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

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.

Students taking the course are expected to:

• 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

• 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

• Introduction to proteomics and tandem mass spectrometry
• Introduction to phosphorylation and characterization of cellular signaling
• Introduction to protein knock-down techniques including validation of knock-down efficiency using Western blotting, PCR or SRM/PRM.
• Introduction to neural differentiation.

• Quantitative proteomics/phosphoproteomics (including purification and characterisation of phosphorylated peptides)
• Tandem mass spectrometry•Bioinformatics (incl. protein/peptide identification and quantification as well as programmes for pathway-analysis)
• Western blotting
• SRM/PRM
• Cell growing
• RNAi knock-down
• (perhaps additional methods)

Planned lessons:
Total number of planned lessons: 70

Hereof:
Common lessons in classroom/auditorium 30
Common lessons in laboratory 40

The course teaching includes lectures, laboratory exercises, and group work. All these elements are designed to enhance students' understanding of molecular biological techniques, including proteome analysis, phosphoproteome analysis, and bioinformatics.

The lectures introduce key topics such as proteomics, tandem mass spectrometry, phosphorylation, and characterization of cellular signaling, as well as neuronal differentiation of stem cells.

The laboratory exercises constitute a central part of the course, where students gain practical skills in proteome analysis, phosphoproteome analysis, immunostaining, and Western blotting. Students are expected to come prepared with knowledge of protocols and methods. Data from the exercises are analyzed in groups and presented on the final day of the course.

In addition to working with data from the laboratory exercises, the group work also involves preparing presentations on one of the laboratory techniques used, as well as a scientific article related to the current topic.

Outside of scheduled teaching hours, students are expected to work independently and in groups to gain a deeper understanding of the course topics.

• Self-study: Students read the provided compendium and research articles and process the lecture topics.

• Preparation and follow-up: Before the laboratory exercises, students prepare by reading and understanding the protocols and reviewing interactive learning materials. After the exercises, they analyze the results and prepare a presentation, contributing to their overall learning.