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 spectra by compound name. MassBank returns the full matching array and ign…

MassBank_search_by_compound tool specification

Tool Information:

  • Name: MassBank_search_by_compound

  • Type: BaseRESTTool

  • Description: Search MassBank Europe spectra by compound name. MassBank returns the full matching array and ignores limit, so ToolUniverse applies exact client-side pagination: start with offset=0 and continue with metadata.next_offset while metadata.has_more is true. metadata.total_results is exact. Returns compound structures, acquisition parameters, and spectral peaks.

Parameters:

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

  • limit ([‘integer’, ‘null’]) (optional) Number of spectra in this client-side page (default 10)

  • offset (integer) (optional) Zero-based spectrum offset. Continue with metadata.next_offset while metadata.has_more is true.

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 spectra by molecular formula. MassBank returns the full matching array and…

MassBank_search_by_formula tool specification

Tool Information:

  • Name: MassBank_search_by_formula

  • Type: BaseRESTTool

  • Description: Search MassBank Europe spectra by molecular formula. MassBank returns the full matching array and ignores limit, so ToolUniverse applies exact client-side pagination: start with offset=0 and continue with metadata.next_offset while metadata.has_more is true. metadata.total_results is exact.

Parameters:

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

  • limit ([‘integer’, ‘null’]) (optional) Number of spectra in this client-side page (default 10)

  • offset (integer) (optional) Zero-based spectrum offset. Continue with metadata.next_offset while metadata.has_more is true.

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)