Gnps Tools

Configuration File: gnps_tools.json Tool Type: Local Tools Count: 4

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_library_record (Type: GNPSTool)

Retrieve a full GNPS library reference spectrum record by its SpectrumID / CCMSLIB accession. GNP…

GNPS_get_library_record tool specification

Tool Information:

  • Name: GNPS_get_library_record

  • Type: GNPSTool

  • Description: Retrieve a full GNPS library reference spectrum record by its SpectrumID / CCMSLIB accession. GNPS (Global Natural Products Social Molecular Networking) hosts the world’s largest community-curated MS/MS reference spectral library. Returns the compound annotation: Compound_Name, Adduct, SMILES, InChI/InChIKey, Ion_Source, Instrument, ionization mode, precursor m/z, charge, contributing PI, library membership (e.g. GNPS-LIBRARY), CAS, and PubMed id. Use this to resolve a CCMSLIB accession (e.g. from a molecular-networking hit) into its annotated reference compound. Example: CCMSLIB00005435737 -> Compound_Name ‘Lovastatin M+H; Mevinolin annotated in standard’, Adduct M+H, library GNPS-LIBRARY; CCMSLIB00000001547 -> ‘3-Des-Microcystein_LR’.

Parameters:

  • spectrum_id (string) (required) GNPS library SpectrumID / CCMSLIB accession (e.g. ‘CCMSLIB00005435737’).

Example Usage:

query = {
    "name": "GNPS_get_library_record",
    "arguments": {
        "spectrum_id": "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)

GNPS_npclassifier_from_smiles (Type: GNPSTool)

NP Classifier: de novo natural-product biosynthetic classification of an arbitrary chemical struc…

GNPS_npclassifier_from_smiles tool specification

Tool Information:

  • Name: GNPS_npclassifier_from_smiles

  • Type: GNPSTool

  • Description: NP Classifier: de novo natural-product biosynthetic classification of an arbitrary chemical structure from its SMILES. Returns the predicted biosynthetic pathway, superclass, and class, plus an is_glycoside flag. Unlike chemical-ontology classifiers, NP Classifier organizes molecules by natural-product biosynthesis (e.g. alkaloids, terpenoids, polyketides), making it the standard for annotating metabolites and natural products in untargeted metabolomics / molecular-networking workflows. Works on any SMILES (no library lookup needed). Example: caffeine SMILES ‘CN1C=NC2=C1C(=O)N(C)C(=O)N2C’ -> class ‘Purine alkaloids’, superclass ‘Pseudoalkaloids’, pathway ‘Alkaloids’, is_glycoside false.

Parameters:

  • smiles (string) (required) SMILES string of the structure to classify (e.g. ‘CN1C=NC2=C1C(=O)N(C)C(=O)N2C’ for caffeine).

Example Usage:

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