SBRI19002U Translational Discovery Omics II
BRIDGE - Translational Excellence Programme
The main themes covered in the course include:
- Mass spectrometry technologies
- Applications of quantitative proteomics in biology
- Epigenetics and proteomics
- Cancer tissue analysis
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 stable isotope labelling and high-resolution mass spectrometry; ii) an overview of the wealth of biological applications that quantitative proteomics screens can be applied in, including proteome quantitation post translational modification (PTM) analysis and protein-protein interaction screens.
Upon completing the course, participants should be able to:
Knowledge
- Demonstrate an understanding of the work-flow of mass spectrometry-based proteomics
- Master the main statistical and deep learning techniques used in the field
- Discuss the models of implementing plasma proteome profiling in the clinic
- Illustrate the uses and special considerations in urinary, cerebrospinal fluid, and other body fluid proteomes
- Oncogenic signalling pathways to identify targetable protein and PTM signatures in cancer patients
- Have basic knowledge in high-throughput assays
Skills
- Use a range of methods for finding, analysing, and integrating heterogeneous biological and medical data in the context of cancer
- Critically evaluate results of such analyses
- Analyse meta-proteomics
- Analyse computational proteomics – raw mass-spectrometry (MS) data processing and bioinformatics
- Use data analysis and visualization programs such as MaxQuant, Perseus, R, and Cytoscape
- Present tissue proteomic data on a specific cancer type for answering biological questions
Competences
- Design cancer tissue sample preparation workflows to preserve in-vivo state of proteome and PTMs
- Perform state-of-the-art liquid chromatography tandem mass spectrometry of clinical samples
- Integrate cancer proteomics data with curated oncogenic signalling pathways
- Acquire, analyse, and interpret plasma proteomics profiling data
- Connect proteomic data to patient diagnoses
- Understand the central aspects of translational omics and be able to discuss and communicate these to other scientists, clinicians, and the public
Geyer, P. E., Holdt, L. M., Teupser, D. & Mann, M. Revisiting biomarker discovery by plasma proteomics. 2017. Molecular Systems Biology. 13, 9, 16 p., 942.
Olsen, J. V. & Mann, M. Status of large-scale analysis of post-translational modifications by mass spectrometry. 2013. Molecular & Cellular Proteomics. 12, p. 3444-52.
Choudhary, C. R., Weinert, B. T., Nishida, Y., Verdin, E. & Mann, M. The growing landscape of lysine acetylation links metabolism and cell signaling. 2014. Nature Reviews. Molecular Cell Biology. 15, 8, p. 536-50 15 p.
- Category
- Hours
- Lectures
- 8
- Class Instruction
- 16
- Preparation
- 5
- Theory exercises
- 4
- Total
- 33
Automatic registration upon appointment in the Translational Excellence Programme
- Credit
- 0 ECTS
- Type of assessment
- Continuous assessmentCourse participationAttendance and active participation
- Exam registration requirements
Participants are automatically registered for the Examination upon course registration.
- Aid
- All aids allowed
- Marking scale
- passed/not passed
- Censorship form
- No external censorship
Criteria for exam assesment
i) an overview of the major high-end quantitative proteomics technologies with focus on stable isotope labelling and high-resolution mass spectrometry;
ii) an overview of the wealth of biological applications that quantitative proteomics screens can be applied in, including proteome quantitation post translational modification analysis and protein-protein interaction screens.
Course information
- Language
- English
- Course code
- SBRI19002U
- Credit
- 0 ECTS
- Level
- Part Time MasterPh.D.
- Duration
- Placement
- Spring
- Schedule
- See course dates and course programme in Absalon
- Course capacity
- 15 participants
- Course is also available as continuing and professional education
- 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
- Jesper Velgaard Olsen (12-6c677572677430716e75677042657274306d7730666d)
- Moreno Papetti (14-6f7174677071307263726776766b42657274306d7730666d)
- Tanveer Singh Batth (7-7731656477776b43667375316e7831676e)