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matchms - Mass Spectrometry Data Processing

Process mass spectrometry spectra, calculate similarities, and harmonize metadata

Tags

Updated: 2026-03-22

Capabilities

Typical Inputs

Typical Outputs

What this skill does

  • load spectra
  • save spectra
  • filter peaks
  • normalize intensities
  • calculate similarity
  • compare spectra
  • standardize metadata
  • derive structures
  • build pipelines
  • plot spectra

Inputs

  • mzML files
  • MGF files
  • MSP files
  • JSON files
  • mzXML files
  • spectra data
  • metadata

Outputs

  • processed spectra
  • similarity scores
  • metadata files
  • chemical structures
  • spectrum plots

Requirements

  • Python 3
  • matchms library
  • rdkit for chemistry

Source

  • Spec: SKILL.md
mass spectrometry
spectral analysis
metabolomics
data processing
compound identification
load spectra
save spectra
filter peaks
normalize intensities
mzML files
MGF files
MSP files
processed spectra
similarity scores
metadata files