Project Overview

As part of the recently funded Marie Curie ProtAIomics project (protaiomics.eu), we invite applications for a PhD position on the topic:

Confidence prediction of fine-tuned AI peptide property models for single-cell proteomics data analysis

The position will be based at the Technical University of Munich (TUM), with a starting date between March and September 2026.

This PhD project aims to establish a (semi-)automatic framework to estimate the confidence of AI model predictions on minimal data. The approach will leverage techniques such as conformal prediction, explicitly considering unknown experimental parameters that influence peptide properties. The resulting confidence intervals will support more accurate data-driven rescoring in proteomics analyses.

Methodology

• Develop methods for model confidence estimation using conformal prediction and related uncertainty quantification techniques.
• Integrate confidence estimation into peptide property prediction workflows.
• Evaluate the methods on diverse datasets, with a focus on single-cell proteomics.

Expected Results

The project will deliver an enhanced data analysis pipeline that improves peptide and protein identification coverage and accuracy—particularly for post-translational modifications. While optimized for single-cell proteomics, the developed methods will be broadly applicable to complex proteomics datasets.

Requirements

Candidates must hold a master’s degree in Data Engineering, Data Science, Bioinformatics, Informatics, or a related discipline. Essential skills include theoretical knowledge of and practical skills in statistical analysis, data mining, data integration, machine learning, programming, deep learning, bioinformatics, confidence/conformal prediction. Additional desirable skills include a sound understanding of proteomic or related technologies as well as basic biological and (bio)chemical concepts. Interest in understanding technologies e.g. proteomics and metabolomics using mass spectrometers is expected. 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 inter-personal communication skills as well as the ability to present in English are also important.

Our offer

You will join a young and highly motivated team of interdisciplinary bioinformaticians who use the latest proteomic approaches to gain insight into the biological processes that govern life. You will further be connected to the Munich Data Science Institute (MDSI) at the Technical University of Munich (TUM) to foster and facilitate exchange. TUM is one of the best academic institutions in Germany and offers a stimulating work environment and excellent future perspectives. 

The position is expected to start March to Sep 2026. 

The Doctoral Candidate will be involved in a Marie-Curie doctoral network(DN). Marie Curie DNs provide a highly competitive salary to the Doctoral Candidates (DCs), including a competitive monthly living and mobility allowance and (if eligible) a monthly family allowance. Marie Curie DN also provides excellent opportunities for scientific and personal development. 

These include:

• Regularly adapted personal career development plans.
• Funding for short stays at top-class research groups in the above-mentioned countries. Found out about potential stays at https://www.protaiomics.eu/project/dc2-tum/
• Regular training events and meetings across Europe.

Equal opportunity

TUM is aiming to increase the proportion of women and, therefore, expressly welcomes applications from women. The position is also suitable for severely disabled persons. Severely disabled applicants will be given preference if their suitability, qualifications and professional performance are otherwise essentially equal.

Application

More details about this position are available here:
➡️ Project DC2 – TUM

Interested candidates are encouraged to apply through the ProtAIomics online application portal by 30 November 2025:
➡️ Apply here

Data Protection Information

When you apply for a position with the Technical University of Munich (TUM), you are submitting personal information. With regard to personal information, please take note of the Datenschutzhinweise gemäß Art. 13 Datenschutz-Grundverordnung (DSGVO) zur Erhebung und Verarbeitung von personenbezogenen Daten im Rahmen Ihrer Bewerbung. (data protection information on collecting and processing personal data contained in your application in accordance with Art. 13 of the General Data Protection Regulation (GDPR). By submitting your application, you confirm that you have acknowledged the above data protection information of TUM.