Time Schedule:
David R. Goodlett
MEDCH 541
Seattle Campus
Covers basics of sample preparation, data generation, instrumentation, ionization, and data interpretation of peptide tandem mass spectra manually. Uses database search engines and bioinformatics in systems biology related proteomics. Prerequisite: MEDCH 530 or permission of instructor. Offered: odd years; Sp.
Class description
MEDCH 541. Mass spectrometry related to current proteomics and protein chemistry methods. Shotgun proteomics and top down protein sequencing to be covered. Basics of mass spectrometry instrumentation and fragmentation methods used in proteomics covered including ESI and MALDI ionization. Basics of sample preparation, data generation and data interpretation of peptide tandem mass spectra manually and via database search engines to be covered. Bioinformatics used in Systems Biology related proteomics efforts will be reviewed. Prerequisite permission of instructor or Med Chem 530. Offered: Spring Quarter of Odd years.
Student learning goals
We will practice manual de novo assingment of amino acid sequence to peptide tandem mass spectra
We will practice interpretation of large proteomic data sets using trans-proteomic pipleine tools such as peptide prophet and protein prophet and SEQUEST, Phenyx, Popitam and more
shotgun proteomic experimentation: students will prepare a sample, analyze it with MS facility staff by LCMSMS and then interpret the data.
when and how to conduct various types of quantitative proteomic experiments
General method of instruction
didactic lectures + guest lectures from local (FHCRC ISB and UW) proteomic experts.
Recommended preparation
some understanding of protein chemistry or basic biochemistry
Class assignments and grading
One take home exam, three lab practicals (ESI and the QTOF, MALDI and the TOF-TOF , dbase searching using SEQUEST and the PROPHETS) and in class homework interpreting tandem mass spectra.
Grade will be a composite of the following: one take home exam, the lab practicals and in class homework interpreting tandem mass spectra
