Overview
Spectral Denoising removes candidate electronic and chemical noise ions from tandem spectra. Denoising Search applies candidate-dependent molecular information during reference-library matching and returns comparisons for raw and denoised spectra.
What can this tool do?
Common uses
- Spectral Denoising removes candidate electronic and chemical noise ions from tandem spectra.
Scientific fit
Primary function
Spectral processing and comparison
Other functions
Metabolite annotation and identification
Data compatibility
Inputs
Mass spectra, Spectral library
Outputs
Mass spectra, Compound list or annotations
Input formats
MSP spectra or peak arrays with formula/SMILES and adduct information
Output formats
Denoised peak arrays and candidate library-match result tables
Scope and considerations
Designed for
- Spectral Denoising removes candidate electronic and chemical noise ions from tandem spectra.
Not designed for
- Formula-independent removal of all interference or proof of a compound identity from an improved matching score alone.
Important requirements
- Python 3.8-3.12 with RDKit and dependencies; chemical denoising needs a molecular formula or SMILES plus adduct information, and search needs a compatible reference library.
Considerations
- Candidate chemistry and precursor tolerances influence which ions are retained. Validate thresholds and preserve original spectra for assessing possible removal of genuine fragments.
Access and documentation
MIT source distribution. External datasets, dependent packages and any hosted routes retain their own terms; software operation was not tested.
License: MIT
Evidence and review
Enveda intake rechecked against official repository documentation, package/license metadata and primary publication identity on 2026-10-27. Editorial source review only; no software execution or independent benchmark. See docs/enveda-expansion-review-2026-10-27-batch3.md.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- Denoising Search doubles the number of metabolite and exposome annotations in human plasma using an Orbitrap Astral mass spectrometer. Nature Methods (2025). doi:10.1038/s41592-025-02646-x
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
- 2026-10-27 · First committed entry
Add 45 source-reviewed Enveda tool entries in third expansion batch
View change · Entry at this revision