Massbank Tools

Configuration File: massbank_tools.json Tool Type: Local Tools Count: 5

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

Available Tools

MassBank_get_record_by_accession (Type: BaseRESTTool)

Retrieve a complete MassBank Europe spectrum record by its accession identifier. Returns the full…

MassBank_get_record_by_accession tool specification

Tool Information:

• Name: MassBank_get_record_by_accession

• Type: BaseRESTTool

• Description: Retrieve a complete MassBank Europe spectrum record by its accession identifier. Returns the full record: title, acquisition parameters (instrument type, MS level, ionization mode, collision energy, precursor type/adduct), the compound block (names/synonyms, molecular formula, exact monoisotopic mass, SMILES, InChI), spectral peaks with the SPLASH hash, and cross-references to external databases (CAS, CHEBI, KEGG, PubChem). Use this to resolve an accession returned by MassBank_spectral_similarity_search, MassBank_search_records_advanced, or MassBank_search_by_compound into a full annotated spectrum. Example: MSBNK-Athens_Univ-AU276601 returns Caffeine (formula C8H10N4O2, mass 194.0803756), LC-ESI-QTOF, MS2, [M+H]+, with links to CAS 58-08-2 and CHEBI:27732.

Parameters:

• accession (string) (required) MassBank record accession identifier (e.g., ‘MSBNK-Athens_Univ-AU276601’, ‘MSBNK-BAFG-CSL2311094669’). These are returned by the MassBank search tools.

Example Usage:

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

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)

MassBank_search_records_advanced (Type: BaseRESTTool)

Filtered search of the MassBank Europe spectral library using one or more criteria combined as AN…

MassBank_search_records_advanced tool specification

Tool Information:

• Name: MassBank_search_records_advanced

• Type: BaseRESTTool

• Description: Filtered search of the MassBank Europe spectral library using one or more criteria combined as AND filters. Filters: exact_mass (+ mass_tolerance in Da), peaks (m/z fragment peak), neutral_loss (m/z difference), ion_mode (POSITIVE/NEGATIVE), ms_type (MS, MS2, MS3), instrument_type, substructure (SMILES/SMARTS substructure match), contributor, and compound_class. Returns matching MassBank accessions; resolve each to a full annotated spectrum with MassBank_get_record_by_accession. Useful for narrowing candidate spectra when you know a compound’s mass, a diagnostic fragment, a neutral-loss, or a structural motif. Examples (vs ~139006 total records, proving each filters): exact_mass=194.0804 & mass_tolerance=0.005 -> 182; peaks=138.0661 -> 4141; ion_mode=POSITIVE -> 97745; ms_type=MS2 & ion_mode=NEGATIVE -> 38390; substructure=c1ccccc1 -> 81644; neutral_loss=18.0106 -> 9911.

Parameters:

• exact_mass ([‘number’, ‘null’]) (optional) Exact monoisotopic mass to match (Da). Combine with mass_tolerance. Example: 194.0804 for caffeine.

• mass_tolerance ([‘number’, ‘null’]) (optional) Mass tolerance window in Da for exact_mass (e.g., 0.005). Only meaningful together with exact_mass.

• peaks ([‘string’, ‘null’]) (optional) Fragment peak m/z value(s) that must be present (e.g., ‘138.0661’).

• neutral_loss ([‘string’, ‘null’]) (optional) Neutral loss m/z difference that must be present (e.g., ‘18.0106’ for water loss).

• ion_mode ([‘string’, ‘null’]) (optional) Ionization polarity: ‘POSITIVE’ or ‘NEGATIVE’.

• ms_type ([‘string’, ‘null’]) (optional) MS level: ‘MS’, ‘MS2’, or ‘MS3’.

• instrument_type ([‘string’, ‘null’]) (optional) Instrument type filter (e.g., ‘LC-ESI-QTOF’, ‘LC-ESI-ITFT’).

• substructure ([‘string’, ‘null’]) (optional) SMILES/SMARTS substructure that the compound must contain (e.g., ‘c1ccccc1’ for a benzene ring).

• contributor ([‘string’, ‘null’]) (optional) Contributing institution/library filter.

• compound_class ([‘string’, ‘null’]) (optional) Chemical compound class filter.

Example Usage:

query = {
    "name": "MassBank_search_records_advanced",
    "arguments": {
    }
}
result = tu.run(query)

MassBank_spectral_similarity_search (Type: BaseRESTTool)

Identify an unknown metabolite by spectral library similarity search against MassBank Europe. Sub…

MassBank_spectral_similarity_search tool specification

Tool Information:

• Name: MassBank_spectral_similarity_search

• Type: BaseRESTTool

• Description: Identify an unknown metabolite by spectral library similarity search against MassBank Europe. Submit a query MS/MS peak list (m/z and intensity pairs) and receive cosine-scored, ranked library matches (highest similarity first). This is the core unknown-metabolite identification workflow: acquire an MS/MS spectrum of an unknown, then match it against MassBank’s open reference library to find candidate compound identities. Returns a list of records each with a MassBank accession (resolve full compound info with MassBank_get_record_by_accession) and a cosine similarity score in [0,1] (1.0 = identical). Example: peak_list ‘138.0661;100,110.0712;40,195.0877;60’ returns 422 ranked hits, top MSBNK-BAFG-CSL2311094669 at score 0.978714.

Parameters:

• peak_list (string) (required) Query MS/MS peak list as comma-separated ‘mz;intensity’ pairs. Format: ‘mz1;int1,mz2;int2,…’. Example: ‘138.0661;100,110.0712;40,195.0877;60’. Intensities may be absolute or relative; cosine scoring is intensity-weighted.

• peak_list_threshold ([‘number’, ‘null’]) (optional) Minimum cosine similarity score (0-1) for a record to be returned. Higher = stricter. Default 0.5. Lower it (e.g. 0.3) to widen the candidate set, raise it (e.g. 0.8) for high-confidence matches only.

Example Usage:

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

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