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Proteomics in Biomedical Research

Course 2018-2019


Period: 22 October 2018 - 16 November 2018

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, 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 in modern biomedical research. In the LUMC, this is performed at the Center for Proteomics and Metabolomics (CPM).

During this course, a combination of lectures, work groups 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 perform their own small research project under the supervision of CPM tutors.

Course objectives

  • 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
  • Explain experiments and results from practicum
  • Describe background, aim, experimental set up, results and conclusion from experiments in a written report
  • Able to follow an experimental protocol in the lab
  • Participate in discussions during workgroups
  • Explain relation between methodology and a research question
  • Able to work together in a group during practicum


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

Mode of instruction

2 weeks of lectures/self-study/work groups, 1 week of practicals combined with self-study and 1 week of self-study and working on assignments.

Course load

Total course load is the amount of EC’s multiplied with 28 hours.

Assessment method

Written exam. Oral presentation after self-study of a manuscript selected from literature. Written report based on the results of the practicum.


Blackboard will be used during this course.

Reading list

Will be distributed during the course.


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