SBRI19002U Translational Discovery Omics II – Proteomics

Volume 2025/2026
Education

BRIDGE – Translational Excellence Programme

Content

The aim of the course is to provide the participants with:

i) An overview of the major high-end quantitative proteomics technologies with a focus on mass spectrometry-based proteomics; 

ii) An overview of key applications of quantitative proteomics exemplified with studies on cellular signalling, analysis of patient samples and single-cell proteomics;

iii) An introduction to clinical sample handling for proteome analysis, hands-on plasma proteomics workflow and processing of proteomics data at different levels.

 

The main themes covered in the course include:

  • Principles of mass spectrometry technologies, protein sequencing and quantitation.
  • Introduction to proteomics and applications in biology including examples with translational impact between industry/clinics and academia.
  • Best practices for clinical sample handling.
  • Hands-on exercise demonstrating a typical plasma proteomics workflow.
  • Data analysis and visualisation of proteomics data using standard-in-the-field software.
Learning Outcome

Upon completing the course, participants should be able to:

 

Knowledge

  • Demonstrate a basic understanding of different mass spectrometry-based proteomics workflows, experimental design, pre-analytical variability and methods including hands-on experience with plasma proteomics.
  • Have a general understanding of the main statistical concepts required for proteomics data analysis.
  • Understand the role of the proteome in protein signalling pathways in health and disease.

 

Skills and Competences

  • Perform mass spectrometry-based proteome analysis of biological and clinical samples.
  • Process raw mass spectrometry data and obtain peptide and protein identification from proteome analysis using available software tools (Spectronaut or DIA-NN).
  • Use data analysis and visualisation programmes such as Perseus to explore and perform basic bioinformatic analysis of mass spectrometry data.
  • Understand the important aspects of translational omics with a focus on clinical sample handling, the importance of pre-analytical variability and be able to discuss and communicate these to other scientists, clinicians, and the public.
  • Critically evaluate proteomic results and interpretation of downstream data analysis to answer biological questions and hypotheses.

The course literature will be listed on Absalon.

Participants must meet the admission criteria of the BRIDGE – Translational Excellence Programme (Fellowship or BRIDGE Omics Programme).
The course is organised as a mix of lectures, practical exercises, and laboratory work.

Lectures will introduce state-of-the-art proteomics, applications, and data analysis tools and include guest lecturers from academia/industry presenting proteomics work with translational impact. Practical exercises will allow course participants to learn by doing, using concrete examples related to the course content. Moreover, a significant part of the course will include a group work-based lab exercise, with hands-on training in clinical sample handling and proteome analysis, supervised by specialists in the field.

The course will end with an evaluation, where participants must reflect on the course learning outcomes and provide feedback for course development.
  • Category
  • Hours
  • Lectures
  • 9,5
  • Class Instruction
  • 1
  • Preparation
  • 4
  • Practical exercises
  • 4,5
  • Laboratory
  • 4
  • Total
  • 23,0
Oral
Continuous feedback during the course of the semester
Credit
0 ECTS
Type of assessment
Continuous assessment
Requirement to attend classes
Type of assessment details
Attendance and active participation are required. By active participation the participant must demonstrate:

i) An overview of the major high-end quantitative proteomics technologies (label-free and tandem mass tag labelling) used to analyse patient and biological samples via high-resolution mass spectrometry.

ii) Knowledge of standard go-to software solutions for raw mass spectrometry data analysis, including downstream software packages for data interpretation and basic visualisation.

iii) An understanding of important factors influencing pre-analytical sample variability and optimal experimental design for the analysis of clinical samples.

iv) Knowledge of biological applications using quantitative proteomics, including proteome quantitation and functional protein interaction networks.
Examination prerequisites

Participants are automatically registered for the examination upon admission to the BRIDGE – Translational Excellence Programme (Fellowship or BRIDGE Omics Programme).

Aid
All aids allowed
Marking scale
passed/not passed
Censorship form
No external censorship
Criteria for exam assesment

Active contribution and course participation according to the BRIDGE Guidelines and Practicalities.