Description MS-Net is a KNIME workflow for confident metabolite annotation in LC-MS/MS untargeted metabolomics. It combines mass spectral similarity networks, molecular structure similarity, and taxonomic knowledge to prioritize structural annotations within large candidate spaces. Key Features Network-based annotation propagation from high-confidence seeds (spectral library matches, authentic standards) Multi-level confidence scoring system (Levels 1-5) with taxonomic enrichment Composite Link Score integrating Tanimoto similarities (full-molecule + scaffold), MS/MS cosine similarity, and in silico confidence Taxonomic filtering via Coconut 2.0 natural products database Rich metadata output with ClassyFire and NPClassifier chemical ontologies and Database identifiers (CID, Kegg...) Compatible with LC-MS processing tools: MZmine, MS-DIAL, Sirius-CSI, MS-Finder Requirements Software KNIME Analytics Platform ≥ 5.2 (https://www.knime.com) Input Data Sources MZmine or MS-DIAL: Feature detection, MS/MS spectral library matching, molecular networking Sirius ≥ 5.8 or MS-Finder: In silico structure prediction with CSI:FingerID and MSNovelist Quick Start Read the tutorial Install KNIME 5.2+ and required extensions Import workflow into KNIME (File → Import KNIME Workflow) For MZmine/MSDial and Sirius-based annotation: MSNet-Sirius.knwf For MSDial and MSFinder-based annotation: MSNet-MSFinder.knwf Configure input file paths (feature table, MSS network, Sirius annotations) Adjust parameters (taxonomic filters, α weighting, fingerprint type) Execute workflow Typical runtime: 5-30 minutes, depending on dataset size Outputs Annotated feature table with confidence levels and chemical metadata Feature intensity matrix for statistical analysis Mass spectral similarity network with annotations Tanimoto structural similarity network Summary statistics and annotation quality metrics Citation If you use MS-Net in your research, please cite: Pereira Francisco V, Duthen S, Crossay E, et al. (2025)Pereira Francisco, Duthen, Crossay et al. MS-Net: Multi-Similarity based network annotation for untargeted metabolomics, 27 November 2025, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-8174529/v1] Workflow DOI: 10.5281/zenodo.17669288 Documentation Full documentation, including detailed installation instructions, parameter optimization guides, troubleshooting tips, and example datasets is provided in the accompanying README.md file. Contact: guillaume.marti@utoulouse.fr License CeCILL-B Free Software License Agreement Version v1.0.0 (Initial release) Compatible with KNIME ≥ 5.2 Keywords: metabolomics, mass spectrometry, annotation, molecular networking, Tanimoto similarity, natural products, KNIME, workflow Upload Contents: MS-Net_workflow.knwf - Main KNIME workflow Quick reference.md - Short documentation TutoMS-Net: Complete step-by-step guide based on MZ-Mine/Sirius annotation processing MZbatch files: Import in MZmine for raw LC-MS data processing