BMB542: Biomedical mass spectrometry – principles and applications

The course has limited seats and in case of too many applications, priority is given to the timely registration by date of registration.

• Have knowledge of organic chemistry, biochemistry, cell biology, biomedicine, as well as basic skills within mathematics, physics and statistics, corresponding to the courses in the first five semesters of a science degree at SDU.
• Have basic computer skills
• Have knowledge of the chemical structure of biomolecules including metabolites, drugs, lipids, proteins and nucleic acids
• Be able to use chemical and biochemical terminology and biomedical concepts.
• Have an understanding of the structure of molecules and cells, metabolism and other biochemical processes and basic cell signalling mechanisms.

The course builds on the knowledge acquired in the courses in cell biology, chemistry and biochemistry in the first five semesters of the bachelor programme, and gives an academic basis for studying the topics protein chemistry and proteome analysis, that are part of the degree. In addition, the course gives the academic basis for carrying out research projects and master projects with biomedical mass spectrometry, e.g. the topics metabolomics, lipidomics, protein chemistry/proteomics and computational biomedicine.

• Understand and describe common ionisation methods (ESI, MALDI, EI/CI)
• Understand the importance of correct sample preparation, including understanding the physico-chemical parameters that affect ionisation of biomolecules and matrix effects.
• Outline the principles of gas phase separation of ions in electric and magnetic fields.
• Describe the structure of mass spectrometers and tandem mass spectrometers including hybrid instruments
• Interpret mass spectra both manually and using computational tools
• Understand the principles of molecular structure determination using mass spectrometry
• Understand the principles of quantitative determination of biomolecules using internal standards and stable isotopes.
• Select the best mass spectrometry technique to study a given class of biomolecules e.g. drugs, proteins, peptides, lipids, metabolites, nucleic acids.
• Evaluate and suggest how Mass spectrometry can be used as a central method in specific biological and biomedical research projects.

• Short introduction to mass spectrometry and its many uses
• History and development of mass spectrometry
• Chemical structures and stable isotopes
• Sample preparation, biomolecules
• Separation methods (LG, GC, electrophoresis) and mass spectrometry
• Ionisation methods with main focus on ESI and MALDI
• Mass analysors (TOF, quadropole, orbitrap etc.) and their specifications
• Hybrid mass spectrometers
• Tandem mass spectrometers
• Interpretation of mass spectra of biomolecules
• Biomolecular structure determination by tandem mass spectrometry
• Data analysis, computational tools and statistics
• Cutting edge mass spectrometry methods and development

• Analysis of drugs and their secondary metabolites
• Qualitative and quantitative analysis of metabolites and lipids
• Protein chemistry and protein structure analysis by mass spectrometry including peptide sequencing by tandem mass spectrometry
• Qualitative methods for stable isotope labelling
• The post-translational and chemical modifications of proteins
• Imaging mass spectrometry
• Forensic science, drug abuse, poisoning etc.
• Food analysis

Planned lessons:
Total number of planned lessons: 32
Hereof:
Common lessons in classroom/auditorium: 26
Common lessons in laboratory: 6

The common lessons is based on lectures which will introduce the basic concepts and methods. The lectures will be followed up by three mandatory two-hour demonstrations in the laboratory, which are then followed by one tutorial with assignments and data interpretation. In addition, there will be another three tutorials focused on interpretation of mass spectra and training in the use of data analysis tools. Thus, both theoretical and practical knowledge is obtained, as well as skills within data analysis and interpretation.

• Reading of scientific material: book and selected review papers and research papers
  
• Repetition of scientific material, in connection with tutorials and lab demonstrations
• A limited number of home assignments