Our research:

Join a world leader in mass spectrometry-based proteomics. The Department of Proteomics and Signal Transduction at the Max Planck Institute of Biochemistry (MPIB), led by Prof. Dr. Matthias Mann, has shaped the field for over two decades — from pioneering computational proteomics to building some of the most advanced analytical workflows in the world. Our work spans from fundamental technology development to direct biomedical application, and our methods are used by laboratories and clinical groups globally.

Beyond experimental innovation, our lab develops and maintains the AlphaX ecosystem (github.com/MannLabs) — a growing suite of open-source Python tools that powers the full proteomics data analysis pipeline: from raw data access and deep learning-based peptide property prediction through DIA search engines, quantification, and statistical analysis to visualization and biological interpretation. These tools are used by hundreds of labs worldwide and are published in leading journals. We are looking for a talented computational scientist or software engineer to help shape the next generation of this platform.

What you will do:

You will join a team of computational scientists and experimentalists building software that is used at the cutting edge of biomedical research. This is an opportunity to work on challenging, real-world problems in scientific computing — from algorithm design and deep learning integration to building tools that thousands of researchers depend on daily. The role offers deep exposure to AI, high-performance computing, and large-scale data processing in a world-class research environment.

Depending on your interests and strengths, your work will include:

• Designing and developing core components of the AlphaX ecosystem, with a focus on performance, modularity, and scientific rigor.
• Implementing and optimizing algorithms for mass spectrometry data processing, including signal processing, identification, and quantification at scale.
• Integrating deep learning models into production-ready analysis pipelines.
• Building intuitive interfaces and visualization tools that make advanced analyses accessible to experimental scientists.
• Contributing to the open-source community through well-documented code, tutorials, and user engagement.

No prior knowledge of proteomics or mass spectrometry is required — what matters is strong engineering instincts, intellectual curiosity, and the drive to build something that has real scientific impact.

Requirements:

• PhD or Master's degree in computer science, physics, mathematics, engineering, or a related quantitative field.
• Strong software engineering skills in Python and AI assisted coding, including experience with package development, testing, and version control (Git/GitHub).
• Experience with scientific computing (NumPy, pandas, Mojo) and/or deep learning frameworks (PyTorch) is a strong plus.
• Demonstrated ability to write clean, maintainable, well-tested code — whether through open-source contributions, published software, or industry experience.
• Curiosity and enthusiasm to learn a new scientific domain.
• Excellent communication skills in English.

Our offer:

This position offers a unique combination: the intellectual freedom and scientific depth of a Max Planck research environment with the software engineering challenges and professional development opportunities typically found in top tech companies. You will build widely used open-source tools, publish in leading journals, work alongside world-class scientists, and develop skills that are highly valued in both academia and industry.

The position is available from June 1, 2026. Salary follows the German public pay scale (TVöD), depending on experience and qualification. The Max Planck Society strives for gender equality and diversity and encourages applications from all backgrounds. Applications from severely disabled persons are expressly welcome. For further information about MPIB, please see http://www.biochem.mpg.de.