Sharing data and reference knowledge
Preserve data and connect reference evidence.
How to choose a resource
Repositories preserve experimental files, reference spectra support annotation, and knowledgebases connect molecular evidence to its reported context. These resources serve different purposes, but all depend on clear metadata and traceable evidence.
Distinguish depositing a dataset from preparing a reference spectrum or contributing a biological annotation. Keep the source files, identifiers, and supporting evidence connected.
Tools & resources
21 entriesMassIVE
Free web serviceA public repository for depositing, preserving, browsing, downloading, and reusing mass-spectrometry datasets, including datasets connected to GNPS analyses.
Deposit & access MS datasetsMSMS-Chooser
Free web serviceA GNPS workflow for automatically selecting candidate reference MS/MS spectra from LC-MS data of known standards using supplied molecular structures and expected precursor masses.
Prepare reference spectraCMMC-KB
Free web serviceA community-curated knowledgebase for microbial metabolites that links reference MS/MS evidence, microbial producers, annotations, and GNPS2 analysis resources.
Curated metabolite knowledgeMassBank
Free web serviceFind and download open reference mass spectra with compound and acquisition metadata.
Open reference mass spectraMoNA
Free web serviceSearch aggregated mass spectra and download reference libraries for local annotation workflows.
Aggregated spectral librariesMetaboLights
Free web serviceDeposit and find metabolomics studies with experimental files and structured sample and assay metadata.
Studies & structured metadataMetabolomics Workbench
Free web serviceDeposit, discover and retrieve metabolomics studies through the National Metabolomics Data Repository.
Study repository & data accessHMDB
Free web serviceFind chemical, biological and spectral reference information for human metabolites.
Human metabolite referencePubChem
Free web serviceSearch chemical structures, identifiers, properties and contributed annotations.
Chemical identities and cross-referencesChEBI
Free web serviceLook up curated chemical entities, names and ontology relationships.
Chemical ontology and identifiersReactome
Free web serviceExplore curated metabolic and signaling reactions with literature-linked pathway context.
Curated biological pathwaysWikiPathways
Free web serviceFind and contribute biological pathway diagrams and machine-readable pathway knowledge.
Community-curated pathway mapsLIPID MAPS
Free web serviceFind lipid structures, classifications, nomenclature guidance and lipidomics analysis resources.
Lipid structures and nomenclatureLipidBlast
Free web serviceUse an in-silico tandem mass-spectral library to support lipid annotation.
Predicted lipid MS/MS libraryFooDB
Free web serviceExplore food constituents, chemical properties and reported dietary sources.
Food compounds and dietary sourcesNatural Products Atlas
Free web serviceExplore structures and literature for bacterial and fungal natural products.
Microbial natural-product structuresLOTUS
Free web serviceConnect natural-product structures, organism occurrences and literature references.
Natural products and organism linksCOCONUT
Free web serviceSearch an aggregated, curated collection of natural-product structures and source records.
Aggregated natural-product referenceRefMet
Free web serviceMap metabolite names to a standardized reference nomenclature for cross-study comparisons.
Standardize metabolite namesLipidLynxX
Open sourceConvert, cross-match and link lipid names across supported nomenclatures before downstream MS lipidomics interpretation.
Convert and cross-match lipid namesGoslin
Open sourceLipid shorthand grammars and parser implementations for validating and normalizing names in MS lipidomics workflows.
Validate lipid shorthand nomenclature