Documented workflows
Published software workflows and their original methodological context. Check current software documentation for version-specific changes.
Structure database search with CSI:FingerID and COSMIC
CSI:FingerID predicts molecular fingerprints from fragmentation-tree information and uses them to rank candidate structures in molecular databases. The COSMIC workflow adds confidence estimation to help distinguish particularly trustworthy structure-database annotations from ambiguous candidate lists.
- Establish candidate molecular formulas
Run SIRIUS formula annotation and retain plausible precursor formulas for structure analysis.
- Predict molecular fingerprints with CSI:FingerID
Use fragmentation-tree-derived information and machine learning to predict structural fingerprint properties from the MS/MS spectrum.
- Search molecular-structure databases
Rank database candidates whose structural fingerprints agree with the predicted fingerprint and molecular formula.
- Apply COSMIC confidence scoring
Evaluate CSI:FingerID structure candidates with COSMIC to identify predictions that meet stronger confidence criteria and to separate high-confidence from ambiguous assignments.
- Validate prioritized structures
Review candidate structures and corroborate important annotations with spectral standards, retention behavior, orthogonal data, or other appropriate evidence.
Requirements
- A plausible molecular formula and informative high-resolution MS/MS spectrum; CSI:FingerID/COSMIC are webservice-backed SIRIUS features requiring appropriate account/license access.
Considerations
- The method is constrained by the candidate structure databases being searched; compounds absent from those databases cannot be returned as exact database candidates.
- A high computational confidence score should still be reported as an annotation unless the identification level is supported by appropriate orthogonal evidence.
Hoffmann MA, Nothias L-F, Ludwig M, et al. High-confidence structural annotation of metabolites absent from spectral libraries. Nature Biotechnology 40, 411–421 (2022).
Read the source methodOverview
CSI:FingerID predicts structural fingerprints from fragmentation-tree information and uses those fingerprints to search and rank candidate molecular structures in databases. In current SIRIUS releases it is a webservice-backed component of the structure-database search workflow rather than a standalone end-user application. It does not resolve stereochemistry and should be interpreted as ranked computational structure evidence rather than definitive identification.
What can this tool do?
Common uses
- Rank molecular-structure database candidates from accurate-mass MS/MS spectra.
- Predict molecular fingerprints that summarize structural properties inferred from fragmentation data.
- Provide structure-candidate rankings used by the SIRIUS COSMIC workflow and downstream interpretation.
- Prioritize database candidates for follow-up confirmation with standards or orthogonal measurements.
Scientific fit
Primary function
Metabolite annotation and identification
Other functions
Machine learning and prediction, Spectral processing and comparison
Analysis types
Untargeted metabolomics, Metabolite profiling
MS level
MS/MS
Acquisition
Data-dependent acquisition (DDA), Targeted MS/MS, General or unspecified acquisition
Ion mobility
Ion mobility not required
Data compatibility
Inputs
Mass spectra
Outputs
Molecular structures, Compound list or annotations, Human-readable report
Input formats
mzML, mzXML, MGF, MSP, SIRIUS project with formula candidates
Output formats
CSV or TSV, JSON, SIRIUS structure-candidate tables
Scope and considerations
Designed for
- Database-backed candidate structure identification of small molecules from informative, high-accuracy MS/MS spectra.
Not designed for
- Unrestricted de novo generation of structures absent from the searched candidate database.
Important requirements
- SIRIUS-compatible high-resolution MS/MS data, a SIRIUS account/license for the webservice, and a molecular formula or formula candidates.
Considerations
- CSI:FingerID does not determine stereochemistry and cannot identify structures absent from the searched databases.
- Ranking accuracy depends on spectral information content, molecular-formula quality, and candidate-database composition.
- Record the candidate database and formula settings, and inspect competing structures before interpreting the highest-ranked hit.
Education
Learn this tool
External tutorials and workshops collected by Navigator. Entries marked Needs review have not been checked end to end.
Access and documentation
CSI:FingerID is accessed through the SIRIUS web services; current webservice features are free for academic use, with separate non-academic licensing.
Evidence and review
Documentation-based editorial pass on 6 September 2026: scope, interpretation limits and practical use reviewed against the linked official documentation and cited literature. Software execution, service availability and developer verification were not assessed.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- Dührkop K, Shen H, Meusel M, et al. Searching molecular structure databases with tandem mass spectra using CSI:FingerID. Proc Natl Acad Sci U S A 112, 12580-12585 (2015). doi:10.1073/pnas.1509788112
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