Instructors:

Giselle Knudsen, University of California San Francisco
Katalin Medzihradszky, University of California San Francisco
Darryl Pappin, Cold Spring Harbor Laboratory

Part-Time Instructors:

Erik Soderblom, Duke University
Will Thompson, Duke Center for Genomic and Computational Biology

This intensive laboratory and lecture course will focus on cutting-edge proteomic approaches and technologies.

Students will gain practical experience isolating, purifying and identifying protein complexes: sample-preparation with in-solution digestion will be performed, then students will be trained using high-sensitivity nano HPLC coupled with nanospray-ESI and tandem mass spectrometry analysis. Different search engines and bioinformatic approaches will be introduced for data evaluation. Students will be shown how to recognize unexpected post-translational modifications. Diverse techniques for PTM peptide enrichment, including affinity chromatography for phosphopeptides and immuno-enrichment of GlyGly-Lys, methyl-Arg, and phospho-Tyrpeptides, and the characterization of the resulting complex mixtures, including site assignments, will be performed. For shotgun proteomic analysis sections, students will use label-free and covalent isotopic-labeling quantitative approaches to profile changes in protein complexes and whole proteomes. In a section focused on targeted proteomics, students will learn to analyze and process shotgun proteomic data for the development of SRM/PRMassays that accurately identify and quantify targeted proteins. Students will design transitions for selected peptides and perform SRM/PRM analyses. They will learn to process and interpret the acquired data to measure changing quantities of targeted peptides in a variety of biological samples, and specifically spend significant time using Skyline for both MS1 and MS2 data analysis.  For all sections of the course, a strong emphasis will be placed on data analysis. There will be opportunity to discuss and provide feedback on individual research projects, and students will have the opportunity to learn to process their own data (acquired outside the course) in Skyline if so desired.

An industrial lecture series will be delivered by drug discovery scientists. The students will get in depth knowledge about chemoproteomics techniques routinely used in industry,  and how they are used to profile compounds and potential protein targets. This will be followed by lab work on in-lysate affinity enrichment techniques and a deep dive into data analysis. This will broaden students’ vision towards chemoproteomics application in drug discovery programs.

A series of outside lecturers will discuss various proteomics topics including: de novo sequence analysis, intact protein analysis, advanced mass spectrometry methods, glycosylation, and functional proteomics. The aim of the course is to provide each student with the fundamental knowledge and hands-on experience necessary for performing and analyzing proteomic experiments. The overall goal is to train students to identify new opportunities and applications for proteomic approaches in their biological research.