Software Developed at the DTU Metabolomics Core

MolNetInvert / Metadata-Based Molecular Networks (MBMN)

• From MolNetInvert: A Tool for Creating Metadata-Based Molecular Networks and Their Applications in Large Microbial Datasets. ChemRxiv
• Developed by Aaron J. C. Andersen. In collaboration with Johan V. Christiansen, Manca Vertot and Scott A. Jarmusch
• What it does: Generates Metadata-Based Molecular Networks (MBMN) by reorganizing molecular networks so that clustering is driven by metadata (e.g., biological conditions, sample type), not just spectral similarity.
• Why it’s useful: This approach simplifies very complex networks, gives meaning to singleton nodes, and helps highlight meaningful relationships linked to metadata. Useful for interpreting large untargeted metabolomics datasets from microbial systems.

Information and access to software can be found on ChemRxiv

Dynamic Cluster Analysis (DCA)

• Based on Dynamic Cluster Analysis: An Unbiased Method for Identifying A+2 Element Containing Compounds in Liquid Chromatographic High-Resolution TOF Mass Spectrometric Data. Analytical Chemistry
• Developed by Aaron J. C. Andersen. In collaboration with Per Juel Hansen, Kevin Jørgensen, and Kristian Fog Nielsen
• What it does: Automatically detects and filters metabolite features that contain A+2 isotopic patterns (e.g., Cl, Br, S) using isotope cluster spacing, monoisotopic mass, and intensity ratios
• Why it’s useful: Enhances the identification of metabolite classes that would otherwise be hidden in complex mass spectra, making high-resolution LC-MS data more interpretable in untargeted workflows

Information on the software can be found here and access to software can be found here.

IsoPat

IsoPat is a python-based windows application for calculating isotope patterns from molecular formulas developed by Aaron J. C. Andersen.

• What it does: Generates isotope patterns from molecular formulas, with functionality for calculating convoluted isotopes from simulated co-eluting compounds, as well as, 13C enrichment calculations 
• Why it’s useful: This software allows for the full visualization of a mass spectra, including multiple adducts and co-eluting compounds all in one simulation. This differs from traditional isotope calculators that limit the user to visualize one chemical species at a time (e.g., [M+Na]+). With IsoPat, it is possible to visualize up to four adducts at once, as well as simulate a co-eluting compound, all in one spectrum. 

Information and access to software can be found on ResearchGate

MetaTrace: In-House Scientific Data Management & LIMS System

MetaTrace is our custom-built scientific data management and laboratory information management system, designed specifically for the needs of the Department by Aaron J. C. Andersen.
Key features include:

• Secure sample and project tracking from submission to reporting
• Automated metadata handling for LC-MS, GC-MS, MALDI imaging, and HPLC workflows
• Integration with instrument output directories and processing pipelines
• Support for archiving raw data, processed files, metadata, and reports
• User-level access control and project-based data sharing
• Audit trails and reproducibility tools for research transparency

MetaTrace ensures that all analytical and sample metadata are well structured, traceable, and easily retrievable, supporting robust data integrity across research and contract projects.

Ongoing Development

The Metabolomics Core continues to expand the functionality of its software ecosystem, focusing on:

• Enhanced MS/MS spectral dereplication
• CCS-assisted annotation for TIMS data
• Developments MALDI imaging workflows from acquisition to data analysis
• Integration with our Microbial Secondary Metabolite MS Database