteomics.


Mackie, M. , Rüther, P. , Samodova, D. , Di Gianvincenzo, F. , Granzotto, C. , Lyon, D. , Peggie, D. ., Howard, H. , Harrison, L. , Jensen, L. ., Olsen, J. . and Cappellini, E. (2018), Palaeoproteomic Profiling of Conservation Layers on a 14th Century Italian Wall Painting. Angew. Chem. Int. Ed.. Accepted Author Manuscript. . doi:10.1002/anie.201713020

Batth, T. S. et al. Protein Aggregation Capture on Microparticles Enables Multipurpose Proteomics Sample Preparation. Mol. Cell. Proteomics 18, 1027–1035 (2019)

Cappellini, E. et al. Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny. Nature 574, 103–107 (2019)

Bekker-Jensen, D. B. et al. A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients. bioRxiv 860643 (2019) doi:10.1101/860643




At: University of Copenhagen

Supervisor: Jesper V. Olsen