Biological Mass Spectrometry Imaging
PhD School at the Faculty of SCIENCE at University of Copenhagen
This is a toolbox course where 80% of the seats are reserved to PhD students enrolled at the Faculty of SCIENCE at UCPH and 20% of the seats are reserved to PhD students from other Danish Universities/faculties (except CBS). Seats will be allocated on a first-come, first-served basis and according to the applicable rules.
Anyone can apply for the course, but if you are not a PhD student at a Danish university (except CBS), you will be placed on the waiting list until enrollment deadline. After the enrollment deadline, available seats will be allocated to applicants on the waiting list.
Aim and Content
This advanced biological imaging course module gives a theoretical and hands-on introduction to metabolite imaging of biological samples using mass spectrometry imaging. The course aims to introduce the basic concepts of the technology, including choice of appropriate approach for a given sample type.
The course gives an introduction to mass spectrometry imaging and the different types of instruments within this technology and provides an overview of strengths and weaknesses of the methods, including what can and cannot be detected, and how they complement each other. In the course, we go through all steps of selecting appropriate methods, sampling and preparing specimens, and sample analysis and data analysis. These steps will all be demonstrated in the hands-on part of the course. While this part will mainly focus on plant and possibly microbial samples, we will also explain which approaches to sample preparation are appropriate for different types of specimens and demonstrate some that work well for animal samples.
Learning outcomes
Intended learning outcome for the students who complete the course:
Knowledge
• Understand basic concepts of mass spectrometry imaging (MSI)
• Know different approaches to sample preparation and MSI analysis and how/why they are appropriate for specific sample types
• Understand the possibilities and limitations of the technology
Skills
• Read, understand and evaluate scientific papers that utilize MSI within the student’s own field
• Design a MSI experiment with sampling, sample preparation and sample analysis based on knowledge of the sample type, metabolite(s) of interest and characteristics and limitations of the chosen methods
• Carry out basic sample preparation
• Carry out basic MSI data analysis and understand how the results can and cannot be interpreted
Competences
• Able to explain the different approaches and/or instruments for sample preparation and MSI analyses
• Able to evaluate the suitability of the different approaches to answer biological questions within the student’s own field of research
• Able to advice on general suitability of the different approaches to answer scientific questions in other biological sciences
Target Group
Students that either:
- Have MSI instruments at their home institution and plan to use it in their projects, or…
- Are interested in initiating collaboration with the host lab, the PlantMSI facility headed by the course responsible (mainly plant science students), or…
- Use other mass spectrometry technologies in their science and want to learn about MS imaging
Recommended Academic Qualifications
Open for master and PhD students after taking the UCPH’s basic Biological Imaging module (course number X) or if the relevant knowledge was acquired in another way, e.g., through related courses at UCPH or other universities. If in doubt, please contact nnb@plen.ku.dk.
Research Area
Relevant for students within Plant Science, Biology, Biology-Biotechnology, Medicine and Technology, Molecular Biomedicine, Pharmaceutical Sciences.
Teaching and Learning Methods
Lectures, demonstrations, hands-on practical exercises, theoretical exercises.
Students will prepare samples, analyze samples and data and present their work in a written report.
Type of Assessment
Written report. The report must be evaluated as “passed” for the course to be completed.
Literature
Relevant background material and journal articles will be electronically available at the start of the course.
Course coordinator
Nanna Bjarnholt, Associate Professor, nnb@plen.ku.dk
Guest Lecturers
Associate Professor Christian Janfelt, Dept. of Pharmacy, SUND, KU. Lectures on animal MSI and specific types of instrumentation.
Possible also guest lecturers from SDU (protein MSI) and/or DTU (microbial MSI)
Dates
25 May - 10 June 2026 (last 3 weeks of block 4).
Expected frequency
To be held every year
Course location
Frederiksberg Campus
Course fee
• Participant fee: 750 DKK - All participants are charged for instrument-time & laboratory expenses for this course module.
• PhD student enrolled at SCIENCE: 0 DKK
• PhD student from Danish PhD school Open market: 0 DKK
• PhD student from Danish PhD school not Open market: 3000 DKK
• PhD student from foreign university: 3000 DKK
• Master's student from Danish university: 0 DKK
• Master's student from foreign university: 3000 DKK
• Non-PhD student employed at a university (e.g., postdocs): 3000 DKK
• Non-PhD student not employed at a university (e.g., from a private company): 8400 DKK
Cancellation policy
• Cancellations made up to two weeks before the course starts are free of charge.
• Cancellations made less than two weeks before the course starts will be charged a fee of DKK 3.000
• Participants with less than 80% attendance cannot pass the course and will be charged a fee of DKK 5.000
• No-show will result in a fee of DKK 5.000
• Participants who fail to hand in any mandatory exams or assignments cannot pass the course and will be charged a fee of DKK 5.000
Course fee and participant fee
PhD courses offered at the Faculty of SCIENCE have course fees corresponding to different participant types.
In addition to the course fee, there might also be a participant fee.
If the course has a participant fee, this will apply to all participants regardless of participant
type - and in addition to the course fee.