construct_massbank_database: Construct a Spectral Database from MassBank Data
In tidymass/metid: Metabolite identification based on MS1 and MS2 spectra

construct_massbank_database

R Documentation

Construct a Spectral Database from MassBank Data

Description

This function constructs a spectral database from MassBank data, specifically formatted as a 'databaseClass' object. The database contains metabolite information and MS2 spectral data for both positive and negative ionization modes.

Usage

construct_massbank_database(
  file,
  only.remain.ms2 = TRUE,
  path = ".",
  version = "0.0.1",
  source = "MassBank",
  link = "https://massbank.eu/MassBank/",
  creater = "Xiaotao Shen",
  email = "xiaotao.shen@outlook.com",
  rt = FALSE,
  threads = 5
)

Arguments

`file`	A character string specifying the path to the MassBank data file (MSP format).
`only.remain.ms2`	A logical value indicating whether to retain only the metabolites with MS2 spectra. Defaults to 'TRUE'.
`path`	A character string specifying the path where the database will be saved. Defaults to the current working directory ('"."').
`version`	A character string specifying the version of the database. Defaults to '"0.0.1"'.
`source`	A character string specifying the source of the database. Defaults to '"MassBank"'.
`link`	A character string specifying the URL of the source database. Defaults to '"https://massbank.eu/MassBank/"'.
`creater`	A character string specifying the creator of the database. Defaults to '"Xiaotao Shen"'.
`email`	A character string specifying the email of the creator. Defaults to '"xiaotao.shen@outlook.com"'.
`rt`	A logical value indicating whether retention time (RT) information is available. Defaults to 'FALSE'.
`threads`	An integer specifying the number of threads to use for parallel processing. Defaults to '5'.

Details

The function reads MassBank data in MSP format and constructs a 'databaseClass' object. It processes both positive and negative ionization modes, and optionally filters out metabolites that do not have MS2 spectra if 'only.remain.ms2' is set to 'TRUE'.

The MassBank data is organized into metabolite information and corresponding MS2 spectra. The spectra are stored in the 'Spectra.positive' and 'Spectra.negative' slots based on their ionization modes.

Value

A 'databaseClass' object containing the MassBank database, with metabolite information and MS2 spectral data.

Examples

## Not run: 
# Construct a database from a MassBank file
massbank_db <- construct_massbank_database(file = "MassBank.msp", only.remain.ms2 = TRUE)

## End(Not run)

tidymass/metid documentation built on Oct. 8, 2024, 10:32 p.m.