Massbank Tools

Configuration File: massbank_tools.json Tool Type: Local Tools Count: 2

This page contains all tools defined in the massbank_tools.json configuration file.

Available Tools

MassBank_search_by_compound (Type: BaseRESTTool)

Search MassBank Europe mass spectrometry spectral library by compound name. MassBank is an open-a…

MassBank_search_by_compound tool specification

Tool Information:

  • Name: MassBank_search_by_compound

  • Type: BaseRESTTool

  • Description: Search MassBank Europe mass spectrometry spectral library by compound name. MassBank is an open-access mass spectrometry reference spectral library for metabolomics, exposomics, and environmental chemistry. Returns MS/MS spectra records with compound information (SMILES, InChI, formula, exact mass), acquisition parameters (instrument type, MS level, ionization mode, collision energy), and spectral peaks. Useful for identifying unknown metabolites or environmental contaminants.

Parameters:

  • compound_name (string) (required) Compound name to search for (e.g., ‘aspirin’, ‘caffeine’, ‘glucose’, ‘PFAS’)

  • limit ([‘integer’, ‘null’]) (optional) Maximum number of spectra to return (default 10)

Example Usage:

query = {
    "name": "MassBank_search_by_compound",
    "arguments": {
        "compound_name": "example_value"
    }
}
result = tu.run(query)

MassBank_search_by_formula (Type: BaseRESTTool)

Search MassBank Europe spectral library by molecular formula. Returns all mass spectra records fo…

MassBank_search_by_formula tool specification

Tool Information:

  • Name: MassBank_search_by_formula

  • Type: BaseRESTTool

  • Description: Search MassBank Europe spectral library by molecular formula. Returns all mass spectra records for compounds with the specified molecular formula. Useful when you know the formula of an unknown compound and want to find candidate matches in the MS spectral library.

Parameters:

  • formula (string) (required) Molecular formula (e.g., ‘C9H8O4’ for aspirin, ‘C8H10N4O2’ for caffeine, ‘C6H12O6’ for glucose)

  • limit ([‘integer’, ‘null’]) (optional) Maximum number of spectra to return (default 10)

Example Usage:

query = {
    "name": "MassBank_search_by_formula",
    "arguments": {
        "formula": "example_value"
    }
}
result = tu.run(query)