Metabolomics Core Facility

Metabolomics is the study of variations in endogenous metabolites in biological materials; such as cells, tissues and body fluids. The metabolome represents the complete set of metabolites in a biological cell, tissue, organ or organism, which are the products of cellular processes. Metabolic profiling can give an instantaneous snapshot of the physiology of that cell, and thus, metabolomics provides a direct “functional readout of the physiological state” of an organism. This in turn can provide key information relating to changes in cell and tissue function during, for example, differentiation and disease development.

The overall goal of the Metabolomics facility is to use and develop mass spectrometry based methods to characterize the relationship between lipid/small molecule metabolism and cardio-pulmonary diseases. The clinical translation of the results from these studies can deliver new diagnostic tests as well as identify new targets for therapeutic interventions to treat chronic disease. Our core facility is equipped with four state-of-the-art mass spectrometers, which are used for the identification and quantification of small molecules, metabolites and lipids.

The IVS Metabolomics Core facility is specialized in the quantification of hundreds of metabolites, in particular oxylipins (which are lipid mediators with polyunsaturated fatty acid residues), acyl-CoAs, amino acids, secondary amines, complex lipids and metabolites of the TCA cycle, pentose phosphate pathway and glycolysis. We also perform 13C-tracing/flux analysis for specific molecules e.g. 13C-glucose. Standard procedures are also in place to extract metabolites from a variety of biological fluids and tissues, e.g. from human plasma, skin, brain, heart and cell culture. The core facility is continually expanding its expertise and is open to collaboration with external groups on a fee-for-service basis (contact:

For those more interested in the technical details…

The MCore uses a positive pressure 96-well plate manifold (or a unit for single tubes) for solid phase extraction, and an advanced solvent-resistant freeze dryer system (condenser temperature of down to -105°C) for sample enrichment. Once the metabolites are extracted, they are transferred to MS Vials or 96-well plates and placed into an auto sampler, which injects a small sample volume into the LC/MS or GC/MS system. For targeted compound screenings, we use the 1290 Infinity II Bio HPLC System coupled to a 6495 QQQ and the 1290 Infinity System coupled to a QTrap5500. For untargeted metabolomics, we use the Orbitrap QExactive classic mass spectrometer coupled to ultra-high performance liquid chromatography (nano or standard flow) and the ISQ7000 single-quadrupole gas chromatography mass spectrometer coupled to a TRACE1300.