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 identify biomarkers or discover new metabolites, which provides information to help understand biological pathways. Metabolomics can also be used to establish the metabolite profile of a sample, or compare biological groups. In this case, the metabolome of a control can be contrasted to the metabolome of an experimental group exposed to an external stimulus (a drug treatment, an environmental stress, or a pathology) to gain information about an organism response to biotic stresses. Metabolomics can also be used to explore responses to non-biological stimuli, such as food processing.

Altogether, metabolomics has a broad range of applications across several areas, ranging from biology, to biochemistry, medicine, pharmaceutics, food, and nutrition.

Metabolomics can be combined with genomics, transcriptomics and proteomics studies to provide comprehensive insights into biological processes.


Image: The relationship between the genome, proteome and metabolome (Wang and Gerszten, 2008. Nature 451, 949–952.doi:10.1038).

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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.

> 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.
> 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

Non-targeted metabolomics is the analysis of all measurable molecules in a sample, including unknown chemical. Comprehensive in nature, non-targeted metabolomics is used in descriptive studies, in the discovery phase of an experiment, or when there is no expectation for the outcome of a particular treatment. Untargeted metabolomics must be coupled to advanced chemometric techniques and statistical analyses, such as multivariate analyses, to reduce the extensive datasets generated into a smaller set of manageable signals.

·   Targeted metabolomics profiling

Targeted metabolomics is the measurement of chemically characterized and biochemically annotated metabolites. It can be used for hypothesis-driven experiments, which may include the validation of untargeted analyses. Targeted metabolomics profiling can be used to monitor changes of specific metabolites in an organism before and after treatment. Targeted metabolomics is specific and sensitive: it provides very accurate quantitation for a range of known metabolites involved in specific pathways of interest.

Targeted metabolomics can also be used for relative or absolute quantitation of metabolites in a sample. For quantitation parallel reaction monitoring (PRM), 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 ( or 607-254-4784).
We also have office hours every Tuesday and Thursday afternoon in the Biotech building.

The facility is equipped with two complementary systems:

> UHPLC / MS system: Thermo Scientific™ Vanquish™ Horizon UHPLC / Thermo Scientific™ Q Exactive™ HF hybrid quadrupole-Orbitrap mass spectrometer

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.

> GC-MS system

The Exactive GC system is an easy-to-use, dedicated GC-MS that provides an unprecedented level of highly sensitive, routine grade performance for both targeted and non-targeted analysis, along with high confidence quantitation for the ultimate sample analysis workflow. This is achieved through the superior resolving power, mass accuracy, linear dynamic range and sensitivity that only Orbitrap technology can deliver, combined with the intelligent data processing workflows provided by Thermo Scientific™ TraceFinder™ software.


Thermo Scientific™ Vanquish™ Horizon UHPLC

Designed with innovative technology and fine detail, the Thermo Scientific™ Vanquish™ Horizon UHPLC System delivers a new standard in high-end UHPLC—more results with better separations and easier interaction simultaneously, without compromise.

·      Higher pump pressure: 1500 bar (22,000 psi) pump pressure

·      Higher flow rate: up to 5mL/min

·      More solvent channels: 2x3

·      Up to nine different solvent combinations without stopping your experiment to replace solvents

·      Two thermostating modes: still air and forced air

·      Temperature range from 5°C to 120°C

·      Active preheating

Thermo Scientific™ Q Exactive™ HF hybrid quadrupole-Orbitrap mass spectrometer

The Thermo Scientific™ Q Exactive™ HF hybrid quadrupole-Orbitrap mass spectrometer features an ultra-high-field Orbitrap analyzer which doubles its speed and resolution – more samples run and amazing data quality. Built on the proven performance of the Q Exactive Plus platform, the Q Exactive HF mass spectrometer utilizes the same active beam guide technology and advanced quadrupole design for very stable system operation and exceptional analytical performance. The Q Exactive HF mass spectrometer is designed for your toughest discovery and quantitation challenges where the combination of speed and highest performance are essential for the highest quality scientific results.

·      Resolution: 240,000 at m/z 200

·      Mass range: 50 to 6,000 m/z

·      Scan rate: Up to 40 Hz at resolution setting of 7,500 at m/z 200

·      Mass accuracy: Internal: < 1 ppm RMS

·      External: < 3 ppm RMS

·      Sensitivity MS/MS: 100 fg reserpine on column S/N 150:1

·      SIM: 50 fg reserpine on column S/N 150:1

·      Dynamic range > 5,000:1

·      Polarity switching: One full cycle in < 1 sec (one full positive mode scan and one full negative mode scan at a resolution setting of 60,000)

·      Multiplexity:  Up to 10 precursors/scan

Thermo Scientific™ Exactive™ GC Orbitrap™ GC-MS system

The Exactive GC system utilizesthe Thermo Scientific™ TriPlus™ RSH autosampler, a robotic sample handling to expand automated capabilities. Your results benefit from improved precision and reproducibility.

·      Resolving Power: 50,000 @ m/z 272

·      Mass Range: 30 to 3,000 m/z

·      Scan Rate: Up to 18 Hz at resolution setting of 12,500 @ m/z 272

·      Mass Accuracy**:

o   Internal: <1 ppm RMS

o   External: <3 ppm RMS

·      Quantitative Dynamic Range*: >106

·      In-Spectrum Dynamic Range: >5000:1

*Under defined conditions

**Under conditions defined in 1 μL, 100 fg/μL octafluoronaphthalene EI Full MS installation specification

·      Automate basic sample and standards preparation procedures such as dilution, internal standard addition, and derivatization.

·      High precision injection from low volumes to maximize your analysis opportunities with your most precious samples.

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.