construct_database: Construct a Mass Spectra Database
In tidymass/metid: Metabolite identification based on MS1 and MS2 spectra

construct_database

R Documentation

Construct a Mass Spectra Database

Description

This function constructs a spectral database from provided metabolite information and MS2 spectra in both positive and negative modes. The database is created as a 'databaseClass' object, including metadata, spectra information, and spectral data for metabolites.

Usage

construct_database(
  path = ".",
  version = "0.0.1",
  metabolite.info.name = "metabolite.info.csv",
  source = "Shen Lab",
  link = "http://snyderlab.stanford.edu/",
  creater = "Xiaotao Shen",
  email = "xiaotao.shen@outlook.com",
  rt = TRUE,
  mz.tol = 15,
  rt.tol = 30,
  threads = 3
)

Arguments

`path`	A character string specifying the path to the folder containing the metabolite information and MS2 data files. Defaults to the current working directory ('"."').
`version`	A character string specifying the version of the database. Defaults to '"0.0.1"'.
`metabolite.info.name`	A character string specifying the file name of the metabolite information (CSV format). Defaults to '"metabolite.info.csv"'.
`source`	A character string specifying the source of the database. Defaults to '"Shen Lab"'.
`link`	A character string specifying the link to the source of the database. Defaults to '"http://snyderlab.stanford.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 '"xiaotao.shen@outlook.com"'.
`rt`	A logical value indicating whether the retention time (RT) information is available. Defaults to 'TRUE'.
`mz.tol`	A numeric value specifying the tolerance for matching the mass-to-charge ratio (m/z). Defaults to '15'.
`rt.tol`	A numeric value specifying the tolerance for matching the retention time (RT). Defaults to '30'.
`threads`	A numeric value specifying the number of threads to use for parallel processing. Defaults to '3'.

Details

The function reads the metabolite information and MS2 spectra from the specified path. It checks for the required files ('metabolite.info.csv', 'POS', and 'NEG' folders) and loads the MS2 data from mzXML or MGF files. The spectra are matched to the metabolites based on mass-to-charge ratio (m/z) and retention time (RT) tolerances.

- **Positive Mode**: The function reads and processes spectra files in the 'POS' folder. - **Negative Mode**: The function reads and processes spectra files in the 'NEG' folder.

The function uses matching algorithms to associate the metabolites with their corresponding MS2 spectra, based on the provided tolerances.

Value

A 'databaseClass' object containing the constructed database, including metadata, spectra information, and MS2 spectral data for both positive and negative modes.

Author(s)

Xiaotao Shen xiaotao.shen@outlook.com

Examples

## Not run: 
# Construct a database from the current working directory
db <- construct_database(path = ".", version = "1.0.0", 
metabolite.info.name = "metabolite_info.csv")

## End(Not run)

tidymass/metid documentation built on Sept. 14, 2024, 4:43 p.m.