Can I perform mass spectrometry searches with this skill?

Yes, you can search for compounds by mass-to-charge ratio (m/z) using specific ion adducts (like M+H or M-H) and defined mass tolerance levels.

What is the primary data source for this skill?

The skill accesses the NIH Common Fund-sponsored Metabolomics Workbench hosted at UCSD, which contains over 4,200 processed research studies.

How does the skill handle metabolite name standardization?

It utilizes the RefMet database to match common metabolite names to a standardized nomenclature across four structural resolution levels.

Can I filter studies by specific analytical platforms?

Yes, you can filter results by analytical methods such as LC-MS, GC-MS, and NMR, as well as by ionization polarity and chromatography type.

Metabolomics Workbench Database

Name: Metabolomics Workbench Database
Author: lingxling

bylingxling

•

Data Science & ML

Connects to the NIH Metabolomics Workbench REST API to query metabolite data, experimental studies, and standardized nomenclature.

This skill integrates the NIH Metabolomics Workbench into Claude, providing seamless programmatic access to a massive repository of over 4,200 metabolomics studies. It enables researchers to retrieve compound structures, standardize chemical names using RefMet, perform precise mass spectrometry searches by m/z, and access comprehensive study metadata and experimental factors. It is an essential tool for biomarker discovery, metabolic pathway analysis, and cross-referencing metabolite identifiers across major databases like PubChem, KEGG, and HMDB directly within a coding workflow.

Key Features

01Mass spectrometry (m/z) precursor ion searches with custom adducts

0239 GitHub stars

03Advanced study filtering by analytical methods, species, and disease states

04Metabolite structure retrieval in MOL and PNG formats via registry IDs

05RefMet nomenclature standardization for consistent metabolite classification

06Access to 4,200+ processed metabolomics studies and raw experimental data

Use Cases

01Retrieving gene-protein-metabolite associations for pathway analysis

02Standardizing multi-source metabolite datasets using RefMet systematic nomenclature

03Identifying unknown metabolites from experimental mass-to-charge ratios

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add lingxling/awesome-skills-cn metabolomics-workbench-database

For use in Claude.ai and ChatGPT

Key Features

01Mass spectrometry (m/z) precursor ion searches with custom adducts

0239 GitHub stars

03Advanced study filtering by analytical methods, species, and disease states

04Metabolite structure retrieval in MOL and PNG formats via registry IDs

05RefMet nomenclature standardization for consistent metabolite classification

06Access to 4,200+ processed metabolomics studies and raw experimental data

Use Cases

01Retrieving gene-protein-metabolite associations for pathway analysis

02Standardizing multi-source metabolite datasets using RefMet systematic nomenclature

03Identifying unknown metabolites from experimental mass-to-charge ratios

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add lingxling/awesome-skills-cn metabolomics-workbench-database

For use in Claude.ai and ChatGPT