PhD Position in Method Development for Peptide Ionization and Fragmentation

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 structurefunction 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.

Applicationsalaryetc.

Appointment as a PhD Research Fellow is for three years. Employment stops automatically at the end of the period. The holder of the scholarship is not allowed to have other paid employment during the three-year period.

The salary for PhD students in Denmark is competitive compared to other European countries. As of 1 April 2025 the gross monthly salary is approximately 30841.76 DKK (4100 EUR) depending on prior experience and includes pension contributions. Note: Living costs in Denmark are relatively high but so is the salary and social security coverage.

The successful applicant will be employed in accordance with the agreement on salaried PhD scholars 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 successful candidate will be enrolled at this university in accordance with faculty regulations and the Danish Ministerial Order on the PhD Programme at the Universities (PhD order).

Further information about the PhD-study can be found at thehomepage of the University.

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

Application must be in English and made in the form of a Declaration of Interest including the following:

A letter stating your specific interest motivation and qualifications for the project in question (max. two pages) (please attach this under box Application form).

Detailed CV including personal contact information.

Copies of diplomas Bachelor as well as Masters degree including transcripts of notes/grades.

At least one signed reference letter. Should your referees wish to send their letter directly to us please have them use e-mail: sinerr@ mentioning your name and the title of the position in the subject line. And please note that these also need to reach us before deadline.

Shortlisting may be used in the assessment process.

Incomplete applications and applications received after the deadline will neither be considered nor also applies to reference letters.

Applications will be assessed by an expert assessor/committee. Applicants will be informed of their assessment by the university.

Applications should be sent electronically via the link Apply now. The faculty expects applicants to read the information How to apply before applying. Please note that the application documents should be in pdf-format and attached as three documents: motivation letter CV and the remaining documents.

We recommend that as an international applicant you take the time to visitWork in Denmarkwhere you will find information and facts about moving to working and living in Denmark as well asthe International Staff Office at SDU.

Contact information

For further inquiries please contact:

Prof. Frank Kjeldsen
Department of Biochemistry and Molecular Biology
University of Southern Denmark
frankk@

Department of Biochemistry and Molecular Biology University of Southern Denmark
Location: Odense Denmark
Application Deadline: 27 February 2026
Starting Date: 15 April 2026 or soon thereafter