PhD Position in Experimental Mass Spectrometry-Based Proteomics

Starting Date: 1 February 2026 or soon thereafter.

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.

For further information please contact Professor Frank Kjeldsen Protein Research Group University of Southern Denmark at

Application salary etc.

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: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.