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:
- 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
- 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
- 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.
- Class Instruction
- Theory exercises
Automatic registration upon appointment in the Translational Excellence Programme
- 0 ECTS
- Type of assessment
- Continuous assessmentCourse participationAttendance and active participation
- Exam registration requirements
Participants are automatically registered for the Examination upon course registration.
- 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.