Chem219: Mass Spectrometry and Proteomics

Course Description: Mass spectrometry embodies a suite of key, enabling technologies required for advanced studies in protein and cell biology, proteomics and epigenetics.

This course will cover the fundamental principles as well as the relative merits of currently important instrument platforms in mass spectrometry for protein sequence and complex mixture analysis, assignment of posttranslational modifications and relative quantitation.

Methods for sample preparation and mass spectral data acquisition will be discussed together with how our UCSF bioinformatics tool box is employed to aid the interpretation and presentation of mass spectral information.

Simultaneously, there will also be a series of laboratory sessions in which participants will gain hands on experience with the entire protein analysis/characterization process starting from an unknown sample[IP, complex, gel band/spot (either your own or one provided)] , through sample digestion, chromatographic separation and data acquisition, processing and results interpretation.

Time will be scheduled the last couple of days to be devoted to oral presentations of each participant’s experimental results to the class for class discussion in lieu of examination.

Course Calendar — Spring 2010

Mon March 29	Tue March 30	Wed March 31	Thu April 1	Fri April 2	Sat April 3	Sun April 4
Discussions	Lecture 1 MS Intro (pdf)	Lecture 2 Sample Prep (pdf)	Lab 1 Digest Samples (pdf) Group 1 starts 9am Group 2 starts 1pm	Lab 2 Extract Peptides (pdf) Group 1 starts 9am Group 2 starts 1pm
Mon April 5	Tue April 6	Wed April 7	Thu April 8	Fri April 9	Sat April 10	Sun April 11
	Lecture 3 Protein Identification (pdf)	Protein Prospector Training (10am -) (pdf)		Lecture 4 Post-translational Modifications (pdf)
Mon April 12	Tue April 13	Wed April 14	Thu April 15	Fri April 16	Sat April 17	Sun April 18
	Lecture 5 Quantification (pdf)

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 2010 lectures will be held 12 noon - 2pm on the Mission Bay Campus in Genentech Hall Room GH-271.

Lecture	Lecturer	Topic
1 (Tu.3/30)	Al Burlingame	Mass Spectrometry Fundamentals: Ionization, Instrumentation; ion optics, resolution and mass accuracy; why these are important at protein vs peptide level.
2 (Wed.3/31)	Shenheng Guan	Sample preparation: Gels and Chromatography; IP/Tags. Digestion. What shouldn't be in the sample - Contaminants.
3 (Tu.4/6)	Mike Baldwin	Protein Identification. Basics of peptide fragmentation. Database searching. How to measure the reliability of assignments.
4 (Fri.4/9)	Mike Baldwin	PTMs: Protein vs peptide analysis. PTM enrichment, modification specific scans/ions.
5 (Tu.4/13)	Shenheng Guan	Quantitation strategies.