Translational Discovery Omics II

Course content

The main themes covered in the course include:

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

BRIDGE - Translational Excellence Programme

 

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

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.

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

Oral
Continuous feedback during the course of the semester
ECTS
0 ECTS
Type of assessment
Continuous assessment
Course participation
Attendance and active participation
Aid
All aids allowed
Marking scale
passed/not passed
Censorship form
No external censorship
Criteria for exam assessment

 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.

Part time Master and Diploma courses

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