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Liquid Chromatography – Quadrupole – Time of Flight Mass Spectrometer (LC/Q-TOF-MS)

A versatile 1290 Infinity II LC coupled to a 6545 Q-TOF LC/MS system for the sensitive untargeted metabolomics enabling structural elucidation in any kind of samples and for a wide variety of metabolites by the use of different LC methods.

Liquid Chromatography – Ion Mobility – Quadrupole-Time of Flight Mass Spectrometer (LC/IMS-Q-TOF-MS)

An ultra-selective system combining liquid chromatography, ion mobility and high resolution mass spectrometry. This system offers the versatility and separating performance of the 1290 Infinity II LC coupled to the 6560 Ion Mobility (IM) Q-TOF LC/MS, which offers a new dimension of separation of molecular species in the ion mobility stage together with the capabilities of the quadrupole and the time of flight analysers. This system can uncover structural information that cannot be achieved with other mass spectrometers.

Liquid Chromatography – Triple Quadrupole Mass Spectrometer (LC/QqQ-MS)

LC 1260 Infinity system coupled to a 6470 Triple Quad LC/MS. Different chromatographic methods can be performed for the separation of compounds with different chemical properties in targeted metabolomics studies with the best sensitivity and selectivity.

Our versatile 1290 Infinity system coupled to a 6460 Triple Quad LC/MS. This equipment can be operated with different chromatographic methods for the separation of compounds of different chemical properties in targeted metabolomics studies with the highest sensitivity and selectivity.

Gas Chromatography – Quadrupole – Time of Flight Mass Spectrometry (GC/Q-TOF-MS)

A powerful 7890B GC System coupled to a 7250 Accurate Mass Q-TOF GC/MS system enabling untargeted metabolomics analyses and structural elucidation of polar and non-polar compounds in a variety of samples, such as plasma, serum, urine, brain, liver, lung, cells, culture media, etc. The system is combined to a multipurpose autosampler enabling the automatic sample preparation prior the injection.

An extremely robust and sensitive 8890 GC System coupled to a 5977B GC/MSD mass spectrometer with a single quadrupole and a 7693A. Autosampler for 150 samples, enabling the determination and quantitation of polar and non-polar compounds in any kind of sample.This system can be used for targeted and untargeted metabolomics.

Capillary Electrophoresis – Time of Flight Mass Spectrometry (CE/TOF-MS)

Two 7100 Capillary electrophoresis coupled to a 6224 TOF MS and 6230 TOF MS detectors for untargeted metabolomics and highly resolutive separations of ionisable compounds in several types of biological samples, with high mass accuracy and sensitivity.

Sample preparation

Sample preparation picture

Our laboratory counts with all the means for the sample treatment of a variety of biological species before the analysis in our multiplatform metabolomic facilities. This includes a Bravo Automated Liquid Handling Platform for the automatic preparation of liquid samples, a lyophilizer (CoolSafe Pro 110-4 Freeze Dryer), two speed-vacs (HyperVAC model VC2124 centrifuge vacuum concentrator and Savant SPD121P Speed Vac), a sample homogenizer (Tissuelyser LT), a cryogenic pulverizer (Covaris cryoPREP) and centrifuges and ultra-microcentrifuges among others.

Data Treatment

Data treatment picture

Metabolomics, the study of small molecules in an organism associated to metabolic pathways, provides a link between genotype and phenotype. Metabolomic analysis generates large-scale and complex datasets. Therefore, various data analysis tools are needed to extract biologically relevant information. The data analysis workflows in metabolomics studies are generally complex and involve several steps. CEMBIO members are used to handle and discuss the data analysis strategies for metabolomics experiments. As part of our collaboration in a research study we can discuss and apply the available tools for data analysis, perform metabolite identification and participate in the biological interpretation of metabolomics data.

CEU Mass Mediator

CEU Mass Mediator


CEU Mass Mediator is a tool for searching metabolites in different databases (Kegg, HMDB, LipidMaps, Metlin, MINE and an in-house library). This is specially designed for searches through experimental masses obtained from mass spectrometry techniques.

CEU Mass Mediator unifies compounds from different sources based on the InChI Key. It will save time to researchers which have to find the compounds in the databases one by one and unifying them manually as well as it reduces the risk of a wrong manual unification.

The LC-MS Advanced search calculates a scoring for the annotations based on three aspects:
1. Probability of the compound to form a specific adduct.
2. Presence of other adducts coming from the same signal in the same RT window.
3. RT of the lipids with the same head depending on the number of carbons and double bonds (and, consequently, the hydrophobicity of them).
A final score is calculated based on these three aspects (see manual for more information).

1. A CE-MS search service using experimental information from different set-ups.
2. A Lipid Annotation Service (LAS) for annotating lipids using a totally isolated docker implemented in Prolog and applying the same rules than the LC-MS batch advanced search.
3. A pathway displayer for sorting the most relevant pathways in a set of compounds.
4. Identification of oxidized glycerophosphocholines (oxPCs) based on the MS/MS spectrum.
5. A spectral quality controller to measure the reliability of a spectrum for identification.


CEU Mass Mediator website