Skill UI

Access HMDB to search over 220K human metabolites by name, ID, structure, disease or specimen, retrieve chemical/clinical/pathway data, and download spectra for metabolomics workflows.

Query the NIH Metabolomics Workbench via REST API to fetch metabolites, RefMet nomenclature, mass-spec searches, and detailed study datasets for biomarker discovery and metabolomics research.

PyOpenMS provides Python bindings for OpenMS to drive complete mass spectrometry workflows, covering data IO, spectral processing, feature/peptide-protein identification, quantitation, and metabolomics pipelines.

Matchms is an open-source Python library designed for comprehensive mass spectrometry data processing. It handles spectrum comparison, calculates various similarity scores (like cosine and modified cosine), and aids in identifying unknown compounds. It is highly valuable for metabolomics and spectral library searching pipelines.

A comprehensive Python wrapper for OpenMS, designed for sophisticated computational mass spectrometry workflows. It supports end-to-end analysis in proteomics and metabolomics, enabling feature detection, peptide/protein identification, quantitative analysis (label-free/isobaric), and adduct/accurate mass annotation. Ideal for researchers processing complex LC-MS/MS raw data and running high-level pipelines.