The position

Beyond the proteins listed in standard reference catalogs, many small open reading frames (smORFs) scattered across the genome are translated into microproteins, small proteins that those catalogs miss. Some of these microproteins are secreted or diffuse between cells, where they can act as signals, yet they are hard to detect because they are scarce and short-lived. Capturing them calls for specialized chemistry: bioorthogonal tagging introduces a small chemical handle into newly made proteins so they can be labeled and pulled out of a complex mixture, while crosslinking mass spectrometry (XL-MS) chemically locks protein-protein contacts in place so that the receptors a microprotein binds can be identified.

This project will systematically capture and characterize diffusible microproteins and the cellular receptors they engage by combining bioorthogonal labeling with XL-MS in cancer cell co-culture models, building an atlas of secreted microproteins in the tumor microenvironment. It sits within ORFeus Work Package 1, which combines computational prediction with experimental validation to map the dark proteome, and it feeds the wider network: the secreted microproteins it identifies become priority targets for synthetic binder design and therapeutically relevant candidates for the antigen presentation studies elsewhere in the consortium.

Main tasks

● Establish workflows that introduce minimal bioorthogonal chemical handles into microproteins, and use crosslinking mass spectrometry to systematically identify microprotein interatomes, e.g. with cell-surface receptors involved in cell-cell communication.

● Apply these methods, together with cell-type specific proteome labeling, to map microprotein-mediated cell-cell communication in the tumor microenvironment.

● Develop analysis workflows to mine generated and public proteomics datasets for microproteins and interactors, build a comprehensive atlas of cell-cell communication microproteins, identify evolutionary conserved patterns and structural themes.

● Identify novel diffusible tumor biomarkers and hand them on as priority targets for the synthetic binder design of other doctoral candidates (DCs) in the network, here DC6, and as therapeutically relevant candidates for the antigen presentation studies of DC14 and DC15.

● Collaborate across the ORFeus network, contribute the secreted microprotein atlas and XL-MS interaction datasets to the shared ORFeome platform, and produce the project's scientific report.

Methods and platforms: bioorthogonal non-canonical amino acid (ncAA) labeling, crosslinking mass spectrometry (XL-MS), and quantitative mass-spectrometry proteomics, applied in cancer cell co-culture models with Cre-dependent proteome labeling, data-independent acquisition (DIA) for unbiased profiling, and complementary proximity-labeling approaches (APEX, BioID), sharing data through the ORFeome platform.

Secondment: you will spend around three months at an industry partner, developing proteomics workflows for diffusible microprotein biomarker discovery. You will also be guided by an independent academic advisor, with the possibility of a short, primarily virtual research exchange to strengthen the project.

Your profile

MSCA eligibility

You must meet all of the following on your recruitment date:

● You do not already hold a doctoral degree. If you have defended a doctoral thesis but the degree has not yet been formally awarded, you are not eligible.

● Mobility rule: you must not have lived or carried out your main activity (work, studies, and so on) in Germany for more than 12 months in the 36 months immediately before your recruitment date. Compulsory national service, short stays such as holidays, and time spent in a procedure to obtain refugee status under the Geneva Convention do not count toward the 12 months.

● You hold, or will hold before the start date, a degree that formally entitles you to enroll in a doctorate, and you can enroll in the doctoral program at the University of Freiburg.

Candidates of any nationality may apply. There is no limit on prior research experience, as long as you do not already hold a doctorate.

Project-specific profile

● A master's degree (or equivalent) in biochemistry, chemical biology, molecular biology, cell biology, proteomics, or a related life-science field.

● Hands-on laboratory experience in cell culture and protein biochemistry, and familiarity with mass-spectrometry-based proteomics.

● Basic knowledge in scientific programming and data analysis with Python and/or R

● Desirable: Experience with proteomics and/or Ribo-seq data analysis, machine learning and AI, structure prediction, bioorthogonal or non-canonical amino acid labeling, crosslinking mass spectrometry (XL-MS), proximity labeling, cancer cell co-culture models, protein purification techniques

● A strong interest in microproteins and the dark proteome.

● Good written and spoken English.

● Motivation for interdisciplinary, collaborative research, and willingness to travel for the secondment and network events.

What we offer

A full-time employment contract for 36 months as a salaried researcher, with full social security coverage, under the rules of the Marie Skłodowska-Curie Actions. This is a paid employment contract, not a stipend or scholarship.

The salary has a living allowance and a mobility allowance, plus a family allowance if you have family obligations when you are recruited. The indicative gross salary for this position is 4.768 EUR per month. This is what you are paid before income tax and your own social-security contributions are deducted.

Beyond salary, you will receive:

● Supervision by a world-leading, interdisciplinary supervisory team.

● A secondment of around three months with an ORFeus industry partner.

● A structured training program: network-wide schools, transferable-skills training, workshops, and international conferences.

● Enrollment in a doctoral program leading to a PhD.

● Center Welcome Service: Support for Visas and Immigration, Citizen’s Office, Language Schools

● The Graduate Centre (GraCe) offers transdisciplinary advising, qualification and access to various programs and support services: AdvanceMet Mentoring Program, Equal Opportunities Office, Family Service, Legal Advice, Psychotherapeutic Counselling, Start-Up Consulting, University Sports

Working at the University of Freiburg

The University of Freiburg (Albert-Ludwigs-Universität Freiburg) is a research-intensive university in Germany, with strong programs in the life sciences, molecular biology, and biomedical research. In the Cluster of Excellence CIBSS (Centre for Integrative Biological Signalling Studies), researchers from the Biology and Medical Faculty, as well as the Max Planck Institute for Immunobiology and Epigenetics, focus on the question how signals orchestrate multicellular life from molecules to organisms.

You will join the Epigenetics, Synthetic and Systems Biology Group of Prof. Simon Elsässer, which employs a wide range of modern ‘Omics methodologies to study gene expression and regulation, signaling and cell-cell communication. Your research will leverage state-of-the-art infrastructure and instrumentation available in the group and in-house facilities. You will work closely with the group of Prof. Jyoti Choudhary at The Institute of Cancer Research, who brings complementary mass-spectrometry proteomics platform expertise. You will enroll as a PhD candidate at the University of Freiburg Spemann Graduate School of Biology and Medicine (SGBM).