Application Deadline: April 1st, 2023
Arrival: August 9th by 6pm ESTDeparture: August 22nd around 12pm EST
CSHL Courses are intensive, running all day and often including evenings and weekends; students are expected to attend all sessions and reside on campus for the duration of the course.
Robert Chalkley, University of California San Francisco
Darryl Pappin, Cold Spring Harbor Laboratory
Chad R. Weisbrod, National High Magnetic Field Laboratory
COVID-19: All participants planning to attend in-person will be required to attest to recent COVID vaccination (within one year of the course’s start date) with an FDA or WHO approved vaccine. Additional safety measures will be in line with current NY and Federal Guidelines applicable in Summer 2023.
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.