Chem219: Mass Spectrometry and Proteomics
This course will next be taught in the Spring Quarter of 2010. Below is the course description and schedule for last year's course. It is anticipated that the 2010 course will follow a similar schedule.
Course Description: Mass spectrometry is a key, enabling technology in most proteomic analyses. This course will cover the fundamentals and applications of mass spectrometry in protein identification and peptide sequence analysis. Current instrument designs, their analytical properties and relative merits will be discussed, methods for sample preparation and mass spectral data acquisition will be reviewed, and then methods and software for data analysis will be presented. Techniques specific for analysis of post-translational modifications (PTMs) and quantitative comparisons of protein composition will also be summarized.
Simultaneously, there will also be a series of laboratory sessions in which attendees will be able to go through the entire sample analysis process starting from a gel band/spot (either their own or one provided), through sample digestion, data acquisition, analysis and interpretation. At the end of this, participants will be expected to give an oral presentation of their results for class discussion in lieu of examination.
Course Calendar — Spring 2009
| Mon May 11 |
Tue May 12 |
Wed May 13 |
Thu May 14 |
Fri May 15 |
Sat May 16 |
Sun May 17 |
| Lecture 1 Intro |
Lecture 2 Sample Prep |
Digest Samples |
Extract Peptides & Acquire Data (Lab) |
|||
| Mon May 18 |
Tue May 19 |
Wed May 20 |
Thu May 21 |
Fri May 22 |
Sat May 23 |
Sun May 24 |
| Lecture 3 Protein Identification |
Data Analysis & Training (Lab) |
Lecture 4 Post-translational Modifications |
Lecture 5 Quantitation |
|||
| Mon May 25 |
Tue May 26 |
Wed May 27 |
Thu May 28 |
Fri May 29 |
Sat May 30 |
Sun May 31 |
| Present Results |
KEY: Dates highlighted in AQUA are set aside to Analyze Results and Prepare Final Presentation.
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 Robert Chalkley, so that instructors can have an idea of the number of people who will attend.
Lecture Schedule: Spring 2009 lectures will be held 10am - 12noon on the Mission Bay Campus in Genentech Hall Room GH-S271.
| Lecture | Lecturer | Topic |
|---|---|---|
| 1 (Mon.5/11) |
S. Guan | Mass Spectrometry Fundamentals: Instrumentation; ion optics, resolution and mass accuracy; why these are important at protein vs peptide PTM level. |
| 2 (Wed.5/13) |
R.Chalkley | Sample preparation: Gels and Chromatography; IP/Tags. What shouldn't be in the sample. Contaminants. Digestion. Cross-linking studies. |
| 3 (Mon.5/18) |
R.Chalkley | Protein Identification: Database searching. Basics of peptide fragmentation. How to measure the reliability of assignments. |
| 4 (Wed.5/20) |
K.Medzihradszky | PTMs: Protein vs peptide analysis. PTM enrichment, modification specific scans/ions. |
| 5 (Fri.5/22) |
A.Falick | Quantitation strategies. |