Exploring spectral relationships
Find relationships and patterns in spectra.
How to choose a resource
Tandem mass spectra contain fragmentation information that can help investigate related molecules. Molecular networking organizes spectra by similarity, while a query language can find spectra containing a specified pattern. These approaches help prioritize signals for closer inspection.
Decide whether you need to explore relationships across a dataset or test a specific spectral pattern. Similarity or a query match alone does not establish a complete structure.
Analytical strategies
Understand the method, then choose its software implementation.
Tools & resources
17 entriesGNPS
Free web serviceA web-based mass-spectrometry ecosystem for molecular networking, spectral-library search, repository-scale search, interactive visualization, knowledgebase curation, and public-data integration.
Molecular networking & librariesGNPS2 Classical Molecular Networking
Free web serviceGNPS2 workflow for organizing MS/MS spectra into molecular families using pairwise spectral similarity and spectral-library searching.
Spectrum-centric molecular networkingGNPS2 Feature-Based Molecular Networking workflow
Free web serviceDedicated GNPS2 workflow that combines an aligned LC-MS feature table with MS/MS spectra to build quantitative molecular networks.
Quantitative feature-based networkingMassQL
Open sourceAn open-source, instrument-independent query language and software ecosystem for searching mass-spectrometry data using reusable MS1, MS/MS, chromatographic, and ion-mobility patterns.
Chemical-pattern queriesmatchms
Open sourceBuild Python workflows for spectral cleaning, metadata harmonization and MS/MS similarity scoring.
Clean and compare MS/MS spectraSpec2Vec
Open sourceCompare tandem mass spectra using embeddings learned from recurring peaks and neutral losses.
Learned spectral similarityMS2DeepScore
Open sourceEstimate molecular structural similarity from pairs of tandem mass spectra.
Predict structural similarityMS2LDA
Source available with restrictionsFind recurring patterns of fragments and neutral losses across tandem mass spectra.
Discover recurring substructure motifsMolNetEnhancer
Source available with restrictionsCombine molecular networking, substructure motifs and chemical classifications into annotated networks.
Combine network annotation evidenceMolNetInvert
Open sourceCreate metadata-based molecular networks from GNPS networks or feature tables to explore how metabolites are distributed across sample groups.
Explore metadata-based molecular networksPostMN MassQL
Free web serviceRun MassQL chemical-pattern queries directly on consensus spectra produced by GNPS molecular networking.
Query processed networking spectraMulti-step MassQL
Free web serviceApply a predefined sequence of MassQL queries to GNPS2 networking spectra to investigate bile acids and their isomers.
Bile-acid query sequencesMassQL Playground
Free web serviceBrowser-based MassQL query editor and runner for exploring fragmentation patterns in local mass-spectrometry files.
Query local spectra in the browserGNPS2 MassQL Analysis
Free web serviceHosted interface for exploring MS/MS spectral libraries with MassQL and using LLM assistance to draft or explain queries.
Explore library queries with assistanceTinyMass
Free web serviceHosted utility for sharing mass spectra through reusable spectrum identifiers in the GNPS2 ecosystem.
Share an individual spectrumMetGem
Open sourceLocal desktop generation and exploration of MS/MS similarity networks and two-dimensional spectral projections.
Local MS/MS network generationCytoscape
Open sourceDesktop network visualization and analysis for exploring MS molecular networks alongside feature annotations and sample metadata.
Explore and style molecular networks