Services, instruments and software

Why metabolomics?

Metabolomics is the characterization of the complex mixture of metabolites in biofluids, cells and tissues. Metabolomics can be used to compare biological groups, identify biomarkers, understand biological pathways, or discover new metabolites. Metabolomics provides an unprecedented way to look at the relationship between phenotypes and genotypes, and further understand biological mechanisms.

Capturing the metabolome with its diversity of structures and physicochemical properties requires multiple technologies. The identification of unknown metabolites in complex samples without available spectral libraries and databases can be challenging. We are happy to work with you and explore solutions for your research project.






We offer a comprehensive range of services

From study design to results interpretation, our facility offers you a state-of-the-art metabolomics analysis, with:

  •       Consultation for experimental design

The diversity in structures and chemical properties requires multiple technologies and strategies to capture a full metabolome. We will help you find the approach that fits your research needs.

  •     Help for sample preparation

Sample preparation is one of the most crucial steps of a metabolomics analysis. We put our expertise to your service for an optimal sample preparation.

  •    Sample analysis

                         - Untargeted metabolomics profiling

For discovery screening of metabolites associated with specific treatment or specific biological phenotypes.

               - Targeted metabolomics profiling

For large-scale validation of known compounds: Targeted metabolomics profiling.

       - Small molecule quantitation

This targeted analysis is used for either relative or absolute quantitation of metabolites in a sample. We use parallel reaction monitoring (PRM) for the quantitation, a technique offering both increased selectivity and higher dynamic range.

  •       Data interpretation

We help you transform raw data into meaningful biological information. Our software toolbox includes methods for visualization, annotation and enrichment analysis for relevant pathways. Our expertise covers metabolite profiling analysis, spectral library-based compound identification. We also provide statistical analyses based on nested or non-nested experimental design.


If you aren’t sure what is the right analysis for you, please don’t hesitate to contact us. We also have office hours every Tuesday and Thursday afternoon in Biotech 139.


Our cutting-edge instruments

The facility is equipped with two complementary systems:


  •         The Vanquish™ UHPLC system with Diode Array Detector (DAD) coupled with Q Exactive™ HF

We use this system for discovery screening and untargeted metabolomics profiling. We can also use it for targeted metabolomics profiling and small molecule quantitation. It relies on UHPLC-MS/MS with high mass accuracy and high resolution capabilities.

  •         The UltiMate3000 2DLC coupled with 4000 Q Trap

This system, a hybrid triple-quadrupole (QqQ) with linear ion trap, is valuable for large-scale, high-throughput small molecule/peptide quantitation and profiling analyses. It is also useful for target-based small molecule identification/validation in complex samples, as well as hypothesis-driven characterization of peptide modifications in QqQ- Infinity DAD mode.


We are regularly updating our equipment to follow technological development and users’ demand.

We will acquire an GC-MS in a few months The instrument capability will be complementary with the existing one from our current LC-MS systems.

GC-MS combines the features of gas-chromatography and mass spectrometry to identify different substances within a test sample. Apolar, volatile compounds such as terpenes are ideally analyzed by GC/MS.




The facility uses an array of commercial software for a flawless and seamless analysis of your raw samples to meaningful results.


Compound Discoverer 2.0

“Streamline and customize high resolution accurate mass data analysis with Thermo Scientific™ Compound Discoverer™ small molecule identification software. Compound Discoverer empowers researchers to strategically collect, organize, store, and analyze data for both targeted and untargeted workflows. The software simplifies data processing for complex data with its customizable node-based workflows, integrated compound identification capabilities, and statistical analysis. Compound Discoverer offers a suite of tools for studies on metabolism, unknown metabolomics, impurities and degradants, extractables and leachables, environmental and food safety research, and forensic toxicology.” – Thermo Scientific

TraceFinder 4.1

“Offer increased flexibility and an array of capabilities in performing targeted screening and routine quantitation with either high resolution accurate mass (HRAM) and/or triple stage quadrupole (TSQ) mass spectrometers with Thermo Scientific™ TraceFinder™ Software. Not only does TraceFinder provide method development tools for all molecule types, it also generates new methods from existing data. From pharma/biopharma to food safety, from environmental safety to clinical research and forensic technology, TraceFinder ensures increased productivity for your analytical laboratory, enabling you to address analytical challenges today and tomorrow.” – Thermo Scientific


Welcome to Dr. Elena Diaz-Rubio, the new dedicated mass spectrometrist for the metabolomics facility! Elena will be joining us on 10/16/2017.