Find your next step in metabolomics.

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Define a spatial sampling scheme
2. Extract and profile each location
3. Process and annotate features
4. Map molecular features onto the physical modelPublished resources: `ili (Find learning resources)Explore alternatives: Visualization and reporting

+ 1 more workflow step on the Strategy page.

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Generate fractions and quantitative bioassay data
2. Acquire untargeted LC-MS/MS profiles
3. Detect and quantify featuresPublished resources: MZmine (Find learning resources) · OpenMS (Find learning resources)Explore alternatives: Preprocessing and feature extraction · Workflow management and reproducibility
4. Calculate feature–bioactivity associationsPublished resources: Bioactive Molecular Networks Jupyter workflow

+ 2 more workflow steps on the Strategy page.

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Prepare matched network and abundance data
2. Score proportional changesPublished resources: Chemical Proportionality (ChemProp) (Find learning resources)Explore alternatives: Statistical analysis
3. Investigate candidate transformations

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Prepare identified metabolites and statistics
2. Construct chemical setsPublished resources: ChemRICH
3. Evaluate and interpret enrichmentPublished resources: ChemRICH

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Select a functional-group-specific probe
2. Encode metabolites by covalent derivatization
3. Capture and clean up the encoded submetabolome
4. Release and analyze derivatives by LC-MS/MS

+ 1 more workflow step on the Strategy page.

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Profile colonies by MALDI-MS1Published resources: IDBac
2. Select small-molecule precursors for fragmentationPublished resources: IDBac
3. Acquire MALDI-MS/MS spectra
4. Run downstream GNPS2 molecular networkingPublished resources: GNPS (Find learning resources)Explore alternatives: Molecular networking and chemical similarity

+ 1 more workflow step on the Strategy page.

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Match the two measurement tables
2. Fit and evaluate the conditional modelPublished resources: mmvec
3. Prioritize and validate associations

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Preserve spatial correspondence
2. Measure chemistry and microbial identity
3. Register and compare images

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Generate matched unlabeled and uniformly 13C-labeled biological material
2. Prepare defined isotope mixtures
3. Run the candidate untargeted workflow
4. Credential biological features

+ 1 more workflow step on the Strategy page.

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Prepare representative pooled QC material
2. Acquire individual study samples by DIA
3. Acquire pooled QC samples by DDA
4. Integrate DDA and DIA informationPublished resources: DaDIA.R

+ 1 more workflow step on the Strategy page.

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Epoxidize unsaturated fatty acids
2. Fragment epoxide products
3. Assign double-bond positions

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Process LC-MS/MS data into aligned featuresPublished resources: MZmine (Find learning resources) · MS-DIAL (Find learning resources) · xcms (Find learning resources) · OpenMS (Find learning resources)Explore alternatives: Preprocessing and feature extraction · Workflow management and reproducibility
2. Export FBMN inputsPublished resources: MZmine (Find learning resources) · MS-DIAL (Find learning resources) · xcms (Find learning resources) · OpenMS (Find learning resources)Explore alternatives: Preprocessing and feature extraction · Workflow management and reproducibility
3. Run the FBMN workflow in GNPS2Published resources: GNPS2 Feature-Based Molecular Networking workflow (Find learning resources)Explore alternatives: Molecular networking and chemical similarity
4. Overlay spectral-library annotationsPublished resources: GNPS2 Feature-Based Molecular Networking workflow (Find learning resources)Explore alternatives: Molecular networking and chemical similarity

+ 1 more workflow step on the Strategy page.

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Define significant and background features
2. Map candidate metabolites to a networkPublished resources: mummichog (Find learning resources)Explore alternatives: Pathway and biological interpretation
3. Evaluate network and pathway enrichmentPublished resources: mummichog (Find learning resources)Explore alternatives: Pathway and biological interpretation
4. Validate prioritized hypotheses

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Detect and align LC-MS/MS featuresPublished resources: MZmine (Find learning resources)Explore alternatives: Preprocessing and feature extraction
2. Annotate ion identitiesPublished resources: MZmine (Find learning resources)Explore alternatives: Preprocessing and feature extraction
3. Export FBMN and ion-identity edgesPublished resources: MZmine (Find learning resources)Explore alternatives: Preprocessing and feature extraction
4. Build the ion identity molecular networkPublished resources: GNPS (Find learning resources)Explore alternatives: Molecular networking and chemical similarity

+ 1 more workflow step on the Strategy page.

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Label samples and reference
2. Mix labeled material
3. Separate and measure isotope pairs
4. Calculate comparative abundances

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Acquire the initial DDA run
2. Convert acquired spectraPublished resources: msconvert (Find learning resources)Explore alternatives: Data conversion and import
3. Generate the next exclusion listPublished resources: IE-Omics
4. Import the list and repeat acquisition

+ 1 more workflow step on the Strategy page.

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Acquire an MS1 survey
2. Prepare features for scheduling
3. Optimize successive acquisition pathsPublished resources: MS2Planner (Find learning resources)Explore alternatives: Data acquisition and instrument control
4. Export instrument inclusion listsPublished resources: IODA_MS

+ 1 more workflow step on the Strategy page.

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Switch nutrient isotope labeling
2. Sample the labeling time course
3. Measure labeling and pool sizes
4. Fit the specified kinetic model

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Acquire spatial metabolite maps
2. Prioritize spatially informative features
3. Acquire complementary LC-MS/MS data
4. Build molecular networksPublished resources: GNPS (Find learning resources)Explore alternatives: Molecular networking and chemical similarity

+ 1 more workflow step on the Strategy page.

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Profile a genetically diverse strain collection
2. Mine genomes for biosynthetic gene clustersPublished resources: antiSMASH BiG-SCAPE
3. Organize metabolite features or molecular familiesPublished resources: GNPS (Find learning resources)Explore alternatives: Molecular networking and chemical similarity
4. Score BGC–metabolite co-occurrencePublished resources: NPLinker

+ 1 more workflow step on the Strategy page.

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Collect fractions during LC-MS/MS
2. Measure reporter responses
3. Align activity with chemistry

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Acquire MS/MS spectra from complex extracts
2. Add reference spectra
3. Build a spectral molecular networkPublished resources: GNPS (Find learning resources)Explore alternatives: Molecular networking and chemical similarity
4. Dereplicate known chemistry and related analogues

+ 1 more workflow step on the Strategy page.

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Prepare aligned inputs
2. Collect complementary annotationsPublished resources: GNPS (Find learning resources) · SIRIUS (Find learning resources)Explore alternatives: Metabolite annotation and identification · Molecular networking and chemical similarity
3. Combine evidence and prioritizePublished resources: MS2DECIDE (Find learning resources)Explore alternatives: Metabolite annotation and identification
4. Review candidates

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Separate metabolites by LC
2. Adjust post-column pH
3. Infuse the metal of interest
4. Process features and ion identitiesPublished resources: MZmine (Find learning resources)Explore alternatives: Preprocessing and feature extraction

+ 2 more workflow steps on the Strategy page.

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Acquire lipids under OzID-compatible conditions
2. Collect diagnostic OzID fragments
3. Resolve and score double-bond assignmentsPublished resources: LipidOz
4. Validate structural isomers

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Photochemically modify lipid double bonds
2. Fragment reaction products
3. Interpret diagnostic fragments

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Acquire paired molecular and optical images
2. Register images and derive paired features
3. Fit ion-specific cross-modal models
4. Evaluate reconstruction and spatial reliability

+ 2 more workflow steps on the Strategy page.

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Interleave representative QC injections
2. Prepare aligned feature intensitiesPublished resources: xcms (Find learning resources)Explore alternatives: Preprocessing and feature extraction
3. Fit QC correction curves
4. Correct and assess reliability

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Prepare representative reference pools
2. Build the polar feature listPublished resources: xcms (Find learning resources) · CAMERA (Find learning resources) AcquireXExplore alternatives: Preprocessing and feature extraction
3. Curate reference targetsPublished resources: DecoID Lipid Annotator
4. Extract cohort peak areasPublished resources: Skyline (Find learning resources)Explore alternatives: Quantification and targeted analysis

+ 1 more workflow step on the Strategy page.

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Prepare candidate lists
2. Score spectral candidatesPublished resources: IOKR
3. Learn and integrate retention preferences
4. Review ranked assignments

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Generate or obtain a reference MS/MS spectrumPublished resources: MSMS-Chooser (Find learning resources)Explore alternatives: Spectral processing and comparison
2. Select a representative reference spectrumPublished resources: MSMS-Chooser (Find learning resources)Explore alternatives: Spectral processing and comparison
3. Search public MS/MS dataPublished resources: MASST (Find learning resources) · GNPS (Find learning resources) · MassIVE (Find learning resources)Explore alternatives: Data management and sharing · Molecular networking and chemical similarity · Reference data and database search
4. Contextualize matches with sample metadataPublished resources: Pan-ReDU (Find learning resources)Explore alternatives: Data management and sharing

+ 2 more workflow steps on the Strategy page.

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Acquire MALDI images
2. Acquire immunophenotypes
3. Register images and segment cells
4. Assign metabolite signals

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Prepare precursor-linked spectraPublished resources: xcms (Find learning resources)Explore alternatives: Preprocessing and feature extraction
2. Learn recurring motifsPublished resources: MS2LDA (Find learning resources)Explore alternatives: Spectral processing and comparison
3. Interpret and inspect assignmentsPublished resources: MS2LDA (Find learning resources)Explore alternatives: Spectral processing and comparison

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Acquire microscopy of the same cells
2. Segment individual cells
3. Acquire MALDI mass spectrometry imaging
4. Register optical and MSI coordinate systems

+ 2 more workflow steps on the Strategy page.

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Select and feed a stable-isotope precursor
2. Detect isotope incorporation
3. Acquire and compare MS/MS spectra
4. Build a molecular networkPublished resources: GNPS (Find learning resources)Explore alternatives: Molecular networking and chemical similarity

+ 1 more workflow step on the Strategy page.

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Build suspect lists
2. Acquire UHPLC-HRMS/MS data
3. Filter chromatographic features for peak quality
4. Compare candidates with suspect and endogenous lists

+ 2 more workflow steps on the Strategy page.

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Construct target and decoy assaysPublished resources: OpenMS (Find learning resources) · SIRIUS (Find learning resources)Explore alternatives: Metabolite annotation and identification · Workflow management and reproducibility
2. Extract DIA chromatogramsPublished resources: OpenMS (Find learning resources)Explore alternatives: Workflow management and reproducibility
3. Score and filter resultsPublished resources: OpenMS (Find learning resources)Explore alternatives: Workflow management and reproducibility

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Generate candidate structural annotations
2. Retrieve candidate biological-source informationPublished resources: LOTUS (Find learning resources) · Natural Products Atlas (Find learning resources)Explore alternatives: Reference data and database search
3. Calculate taxonomic relevance
4. Rerank candidates

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Acquire MALDI protein fingerprints from individual isolatesPublished resources: IDBac
2. Group taxonomically similar isolatesPublished resources: IDBac
3. Acquire specialized-metabolite profilesPublished resources: IDBac
4. Compare chemical overlap within taxonomic groupsPublished resources: IDBac

+ 1 more workflow step on the Strategy page.

Alternative searches use the recorded tool function; check inputs, outputs and acquisition compatibility before substituting.

1. Introduce and measure the nutrient tracer
2. Image tissue isotopologues
3. Validate signals and map labelingPublished resources: IsoScope