• Cultivation of human cells and in-cell crosslinking under basal and altered conditions (e.g. drug treatment, stress)
• Optimization and benchmarking of chemical and photoactivatable crosslinking reagents with regard to efficiency, membrane permeability, and biological relevance
• Combining crosslinking with subcellular fractionation (cytosol, nucleus, membranes) to enrich compartment-specific protein complexes
• Sample preparation for proteome-wide crosslinking mass spectrometry (digestion, enrichment, multidimensional fractionation) and LC-MS/MS measurements (Orbitrap, Astral)
• Data analysis using xiSEARCH/xiFDR and contribution to improving spectrum assignment and false discovery rate (FDR) estimation, including through systematic investigation of artifacts such as non-covalently associated peptide pairs
• Validation of crosslinking data against known complexes and comparison with CF-MS and AP-MS data from project partners; preparation of distance restraints for structural modeling
• Close collaboration within an international consortium, open sharing of data and protocols (EMBL-EBI/PRIDE), and presentation and publication of results
• There is an opportunity to pursue a doctoral degree

• Successfully completed university degree (Master, Diplom, or equivalent) in biotechnology, biochemistry, chemistry, or a closely related discipline
• Practical experience in mass spectrometry-based proteomics (sample preparation, LC-MS/MS, data analysis)
• Solid laboratory experience with biochemical and cell biological methods (e.g. cell culture, protein expression and purification)
• Very good command of written and spoken English

Desirable criteria:

• readiness to develop expertise in crosslinking mass spectrometry, structural proteomics, and integrative structural modeling
• An independent, meticulous, and structured approach to work, along with strong teamwork and communication skills
• Experience with crosslinking mass spectrometry or the analysis of artifacts in LC-MS data (e.g. non-covalently associated peptides)
• Experience with proteomics data analysis software (e.g. DIA-NN, Xcalibur), programming skills (e.g. Python), and structural visualization (e.g. ChimeraX)
• Knowledge of human cell models, for example in stem cell research or tissue engineering
• Knowledge of German

Please send your application with the reference number and the usual documents only by email (compiled into a single PDF document, max. 5 MB) to Prof. Dr. Juri Rappsilber via sekretariat@bioanalytik.tu-berlin.de.

By submitting your application via email you consent to having your data electronically processed and saved. Please note that we do not provide a guaranty for the protection of your personal data when submitted as unprotected file. Please find our data protection notice acc. DSGVO (General Data Protection Regulation) at the TU staff department homepage: https://www.abt2-t.tu-berlin.de/menue/themen_a_z/datenschutzerklaerung/.

To ensure equal opportunities between women and men, applications by women with the required qualifications are explicitly desired. Qualified individuals with disabilities will be favored. The TU Berlin values the diversity of its members and is committed to the goals of equal opportunities. Applications from people of all nationalities and with a migration background are very welcome.

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