Annotating molecules
Explore formulas, structures, and chemical classes.
How to choose a resource
Annotation tools help connect measured signals to molecular formulas, candidate structures, or chemical classes. These are different levels of information. A class prediction can be useful even when an exact structure remains unknown; a ranked structure candidate still needs supporting evidence.
Match the tool to the question you can answer with your data: formula, chemical class, database candidate, or a possible modification of a known molecule.
Tools & resources
15 entriesSIRIUS
Free for academic useA cross-platform small-molecule MS/MS framework for LC-MS preprocessing, molecular-formula annotation, spectral-library searching, structure-database searching, compound-class prediction, confidence scoring, and de novo structure generation.
Formula & structure annotationLipidOz
Open sourceDetermine lipid carbon–carbon double-bond positions using diagnostic ozone-induced dissociation data.
Metabolite annotation and identificationCSI:FingerID
Free for academic useA SIRIUS-integrated machine-learning method and webservice for predicting molecular fingerprints from MS/MS data and ranking candidate structures from molecular-structure databases.
Structure database searchCANOPUS
Free for academic useA SIRIUS-integrated machine-learning method and webservice for predicting compound classes directly from high-resolution MS/MS data without requiring an exact database structure match.
Chemical-class predictionMSNovelist
Free for academic useA SIRIUS-integrated de novo structure-generation method that proposes molecular structures from a predicted molecular formula and CSI:FingerID fingerprint when database search is insufficient.
De novo structure candidatesModiFinder
Free web serviceA GNPS2-associated computational tool for localizing structural modification sites by aligning MS/MS spectra of a known compound and a structurally related unknown analogue.
Modification-site localizationMetFrag
Open sourceRank candidate molecular structures by comparing predicted fragments with an experimental MS/MS spectrum.
Fragment-based structure rankingMS-FINDER
Source available with restrictionsExplore formula and structure candidates using fragmentation rules and EI-MS or MS/MS library searches.
Formula & structure interpretationCFM-ID
Free web servicePredict tandem mass spectra, annotate fragments and rank candidate structures for small molecules.
Predict spectra and rank structuresmetID
Open sourceAnnotate LC-MS features using accurate mass, retention time and tandem mass spectra in R.
Match mass, retention and MS/MSMIST
Source available with restrictionsPredict molecular fingerprints from tandem mass spectra and retrieve candidate structures.
Fingerprint prediction from MS/MSBUDDY / msbuddy
Open sourceGenerate and rank molecular formula annotations for small-molecule mass-spectrometry queries.
Molecular formula candidatesMetaboAnnotation
Open sourceMatch metabolomics features and spectra against reference values through a unified R interface.
Reproducible matching in RMS2Query
Open sourceMS/MS analogue-search tool that combines learned spectral similarity and precursor-mass information to retrieve structurally related reference compounds.
Find spectral matches & analoguesNPClassifier
Open sourceDeep neural-network tool that classifies natural-product structures into biosynthetic pathways, superclasses and structural classes.
Classify supplied natural-product structures