Meetings & Courses Program

Crossroads of Biology

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Proteomics
August 5 - 19, 2025

Key Dates
Application Deadline:  March 31, 2025
Arrival: August 5th by 6pm EST
Departure: August 19th 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
Chad R. Weisbrod, National High Magnetic Field Laboratory
Cassandra Wong, Lunenfeld-Tanenbaum Research Institute, Canada

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.

2024 Invited Speakers Include:
Angelo Andres, AstraZeneca, Waltham, MA 
Sophia Chung, AstraZeneca, Waltham, MA 
Paolo Cifani, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 
Karl Clauser, Broad Institute of MIT and Harvard, Cambridge, MA 
Ugo Dionne, Lunenfeld-Tanenbaum Research Institute, Toronto, Canada 
Jennifer Geddes-McAlister, University of Guelph, Guelph, Canada 
Aarti Kawatkar, AstraZeneca, Waltham, MA 
Julia Kitaygorodsky, Lunenfeld-Tanenbaum Research Institute, Toronto, Canada 
Alissa Nelson, Cell Signaling Technology, Danvers, MA 
Fiona Pachl, AstraZeneca, Waltham, MA 
Lindsay Pino, Talus Biosciences, Seattle, WA 
Michael Trnka, University of California San Francisco, San Francisco, CA 

This course is supported with funds provided by: National Institute of Child Health & Human Development

Support & Stipends:

On average, 50% of trainees receive some 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): $4,650 USD

No fees are due until you have completed the full application process and are accepted into the course.

Before applying, ensure you have (all due March 31):
  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: