Browse the catalogue

Explore tools by what they do and strategies by the scientific problem they address.

Tool functions

Broad tasks performed by software, databases, services, and other tools.

Data acquisition and instrument controlInstrument control, acquisition methods, or real-time acquisition support.7 Data conversion and importConversion between vendor, open, tabular, or exchange formats.16 Preprocessing and feature extractionPeak detection, deconvolution, alignment, grouping, or gap filling.51 Quality control and filteringQC assessment, contaminant or blank filtering, drift detection, or diagnostic reporting.36 Normalization and batch correctionSignal normalization, scaling, drift correction, or batch-effect adjustment.14 Quantification and targeted analysisCalibration, integration, targeted quantification, or assay processing.9 Metabolite annotation and identificationFormula assignment, structure elucidation, library matching, or confidence assessment.86 Spectral processing and comparisonSpectrum cleaning, similarity scoring, prediction, interpretation, or library generation.63 Molecular networking and chemical similarityNetwork-based organization or exploration of spectra, features, or chemical relationships.24 Statistical analysisUnivariate or multivariate statistics, hypothesis testing, or exploratory analysis.32 Machine learning and predictionClassification, regression, feature selection, embedding, or predictive modeling.36 Pathway and biological interpretationEnrichment, pathway mapping, reaction analysis, or biological interpretation.15 Isotope tracing and flux analysisStable-isotope correction, isotopologue analysis, flux estimation, or metabolic modeling.6 Visualization and reportingFigures, dashboards, interactive exploration, automated reports, or publication outputs.56 Data management and sharingMetadata handling, deposition, retrieval, interoperability, or FAIR data support.28 Workflow management and reproducibilityPipeline execution, provenance, containers, notebooks, or reproducible environments.18 Reference data and database searchSearch and retrieval of metabolite, spectrum, pathway, reaction, or ontology records.42 Multi-omics integrationIntegration of metabolomics with genomics, transcriptomics, proteomics, microbiome, or other data.13

Tool platforms

Analytical technologies supported by tools.

LC-MS145 GC-MS18 CE-MS3 Direct-infusion MS15 MALDI-MS4 Imaging mass spectrometry20 Multiple analytical platforms31 Platform-independent84

Strategy objectives

Scientific questions and transferable strategies represented by strategies.

Metabolite annotation8 Structure elucidation3 Dereplication1 Molecular-family discovery1 Metal-binding compound discovery1 Chemical-reactivity profiling2 Biotransformation analysis1 Analytical quality control1 Phenotype association3 Host–microbe interaction1 Natural-product discovery6 Stable-isotope tracing3 Flux analysis1 Spatial metabolomics4 Single-cell metabolomics2 Reverse metabolomics1 Exposomics1

Strategy components

Experimental and computational stages included in strategies.

Sample preparation18 Chromatography8 Post-column modification or infusion1 Data acquisition30 Preprocessing and feature extraction20 Quality control6 Annotation or identification23 Spectral search8 Molecular networking10 Repository-scale mining1 Metadata analysis13 Statistical analysis17 Biological validation13 Data and workflow sharing6

Strategy sample types

Sample matrices represented by published strategies.

Serum1 Urine1 Saliva1 Feces or stool1 Tissue or biopsy4 Cells or cell pellets1 Microbial culture or biomass7 Plant tissue1 Water or aquatic sample1 Synthetic or analytical standards2 Other biofluid1 Other or broadly applicable1

Strategy biological contexts

Broad biological systems and study contexts represented by strategies.

Human3 Animal2 Microbial8 Plant3 Fungal3 Marine1 Environmental2 Host–microbe interaction1 Synthetic or reference material2 Broadly applicable15