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 chemical and physical principles of negative ion mode LC-MS/MS-based peptide analysis. The project combines method development and mechanistic exploration with downstream applications in proteome characterization.

Proteomics today captures only half the story. By focusing almost exclusively on positively charged peptides, current approaches miss a large class of acidic biomolecules. This project challenges that paradigm and explores negative ion mode LC-MS/MS to reveal new molecular insights and enable broader biological discovery

This PhD position is part of a vibrant research environment involving other researchers working on closely related topics. You will be enrolled in the Protein Research Group (PRG) – known internationally for its contributions to proteomics and biological mass spectrometry – ensuring daily interaction, idea exchange, and collaboration across both wet-lab and computational projects.

Responsibilities

The PhD student will be expected to:

• Plan and conduct LC-MS/MS-based proteomics experiments, primarily in negative ion mode

• Investigate gas-phase peptide behavior and fragmentation

• Characterize how physicochemical parameters influence ionization efficiency and detectability

• Explore how different ion activation methods affect peptide fragmentation, including work with a next-generation multi-mode trap instrument supporting both collisional- and electron-based dissociation

• Contribute to structured spectral annotation supporting advanced downstream data analysis (in collaboration with a dedicated postdoc)

• Present research findings through peer-reviewed publications and international conferences

• Complete PhD coursework (~30 ECTS) and contribute to teaching and dissemination activities.

Required Qualifications

• MSc degree in proteomics, protein chemistry, analytical chemistry, or gas-phase chemistry

• Documented hands-on experience with mass spectrometry-based proteomics

• Proficiency in database searching and peptide identification

• Familiarity with LC-MS/MS workflows, chromatographic methods, and sample preparation

Desirable Qualifications

• Prior experience with negative ion mode MS is an advantage

• Interest in computational proteomics workflows

• Programming or scripting skills (e.g., Python, R) for data processing and visualization

• Strong analytical mindset and ability to collaborate across disciplines

What We Offer

• Innovative Research Project: Engage in fundamental discovery in peptide chemistry and MS methodology

• Advanced Instrumentation: Access Orbitrap Eclipse, Orbitrap Astral, TIMSTOF Ultra2, and more

• Collaborative Environment: Work in a shared lab with over 40 researchers, PhD students, and postdocs

• Mentorship and Training: Receive strong supervision and support in experimental proteomics

• International Outlook: Present at leading conferences and engage in global collaborations

• Attractive Conditions: Competitive salary and social benefits under Danish agreements (see below for more details), including relocation and visa support

About the Research Group

The Protein Research Group (PRG) at the University of Southern Denmark is internationally recognized for its pioneering work in proteomics, mass spectrometry, and protein chemistry. The group has a broad portfolio spanning structure-function analysis, post-translational modifications, quantitative proteomics, environmental research, biomedical research, and gas-phase chemistry.

Located in Odense, the PRG offers a stimulating and inclusive research environment, where interdisciplinary collaboration and mentorship are central. The group currently comprises eight research teams, with more than 40 researchers and students, and close interaction and shared laboratory space foster innovation and synergy.