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AIMMS excels in measuring molecules and their effect on biological systems. 

We can monitor molecules in complex samples or in single cells, from chemicals to metabolites, RNA or proteins. We have sensitive assays to measure the impact of molecules on biological functions, from growth to toxicity to endocrine disruption.


  • Effect Directed Analysis (EDA)

  • Analytical chemistry

  • (Cell) Biology

  • Single-cell

Effect Directed Analysis (EDA)

In effect-directed analysis, we combine chromatography for fractionation of complex samples, and split these fractions for simultaneous functional assessment (cell-based assay) and compound identification (using mass spec). 

In this way we can identify bioactive compounds in complex samples such as environmental samples, snake venoms, foods or body fluids.

Analytical chemistry

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Mass spec-based methods

We have advanced analytical methods for metabolomics, proteomics and glycomics for the analysis of human fluids, intracellular metabolites, tissues and cell culture media. We hyphen separation techniques as HPLC, CE and GC with high-end (tandem) mass spectrometry (high-resolution, ion mobility and UVPD/IRMPD). We also have MS-based imaging facilities.

Contacts: Pim Leonards, Govert Somsen, Sofia Moco

NMR and crystallography

We have 300 – 600 MHz NMR machines for compound identification and analysis of complex fluids for metabolite quantification. 

For protein structure determination, the workflow includes liquid handling for sample crystallization, optimizing crystals, crystal handling including cryo-protection and storage. Diffraction analysis and data collection is done on an in-house, state of the art Bruker D8 Quest X-ray source attached to an cutting edge PhotonII detector including downstream software suits for structure determination. 

Contact: Elwin Janssen (


MIMETAS OrganoPlate® Challenge Winner Selected

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Congratulations to Elisabeth Naderlinger, Lenya de Brouwer, and Olivia Klatt for winning the MIMETAS-AIMMS VU OrganoPlate® Platform Proposal Contest! 🎉 The idea for the MIMETAS-AIMMS…

Kickstarting the animal to plant protein transition

| Challenges, Food, Human health & food | No Comments
When ten bright minds come together for two full days, innovation is bound to prosper! The first AIMMS hackathon revolved all around finding alternative protein…

(Cell) Biology

AIMMS has an array of methods, model systems and assays to monitor the impact of molecules on biological function. These include 

  • multicellular systems such as Zebrafish (contact Wilbert Bitter), C elegans (contact Samantha Hughes), organ-on-a-chip (contact Paul Jennings)
  • cellular systems such as iPSC cells (, cell (co-)cultures, complex in vitro models (contact Timo Hamers), organoids (Anja Wilmes), bioreactors and microfluidic setups (Bas Teusink)
  • biochemical assays, including (receptor) binding & enzyme assays (Iwan de Esch), (GPCR) signalling, nanobodies (Martine Smid), Seahorse analyzer for metabolic functions (Paul Jennings).


We have different methods to analyze biological states at the single cell level, largely based on fluorescent probes and biosensors in combination with flow cytometry and advanced (high content) microscopy. We collaborate closely with the AUMC technology center in the same O2 building. We combine these techniques with the cell-based methods. We have dedicated image-analysis tools and expertise based on AI/ML techniques to turn images into quantitative data.



Fluorescent protein based biosensors allow the dynamic, continuous, measurement of specific metabolites at single cell and even cell-compartment resolution. We apply , test, improve and develop such biosensors in house. Examples are sensors for pH, cAMP, ATP and recently glucose.

Intracellular pH in yeast cells analyzed with dynamic flow cytometry reveals two distinct subpopulations. (contact: Johan van Heerden, Bas Teusink)


RNAs can be detected at a single molecule level with RNA-FISH, which counts single mRNA molecules in fixed cells. We have this technique operational for bacteria, yeasts and fungi, and mammalian cells. We can also measure RNAs with time-lapsed microscopy using (variations of) the MS2 system. (contact: Evelina Tutucci)

Example of RNA-FISH in yeast: CLN2 mRNA smFISH (yellow), Tubulin IF (magenta), DAPI (blue), DIC (gray)

Sample projects

Meet the Scientist: Thomas Hansen

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Thomas Hansen Assistant Professor in the Synthetic Organic Chemistry & Catalysis Group "People with different personal, cultural, and scientific backgrounds bring unique insights...the beauty of…
Sofia discussing metabolism with PhD candidate Victoria Pozo Photo credit: David Poole III

Meet the Scientist: Sofia Moco

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Sofia Moco PI at the Chemistry and Pharmaceutical Sciences department of the VU. Birthplace:  Portugal "I was always curious about how things work, and somehow…

Do NMR Experiments with AIMMS

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Interested in using our NMR equipment? Nuclear Magnetic Resonance (NMR) spectroscopy is widely used to determine the structure of organic molecules and is closely tied to…

Using metabolomics to study the dynamics of metabolism

| Fermentation, Food, Research | No Comments
Dysregulation of metabolism is closely linked to the development of various diseases and lifetime changes, including metabolic disorders, cancer, and ageing. Understanding the nuances of…

AIMMS researchers win €5M NWO Perspective Grant for the plant-based fermentation proposal

| Fermentation, Food, Research | No Comments
This week The Netherlands Organisation for Scientific Research (NWO) granted the FERMI Perspective proposal led by Herwig Bachmann from the Systems Biology Lab. The project…

Stringing Science Together: Bead-azzling Macrocyclization for Biochemistry Bling!

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Imagine making a necklace. You start with various colors and shapes of beads, and you decide which specific beads you want to connect to form…