Key Dates
Application Deadline: April 1st, 2023
Arrival: August 9th by 6pm EST
Departure: 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.
Instructors:
Robert Chalkley, University of California San Francisco
Darryl Pappin, Cold Spring Harbor Laboratory
Chad R. Weisbrod, National High Magnetic Field Laboratory
Cassandra Wong, Lunenfeld-Tanenbaum Research Institute, Canada
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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.
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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 will be trained using high-sensitivity nano LC-ESI-MS and tandem mass spectrometry. An introduction to manual interpretation of data will be followed by training in different search engines and bioinformatic approaches for data evaluation. Students will use label-free and covalent isotopic-labeling quantitative approaches to profile changes. This will include a section using Skyline to quantify peptides at the MS1 level, development of PRM targeted assays for quantification at the MS2 level, and an introduction to DIA analysis for more comprehensive fragmentation analysis. Students will be shown how to recognize unexpected post-translational modifications. Diverse techniques for PTM peptide enrichment, including affinity chromatography and immune-enrichment will be carried out and the characterization of the resulting complex mixtures, including site assignments will be performed. For training in protein complex and interaction analysis, students will process and analyze proximity-labeled samples and learn how to evaluate the specificity of results.
A section on intact protein or large peptide analysis will demonstrate the benefits of this approach and cross-linking analysis for structural studies will also be discussed.
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 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.
2023 Speakers Include:
Angelo Andres, AstraZeneca,
Paolo Cifani, Cold Spring Harbor Laboratory
Karl Clauser, Broad Institute of MIT and Harvard
Jennifer Geddes-McAlister, University of Guelph, Guelph, Canada
Casey Greene, University of Colorado, Anschutz Medical Campus
Ventzi Hristova, AstraZeneca
Julia Kitaygorodsky, Sinai Health, Toronto, Canada
Paraveen Kumar, AstraZeneca
Alissa Nelson, Cell Signaling Technology
Lindsay Pino, Talus Biosciences,
Reuben Samson, Sinai Health, Toronto, Canada
Meha Singh, AstraZeneca
Michael Trnka, University of California San Francisco