June 10 - 25, 2023

Key Dates:
Application Deadline: March 1, 2023
Arrival: June 9th by 6pm EST
Departure: June 25th 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.

Justin Cross, Memorial Sloan Kettering Cancer Center
Adam Rosebrock, Maple Flavored Solutions

Ifat Abramovich, Technion, Israel Institute of Technology
Amy Caudy, Maple Flavored Solutions, LLC

David Sumpton, Cancer Research UK, Beatson Institute for Cancer Research


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.

Follow us on Twitter @cshlmetabo

Advances in genomics, transcriptomics, and proteomics have enabled both broad and deep analysis of genomes and their encoded proteins. Metabolomics focuses on measuring the biochemical contents and activities of cells, tissues, and organisms.  Biochemical phenotypes represent a unique view into the dynamic state of biological systems, and are relevant to a range of fields, from model organisms to patients, from bioprocess to bedside. 

CSHL's Metabolomics Course combines theoretical and practical training including hands-on experience with a range of cutting-edge approaches to interrogate biochemical state.  Mass spectrometry (MS) is currently the most powerful and flexible approach in the metabolomics toolbox; students will become proficient in the generation and analysis of both gas-chromatography (GC) and liquid-chromatography (LC) mass spectrometry data.  New biochemistry awaits discovery, even in well characterized systems.  Participants will learn how to quantitate known metabolites in complex biological samples and how to discover and characterize unknown compounds using LC- and GC- mass spectrometry.  

Metabolomics makes use of many complementary tools in addition to mass spectrometry.

Students will gain hands-on experience in:

  • Gain hands-on experience with multiple LC- and GC- mass spectrometers to directly measure metabolites and metabolic flux
  • Engage in friendly competition to develop practical chromatographic separations
  • Measuring metabolic state in live cells using the Agilent Seahorse XF platform

The Metabolomics Course integrates practical lab sessions, hands-on data analysis, and lecture-based learning. Students have the opportunity to interact with instructors and TAs as well as a diverse panel of field-leading guest speakers who present both formal talks and a nuts-and-bolts view of metabolomics in their labs.

Objectives for Students:

  • Become proficient in quantitative and qualitative analysis of GC- and LC-MS data using vendor and open-source tools
  • Understand the use cases and limitations of currently available metabolomics instrumentation and be able to identify the right approach for a given question
  • Learn key factors in experimental design and sample preparation that enable collection of interpretable and actionable metabolomics data
  • Gain the core knowledge and vocabulary required to fruitfully interact with other researchers in the metabolomics field

Past lab exercises have included:

  • Development of mass spectral transitions for targeted metabolite analysis using a triple-quadrupole LC-MS.
  • Full scan/untargeted analysis of gene knockout/drug treatment, including follow-up characterization of significantly changed metabolites by tandem mass spectrometry and other methods for identification.
  • Identification of significantly changed metabolites and pathways in perturbed biological systems including the development of a targeted methods for new analytes by triple-quadrupole LC-MS.
  • Determination of analytical specifications of merit (LOD/LOQ/IDL), linearity, and steps necessary for method validation.
  • Measurement of metabolite flux using stable isotope labeling (kinetic flux profiling).
  • Determination of reaction kinetics using enzyme assays.
  • Determination of glycolytic and respiratory rate by Seahorse XF analysis.
  • Development of optimized chromatographic and ionization conditions for separation of both focused and multi-analyte analyses.
  • Identification of metabolic constituents of complex fermentation products.

Successful course participants have come from a range of backgrounds:

The goal of this course is to make students proficient in metabolomic analysis. Applicants do not need to have prior experience in metabolomics or mass spectrometry. Alumni range in age from senior graduate students through full professors and established industrial scientists.

Data analysis is a large and growing part of the field; quantitative biologists who wish to gain hands-on experience in data generation are encouraged to apply. Strong applicants typically have a:

  • Background in a field of biology, chemistry, or computation that will add to the rich dialogue among course participants
  • Desire to incorporate metabolomics into their own research in the near future
  • Research project or program that would benefit from metabolic experimental approaches and from the interaction with like-minded students and instructors

Multiple hardware platforms are typically represented in the course.  Past years have provided hands-on experience with GC-MS, LC- time-of-flight, triple-quadrupole (Agilent Technologies) and Q-Exactive High Resolution Accurate Mass instruments (Thermo Scientific), and Seahorse extracellular analysis (Agilent Technologies).

2023 Confirmed Speakers:
Allegra Aron, UC San Diego
Bryson Bennett, Calico Life Sciences, LLC
Michelle Clasquin, Pfizer
Alex Dexter, National Physical Laboratory, United Kingdom
Annie Evans, Metabolon
Teresa Fan, University of Kentucky
Eyal Gottlieb, Technion Israel Institute of Technology, Haifa, Israel 
Kayvan Keshari, Memorial Sloan Kettering Cancer Center
Ryan Sheldon, Van Andel Institute
Matthew Vander Helden, MIT
Johan Vander Voorde, Beatson Cancer Institute, Glasgow, United Kingdom 

Support & Stipends:

We would like to acknowledge the following companies that provided invaluable support:
Agilent Technologies, Thermo Fisher Scientific
Agilent Technologies, Thermo Fisher Scientific

Major support provided by:  Helmsley Charitable Trust and Howard Hughes Medical Institute.


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): $4,660

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

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: