alterlab-matchms

# Matchms ## Overview Matchms is an open-source Python library for mass spectrometry data processing and analysis. Import spectra from various formats, standardize metadata, filter peaks, calculate spectral similarities, and build reproducible analytical workflows. ## When to Use This Skill Use this skill when the user wants to: - Load, clean, and harmonize MS/MS spectra (MGF, MSP, mzML, mzXML, JSON, USI) and their metadata - Score spectral similarity (cosine, modified cosine, neutral-loss cosine) between queries and a reference library - Annotate unknown metabolites by library matching, or derive InChI/InChIKey/fingerprints from spectrum metadata - Build reproducible preprocessing pipelines (`SpectrumProcessor`) for metabolomics spectra ### Does NOT Trigger | Scenario | Use Instead | |----------|-------------| | Full LC-MS/MS proteomics or feature-detection pipelines (peptide ID, quantification, raw-file processing) | `alterlab-pyopenms` | | Looking up a metabolite's reference record, pathways, or published spectra in HMDB | `alterlab-hmdb` | | Querying Metabolomics Workbench studies, RefMet names, or m/z mass searches | `alterlab-metabolomics-wb` | | Structure-level cheminformatics on the annotated compounds (substructure, descriptors) | `alterlab-rdkit` | ## Core Capabilities ### 1. Importing and Exporting Mass Spectrometry Data Load spectra from multiple file formats and export processed data: ```python from matchms.importing import load_from_mgf, load_from_mzml...