Project Description

We invite applications for a postdoctoral position in experimental mass spectrometry-based proteomics, focused on peptide ionization, charge state behavior, and fragmentation mechanisms in LC-MS/MS.

The project addresses fundamental limitations in current proteomics workflows, which rely almost exclusively on positive ion mode and therefore systematically underrepresent acidic peptides and selected post-translationally modified species. The overarching goal is to develop experimentally driven strategies, grounded in gas-phase ion chemistry, that improve peptide and proteome coverage by exploiting negative ion mode and advanced fragmentation methods.

Within this framework, the postdoc will drive method development and high-level experimental MS studies, including systematic investigations of charge state distributions, fragmentation behavior under collisional- and electron-based dissociation, and differentiation of peptide isoforms and PTMs using negative ion mode workflows.

Research Environment and Collaborative Structure

The position is embedded within the Protein Research Group (PRG) at the University of Southern Denmark – an internationally recognized center for biological mass spectrometry and proteomics. PRG consists of eight PI-led research teams and more than 50 researchers and students, providing a highly interactive and collaborative research environment.

The postdoc will play a central experimental role in the project and work closely with a dedicated postdoc supporting advanced computational analysis and interpretation of data. The position offers substantial scientific independence, with opportunities to shape experimental directions and contribute to the strategic development of the research program.

Responsibilities

• Design, execute, and interpret advanced LC-MS/MS experiments, with emphasis on negative ion mode

• Develop and optimize fragmentation strategies for peptide analysis under collisional- and electron-based dissociation regimes

• Investigate gas-phase chemistry of peptide ions, including charge state behavior and fragmentation pathways

• Independently operate, optimize, and troubleshoot state-of-the-art MS instrumentation, including Orbitrap platforms and TIMSTOF OmniTrap MS

• Curate high-quality MS/MS datasets and perform detailed fragment ion interpretation

• Collaborate with computational researchers on downstream data interpretation and methodological refinement.

• Publish results in peer-reviewed journals and present findings at international conferences

Required Qualifications

• PhD in proteomics, analytical chemistry, physical chemistry, or a closely related discipline

• Strong experimental background in peptide-based mass spectrometry

• Solid understanding of peptide ionization and fragmentation mechanisms 

• Proven experience with LC-MS/MS troubleshooting and method development

• Strong analytical skills and experience in fragment ion interpretation and data curation

• Ability to work independently and drive complex experimental projects

Desirable Qualifications

• Experience with negative ion mode proteomics

• Knowledge of gas-phase chemistry of peptide ions

• Familiarity with advanced MS platforms (Orbitrap, TIMSTOF, multi-mode traps)

• Interest in collaborating with computational scientists 

• Experience with PTM analysis or peptide isomer differentiation

What We Offer

• Scientifically ambitious project at the forefront of proteomics method development

• Access to cutting-edge MS instrumentation, including latest-generation Orbitrap systems and TIMSTOF OmniTrap

• High degree of scientific independence and ownership of experimental work

• Close collaboration with both experimental and computational researchers

• Strong international research environment and opportunities for career development

• Competitive salary and benefits according to Danish collective agreements, including relocation and visa support

About the Protein Research Group

The Protein Research Group (PRG) at SDU is internationally recognized for pioneering work in biological mass spectrometry, protein chemistry, and proteomics. Research spans gas-phase chemistry, peptide and protein fragmentation, PTMs, quantitative proteomics, and translational applications in health and disease.

Located in Odense, PRG fosters an open, inclusive, and collaborative research culture with a strong emphasis on scientific rigor, mentoring, and interdisciplinary exchange.

Application deadline: 4th of March 2026 at 23:59 hours local Danish time

Please see the full call, including how to apply, on https://fa-eosd-saasfaprod1.fa.ocs.oraclecloud.com/hcmUI/CandidateExperience/da/sites/CX_1001/job/3637/?utm_medium=jobshare