Universiteit Leiden

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Metabolomics and Analytics Centre

Metabolomics Facility

The Biomedical Metabolomics Facility Leiden (BMFL) is the core metabolomics facility of Leiden University and the Metabolomics and Analytics Centre (MAC). We offer a highly structured environment for advanced MS-based metabolomics studies and build on fully validated, state-of-the-art assays that each cover a part of the human metabolism and together span the complete human metabolome. BMFL is particularly suited towards biomarker discovery of human disease and health.

Our clients include internal and external academic collaborators as well as pharmaceutical and industrial partners from all over the world. The BMFL team offers the complete track from involvement in experimental design, study set-up and sample collection to the actual measurements, data analysis, identification of unknown compounds and comprehensive feedback on the results. We work according to ISO17025 guidelines and employ rigorous quality standards, working with validated methods. In close collaboration with our partners, BMFL defines a tailor-made approach that offers the best fit between your biological question and optimal use of the potential of our highly advanced facilities. 

Photo by Thijs Rooimans

BMFL does not only perform routine measurements but also operates at the frontier of metabolomics developments. Being embedded in the university ensures that new technological opportunities are quickly recognized and further developed into new platforms. The BMFL portfolio is therefore continuously improved and expanded. Major research efforts in miniaturization and automation of methods, increasing sensitivity and coupling to organ-on-a-chip are currently being performed jointly with researchers in MAC. 

If you are interested in our services, we will discuss the details of your request including your proposed study design. We recommend our clients to follow our study design guidelines. These include sufficiently sized cohorts sampled from the general population, well-defined time periods and sampling points.  

After agreement of the details, all necessary documentation is arranged together with our project manager.  

Sample matrices

Our metabolomics services are compatible with the following sample matrices: 

  • Blood plasma (preferably EDTA) 

  • Blood serum 

  • Urine 

  • Cells and cell medium 

  • Cerebrospinal fluid 

  • Saliva 

The following sample matrices are compatible but currently under development and/or available for surcharge:  

  • Feces 

  • Blister fluid 

  • Whole blood 

  • Zebrafish 

  • Brain tissue 

  • Organoids 

If you have another sample matrix, please contact the facility manager to discuss its compatibility with our assays. Our experienced team of researchers will investigate your sample matrix upon request. All our projects include study specific pooled quality control (QC) samples and laboratory specific QC samples for data quality assessment. 

Read more about sample submission (checklist)

Photo by Thijs Rooimans

Metabolomics is a technology which measures low molecular weight (<1500 Da) molecules that enable us to reveal the functionality and dynamics of metabolite pathways and networks from a systems biology point of view. It provides a readout for the unique chemical fingerprints that specific cellular processes leave behind. Applying metabolomics to investigate health and disease allows to reveal pathogenic metabolism related to the phenotype of the disease. These studies contribute to finding biomarkers useful in: diagnosis, disease severity prediction, measurement and prediction therapeutic intervention, therapeutic targets identification, and risk stratification. Continuous metabolomic measurements in a personalized medicine setting will enable us to differentiate between homeostasis, allostasis and disease, equipping us with the tools for early detection of health perturbations. The diversity of the human metabolome requires tailor-made metabolomics approaches targeting specific compound classes to achieve robust metabolic profiles that collectively can provide a comprehensive readout.  

Targeted metabolomics focuses on a predefined set of metabolites covering specific metabolic pathways, and analyses these using optimized sample preparation methods in tandem with cutting-edge analytical technology. When prior biological knowledge is available targeted metabolomics enables us to target specific pathways and to study their response within the biological question.  

Untargeted metabolomics allows screening of a broad range of different metabolite classes used in discovery-based studies and/or when no previous knowledge of the metabolites of interest is available.  

We offer three different types of metabolomics assays: targeted metabolomics, untargeted metabolomics, and research metabolomics assays. The research metabolomics assays are not validated but will be performed by a MAC researcher according to professional scientific standards (good research practices). All assays are performed on state-of-the-art Ultra-High Performance Liquid Chromatography Mass Spectrometry (UHPLC-MS) instrumentation.  

Read more about our assays:


Photo by Thijs Rooimans

Quality assessment

In-house developed software is not only used for evaluation of the instrument performance prior to analysis but also for integration of metabolite signals and assessment of the data quality prior to reporting. Programming languages R and Python are used for these software tools coupled to graphical user interface for our researchers to use. Instrument performance is assessed prior to analysis of study samples. In addition, newly acquired data files are collected in a data lake and processed instantly to monitor the measurements real-time. Our data quality control pipeline provides correction for analytical variation, data monitoring by means of quality control reports and data standardization. This ensures robust data that enables truly comparative studies.

Read more about reporting of studies

Reporting and statistical services

We offer consultations for statistical analysis as well as meticulous feature identification, annotation, classification. During the statistical consulting we can provide guidelines, workflows and best practices for the necessary pre-processing steps that are involved in preparing the data for downstream analyses. We can advise on data transformations, normalizations and methods to use for biomarker identification, feature selection and general associations of metabolites with the phenotypes under investigation.  

Important publications

Method publications: 

Application publications: 

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