construct_mona_database: Construct a Spectral Database from MoNA Data

In tidymass/metid: Metabolite identification based on MS1 and MS2 spectra

Construct a Spectral Database from MoNA Data

Description

This function constructs a spectral database from MoNA (MassBank of North America) 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_mona_database(
  file,
  only.remain.ms2 = TRUE,
  path = ".",
  version = "0.0.1",
  source = "MoNA",
  link = "https://mona.fiehnlab.ucdavis.edu/",
  creater = "Xiaotao Shen",
  email = "[e-mail]",
  rt = FALSE,
  threads = 5
)

Arguments

file	A character string specifying the path to the MoNA 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 '"MoNA"'.
link	A character string specifying the URL of the source database. Defaults to '"https://mona.fiehnlab.ucdavis.edu/"'.
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 '"[e-mail]"'.
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 MoNA 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 MoNA 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 MoNA database, with metabolite information and MS2 spectral data.

Examples

## Not run: 
# Construct a database from a MoNA file
mona_db <- construct_mona_database(file = "MoNA.msp", only.remain.ms2 = TRUE)

## End(Not run)

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