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Spectral processing and comparison

SIMILE

A Python library for relating fragmentation spectra using statistically assessed fragment and neutral-loss relationships, including pairwise and multiple spectral matching.

Platform-independentUntargeted metabolomicsPython packageSource available with restrictions
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Overview

SIMILE compares fragmentation spectra through relationships among fragment ions and estimates statistical significance of their alignment. Its Python implementation produces similarity/matching matrices, scores and matching-ion reports for spectral interpretation.

What can this tool do?

MS/MS processing

Common uses

  • Detect significant relationships among MS/MS spectra despite multiple structural differences.

Scientific fit

Primary function

Spectral processing and comparison

Other functions

Metabolite annotation and identification

Analysis types

Untargeted metabolomics

Data compatibility

Inputs

Mass spectra

Outputs

Statistical results

Input formats

Python fragment-mass arrays and optional precursor-mass arrays

Output formats

Similarity/matching matrices, p-values and matching-ion data frames

Scope and considerations

Designed for

  • A Python library for relating fragmentation spectra using statistically assessed fragment and neutral-loss relationships, including pairwise and multiple spectral matching.

Not designed for

  • Experimental validation of molecular identity or a general guarantee that a low p-value establishes structural equivalence.

Important requirements

  • The documented Python environment, arrays of fragment m/z values with optional precursor masses, and appropriate tolerances and significance-testing settings.

Considerations

  • Interpret significance in the context of the null model and multiple comparisons. The current V2 matching procedure differs from the original paper, and the supplied environment uses older dependencies.

Access and documentation

Primary accessDocumentation

README and pyproject label the code Modified BSD, but the linked license.txt is absent from the current repository. Exact terms need clarification; no precise SPDX license or unrestricted grant is inferred. Record the implementation version because V2 changes matching/statistics.

License: Modified BSD (full terms not located)

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-batch2.md.

Core publications

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

  1. SIMILE enables alignment of tandem mass spectra with statistical significance. Nature Communications (2022). doi:10.1038/s41467-022-30118-9

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 24 reviewed Enveda tools in a separate second batch

    View change · Entry at this revision

Full GitHub history