PhD Position in Method Development for Peptide Ionization and Fragmentation i Odense

Project Description

We invite applications for a fully funded PhD position in experimental proteomics. The successful candidate will contribute to a fundamental research program exploring the chemical and physical principles of peptide ionization and fragmentation in LC-MS/MS – with particular emphasis on the analytical potential of negative ion mode.

Current proteomics workflows rely almost exclusively on positive ion mode, which leads to systematic underrepresentation of acidic peptides and other biomolecules. This project aims to address that gap through novel method development and mechanistic investigations of ionization and fragmentation behavior.

Areas of investigation may include modulation of peptide properties to direct fragmentation pathways and the differentiation of isomeric peptide forms using advanced dissociation techniques. These directions are flexible, and the PhD candidate will play a central role in shaping and executing the experimental strategy.

Research Environment and Collaborative Structure

The position is embedded in the Protein Research Group (PRG), an internationally recognized center for proteomics and biological mass spectrometry. The group comprises eight PI-led teams and more than 50 researchers and students, offering a dynamic, interdisciplinary, and collaborative research environment with access to cutting-edge instrumentation.

The PhD student will be responsible for the core experimental work: planning and executing LC-MS/MS experiments, generating high-quality MS/MS spectra, and contributing to structured spectral annotation. A dedicated postdoctoral researcher will support computational development, and the PhD candidate is expected to engage in active collaboration while maintaining full ownership of their own research project.

Responsibilities

• Design and execute LC-MS/MS-based proteomics experiments (primarily in negative ion mode)
• Independently operate and optimize chromatographic and mass spectrometric instrumentation
• Investigate how physicochemical properties affect ionization and peptide fragmentation
• Explore alternative ion activation methods, including next-generation multi-mode trap instruments supporting both collisional- and electron-based dissociation
• Contribute to spectral annotation workflows in collaboration with a computational postdoc
• Disseminate findings through peer-reviewed publications and international conferences
• Complete PhD coursework (~30 ECTS), and participate in teaching and scientific outreach activities

Required Qualifications

• MSc degree in proteomics, analytical chemistry, protein chemistry, or a closely related field
• Strong hands-on experience with mass spectrometry-based proteomics
• Demonstrated ability to independently operate and troubleshoot mass spectrometry and chromatography instrumentation
• Solid understanding of database searching and spectral interpretation
• Capacity for critical thinking, clear documentation, and structured experimental design

Desirable Qualifications

• Experience with or interest in gas-phase fragmentation mechanisms and ion chemistry
• Interest in computational proteomics, spectral library development, or fragmentation modeling
• Programming/scripting skills (e.g., Python, R) for data handling and visualization
• Strong interpersonal and cross-disciplinary collaboration skills

What We Offer

• Innovative Research Framework: Contribute to next-generation methods in proteomics
• Advanced Instrumentation: Access to Orbitrap Eclipse, Orbitrap Astral, TIMSTOF Ultra2, and more
• Collaborative Culture: Work in a shared lab with over 50 researchers across experimental and computational fields
• Strong Mentorship: Active supervision and scientific development support
• International Outlook: Participate in global scientific networks and conferences
• Attractive Conditions: Competitive salary and benefits (including pension, health coverage, and relocation/visa support in accordance with Danish regulations)

About the PRG

The Protein Research Group (PRG) at SDU is internationally recognized for pioneering work in biological mass spectrometry, protein chemistry, and biomedical proteomics. Research projects span protein structure–function relationships, post-translational modifications, gas-phase chemistry, and translational proteomics. Located in Odense, the group fosters an open and inclusive culture with a strong emphasis on interdisciplinary collaboration and mentorship.

Application deadline: 27h of February 2026 at 23:59 hours local Danish time

Please see the full call, including how to apply, onhttps://fa-eosd-saasfaprod1.fa.ocs.oraclecloud.com/hcmUI/CandidateExperience/da/sites/CX_1001/job/3590/?utm_medium=jobshare