Gnps Tools

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

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

Available Tools

GNPS_compare_spectra (Type: GNPSTool)

Compare two MS/MS spectra from the GNPS spectral library using Universal Spectrum Identifiers (US…

GNPS_compare_spectra tool specification

Tool Information:

  • Name: GNPS_compare_spectra

  • Type: GNPSTool

  • Description: Compare two MS/MS spectra from the GNPS spectral library using Universal Spectrum Identifiers (USIs). Returns metadata for both spectra (precursor m/z, peak counts) and a link to the interactive mirror plot visualization. Useful for assessing spectral similarity between known and unknown compounds in metabolomics workflows.

Parameters:

  • usi1 (string) (required) First spectrum USI. Example: ‘mzspec:GNPS:GNPS-LIBRARY:accession:CCMSLIB00005435737’.

  • usi2 (string) (required) Second spectrum USI. Example: ‘mzspec:GNPS:GNPS-LIBRARY:accession:CCMSLIB00000579622’.

Example Usage:

query = {
    "name": "GNPS_compare_spectra",
    "arguments": {
        "usi1": "example_value",
        "usi2": "example_value"
    }
}
result = tu.run(query)

GNPS_get_spectrum (Type: GNPSTool)

Retrieve a mass spectrometry (MS/MS) reference spectrum from the GNPS spectral library using a Un…

GNPS_get_spectrum tool specification

Tool Information:

  • Name: GNPS_get_spectrum

  • Type: GNPSTool

  • Description: Retrieve a mass spectrometry (MS/MS) reference spectrum from the GNPS spectral library using a Universal Spectrum Identifier (USI). Returns precursor m/z, charge, number of peaks, m/z range, and the top 20 peaks by intensity. GNPS is the world’s largest community-curated spectral library for metabolomics and natural products research. Example: ‘mzspec:GNPS:GNPS-LIBRARY:accession:CCMSLIB00005435737’ retrieves a reference spectrum with precursor m/z 405.264 and 83 peaks.

Parameters:

  • usi (string) (required) Universal Spectrum Identifier. Format: ‘mzspec:GNPS:GNPS-LIBRARY:accession:CCMSLIB{id}’. Example: ‘mzspec:GNPS:GNPS-LIBRARY:accession:CCMSLIB00005435737’.

Example Usage:

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