Recent research in cancer biology, aging, microbial pathogenesis, and many other areas has revealed a key role for small molecule and lipid metabolites. The Metabolite Profiling Core Facility (Metabolomics Core Facility) was established in 2013 to support studies in this rapidly developing field.

Due to the extreme chemical diversity of small molecule and lipid metabolites – which greatly exceeds that of proteins and nucleic acids – the facility operates on a collaborative model in which experimental design, sample preparation, data collection, and data analysis are tailored to each study. We serve the Whitehead as well as the larger MIT community and external collaborators.

The facility is managed by Caroline A. Lewis, Ph.D., and employs two full time technicians, Tenzin Kunchok and Kayla Crowder, Ph.D.
The faculty advisor for the facility is Prof. David M. Sabatini, M.D., Ph.D.

Webinar by Lisa Freinkman, Ph.D. (former Core Director)

An introduction to LC/MS-based metabolomics and an overview of the WI metabolomics facility.

The Metabolite Profiling Core Facility houses three liquid chromatography / mass spectrometry (LC/MS) systems.

We have two Thermo Scientific QExactive Orbitrap mass spectrometers and one Thermo Scientific Orbitrap ID-X mass spectrometer, all of which are capable of measuring mass-to-charge ratios with less than 5 ppm error and a resolution of up to 140,000 and can also collect MS/MS fragmentation data. Each mass spectrometer is coupled to a Dionex UltiMate 3000 ultra-high performance liquid chromatography (UPLC) system designed for pressures up to 1000 bar, permitting rapid separation times of ~30 minutes per sample.

Together with a library of several hundred synthetic standards, the combination of exact mass, fragmentation, and chromatographic retention time data permits the positive identification of most common cellular metabolites. Operating the mass spectrometers in either targeted or full-scan mode enables both hypothesis-driven and hypothesis-generating (untargeted) experiments to be performed.

It is important to document use of the Whitehead Metabolite Profiling Core Facility in each publication, poster presentation or oral presentation. This helps us to be recognized by the institute and facilitates funding, and allows us to continue to support your research.
When data provided by the Metabolite Profiling Core Facility results in a publication, please contact us to let us know, and acknowledge the Core in your manuscript using a simple statement, such as the following:

“We thank the Metabolite Profiling Core Facility at the Whitehead Institute for running metabolomics samples and for data analysis”.

When a member of the Core has contributed significantly to a project, consider making them a co-author. The members of the Metabolite Profiling Core Facility are valued scientists; as such, their contributions to projects deserve to be recognized like any other co-author. For guidelines on including Core Facility personnel as co-authors, please see recommendations made by the Association for Bimolecular Resource Facilities (ABRF).