BMB535: Experimental Proteomics - Characterization of cellular signaling using quantitative proteomics

• Have knowledge of fundamental molecular biology terms and biochemistry processes (the content of BMB533 and BMB508 is assumed known)


• Be able to use traditional it-tools, including excel


• Active participation is expected, including an oral presentation from the students in groups


• Knowledge regarding general laboratory safety is expected

The course builds on the knowledge acquired in the courses at the second year and combines elements from several courses into one molecular biology problem which is explored experimentally and related to information extracted from relevant literature.

In relation to the competence profile of the degree it is the explicit focus of the course to:

• Ability to independently plan and perform studies with the methods used


• Present and pass on knowledge obtained in the course


• Critically evaluate the results obtained with the methods used in the course


• The course includes laboratory-based projects, providing personal competence in organizing the laboratory work.


• The laboratory projects will be made in teams in order to strengthen their ability to cooperate in all phases of the work.

• Describe the basic principles behind tandem mass spectrometry


• Understand and interpret data generated by tandem mass spectrometry


• Describe different methods used for quantitative proteomics


• Understand the role of post-translational modifications in cellular signaling in eukaryotic cells


• Understand the principle of the characterization of phosphorylated proteins by tandem mass spectrometry, including enrichment of phosphorylated peptides


• Understand the principles of working with cell cultures and protein knock-down


• Explain and perform methods for validation of knock-down experiments, incl. Western blotting, PCR and Selected/Parallel Reaction Monitoring (SRM/PRM)


• Use the bioinformatics programs utilized in the course

• Theory:




• Introduction to proteomics and tandem mass spectrometry


• Introduction to phosphorylation and characterization of cellular signaling pathways


• Introduction to protein knock-down techniques, and validation of knock-down efficiency using Western blotting, PCR or SRM / PRM


• Introduction to neural differentiation




• Methods/Techniques:




• Quantitative proteomics/phosphoproteomics (including purification and characterization of phosphorylated peptides)


• Electrospray tandem mass spectrometry


• Bioinformatics (incl. protein/peptide identification and quantitation and pathway analysis programs)


• Western blotting


• SRM/PRM


• Cell culture


• RNAi knock-down


• (others)

NB: This training course is conducted according to legal safety instructions, but using experimental protocols and chemicals that are suspected to be potentially harmful to pregnant / lactating. Pregnant / nursing students should therefore contact the course coordinator in good time before course registration or as soon as possible.

At the faculty of science, teaching is organized after the three-phase model ie. intro, training and study phase.

Intro phase: 15 hours

Skills training phase: 55 hours, hereof:

• Tutorials: 15 hours
• Laboratory exercises: 40 hours

Activities during the study phase:

• Read the compendium 
• Read a few articles
• Watch a few videos
• Preparation for laboratory work

As the course is an intense summer course, the course days will consist of element both from the intro- and training phase, whereas the study phase will take place both prior and during the course.