Software Developer / Data Engineer in Proteomics

The Chair of Proteomics and Bioanalytics at the Technical University of Munich located in Freising invites applications for a

Software Developer / Data Engineer in Proteomics

We are seeking a talented and motivated individual to join our precision oncology research program. The successful candidate will design and implement computational frameworks for processing, integrating, and analyzing large-scale phosphoproteomics patient data, supporting the discovery of signaling networks and actionable therapeutic targets in cancer.

Key Responsibilities: Develop and maintain scalable data-processing pipelines for mass spectrometry-based phosphoproteomics and related omics data. Design, build, and document database systems and interfaces for managing, visualizing, and mining complex multi-omics datasets. Integrate quantification, annotation, and pathway information with genomic and transcriptomic data relevant to cancer signaling and drug response. Collaborate closely with proteomics experts, cancer biologists, and clinicians to transform experimental data into biologically and clinically meaningful insights. Implement data quality control, and reproducibility workflows in accordance with regulatory requirements. Contribute to the development of APIs, web tools, and dashboards for internal users and collaborators.

Required Qualifications: MSc or PhD in Computer Science, Bioinformatics, Computational Biology, or a related quantitative field. Solid experience in programming and system architecture design (e.g., Python), workflow management tools (e.g., Nextflow) and containerization (e.g., Docker). Strong knowledge of relational database systems and schema design (e.g., MySQL), and web-development (e.g., Vue.js) including data visualization frameworks (e.g., D3.js). Excellent collaborative skills; ability to work in multidisciplinary teams.

Desirable Skills: Familiarity with mass spectrometry-based phosphoproteomics or proteomics data. Understanding of signal transduction networks, kinase–substrate relationships, and phosphoproteomics information resources (e.g., PhosphoSitePlus, KinHub). Experience with cloud or HPC environments for large-scale data analysis.

We are looking for a self-motivated and broadly interested individual with high potential and a strong sense of responsibility. Flexibility and the ability to work in a fast-paced environment on multiple scientific and infrastructure projects are essential. Good inter-cultural and interpersonal communication skills as well as presenting complex data to scientists and clinicians in English are also important.

Our offer: You will join an interdisciplinary team of biochemists, cell biologists, bioinformaticians, and clinicians that uses the latest proteomic approaches to fight cancer. The Technical University of Munich is one of the best academic institutions in the world, and offers a stimulating work environment and excellent future perspectives. The position is initially available for two years but may be extended. The salary follows the TVL scale.

Application Instructions: Please send your CV, a cover letter describing your motivation and relevant experience, links to GitHub repositories or examples of software/pipelines you have developed (if available) and the contact details of two references. Applications should be sent as a single PDF to Matthew The (matthew.the(at)tum.de) and Bernhard Kuster (kuster@tum.de). The position is available immediately and applications will be considered until the position is filled.