Metabolomics Area

Metabolomics is the measurement and quantitation of small molecules or metabolites (< 1500 Dalton). Small molecules may be endogenous compounds involved in cellular metabolism, although they may also come from drugs, food, microbes or the environment. Metabolomics deals with the quantitative global profiling of metabolites, being used extensively to explore the dynamic response of living systems.

The Metabolomics Area is formed by the Metabolomics facility of the COS that covers a wide range of capabilities in metabolome analysis and data handling. The expertise is guaranteed by professionals with extensive experience on mass spectrometry (MS), nuclear magnetic resonance (NMR) and data analysis. The Metabolomics team at COS focuses its activity on profiling and quantifying small, naturally occurring compounds that collectively constitute the so-called metabolome. Small molecules serve as direct signatures of biochemical activity and therefore are easier to correlate with phenotype. Thus, comparative metabolomics provides a powerful strategy for understanding changes associated with a unique phenotype or disease state at the molecular level. Extracting metabolites from tissues, biofluids, or cell cultures and subsequent analyses through liquid and gas chromatography/mass spectrometry (LC/MS and GC/MS) as well as nuclear NMR, allow us to simultaneously analyze many low molecular weight biochemicals. 

To complement LC/MS, GC/MS and NMR profiling, the COS has incorporated two additional components to its research: i) MALDI imaging to localize dysregulated metabolites with micrometre resolution in tissues or cell types and ii) intact tissue NMR using high resolution magic angle spinning (HR-MAS) to characterize such dysregulated metabolites. These complementary technologies offer a powerful approach to investigate the biochemical basis of disease and relies on a unique breadth of training experiences.

The Metabolomics area of the OmicsTech at the COS can guide researchers at any project phase from the design of the experiments to the data analysis.

For further information and discussion of possible ways of collaboration, please contact


Untargeted metabolomics

Untargeted or large-scale metabolite profiling using LC-MS or GC-MS technologies. Its aim is to identify potentially new diagnostic and prognostic biomarkers or uncover previously unknown metabolic pathways.

Targeted metabolomics

Targeted metabolomics using LC-MS or GC-MS provides an absolute quantification of a specific molecule or group of molecules. Concentrations are determined by comparison of samples to calibration curves constructed with authentic chemical standards and chemically similar internal standards. Optimized sample preparation methods are used to maximize the extraction of metabolites and their detection. The COS offers target panels as well as customized analysis.

Targeted metabolomics > MetGC Energy Metabolism

Targeted metabolomics panel that covers 48 metabolites approx.: glycolysis intermediaries, Krebs cycle intermediaries, organic acids, sugars, fatty acids, amino acids, etc.

Targeted metabolomics > MetLC Amino Acid Extend

Targeted metabolomics panel that covers 53 metabolites approx.: amino acids and related metabolites.

Targeted metabolomics > MetLC Acylcarnitine

Targeted metabolomics panel that covers 40 metabolites approx.: carnitine and its short, medium and long-chain acyl derivatives.

Targeted metabolomics > MetLC Bile Acids

Targeted metabolomics panel that covers 14 metabolites approx.: primary and secondary bile acids and their glycine and taurine conjugates.

Targeted metabolomics > MetLC Short Chain Fatty Acids

Targeted metabolomics panel that covers 9 metabolites: acetic acid, propionic acid, butyric acid, isobutyric acid, valeric acid, isovaleric acid, 3-methyl valeric acid, 4-methylvaleric acid and hexanoic acid.

Targeted metabolomics > MetLC Oxylipins

Targeted metabolomics panel that covers around 90 metabolites including HETE, HEPE, HODE, HDHA, DHET, DiHETE, Leukotrienes, lipoxins, Thromboxanes, prostaglandins, resolvins and related metabolites.

Targeted metabolomics > MetLC Polyamines

Targeted metabolomics panel that covers around 15 metabolites from the polyamine metabolome: spermine, spermidine and putrescine, as well as their precursor amino acids and acetyl- derivatives.

Targeted metabolomics > MetLC Methylamines

Targeted metabolomics panel that covers TMAO determination as well as its related metabolites: TMA, choline, carnitine and betaine.

Targeted metabolomics > MetGC Fatty Acids

Targeted metabolomics panel that covers 13 fatty acids: Octanoic acid, myristic acid, palmitic acid, palmitoleic acid, palmitelaidic acid, stearic acid, oleic acid, elaidic acid, linoleic acid, alpha-linolenic acid, arachidonic acid, eicosapentaenoic acid and docosahexaenoic acid.

Targeted metabolomics > MetGC Fatty acid methyl esters (FAMEs)

Targeted metabolomics panel that covers 30 metabolites approx.: total medium- and long-chain fatty acids, from C8 to C24 with or without insaturations.

Targeted metabolomics > MetLC Tryptophan Metabolism

Targeted metabolomics panel that covers 17 metabolites approx.: tryptophan, tryptamine, kynurenine and derivatives, serotonin, and other metabolites involved in the pathway.

Targeted metabolomics > MetLC Urea Cycle

Targeted metabolomics panel that covers 7 metabolites approx.: urea, arginine, ornithine, citrulline, argininosuccinate, fumaric acid and aspartic acid.

Targeted metabolomics > MetLC One-Carbon Metabolism

Targeted metabolomics panel that covers 12 metabolites approx.: includes folic acid cycle (folic acid, THF, 5-methyl-THF), methionine cycle (Met, Cys, SAM, SAH) and associated vitamins (B6, B2) and intermediaries (betaine, choline, dimethylglycine).

Targeted metabolomics > MetLC Neurotransmitters

Targeted metabolomics panel that covers Tyrosine-derived neurotransmitters and intermediaries: tyrosine, tyramine, L-dopa, dopamine, epinephrine, norepinephrine, homovanillic acid, etc.

Targeted metabolomics > Customized analysis

Customized analyses include the development of LC-MS or GC-MS methods and optimized sample preparation methods to provide precise measurement of your metabolites of choice in a wide variety of matrices. Contact us to discuss the approach that best suits your interests.


Lipidomics is a specialized area of metabolomics focused on the analysis of lipids. Lipidomics analysis cover metabolites such as oxylipins, HETEs, fatty acids, bile acids, steroids hormones, lysophospholipids, phospholipids, sphingomyelins, diglycerides and triglycerides.

Lipidomics > MetLC Lipidomics - I

Targeted lipidomics panel that covers 190 compounds aprox.: Oxylipins, fatty acids, bile acids, steroid hormones, lysophospholipids, N-acyl ethanolamines and sphingosine-1P.

Lipidomics > MetLC Lipidomics - II

Targeted lipidomics panel that covers 120 compounds approx.: lysophospholipids, phospholipids, sphingomyelins, cholesteryl esters, diglycerides and triglycerides.

Lipidomics > MALDI Imaging Lipidomics

Imaging and profiling of lipids present in tissue slices using MALDI-TOF/TOF mass spectrometry, for the study of the spatial distribution of molecules within biological tissues.

Nuclear Magnetic Resonance (NMR) spectroscopic profiling

Non-destructive proton nuclear magnetic resonance (1H-NMR) methods may detect metabolites which are present at high concentrations (greater than 10 mM). It allows the rapid, untargeted screening of large numbers of specimens without tedious chemical pre-processing.

13C, 31P, and 19F Nuclear Magnetic Resonance (NMR) analysis

Many isotopes of chemical elements can be used for NMR analysis. Our equipment is not only capable of using +H for NMR analysis, but also other isotopes such as 13C, 31P, and 19F, for pharmaceutical studies, can be used.

Fluxomics by Nuclear Magnetic Resonance (NMR)

Positional Enrichment by Proton Analysis (PEPA) detects the position of carbon label in isotopically enriched metabolites and quantifies fractional enrichment by indirect determination of 13 C-satellite peaks using 1D-1 H-NMR spectra. Different metabolic fluxes can be analysed depending on the metabolite used such as amino acids, lipids, tricarboxylic acids, and glucose.

Bioinformatic Applications

Metabolite identification

Untargeted or large-scale metabolite profiling using LC-MS or GC-MS technologies. Its aim is to identify potentially new diagnostic and prognostic biomarkers or uncover previously unknown metabolic pathways.

Statistical analysis

Univariate and multivariate statistical analyses (PCA, clustering, correlations, PLSDA, …). Mass Profiler Professional (Agilent)-Generic and specific Agilent data-, Gene Spring (Agilent)-Generic and specific Agilent data-, Sieve 1.4 (Thermo)-specific for Thermo LC-MS data.


2 Agilent 6490 Triple Quadrupole with iFunnel technology for LC/MS

The Agilent 6490 Triple Quadrupole mass spectrometer incorporates iFunnel technology to achieve new levels of sensitivity and dynamic range for detection of target compounds in complex matrices. The innovative design of the ion funnel reduces contamination and neutral molecules thus improving overall signal and reducing system noise.

Agilent 6470 Triple Quadrupole for LC/MS

The Agilent 6470 Triple Quadrupole is equipped with an Agilent Jet Stream ion source and a curved geometry collision cell. These innovations enable the reliable detection of target compounds at low levels in diverse matrices, while achieving wide linear dynamic range.

2 Agilent 7000 and 7010 series Triple Quadrupole for GC/MS

The 7000 Series Triple Quadrupole GC/MS is a standalone capillary GC detector used with an Agilent gas chromatograph. Both chemical and electron-ionization modes are available.

Agilent 6550 Quadrupole Time of Flight with iFunnel technology for LC/MS

The Agilent 6550 Q-TOF incorporates iFunnel technology which increases ion transfer and enables higher sensitivity and lower detection levels. It provides both qualitative and quantitative data with high resolution and accurate mass.

Agilent 6546 Quadrupole Time of Flight for LC/MS

The 6546 high resolution mass spectrometer accelerates your lab’s capabilities by enabling comprehensive workflows in metabolomics research, food safety, food authenticity, and environmental screening. With simultaneous high sensitivity, wide dynamic range, high resolution, isotope fidelity, and accurate mass measurements, the resulting high data quality provides the level of confidence you need for fast and simplified data review processes.

Agilent 7250 Quadrupole Time of Flight for GC/MS

The Agilent 7250 GC/Q-TOF system delivers full-spectrum, high-resolution, accurate mass data with a wide dynamic range for identifying and quantifying GC-amenable compounds. This high-resolution GC/Q-TOF enables accurate mass screening by GC/MS and enhanced compound identification through MS/MS, low-energy electron ionization, and complimentary chemical ionization techniques.

Agilent 7200 Quadrupole Time of Flight for GC/MS

The Agilent 7200 Quadrupole Time-of-Flight GC/MS system delivers full-spectrum, high-resolution, accurate-mass data for screening, profiling, and identifying GC-amenable compounds, using both electron and chemical ionization.

Thermo Orbitrap Eclipse Tribrid

An instrument designed with your most difficult analytical challenges in mind, the Thermo Scientific Orbitrap Eclipse mass spectrometer incorporates the latest inventions in ion transmission and control, extended m/z range, and real-time decision making to expand the breadth of your work and push your science beyond today's discovery. This system is ideally suited for proteomics, structural biology, small-molecule, and biopharmaceutical characterization experiments.

Thermo Orbitrap Exploris 480 with Biopharma option

The Orbitrap Exploris 480 mass spectrometer is an advanced, intelligence-driven instrument, with remarkable robustness and built for ultimate performance data certainty is assured with high-resolution accurate mass (HRAM) selectivity and spectral quality.

Orbitrap Thermo Velos Pro

The Orbitrap is an ion trap mass analyser that consists of two outer electrodes and a central electrode, which enables it to act as both an analyser and a detector. Ions entering the Orbitrap are captured through electrodynamic squeezing. These ions then oscillate around the central electrode and in between the two outer electrodes. Different ions oscillate at different frequencies, resulting in their separation. By measuring the oscillation frequencies induced by ions on the outer electrodes, the mass spectra of the ions are acquired using image current detection. Due to its setup, the Orbitrap mass analyser is a Fourier Transform mass analyser analog of FT-ion cyclotron resonance (ICR) technology, yet with smaller instrument size and easier instrument operation.


Two-Dimensional Gas Chromatography coupled to a time-of-flight mass spectrometer. This technology allows the separation of compounds that are not well resolved in one-dimensional gas chromatography.

MALDI-TOF/TOF Bruker UltrafleXtreme

The MALDI (Matrix Assisted Laser Desorption/Ionization) tandem mass spectrometer specially designed for automated MS and MS/MS high throughput identification of samples. Tandem Mass Spectrometry is a technique that utilizes more than one mass selective stage in a mass spectrometer.

2 Bravo liquid handling system

Agilent's automated liquid handling platform for processing up to 96 samples.

Nuclear Magnetic Resonance (NMR) instruments

Two NMR equipments which work at two different frequencies, 500 MHz and 600 MHz. The Bruker 600 MHz Avance III spectrometer is composed by a cryoprobe and a SampleJet robot. The 500 Bruker 500 MHz Avance DRX spectrometer has a 5mm 1H/BB probe with an X-channel tunable from 15N to 31P. This spectrometer is also capable of carrying out both low temperature and high-temperature experiments. It also has an X-PRESS automatic sample changer for high-throughput work.

RMN Systems for automated liquid handling
Gilson 215 Liquid handler

The Gilson 215 Liquid Handler automatically process up to 96 samples directly in the NMR tubs.