The Metabolomics Core Facility: Addressing an exploding demand

Posted on Tuesday, May 25, 2021

Photo of the equipment of the uOttawa Metabolomics Core Facility

By Michelle Read

The team of experts at the uOttawa Metabolomics Core Facility (MCF) is in the throes of a skyrocketing demand.

That’s because metabolomics, or the measurement of metabolites in biological samples, is exploding as a research interest. To help meet demand, MCF launched in 2019 following the acquisition of three state-of-the-art mass spectrometers, thanks to grants from the Canada Foundation for Innovation.

Those grants came via facility director Dr. Julie St-Pierre. For eight years, Dr. St-Pierre was director of the Metabolomics Core at McGill University; in 2017 she was recruited by uOttawa, and set about establishing such a facility at the Faculty of Medicine.

“I was very excited to join the uOttawa research community with its strong leaders in metabolism and mitochondrial research,” says Dr. St-Pierre, a full professor in the Department of Biochemistry, Microbiology and Immunology.

High demand for the powerful technology

Metabolomics is a powerful technology that permits a deep understanding of the metabolic state in physiological and pathological conditions. As such, it is an integral part of systems biology. Dr. St-Pierre was delighted to join the Ottawa Institute for Systems Biology (OISB) upon her recruitment to uOttawa.

“The metabolomics core is the most recent addition to the ‘omics’ suite at OISB,” she says, “which already has cutting-edge lipidomics and proteomics platforms, as well as strong bioinformatics expertise to analyze these large omics data sets.”

Since her arrival, Dr. St-Pierre’s research program has focused on uncovering metabolic vulnerabilities in breast cancer that can be exploited for therapeutic purposes. She also has a particular interest in mitochondrial metabolism.

A busy team is a nice challenge to be facing, according to MCF manager Dr. David Patten.

“The response to the uOttawa MCF opening has been really fantastic,” says Dr. Patten. “There has been zero staff downtime since our opening, so we would like to thank all our users for their exciting research projects and for keeping us quite busy.”

Dr. Patten says the Core was very fortunate to have Dr. Shama Naz join the core right before the pandemic began. Dr. Naz brought over 13 years of mass spectrometry and metabolomics experience, allowing the team to meet the large demand for metabolomics-based research. 

The core provides researchers with equipment and expertise to help analyze healthy and diseased states. Initially, the MCF can help identify metabolites or metabolic pathways that are altered in tissues or biofluids of a particular disease state. Through more advanced techniques, using labeled metabolites, researchers can further tease out intracellular metabolism and measure the flux of metabolites through a particular pathway.  

The far-reaching impact of metabolomics

One of the major focuses of the core is on cancer metabolism, but the research interests of other users have included obesity, mitochondrial biology, blood cells and neurosciences, to name just a few.

Because metabolomics-based research can be applied to an extensive number of fields, MCF’s client base is similarly vast. Many clients are located within the Faculty of Medicine, but others come from other uOttawa faculties, Canadian universities and research institutes and non-profit research organizations.  

“Metabolomics is very complex, but users should not worry—the uOttawa MCF is here to support all your research needs from consultations to study design to data analysis,” explains Dr. Patten. “These services are tailored to the specific project and the metabolic pathways of interest.”

Through the support of the Terry Fox Research Institute and the Canadian Foundation for Innovation, the uOttawa MCF is part of the Metabolomics Innovation Resource of the Goodman Cancer Research Centre (GCRC), the University of Ottawa and the Van Andel Research Institute (VARI), known collectively as MIRGOV. 

The mutual support of the three core facilities helps accelerate method development and aids in method standardization and reproducibility,” says Dr. Patten. “I think this collaboration sets us apart from other core facilities and is a major benefit to our users. “

Dr. St-Pierre is proud that the uOttawa metabolomics core is an integral part of the Terry Fox team grant in oncometabolism, which she co-leads with Dr. Peter Siegel of McGill University.

“As a team, we have made significant contributions to the understanding of metabolism in cancer,” she says.

“All of these discoveries were made possible by having access to state-of-the-art metabolomics capabilities.”

The Metabolomics Core Facility: One of 15 cores at the Faculty of Medicine

With support from affiliated hospital-based research institutes and the University of Ottawa, the Faculty has successfully developed a series of cutting-edge core facilities that bring together state-of-the-art equipment, instrumentation, methodologies and expertise crucial to the success of basic and clinical research activities. These facilities are accessible to all researchers across the University of Ottawa as well as to outside communities on a fee-for-service basis.

To date, 15 cores have been established and a few others are in the planning stages. For each facility, a director and user committees have been appointed to ensure accountability and optimal use for the continued commitment and success of our expanding core facilities.

Animal Behaviour and Physiology

Dr. Stephen Ferguson

Genomics (StemCore):

Dr. Michael Rudnicki


Dr. Theodore Perkins

Cell Biology and Image Acquisition:

Dr. John Copeland

Human Pluripotent Stem Cells:

Dr. William Stanford

Common Equipment and Technical Services:

Dr. Laura Trinkle-Mulcahy

Louise Pelletier Histology Core Facility:

Dr. John Veinot

Containment Level 2+:

Dr. Marc-André Langlois

Preclinical Imaging:

Dr. Richard Aviv

Flow Cytometry and Virometry:

Dr. Kristin Baetz


Dr. Daniel Figeys


Dr. David Lohnes


Dr. Julie St-Pierre

Protein Biophysics/Structural Biology:

Dr. Jean-François Couture

Transmission Electron Microscopy

Dr. Baptiste Lacoste

For more information, please visit the Core Facilities website.

Consider supporting the University of Ottawa.

The Faculty Of Medicine's Greatest Needs fund financially supports the priorities of the Faculty of Medicine.

Meet the Team

uOttawa Metabolomics Core Facility:

  • Dr. Julie St-Pierre - Professor and Director
  • Dr. David Patten – Manager
  • Dr. Shama Naz – Research Associate

Learn more about the team and the Oversight Committee.

To find out more or to access the Core's services:

Metabolomics Core Facility
University of Ottawa
Roger Guindon Hall
451 Smyth Road, Room 1129/1130
Ottawa ON  K1H 8M5

Photo of Dr. Julie-St-Pierre, Dr. David Patten and Dr. Shama Naz

uOttawa Metabolomics Core Facility team: Dr. Julie St-Pierre, director; Dr. David Patten, manager; Dr. Shama Naz, research associate.


A photo of two pieces of metabolomics analysis equipment.

Quadrupole time of flight LC/MS: The MCF's Agilent 6545B Q-TOF is coupled to a 1290 Infinity II liquid chromatography system and the Agilent Jet Stream source. This system is primarily dedicated to targeted metabolomics and stable isotope tracing analysis using hydrophilic interaction chromatography (HILIC) but is also suitable for non-targeted metabolomics. For particular metabolic pathways, or compound classes, new methods can also be developed/optimized according to customers' needs. Learn more about MCF's Instrumentation.

Photo credits: The University of Ottawa Faculty of Medicine


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