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.

Matchms is a powerful Python package designed for importing, cleaning, processing, and comparing tandem mass spectra (MS/MS). It supports various file formats (mzML, MGF) and provides core functionalities including library searching, metadata harmonization, peak filtering, and calculating multiple similarity scores (e.g., Cosine, Neutral-loss). It is essential for metabolomics and mass spectrometry workflows, enabling the construction of structured score matrices and spectral similarity networks.

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.