This function reads Mass Spectrometry (MS) data in MGF format from GNPS, extracts the MS2 spectra, and returns it in a structured format.

read_mgf_gnps(file, threads = 3)

Arguments

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

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.

Details

The function parses MGF files from GNPS, a popular platform for metabolomics analysis. It extracts both the metadata and the MS2 spectra, and organizes the data into a structured format for further processing. Parallel processing is supported to speed up reading large files.

Author

Xiaotao Shen xiaotao.shen@outlook.com

Examples

if (FALSE) { # \dontrun{
# Read MGF data from GNPS
mgf_data <- read_mgf_gnps(file = c("path/to/mgf1.mgf", "path/to/mgf2.mgf"))
} # }