Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Spectral processing and comparison

MSEntropy

An open-source multi-language implementation of spectral entropy, entropy similarity, and flash entropy search for comparing and querying small-molecule mass spectra.

Platform-independentUntargeted metabolomicsPython packageR packageOpen source
Access toolSuggest an update

Overview

MSEntropy implements spectral entropy and entropy-based similarity calculations, with Flash Entropy Search for indexed library comparisons. Python provides the indexed search interface, while R and C/C++ interfaces expose entropy and comparison functions.

What can this tool do?

Spectral-library matchingMS/MS processing

Common uses

  • Calculate spectral entropy and entropy-based similarity between MS/MS spectra.
  • Search spectral libraries with flash entropy search.

Scientific fit

Primary function

Spectral processing and comparison

Other functions

Metabolite annotation and identification, Reference data and database search

Analysis types

Untargeted metabolomics

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, Spectral library

Outputs

Statistical results

Input formats

In-memory m/z-intensity arrays and library spectrum dictionaries

Output formats

Entropy values, similarity arrays and indexed-search scores

Scope and considerations

Designed for

  • Entropy-based spectral comparison and high-speed library searching.

Not designed for

  • Raw chromatographic peak extraction or confirmation of identity solely from an entropy score.

Important requirements

  • Centroid m/z-intensity peak arrays and appropriate mass tolerances; library search additionally requires a prepared reference library and precursor metadata.

Considerations

  • Cleaning, intensity normalization and fragment tolerances affect scores. Confirm that candidate precursor/adduct conditions and reference spectra are appropriate.

Access and documentation

Primary accessSource repository

Apache-2.0 implementation; reference-library availability and licensing are separate from the software license. Language interfaces provide different subsets of functionality.

License: Apache-2.0

Evidence and review

Enveda intake rechecked against official README/documentation, repository access terms and primary publication metadata on 2026-10-27. Editorial source review only; no software execution or independent benchmarking. See docs/enveda-expansion-review-2026-10-27.md.

Core publications

Resource papers, direct updates and tool-specific methods. Selection policy.

  1. Spectral entropy outperforms MS/MS dot product similarity for small-molecule compound identification. Nature Methods (2021). doi:10.1038/s41592-021-01331-z
  2. Flash entropy search to query all mass spectral libraries in real time. Nature Methods (2023). doi:10.1038/s41592-023-02012-9

Related tools

BLINKSimilar function · A Python package for efficient cosine-based similarity scoring and matching of large collections of fragmentation mass spectra, including analog-search workflows.DreaMSSimilar function · A transformer-based framework for learning molecular representations from tandem mass spectra, supporting spectral similarity, clustering, molecular networking, and downstream prediction tasks.FastEISimilar function · Search electron-ionization spectra against a large predicted reference library.FragHubSimilar function · Standardize and combine reference mass-spectral libraries.

Entry history

Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.

  1. 2026-10-27 · First committed entry

    Add 27 source-reviewed tools from Enveda intake

    View change · Entry at this revision

Full GitHub history