read_mgf_mona: Read MGF Data from MoNA

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

Read MGF Data from MoNA

Description

This function reads Mass Spectrometry (MS) data in MGF format from the MoNA (MassBank of North America) database, extracts the MS2 spectra, and returns them in a structured format.

Usage

read_mgf_mona(file, threads = 3)

Arguments

file	A character vector containing file paths to the MGF files from MoNA.
threads	Numeric, the number of threads to use for parallel processing. Defaults to '3'.

Details

The function parses MGF files from MoNA, a public repository of mass spectrometry data, extracts both metadata and the MS2 spectra, and organizes the data into a structured format for further processing. Parallel processing is supported to improve efficiency when handling large datasets.

Value

A list where each element contains the MS2 spectra and related metadata for each entry in the MGF file. Each entry includes:

info	A data frame with metadata (such as m/z, retention time, etc.) for each spectrum.
spec	A data frame containing the 'mz' and 'intensity' values of the MS2 spectrum.

Author(s)

Xiaotao Shen [e-mail]

Examples

## Not run: 
# Read MGF data from MoNA
mgf_data <- read_mgf_mona(file = c("path/to/mgf1.mgf", "path/to/mgf2.mgf"))

## End(Not run)

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