DTU Metabolomics Core

About the DTU Metabolomics Core

The DTU Metabolomics Core provides analytical services to researchers at DTU Bioengineering by integrating major analytical instrumentation under unified management in dedicated laboratories. Our objectives are to ensure efficient use of equipment, maintain a high level of analytical expertise, and support cost-effective operation of advanced analytical systems.

Our Mission

Our mission is to provide researchers access to state-of-the-art analytical instrumentation and methodologies for the comprehensive detection and characterization of secondary metabolites from biological systems, with a strong focus on microbial producers including bacteria, fungi, microalgae, and other microorganisms.

Expertise and Capabilities

Advanced high-resolution mass spectrometry coupled chromatography is central to our work. We have extensive experience in untargeted secondary metabolite profiling and dereplication for novelty assessment, supporting projects ranging from natural product discovery to biosynthetic pathway elucidation.

Key capabilities include:

• LC-HRMS (ESI) for untargeted metabolomics and secondary metabolite discovery
  Using a Bruker timsTOF fleX and Bruker Impact II, each coupled to an Agilent 1290 UHPLC with DAD, we perform high-resolution profiling, MS/MS annotation, and have the ability to use CCS-enhanced identification.
• MALDI Imaging (MSI)
  Our Bruker timsTOF fleX enables high-resolution MALDI imaging for spatial metabolomics, mapping metabolite distributions directly from microbial cultures, tissues, and other biological samples down to 20 µm.
• Semi-preparative HPLC-DAD-MS and purification workflows
  We operate two semi-preparative HPLC systems for isolation and purification of secondary metabolites, supported by our analytical LC-HRMS for purity assessment and method development.
• HPLC-DAD-FLD for initial profiling of newly isolated fungal strains
  In-house experts can distinguish compound classes that aid chemo/taxonomic workflow.
• GC-MS analysis
  A ThermoFisher GC-MS platform enables analysis of lipids, volatile and semi-volatile compounds, complementing our MS capabilities.
• Extensive secondary metabolite reference resources
  We maintain a curated collection of over 1400 natural products and in-house MS/MS libraries, supporting high-confidence dereplication and structural annotation.
• Software Development
  We are actively developing unique software for many applications, from mass spectrometry acquisition and data analysis to scientific data management.
  Additionally, we have strong expertise in sample preparation, including solid-phase extraction (SPE) and other cleanup strategies to reduce matrix effects and maintain instrument integrity.

Access and Use

The Core Facility is open to all researchers following consultation with Metabolomics Core staff. Before initiating work, please consider the following:

• Sample preparation: Consult with us before beginning preparation to avoid contamination issues or loss of analytes.
• Matrix complexity: Inform us if samples contain interfering compounds (e.g., polymers, surfactants, salts) requiring cleanup.
• Data analysis: LC-MS and GC-MS datasets are complex; users are generally responsible for their own data analysis in scientific projects.
• Experimental design: Ensure appropriate controls, blanks, and validation strategies are included.
• Sample labeling: All samples must be submitted with printed labels produced using our label printers.

Please use the Sample Submission Form when submitting samples.

Contract Research

We support a broad range of contract research for industrial and academic partners, including:

• Identification and characterization of unknown compounds in fermentation broths, bioprocess samples, and microbial extracts
• Profiling and dereplication of secondary metabolites for natural product discovery pipeline support
• Development and optimization of sample preparation workflows and chromatographic methods

Recent Publications

Lydicamycins induce morphological differentiation in actinobacterial interactions
Scott A. Jarmusch*, Morten D. Schostag, Zhijie Yang, Jinglin Wang, Aaron J. C. Andersen, Tilmann Weber, Ling Ding
Corresponding author: Scott A. Jarmusch
Affiliations: Natural Product Discovery; Section for Microbial and Chemical Ecology; Department of Biotechnology and Biomedicine; Bacterial Ecophysiology and Biotechnology; Novo Nordisk Foundation Center for Biosustainability; DTU Metabolomics Core; Natural Products Genome Mining; Bioactive Microbial Small Molecules

Penicillium hordei acidification precipitates Bacillus subtilis lipopeptides to evade inhibition
Manca Vertot, Morten D. Schostag, Aaron J. C. Andersen, Jens C. Frisvad, Carlos N. Lozano-Andrade, Scott A. Jarmusch*
Corresponding author: Scott A. Jarmusch
Affiliations: Department of Biotechnology and Biomedicine; Section for Synthetic Biology; Fungal Chemodiversity; IBT Culture Collection of Fungi; Section for Microbial and Chemical Ecology; Bacterial Ecophysiology and Biotechnology; Center for Microbial Secondary Metabolites; DTU Metabolomics Core; Natural Product Discovery; Microbiome Interactions Engineering

Insights into the nature of ichthyotoxins from the Chrysochromulina leadbeateri blooms in Northern Norwegian fjords
Xinhui Wang, Mathias Fon, Aaron J. C. Andersen, Anita Solhaug, Richard A. Ingebrigtsen, Ingunn A. Samdal, Silvio Uhlig, Christopher O. Miles, Bente Edvardsen*, Thomas O. Larsen*
Corresponding authors: Bente Edvardsen, Thomas O. Larsen
Affiliations: Department of Biotechnology and Biomedicine; Section for Microbial and Chemical Ecology; Natural Product Discovery; DTU Metabolomics Core

Phages carry interbacterial weapons encoded by biosynthetic gene clusters
Anna Dragoš*, Aaron J. C. Andersen, Carlos N. Lozano-Andrade, Paul J. Kempen, Ákos T. Kovács, Mikael Lenz Strube*
Corresponding authors: Anna Dragoš, Mikael Lenz Strube
Affiliations: Section for Microbial and Chemical Ecology; Department of Biotechnology and Biomedicine; DTU Metabolomics Core; Natural Product Discovery; Center for Microbial Secondary Metabolites; National Centre for Nano Fabrication and Characterization; Department of Health Technology; Nanocharacterization; Materials at the Interface of Biology; Bacterial Ecophysiology and Biotechnology