June 8 - 24, 2019
Application Deadline: March 1, 2019


Amy Caudy, The Donnelly Centre, University of Toronto, Canada
Justin Cross, Memorial Sloan Kettering Cancer Center
Adam Rosebrock, Stony Brook School of Medicine, State University of New York


Ifat Abramovich, Technion Institute of Technology, Israel
David Sumpton, 
Beatson Institute for Cancer Research, United Kingdom

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

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 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 Metabolomics 2019 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:

  • Measuring metabolic state in live cells using the Agilent Seahorse XF platform
  • Determine reaction kinetics for purified enzymes using in vitro assays
  • Engage in friendly competition to develop practical chromatographic separations

Metabolomics 2019 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 currently available 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 a 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 your 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).

2019 Guest Speakers Include:

Daniel Amador-Noguez, University of Wisconsin-Madison
Michelle Clasquin, Pfizer Inc
Annie Evans, Metabolon
Whei-Mei (Teresa) Fan, University of Kentucky College of Medicine
Eyal Gottlieb, Technion Israel Institute of Technology
Kayvan Keshari, Memorial Sloan Kettering Cancer Center
Tobias Kind, University of California Davis
Kyu Rhee,
Weill Cornell Medical College
Hannes Rost, University of Toronto
Matthew Vander Heiden, Massachusetts Institute of Technology

Support & Stipends:

Major support provided by: National Institute of General Medical Sciences, Helmsley Charitable Trust and Howard Hughes Medical Institute.


Major equipment support provided by: Agilent Technologies, Thermo Fisher Scientific
Donations: Agilent Technologies, Thermo Fisher Scientific

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): $4,645

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 Friday June 7 and plan to depart after lunch on Monday June 24.

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: