Master thesis/semester project in quantitative AP-MS of signaling complexes
TNF-alpha is a cytokine playing a fundamental role in inflammation that induces the formation of a large signaling complex associated with its receptor. The project will primarily entail application of quantitative mass spectrometry methods to obtain detailed information about this large assembly. The student will learn protein purification, experimental and computational aspects of AP-MS and possibly other proteomics techniques. The student is expected to know basics of mass spectrometry and cell culture and have a strong interest in method development.
Tumor necrosis factor-alpha (TNF-alpha) is an extensively studied cytokine that plays a fundamental role in inflammatory processes. Binding of TNF-alpha to TNFRI leads to the formation of a large signaling complexes consisting of about 30 proteins (TNF-RSC). The project will primarily entail method optimization of the current AP-MS (affinity purification coupled to mass spectrometry) workflow as applied to the TNF-RSC to improve its throughput and specificity as well as to obtain both quantitative and structural information about this large assembly.
Dr. Rodolfo Ciuffa and Federico Uliana will jointly supervise the project. Under their supervision, the student will have the opportunity to learn protein purification, experimental and computational aspects of AP-MS and possibly advanced quantitative and structural proteomics techniques. The student is expected to have basic knowledge of mass spectrometry, training in cell culture and a strong interest in method development.
For further information, please send a CV and a motivation statement to Dr. Rodolfo Ciuffa () and Federico Uliana ().
 Brenner, D.; Blaser, H.; Mak, T. W. Regulation of tumour necrosis factor signalling: live or let die. Nat. Rev. Immunol. 2015, 15 (6), 362−374.
Master thesis/semester project focused on method development in chemical cross-linking/mass spectrometry
Most proteins execute their function not in isolation, but in the form of protein complexes. Chemical cross-linking coupled to mass spectrometry is a strategy to learn more about the spatial organization of protein domains or subunits in such protein complexes, and has recently become a powerful tool in structural biology. Our group is one of the world-wide leaders in this field and has contributed to the structural analysis of many important complexes such as proteasomes, ribosomes, chromatin remodeling complexes and others.
We are continuously optimizing our experimental and computational workflows to extract the maximum amount of information from our sample and are looking for students to support us in this endeavor.
The student will learn how to perform cross-linking experiments, process your samples for MS analysis, analyze the samples by LC-MS and perform the data analysis. These projects are the perfect opportunity to get hands-on experience with proteomics methods and mass spectrometry instrumentation. In particular, the student will develop new instrumental methods of analysis and corresponding improvements of the data analysis workflow and will contribute to important projects that will have immediate impact on cutting-edge research in the group. Prior experience with mass spectrometry is not essential, although candidates with basic knowledge of mass spectrometry or proteomics methods are preferred.
For further information, contact )
Walzthoeni T., Leitner A., Stengel F., Aebersold R., Mass spectrometry supported determination of protein complex structure, Curr. Opin. Struct. Biol. 23 (2013) 252-260.
Leitner A., Joachimiak L. J., Unverdorben, P., Walzthoeni T., Frydman J., Förster F., Aebersold R., Chemical cross-linking/mass spectrometry targeting acidic residues in proteins and protein complexes, Proc. Natl. Acad. Sci. USA 111 (2014) 9455-9460.
Greber B. J., Bieri P., Leibundgut M., Leitner A., Aebersold R., Boehringer D., Ban N., The complete structure of the 55S mammalian mitochondrial ribosome, Science, 348 (2015) 303-308.
Master thesis/semester project in interactomic studies of signaling complexes
APEX is a new proteomic method for the determination of protein-protein interaction based on spatial proximity. In APEX, a 28kDa ascorbate peroxidase is fused to a protein of interest, and, by addition of biotin phenol and H2O2, it does promote the formation of phenol radicals and the labeling of proteins in the proximity of the protein of interest . Proximity labeling has been shown to produce complementary results as compared to traditional affinity purification-based MS approaches . The project will entail the application of both AP-MS and APEX to the three key members of the signaling complex associated with tumor necrosis factor receptor I (TNFRI), a crucial player in inflammation and autoimmune diseases .
The student will be jointly supervised by Dr. Rodolfo Ciuffa and Dr. Martin Mehnert. He/She will have the opportunity to learn the two most powerful interactome-determination methods in proteomics, and apply this knowledge to a key immunological problem. The project will entail a well-structured set of experiments and a subsequent statistical evaluation of the results. The outcome of the project should be the integrative and dynamic interactome map of key factors in inflammation before and after stimulation with cytokines.
The student is expected to have basic knowledge of MS, training in cell culture and a strong interest in protein signaling. He/she will learn, in the course of her/his stay, basic MS workflows and basic and advanced interactome-determination techniques.
For further information, please send a CV and a motivation statement to Dr. Rodolfo Ciuffa () and Martin Mehnert ().
 Hung, V., Udeshi, N. D., Lam, S. S., Loh, K. H., Cox, K. J., Pedram, K., et al. (2016). Spatially resolved proteomic mapping in living cells with the engineered peroxidase APEX2. Nature Protocols, 11(3), 456–475. http://doi.org/10.1038/nprot.2016.018
 Lambert, J.-P., Tucholska, M., Go, C., Knight, J. D. R., & Gingras, A.-C. (2015). Proximity biotinylation and affinity purification are complementary approaches for the interactome mapping of chromatin-associated protein complexes. Journal of Proteomics, 118, 81–94. http://doi.org/10.1016/j.jprot.2014.09.011
 Brenner, D., Blaser, H., & Mak, T. W. (2015). Regulation of tumour necrosis factor signalling: live or let die. Nature Reviews. Immunology, 15(6), 362–374. http://doi.org/10.1038/nri3834
Semester project in identification of plant membrane protein-protein interaction
All plant cells are encapsulated by a cellulose-rich cell wall, which performs many functions in plant growth and development. Despite extensive research, still little is known about the nature of biosynthesis of the most abundant biopolymer on Earth - cellulose. This project is focused on exploring methods of detection of the cellulose synthase complex within the Golgi apparatus in Arabidopsis. The proposed work involves establishment and application of immuno-precipitation of membrane-solubilized protein complex. Initial work will involve detergent selection for proper complex solubilization, after which the student will be performing Affinity Purification Mass Spectrometry (AP-MS) and subsequent data analysis.
) and Dr Martin Mehnert ().
For further background information, please see the following articles:
 Schneider R et al (2016), Cellulose and callose synthesis and organization in focus, what's new?, Curr Opin Plant Biol. Dec;34:9-16.
 Zhang Y et al. (2016), Golgi-localized STELLO proteins regulate the assembly and trafficking of cellulose synthase complexes in Arabidopsis, Nat Commun. 2016 Jun 9;7:11656.
 Li A et al. (2016), Proteomic profiling of cellulase-aid-extracted membrane proteins for functional identification of cellulose synthase complexes and their potential associated- components in cotton fibers, Sci Rep. 2016 May 19;6:26356.
 Song D et al (2010), Characterization of cellulose synthase complexes in Populus xylem differentiation, New Phytol. 2010 Aug;187(3):777-90.
Master Thesis: Population Genetics—Analyzing Proteomics in a Diverse Population to Uncover Mechanisms of Aging
Differences in the natural aging process between individuals vary as a factor of the millions of genetic variants and lifestyle choices that interact up over a lifetime. In this project, we will examine how aging affects transcript, protein, and metabolite expression in the liver over a population of inbred mouse strains which segregate for genetics and for their dietary regimen. The ~2200 mice in this study have lived their natural lifespans (up to ~3 years), and we are now moving into the second part of the study: molecular tissue analysis.
The student will learn how to process samples for mRNA, protein, and metabolite analysis, and integrate these large datasets (~17 million datapoints will be generated) in order to develop and test hypotheses about the aging process. The project will give the student a strong background in bioinformatics, population genetics, mass spectrometry, complex traits, and liver metabolism. Please send a CV and motivation letter to Dr. Evan Williams.
Master Thesis of systems biology to reveal the protein turnover behaviors in human cancer cells.
The student will learn how to efficiently process samples for mass spectrometry analysis at a large scale, how to perform and maintain a mass spectrometer for their own samples in SWATH-MS mode, and how to analyze the data generated using systems biology perspectives.
The quantitative correlation between mRNA and protein provides insightful understanding of different biological systems . The genome-wide protein turnover can be quantified by a pulse-chase experiment and essentially represents another dimension of protein dynamics, compared to the steady proteome regulations. This project (~6 months) will mainly involve how to improve the current pulse labelling SWATH-MS based workflow by a novel method and link the results to the modification states of the proteins. The knowledge acquired will hold promise to sharpen our views in systems biology.
The student is expected to have cell culture skills, to have basic knowledge in MS-based proteomics, and to have a strong interest in systems biology.
Please send your C.V. and a motivation letter to .
 Y Liu, A Beyer, R Aebersold (2016), On the Dependency of Cellular Protein Levels on mRNA Abundance, Cell 165 (3), 535-550
Student project to monitor epigenetic states in melanoma cells using novel proteomic tools.
Cancer is a multifactorial disease characterized by aberrations in genetic and epigenetic processes. While the genetic basis of cancer is now better understood a better understanding of epigenetic processes, its transformation during cancer and its integration with genetic cancer lesions may contribute to developing novel alternative and/or complementary diagnoses and therapies.
We recently obtained funding to monitor epigenetic states in melanoma cells using novel proteomic tools.
The student will learn how to process samples for mass spectrometry analysis, to analyse the resulting proteomic datasets and integrate them into a larger multi-omics framework. The work will be published in a scientific journal and the student will be involved in writing up the manuscript.
Please send your C.V. and a motivation letter to Christian Feller.
Master thesis/ student projects in focusing on method development in the field of phosphoproteomics / phosphopeptide enrichment.
Protein phosphorylation is one the most important post-translational modifications with relevance for many biological processes, e.g. signal transduction. Phosphoproteomics aims to comprehensively characterize this modification by mass spectrometry. To be able to detect phosphorylation events, proteins are enzymatically digested and phosphopeptides enriched by various affinity materials. Our group has a strong track record in developing phosphoproteomics methods and applying them to highly relevant research questions in systems biology and biomedicine.
Currently, we are evaluating different affinity materials based on metal oxides for the analysis of small sample amounts and are looking for students to support us in this endeavor.
You will learn how to perform phosphopeptide enrichment, process your samples for MS analysis, analyze the samples by LC-MS and perform the data analysis. These projects are the perfect opportunity to get hands-on experience with proteomics methods and mass spectrometry instrumentation. You will contribute to important projects that will have immediate impact on cutting-edge research in the group. Prior experience with mass spectrometry is not essential, although candidates with basic knowledge of proteomics methods are preferred.
For further information, contact Dr. Alexander Leitner ().
Jünger M. A., Aebersold R., Mass spectrometry-driven phosphoproteomics: Patterning the systems biology mosaic, WIREs Dev. Biol., 3 (2014) 83-112.
Vaga S. et al., Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast, Mol. Syst. Biol., 10 (2014) 767.
Oliveira et al., Dynamic phosphoproteomics reveals TORC1-dependent regulation of yeast nucleotide and amino acid biosynthesis, Sci. Signal., 8 (2015) rs4.