David R. Goodlett
Covers the basics of modern ionization methods and mass analyzers; small molecule structure assignment, quantitative assay development by LC-MS and metabolomics; quantitative discovery-based proteomics and validation methods; and peptide sequence determination, post-translational modification mapping, and protein structure determination methods. Prerequisite: permission of instructor. Offered: Sp.
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.
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