SBRI19002U  Translational Discovery Omics II

Volume 2019/2020
Education

BRIDGE - Translational Excellence Programme

 

Content

The main themes covered in the course include:

  • Mass spectrometry technologies
  • Applications of quantitative proteomics in biology
  • Epigenetics and proteomics
  • Cancer tissue analysis
Learning Outcome

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.

Participants must meet the admission criteria in BRIDGE - Translational Excellence Programme
The course is organized with a mixture of student-led lectures and scientific seminars by invited speakers including technical lectures about modern proteomics technologies used to study cellular signalling pathways, protein-protein interactions and global proteome changes. In addition, the course will include group work, case studies/journal clubs, demonstrations, and practical exercises provided and supervised by the world leading specialists in the field.
Oral
Continuous feedback during the course of the semester
Credit
0 ECTS
Type of assessment
Continuous assessment
Course participation
Attendance 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.

  • Category
  • Hours
  • Lectures
  • 8
  • Theory exercises
  • 4
  • Preparation
  • 5
  • Class Seminar
  • 16
  • Total
  • 33