SBRI19002U Translational Discovery Omics II - Proteomics
BRIDGE - Translational Excellence Programme
The aim of the course is to provide the participants with: i) an overview of the major high-end quantitative proteomics technologies with focus on mass spectrometry; ii) an overview of key biological applications that quantitative proteomics screens can be applied in, including proteome quantitation, and functional protein interaction networks; and iii) introduction to clinical sample handling for proteome analysis and processing of proteomics data at different levels.
The main themes covered in the course include:
- Mass spectrometry technologies and principles for protein sequencing.
- Introduction to proteomics and applications in biology including examples with translational impact from industry and academia.
- Data analysis and visualization of proteomics data using StringApp and Cytoscape.
- Best practice for clinical sample handling, plasma proteomics hands-on workflow and data analysis.
Upon completing the course, participants should be able to:
Knowledge
- Demonstrate a basic understanding of different mass spectrometry-based proteomics workflows, experimental design 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 protein signalling pathways and functional protein interaction networks 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 different software tools (MaxQuant, Spectronaut).
- Use data analysis and visualization programs such as Perseus, StringApp, and Cytoscape including ability to integrate proteomics data with curated datasets such as signalling pathways and protein-protein interactions.
- Understand the important aspects of translational omics with a focus on clinical sample handling 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.
Course literature will be published on Absalon.
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 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 proteomics analysis supervised by specialists in the field.
The course will end with an evaluation where participants must reflect on course learning outcomes and give feedback for course development.
- Category
- Hours
- Lectures
- 8,5
- Class Instruction
- 2
- Preparation
- 4,5
- Practical exercises
- 7
- Laboratory
- 6
- Total
- 28,0
The BRIDGE – Translational Excellence Programme offers a few selected graduated PhDs
- a two-year postdoctoral fellowship in translational medicine (BRIDGE Programme).
- a package of three courses in Translational Discovery Omics (BRIDGE Omics Programme).
This course is only available to graduated PhDs enrolled in either of the programmes. Fellows and participants enrolled in the programmes are automatically enrolled in this course upon admission to one of the programmes.
For further information about the BRIDGE Programme, please go to the website: www.bridge.ku.dk
For further information about the Omics Programme, please go to the website: www.bridge.ku.dk/about/academic-curriculum/bridgeomics/
- Credit
- 0 ECTS
- Type of assessment
- Continuous assessmentRequirement to attend classes
- Type of assessment details
- Attendance and active participation. 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 for analysing patient and biological samples using high-resolution mass spectrometry.
ii) Knowledge on standard go-to software solutions for raw mass spectrometry data analysis including downstream software packages for data interpretation and basic visualization.
iii) Knowledge of important factors influencing pre-analytical sample variability and optimal experimental design for analysis of clinical samples.
iv) Knowledge of biological applications using quantitative proteomics including proteome quantitation and functional protein interaction networks. - Exam registration requirements
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.
Course information
- Language
- English
- Course code
- SBRI19002U
- Credit
- 0 ECTS
- Level
- Part Time MasterPh.D.
- Placement
- Autumn
- Schedule
- See course dates and course programme in Absalon.
- Course capacity
- 20 participants
Study board
- Study Board for the Professionel Master´s Degree Programmes at The Faculty og Health and Medical Science
Contracting department
- Center for Protein Research
Contracting faculty
- Faculty of Health and Medical Sciences
Course Coordinators
- Kristina Bennet Emdal (kristina.emdal@cpr.ku.dk)
- Jesper Velgaard Olsen (jesper.olsen@cpr.ku.dk)
- Moreno Papetti (moreno.papetti@cpr.ku.dk)