Postdoctoral Researcher in Peptide Ionization and Fragmentation Mechanisms

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.

Why Odense A place to work live and settle

Odense offers an excellent quality of life in a vibrant Danish university city with proximity to nature strong cultural life and easy access to Copenhagen and the rest of Europe. The city is known for being family-friendly internationally oriented and affordable compared to larger metropolitan areas.

For international researchers and accompanying partners or families Odense provides strong support structures career opportunities childcare schools and a welcoming international community.

Learn more about living and working in Odense here:
successful applicant will be employedin accordance withthe agreement between the Ministry of Finance and AC (the Danish Confederation of Professional Associations). Please check links for more information onsalary(only available in Danish)andtaxation.

The application must include the following:

• A curriculum vitae including information onpreviousemployment with start and end dates
• A full list of publicationsstatingthe scientific publications on which the applicant wishes to rely
• Copy of PhD diploma ifPhddiploma has not yet been received please include statement from your supervisor
• Minimum one recommendation letter

Incomplete applications and applications received after the deadline will neither be considered nor evaluated.

Shortlisting may be used as part of the assessment process and an interview may be included in the overall evaluation of the applicants qualifications.

The application and all appendices must be in Danish or English. Applications must besubmittedelectronically using the linkApplynow.Attachedfiles must be in Adobe PDF format. We strongly recommend that you readHow to apply for a position at SDUbefore you apply.

The University wishes our staff toreflectthe diversity of society and thus welcomes applications from all qualified candidates regardless of personal background.

Further informationfor international applicants about entering and working in Denmark can be found on the Universitys website.

Contact Information

For further information please contact:
Prof. Frank Kjeldsen
Department of Biochemistry and Molecular Biology
University of Southern Denmark
frankk@

Location: Odense Denmark
Duration: 2 years with possibility of extension
Starting Date: 15 April 2026 or as soon as possible
Application Deadline: 4 March 2026 at 23.59 Danish time