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Spectral processing and comparison

BLINK

A Python package for efficient cosine-based similarity scoring and matching of large collections of fragmentation mass spectra, including analog-search workflows.

Platform-independentUntargeted metabolomicsPython packageCommand lineNotebook
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Overview

BLINK computes cosine-based spectral similarities and matching-ion counts using a discretized representation of fragmentation spectra. Its experimental REM-BLINK interface also supports analog comparisons using specified mass differences and pretrained regression models.

What can this tool do?

Spectral-library matchingMS/MS processing

Common uses

  • Calculate large numbers of MS/MS similarity scores efficiently.
  • Perform library or analog searches using fragmentation spectra.

Scientific fit

Primary function

Spectral processing and comparison

Other functions

Metabolite annotation and identification

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

MGF, mzML

Output formats

CSV or TSV

Scope and considerations

Designed for

  • Fast spectral similarity and analog-search calculations on MS/MS data.

Not designed for

  • Chromatographic feature extraction or definitive structure identification from similarity alone.

Important requirements

  • Python with the supplied conda environment; query and reference spectra. REM-BLINK additionally needs polarity-specific models and the same ordered mass-difference list used for training.

Considerations

  • Similarity thresholds and interpretation remain dataset- and use-case-dependent.
  • The repository describes its command-line interface as experimental.

Access and documentation

Primary accessDocumentation

The repository includes a Berkeley Lab redistribution license with source/binary notice and non-endorsement conditions. The command-line and pretrained-model interfaces are labelled experimental.

License: BSD-3-Clause-LBNL

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. BLINK enables ultrafast tandem mass spectrometry cosine similarity scoring. Scientific Reports (2023). doi:10.1038/s41598-023-40496-9

Related tools

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.GNPS2 MassQL AnalysisSimilar function · Hosted interface for exploring MS/MS spectral libraries with MassQL and using LLM assistance to draft or explain queries.

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