August 1 - 14, 2017
Application Deadline: April 15, 2017


Giselle Knudsen, University of California San Francisco
Katalin Medzihradszky
, University of California San Francisco
Darryl Pappin, Cold Spring Harbor Laboratory
Will Thompson, Duke Center for Genomic and Computational Biology

Module Leader:
Aarti Kawatkar, AstraZeneca

See the roll of honor - who's taken the course in the past
The 2016 course (including students as co-authors) recently published a joint paper
on the Protein Interaction Reporter (PIR) technology developed in Jim Bruce's lab

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 or FASP protocol 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. They will use affinity chromatography for phosphopeptide enrichment, and the characterization of the resulting complex mixture, including site assignment, 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. Students will learn both single-dimension and multidimensional separation methods. In a section focused on targeted proteomics, students will learn to analyze and process shotgun proteomic data for the development of SRM/MRM assays that accurately identify and quantify targeted proteins. Students will design transitions for selected peptides and perform SRM/MRManalyses. They will learn to process and interpret the acquired data to measure changing quantities of targeted proteins in a variety of biological samples. For all sections of the course, a strong emphasis will be placed on data analysis. There will be opportunity to discuss individual research projects.

A series of outside lecturers will discuss various proteomics topics including: differential gel electrophoresis (DIGE), de novo sequence 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.

Confirmed 2017 Speakers:

Lissa Anderson, National High Magnetic Field Laboratory
Alexander Greninger,
Fred Hutchinson Cancer Research Center
Michelle Heck,
Cornell University
Karl Clauser,
Broad Institute of MIT and Harvard
Charles Farnsworth,
Cell Signaling Technology
Adam Hendricks,
Richard Jacob,
Matrix Science
Tsung-Heng Tsai,
Northeastern University
Andrew Zhang, AstraZeneca

Support & Stipends

Major support provided by the National Institute of Child Health & Human Development

Stipends are available to offset tuition costs as follows:


US applicants (National Institute of Child Health & Human Development)
Interdisciplinary Fellowships (transitioning from outside biology)  & Scholarships (transitioning from other biological disciplines) (Helmsley Charitable Trust)
International applicants (Howard Hughes Medical Institute)

Please indicate your eligibility for funding in your stipend request submitted when you apply to the course. Stipend requests do not affect selection decisions made by the instructors. 

Cost (including board and lodging): $3,810

This button links to a short form which confirms your interest in the course. No fees are due until you have completed the full application process and are accepted into the course.

Students accepted into the course should plan to arrive by early evening on July 31 and plan to depart after lunch on August 14.