The Mayo Clinic Metabolomics Core is an analytic facility that specializes in mass spectrometry techniques for measuring metabolites — small molecules and macromolecules — in biological fluids and tissue extracts.

The core exists as a resource to support investigators at Mayo Clinic as well as external investigators. Analyses are completed in a fee-for-service arrangement, but in many cases, the core's staff contributes in a more collaborative arrangement with substantial input into study design and interpretation of data.

What is metabolomics?

Metabolomics is the measurement and quantitation of small molecules (metabolites). Small molecules may be endogenous chemicals that are involved in cellular metabolism. Metabolites may also come from drugs, food, microbes or the environment.

There are more than 40,000 different metabolites in the human metabolome. The ability to measure these metabolites provides a direct window into cellular metabolism.

Metabolomics can be broadly separated into three main approaches:

  • Untargeted. Untargeted or large-scale metabolite profiling is intended to simultaneously measure the relative abundance of as many metabolites as possible. This approach is ideal for biomarker discovery or uncovering previously unknown metabolic pathways that may contribute to disease or treatments. Untargeted metabolite profiling not only requires sensitive analytic tools but also requires strong informatics support to gain meaningful insights from massive amounts of data.
  • Targeted. In a targeted approach to metabolomics, the core focuses on measuring a specific molecule or group of molecules for quantitation using internal standards. Selectivity and accurate quantitation is the main distinction from an untargeted approach.
  • Metabolite flux. The answers to some scientific questions necessitate going beyond measuring static levels of metabolites. Metabolite levels are determined by the balance between their production and their clearance. In many cases, it's possible to use stable isotope tracers to measure the flux or rate of a particular metabolic process, which provides additional insights into why metabolite concentrations may be altered. The metabolite flux approach has been successfully applied to study protein, glucose and fat metabolism and various aspects of intermediary metabolism in humans, animals and cell culture.

The Metabolomics Core at Mayo Clinic offers services in all three of the aforementioned categories, including statistical analyses and bioinformatics. The core is equipped with a wide selection of mass spectrometers and sample processing equipment to provide a comprehensive service to investigators. Furthermore, the Metabolomics Core has strategic pipelines to the Bioinformatics Core, Proteomics Core and Genome Analysis Core to provide an integrated approach to omics-related research for investigators inside and outside Mayo Clinic.


National Institutes of Health (NIH) Public Access Policy requires that all publication that results from NIH funding be uploaded to PubMed Central. Review the process for uploading publications.

All users of the core must cite the Mayo Clinic Metabolomics Resource Core grant as a funding source in any resulting publications. Use this language:

This publication was made possible by Mayo Clinic Metabolomics Resource Core through grant number U24DK100469 from the National Institute of Diabetes and Digestive and Kidney Diseases and originates from the National Institutes of Health Director's Common Fund.