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Clinical proteomics and biological mass spectrometry

Clinical proteomics and biological mass spectrometry

Course leaders

Patrik Önnerfjord (

Lotta Happonen (


Prof. Johan Malmström (

Target group

PhD students at the Faculty of Medicine


The course equals one week (1.5 ECTS credits). Five days are scheduled as well as some some self-studies.


This course will be given physically and partly digitally.


Autumn 2022. Week 48 (Nov28-Dec2). Self-studies the week before the start of the course are included (about 4 hours), consisting of reading course literature and part one of the assignment. Compulsory attendance all days from 8-16.

Number of participants

Max 16



General information

This is an electable course for PhD students who are interested in learning more about biological mass spectrometry and clinical proteomics. Mass spectrometry (MS) is a technique to measure the molecular weight (m/z) of biomolecules such as proteins or peptides. Proteomics describes the large-scale analysis of proteins in a biological sample and MS based proteomics is used extensively in the life science area with numerous applications spanning from basic research questions to precision medicine e.g. in the hospital where MS is used for bacterial phenotyping in acute sepsis to select the effective drug treatment and thereby save lives. Clinical proteomics focus on clinical samples such as tissues, cells and various biological fluids, that need special considerations to be successful. There are local infrastructures for biological mass spectrometry available at the Medical Faculty: translational proteomics (CTP), structural proteomics (SciLifelab) as well as the national resource for biological MS (BioMS).

The aim of the course is to provide the students with an introduction to current methodologies in the field of proteomics. The students should obtain an overview of typical proteomics applications and be introduced to proteomics experimental workflows to enable the technology to be included in their own research project.


Learning objectives: On completion of the course, the student will be able to:

  • explain the basic principles of mass spectrometry and proteomics
  • understand how biological MS can be used in a wider perspective as for example to obtain critical sequence information from unknown proteins, and how MS can be used to investigate protein structure and protein-protein interactions
  • perform basic MS data analysis including identification and quantification of proteins
  • describe and suggest analytical approaches to biological questions – discuss advantages and limitations
  • participate in scientific discussions regarding proteomics technologies and critically evaluate scientific results
  • plan how to incorporate mass spectrometry/proteomics into your own PhD work and enable this versatile high-performance technology to potentially improve your individual research project

Content and design

The course will cover basic principles of mass spectrometry, separation of proteins and peptides, sample preparation techniques, data acquisition methods, data analysis, analysis of post-translational modifications (PTMs) and bioinformatics analysis. There will also be invited lectures (senior researchers within biological MS and clinical proteomics) that will include specific applications in various research areas.

Learning activities include lectures, group exercises, PBL, instrument demos (to generate MS data) and a round tour at BMC D13. Participants are expected to have access to a laptop.

Furthermore, the course includes one compulsory assignment, in which the doctoral student is to reflect on a research situation (preferably from their own PhD-project) where biological mass spectrometry might be used, present it for the course participants and finally propose in writing how this technology can be used to enrich the previously described research situation.


To pass the course, approved individual assignment is needed in addition to active participation in all course events.


The grades awarded are Pass and Fail.

Admission requirements

Applicants admitted to research studies at the Faculty of Medicine in Lund are prioritized.


Selected research articles and other study materials will be made available before and during the course.

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