Mass Spectrometry of Proteins

Course goals

Upon completion of the course, the student will be able to:

• Describe the basic principles of mass spectrometry
• Explain the operating principles of common MS instruments
• Interpret peptide and protein spectra
• Describe the basics of Proteomics and related MS techniques in Structural Biology
• Explain the operating principles of common chromatography methods in proteomics
• Reason about which type of instrumentation and chromatography can be used for specific MS applications
• Design an experimental setup for an MS experiment

Content

Mass spectrometry (MS) is an important analytical technique for the identification and structure elucidation of biomolecules. Not only can mass spectrometry be used to determine the molecular weight of a compound, but one can also extract information about the functional groups of a compound and often its structure from a fragment spectrum. The application of MS is broad: it is used to map small organic molecules, to study proteins, and even to analyze protein complexes or whole cells. Because MS can measure how this range of biomolecules changes as a function of their cellular environment, it is one of the most important analytical chemical methods in biological and biomedical research.

This course will introduce you to the theoretical background of mass spectrometry and the fundamental processes that take place in a mass spectrometer. In addition, you will learn how mass spectrometry is applied in biological and (bio)medical research. The emphasis is on protein mass spectrometry and the content can be divided into three blocks:
1) Fundamentals and Instrumentation
2) Proteomics by LC-MS/MS
3) MS in structural biology.

Attention is also given to the practicalaspects of MS, such as interpreting spectra, database searching and bioinformatics.

For Chemistry students:
Protein Mass Spectrometry is part of the Biochemistry curriculum and connects to biomolecular chemistry level 1 and Chemical Biology (level 2). The Ethics and Society curriculum line is also covered in the course.

For MBLS students:
The course partially overlaps with MBLS-201 (Biophysical Methods and Structural Biology) but provides a lot more depth on protein mass spectrometry.