Transferable ideas for solving metabolomics problems.

A spatial metabolomics strategy that combines systematic surface sampling, LC-MS/MS, coordinate-aware metadata and 2D/3D molecular mapping to reconstruct the distribution of metabolites and environmental chemicals across physical objects.

Uses: `ili

A transferable natural-product discovery strategy that overlays quantitative bioassay results onto LC-MS feature abundance and MS/MS molecular networks to prioritize molecular families and individual features associated with biological activity.

Uses: MZmine · OpenMS · GNPS · Bioactive Molecular Networks Jupyter workflow

Combine molecular-network edges with abundance changes across ordered samples to prioritize possible chemical transformations.

Uses: Chemical Proportionality (ChemProp)

Group identified metabolites by chemical similarity and test which groups change between study conditions.

Uses: ChemRICH

A functional-group-resolved metabolomics strategy that uses orthogonal chemoselective probes, covalent capture and diagnostic reporter chemistry to enrich and organize otherwise chemically heterogeneous metabolite subsets before LC-MS.

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A miniaturized microbial natural-product strategy that adds MALDI tandem mass spectrometry and GNPS2 molecular networking to IDBac so metabolite families can be preliminarily annotated directly from colonies before fermentation scale-up and extraction.

Uses: IDBac · GNPS

Model paired microbial and MS metabolomics measurements to prioritize conditional co-occurrence relationships between taxa and molecular features.

Uses: mmvec

Combine mass spectrometry imaging with taxon-specific fluorescence labeling to associate spatial chemistry with microbial identity.

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A method-development strategy that uses mixtures of natural-abundance and uniformly 13C-labeled biological extracts to distinguish genuine biological features from artifacts and benchmark untargeted metabolomics workflows.

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A hybrid untargeted acquisition strategy that analyzes individual samples by DIA for broad feature and MS/MS coverage while using pooled quality-control samples by DDA to obtain cleaner fragmentation spectra for annotation.

Uses: DaDIA.R

Convert unsaturated fatty-acid double bonds to epoxides and use diagnostic tandem-MS fragments to distinguish positional isomers.

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A strategy that combines aligned LC-MS feature abundances with MS/MS spectral similarity to explore quantitative molecular families while retaining chromatographic feature identity.

Uses: GNPS2 Feature-Based Molecular Networking workflow · MZmine · MS-DIAL · xcms

Infer pathway and metabolic-network hypotheses from significant untargeted MS features before assigning every metabolite identity.

Uses: mummichog

A strategy extending feature-based molecular networking with MS1-derived ion relationships, linking candidate ion species of the same molecule alongside MS/MS spectral-similarity edges.

Uses: GNPS · MZmine · Cytoscape

Pair light and heavy chemical labels to quantify amine- and phenol-containing metabolites by LC-MS.

Uses:

Use precursors fragmented in earlier injections to guide subsequent DDA runs toward additional ions.

Uses: msconvert · MZmine · IE-Omics · LipidMatch

Plan successive MS/MS acquisitions from an MS1 survey by optimizing precursor schedules across mass and retention time.

Uses: MS2Planner · IODA_MS

Combine isotope-label incorporation kinetics with metabolite pool sizes to estimate cellular fluxes under an explicit kinetic model.

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A multimodal natural-product strategy that uses spatial localization from mass spectrometry imaging to prioritize metabolites for LC-MS/MS molecular networking and structural interpretation.

Uses: GNPS

A natural-product discovery strategy that correlates metabolite occurrence across a strain collection with biosynthetic gene-cluster or gene-cluster-family occurrence to connect chemistry with its likely genetic origin.

Uses: GNPS · NPLinker · MIBiG

Pair rapid chromatographic fraction collection with LC-MS/MS and luminescent bioreporters to connect chemical signals with antibacterial responses.

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A natural-product dereplication strategy that organizes MS/MS spectra by fragmentation similarity and uses reference spectra, standards, or characterized organisms to recognize known molecules and related analogues before isolation.

Uses: GNPS

Tandem mass spectrum to decision (MS2DECIDE) leverages decision theory and expert knowledge to aggregate the outputs of three widely used annotation tools (GNPS, Sirius, and ISDB-LOTUS) and compute a recommendation for targeting natural products with regard to their potential novelty.

Uses: MS2DECIDE · GNPS · SIRIUS · ISDB-LOTUS

A transferable LC-MS strategy that combines post-column pH adjustment and metal infusion with ion identity molecular networking to discover small molecules that bind metals in complex biological samples.

Uses: MZmine · GNPS · MassIVE · Cytoscape

A structural-lipidomics strategy that uses ozone-induced dissociation to generate diagnostic fragments for carbon–carbon double-bond positions that conventional CID-based lipidomics often cannot resolve.

Uses: LipidOz

Couple lipid photochemical derivatization to tandem MS to locate carbon-carbon double bonds.

Uses:

Model spatial relationships between microscopy features and measured ion intensities, then use validated relationships to predict molecular distributions at finer spatial resolution or in unmeasured tissue regions.

Uses: Molecular Image Fusion prototype

Use repeated biological QC injections to estimate and correct feature-specific signal drift along acquisition order.

Uses: xcms

Discover features in pooled reference samples, then extract their signals across a large LC-MS cohort using curated mass and retention-time targets.

Uses: xcms · CAMERA · Skyline · AcquireX

Combine relative LC elution order with MS/MS candidate scores to annotate multiple features jointly.

Uses: IOKR · Retention-order prediction implementation

A discovery strategy that starts from a candidate chemical structure or reference MS/MS spectrum, searches public metabolomics repositories for matching spectra, and uses sample metadata to reveal biological or phenotypic associations.

Uses: MSMS-Chooser · MASST · Pan-ReDU · GNPS

Combine tissue metabolite images with antibody-based cellular phenotypes from imaging mass cytometry.

Uses: MALDI-MSI-IMC analysis scripts

Discover recurring fragment and neutral-loss patterns across MS/MS spectra to propose shared substructures.

Uses: xcms · MzMatch · RMassBank · MS2LDA

A single-cell metabolomics strategy that registers microscopy-derived cell boundaries and morphologic information with MALDI imaging mass spectrometry so spatial ion signals can be assigned to individual cells.

Uses: SpaceM

A biosynthetic discovery strategy that combines stable-isotope precursor feeding with LC-MS/MS molecular networking to identify structurally related metabolites that incorporate a defined biosynthetic building block.

Uses: GNPS

An exposomics strategy that interrogates untargeted UHPLC-HRMS/MS data with curated lists of plausible xenobiotics and metabolites, then applies chromatographic, spectral, and error-control evidence to prioritize candidate exposures.

Uses: Compound Discoverer

Use DDA-derived assay libraries and decoy scoring to control false discoveries during targeted DIA extraction.

Uses: OpenMS · SIRIUS

A metabolite-annotation strategy that reranks candidate natural-product structures by combining spectral or in-silico annotation evidence with the taxonomic distance between the study organism and known producers of candidate compounds.

Uses: LOTUS · Natural Products Atlas

A microbial natural-product discovery strategy that combines MALDI protein fingerprinting with specialized-metabolite overlap to reduce taxonomic and chemical redundancy when constructing or downsizing isolate libraries.

Uses: IDBac

Combine stable-isotope nutrient tracing with MALDI imaging to map labeling patterns within tissue rather than averaging an entire section.

Uses: IsoScope