August 7 - 20, 2019
Application Deadline: April 1, 2019


Giselle Knudsen, Alaunus Biosciences
Robert Chalkley, University of California San Francisco
Darryl Pappin, Cold Spring Harbor Laboratory

Part-Time Instructors:

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

Module Leaders:

Aarti Kawatkar, AstraZeneca

See the roll of honor - who's taken the course in the past

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

Students will gain practical experience in sample preparation with in-solution digestion, then students will be trained using high-sensitivity nano LC-ESI-MS and tandem mass spectrometry. Different search engines and bioinformatic approaches will be introduced for data evaluation. For the shotgun proteomic analysis sections, students will use label-free and covalent isotopic-labeling quantitative approaches to profile changes.

In a section focused on targeted proteomics, students will learn to analyze and process shotgun proteomic data for the development of SRM/PRM assays 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.  Students will be shown how to recognize unexpected post-translational modifications. Diverse techniques for PTM peptide enrichment, including affinity chromatography and immune-enrichment for phosphopeptides will be carried out and the characterization of the resulting complex mixtures, including site assignments, will be performed.

A series of outside lecturers will discuss various proteomics topics including:

  • de novo sequence analysis
  • Intact protein analysis
  • Cross-linking analysis for structural studies
  • Data-independent analysis for comprehensive results across many samples
  • Protein complex analysis

Finally an industrial lecture and practical component by drug discovery scientists will allow participants to understand how chemoproteomics techniques can be routinely used in industry to profile compounds and potential protein targets.

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), if so desired.

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.

2019 Speakers Include:

Lissa Anderson, NHMFL-FSU
Karl Clauser, Broad Institute of MIT and Harvard
Zsuzsanna Darula, the Biological Research Centre, Szeged, Hungary
Charles Farnsworth, Cell Signaling Technology
Adam Hendricks, AstraZeneca
Thomas Liro,
Fiona Pachl,
Brian Searle,
Institute for Systems Biology
Michael Trnka, University of California San Francisco

We anticipate this course will be supported with funds provided by: National institute of Child Health & Human Development

Support & Stipends:

On average, 50% of trainees receive financial support on a needs-basis.

Stipends are available to offset tuition costs as follows-


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): $3,960 

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 August 6 and plan to depart after lunch on August 20.

Before applying, ensure you have:
  1. Personal statement/essay;
  2. Letter(s) of recommendation;
  3. Curriculum vitae/resume (optional);
  4. Financial aid request (optional).
    More details.

If you are not ready to fully apply but wish to express interest in applying, receive a reminder two weeks prior to the deadline, and tell us about your financial aid requirements, click below: