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Proteomics in Biomedical Research


Admission requirements


Period: 25 October 2021 - 19 November 2021

Proteins are the cellular workhorses which are involved in almost every task of cellular life. Hence, their abundance, modification(s) and localization must be tightly controlled and alterations are generally observed during disease onset and progression.
The large scale analysis of proteins – i.e. proteomics – currently relies mainly on mass spectrometric analyses. This is primarily due to the immense improvements in the instrumentation and data analysis platforms in the last decades. On the one hand, these approaches provide information about the identity of proteins in a certain cell or tissue, on the other hand, one can use them to (relatively) quantify proteins and study their post-translational modification. Consequently, mass spectrometry-based proteomics has become an essential part of modern biomedical research. In the LUMC, this is performed at the Center for Proteomics and Metabolomics (CPM).
During this course, a combination of lectures, workgroups, and self-study will be used to introduce mass spectrometry-based proteomics in biomedical research. Starting from the basics of mass spectrometry techniques, the students will be guided through the different aspects of proteomics: protein identification, (relative) quantification and the study of post-translational modifications (e.g. phosphorylation, glycosylation, and ubiquitinylation), including the data analysis pipelines involved. Through the use of examples from literature and ongoing research within the LUMC it will then be demonstrated how proteomics is applied in biomedical research. In addition, the study of HLA (Human Leukocyte Antigen)-peptides in relation to several ongoing studies in the LUMC, e.g. related to auto-immune diseases and the discovery of tumor neo-antigens, will be discussed. Moreover, the application of imaging mass spectrometry of tissue sections will be demonstrated. Finally, the students will have the opportunity to work with proteomics data generated in the CPM-lab, under the supervision of CPM tutors.

Course objectives

This course aims to provide a detailed insight into the application and impact of proteomics in biomedical research, more specifically:

-Explain mass spectrometric platforms for the detection of peptides and proteins
-Explain HLA-peptidomic approaches
-Explain proteomic approaches for protein identification and (relative) quantification
-Explain the application of proteomics to study cell biological questions
-Explain the mass spectrometric analysis of post-translational modification
-Discriminate and explain different data analysis approaches applied in proteomics
-Describe how methodologies were used to investigate a cell biological research question
-Reflection on working in a group
-Explain relation between methodology and a research question
-Participate in discussions during workgroups


All course and group schedules are published on our LUMC scheduling website or on the LUMC scheduling app.

Mode of instruction

3 weeks of lectures/self-study/workgroups. 1 week of self-study, workgroups, and preparation for the exam

Assessment method

Written exam (summative). Oral presentation after self-study of a manuscript selected from literature (formative).

Reading list

Will be distributed during the course.


Registration for FOS courses, H2W, Scientific Conduct, Course on Lab Animal Sciences and CRiP takes place in lottery rounds in the beginning of July. After the lottery rounds: if you want to register for a course you are kindly asked to contact the student administration at