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matchms - Mass Spectrometry Data Processing and Analysis Tool

Process and analyze mass spectrometry data with spectral similarity calculations and metadata harmonization

Tags

Updated: 2026-02-11
mass spectrometryspectral analysisdata processingmetabolomicssimilarity calculation

Capabilities

import mass spectrometry dataexport processed spectraapply spectrum filterscalculate spectral similarities

Typical Inputs

mzML filesMGF filesMSP files

Typical Outputs

processed spectrasimilarity scoresbest matches

What this skill does

  • import mass spectrometry data
  • export processed spectra
  • apply spectrum filters
  • calculate spectral similarities
  • build processing pipelines
  • manage spectrum metadata

Inputs

  • mzML files
  • MGF files
  • MSP files
  • spectral data
  • JSON files

Outputs

  • processed spectra
  • similarity scores
  • best matches
  • processing pipelines
  • filtered data

Requirements

  • Python environment
  • matchms library
  • chemistry dependencies for structure processing

Source

  • Spec: SKILL.md

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