About the Project
The Protein Research Group at the University of Southern Denmark invites applications for a PhD position in advanced mass spectrometry development, with a focus on negative ion mode proteomics to enhance bacterial proteome coverage. This project aims to improve the detection of acidic proteins, contributing to a better understanding of bacterial biology and unlocking new biotechnological applications.

Current proteomics approaches rely almost exclusively on positive ion mode, which leads to inefficient ionization of many acidic peptides. However, acidic and alkaline proteins are almost equally abundant in most organisms, highlighting the need to develop and optimize negative ion mode techniques. This project will advance the next generation of proteomics, bridging this fundamental gap and expanding analytical capabilities.

What We Offer

• Cutting-Edge Research: Work on an emerging area of proteomics with high potential for discovery and application.
• Advanced Methodologies: Develop novel mass spectrometric techniques to improve proteome analysis.
• Collaborative Environment: Join an interdisciplinary team with microbiology, bioinformatics, and mass spectrometry expertise.
• State-of-the-Art Facilities: Access Orbitrap Eclipse, Orbitrap Astral, TIMSTOF Ultra2, and other high-end instrumentation.
• International Exposure: Present findings at leading conferences and collaborate with experienced researchers.
• Benefit from competitive salary and social benefits, including health coverage and support for international candidates (relocation, visa assistance).

Your Role

As a PhD student, you will:

• Develop and optimize negative ion mode mass spectrometry for improved detection of acidic proteins in bacterial proteomes, including different fragmentation experiments, peptide library analysis, and optimizing ionization conditions. The ultimate goal is to integrate key negative ion mode features into computational workflows for enhanced proteome analysis.
• Refine bacterial lysis methods for unbiased protein recovery.
• Establish a high-throughput proteomics platform by integrating positive and negative ion modes and optimizing ultra-short liquid chromatography gradients.
• Publish research in high-impact journals and present findings at international conferences.
• Complete PhD coursework (~30 ECTS) and contribute to teaching and dissemination activities.

Who We Are Looking For

We are seeking a motivated and dedicated candidate with:

• A Master’s degree in Biochemistry, Bioanalytical Chemistry, Biotechnology, or a related field.
• Experience or strong interest in proteomics, mass spectrometry, and/or bioinformatics/computational proteomics.
• A solid understanding of protein chemistry.
• Analytical thinking and problem-solving skills with a passion for scientific research.
• Good communication skills and the ability to work independently and in a team.
• Proficiency in spoken and written English.

About Us

The Protein Research Group (PRG) at the University of Southern Denmark is internationally recognized for its pioneering research in proteomics and mass spectrometry, with a focus on expanding proteome coverage, post-translational modification characterization, and advancing biomedical and technological applications. Our research spans fundamental gas-phase chemistry, protein structural analysis, cancer research, and neuroscience.

Located in Odense, just an hour from Copenhagen, the PRG offers a stimulating and inclusive research environment that values collaboration, mentorship, and professional growth. With a strong emphasis on teamwork and knowledge-sharing, we provide a supportive setting for early-career researchers to develop their expertise, engage in interdisciplinary discussions, and contribute to innovative scientific discoveries.

The PRG consists of eight research groups and over 50 scientists, postdocs, and students, fostering a collaborative and internationally connected research environment. The group maintains strong partnerships with leading international experts, ensuring high-impact contributions to biological mass spectrometry, biomedical research, and clinical proteomics.

Application deadline: 1 June 2025 at 23:59 hours local Danish time 
Please see the full call, including how to apply, on www.sdu.dk