Chem219: Protein Mass Spectrometry and Proteomics
April 1 - 19, 2013
Course Description: Mass spectrometry is comprised of a broad suite of advanced technologies important for identification of unknowns for most classes of biomolecules (and a large number of other molecules as well), the characterization of complex mixtures using chromatography coupled mass spectrometry experiments, studies of their covalent modifications both posttranslational and xenobiotic, the analyses of modification-site-specific protein network kinetics/dynamics and studies of intact protein complexes, e.g. pol II. Proteomics is broadly concerned with the global protein composition of cells, sub-cellular organelles, complexes and machines and how their class functions are modulated by posttranslational dynamics, e.g. kinome homeostasis and dynamics and the effects of molecular defects on aberrant signaling pathways and networks, etc.
This course will focus on the practical aspects, i.e. experimental and spectral interpretation, involved in the identification of proteins and their posttranslational modifications. It will cover the fundamental principles of currently important mass spectrometry instrument platforms. It will provide an overview of key problems that are being tackled and solved at the protein level relevant to cell function/dysfunction; the detection and assignment of protein posttranslational modifications; and studies of site-specific dynamics/relative quantitation.
Methods for sample preparation and mass spectral data acquisition will be discussed together with how our UCSF bioinformatics toolbox (ProteinProspector) may be employed to facilitate the interpretation and presentation of mass spectral information.
Simultaneously, laboratory sessions are required. Participants will gain hands-on experience with the entire protein analysis/characterization processing stream - starting from an unknown sample [IP, complex, gel bands/spots (either your own and/or provided)], through sample digestion, chromatographic separation and data acquisition, processing and results interpretation. Samples will be provided by the course instructors.
Blocks of time will be scheduled for class discussion of the experimental results you obtain.
No need to register! Open to anyone! Free! Turn up only to the lectures you are interested in! Opportunity to analyze your own samples!
If you want to participate in either the lectures and/or the labs please email Al Burlingame, so that instructors can have an idea of the number of people who will attend.
Lecture Schedule: Spring 2013
Wednesdays and Thursdays, 10:00am - 12 noon
Mission Bay Campus, Genentech Hall, Room GH 271.
Labs by arrangement.
| Lecture | Lecturer | Topic |
|---|---|---|
| 1 (Wed.4/3) |
ALB | Mass Spectrometry Fundamentals: Ionization, Instrumentation; ion optics, resolution and mass accuracy; why these are important at protein vs peptide level. |
| 2 (Thu.4/4) |
ALB | Sample preparation: Gels and Chromatography; IP/Affinity Tags. Digestion. What shouldn't be in the sample - Contaminants. |
| 3 (Wed.4/10) |
RJC | Protein Identification. Basics of peptide fragmentation processes. Database searching. How to measure the reliability of assignments. |
| 4 (Thu.4/11) |
JO | PTMs: Posttranslational modifications: Protein vs peptide analysis. PTM enrichment, modification specific scans/ions. |
| 5 (Wed.4/17) |
AU | Quantitation strategies (SILAC, iTRAQ, MRM). |
| 6 (Thu.4/18) |
MT | Architecture of protein complexes and machines. |
Lecturers
| ALB | - | Al Burlingame |
| RJC | - | Robert Chalkley |
| JO | - | Juan Oses |
| MT | - | Mike Trnka |
| AU | - | Anatoly Urisman |