Postdoc: Machine-Learning Proteomics & MS Analytics

Syddansk Universitet; Cortex Park; On-site; DKK 420,000 - 520,000; Full time

Benefits offered by this job

Pension

Competitive salary

Job summary

The Protein Research Group at the University of Southern Denmark invites applications for a postdoctoral position at the interface of computational proteomics, machine learning, and mass spectrometry. You will develop ML methods for peptide fragmentation analysis on large curated MS/MS datasets and work with experimental colleagues to generate data.

Located in Odense, the position offers scientific independence and collaboration across computational and experimental teams, aiming to advance

Qualifications

• PhD in computational proteomics, bioinformatics, ML, computer science, chemometrics, analytical chemistry, or closely related field.
• Strong experience with machine learning/deep learning on complex scientific datasets.
• Ability to independently develop computational solutions from design to evaluation and documentation.
• Proficiency in Python and relevant ML/data science frameworks.
• Experience with preprocessing, curation, and quality control for large, complex datasets.
• Analytical mindset and ability to work independently on computational research problems.
• Interest in computation-chemistry-mass spectrometry interface.

Responsibilities

• Develop computational and ML workflows for large-scale tandem MS data.
• Contribute to structuring, curation, and QC of large MS/MS datasets.
• Build data-driven models for peptide fragmentation using experimental spectra.
• Integrate variables like peptide sequence, precursor charge, collision energy, and PTMs.
• Evaluate model performance with appropriate metrics.
• Extend models toward chemically/biologically relevant peptide classes, incl. PTMs.
• Work independently on model development while collaborating with experimentalists.
• Contribute to reproducible pipelines, data structures, and workflows.
• Disseminate findings through publications, talks, and open resources.

Skills

Machine learning

Python

Data preprocessing

Independent work

Analytical mindset

Mass spectrometry knowledge

Education

PhD in computational proteomics or related field

Tools

Python (scikit-learn, PyTorch)

Job description

The Protein Research Group at the University of Southern Denmark invites applications for a postdoctoral position at the interface of computational proteomics, machine learning, and mass spectrometry. You will develop ML methods for peptide fragmentation analysis on large curated MS/MS datasets and work with experimental colleagues to generate data.

Located in Odense, the position offers scientific independence and collaboration across computational and experimental teams, aiming to advance