idslme / idsl.mxp

A light weight and fast parser for reading mzML, mzXML and netCDF data files

IDSL.MXP

Mass Spectrometry Parser (MXP) by the Integrated Data Science Laboratory for Metabolomics and Exposomics (IDSL.ME) is a tiny parser to extract mass spectra data and metadata table of instrumentational acquisition properties from mzML, mzXML and netCDF mass spectrometry files.

Installation

install.packages("IDSL.MXP")

Note: In case you want to process netCDF/CDF mass spectrometry data by IDSL.MXP, you should also install the RnetCDF package separately using the below command.

install.packages("RNetCDF")

Workflow

To use this package, follow below commands:

path <- “location address of the mass spectrometry file”
MSfileName <- "name of the mass spectrometry file with its extension"
mxpObject <- IDSL.MXP::peak2list(path, MSfileName)

mxpObject is a list with two objects - 1) scanTable, a metadata of different scan properties, and 2) spectraList, a list of m/z and intensity values for each scan.

Visit wiki and Google colab to illustrate performance of IDSL.MXP.

Citation

[1] Fakouri Baygi, S., Kumar, Y. Barupal, D.K. IDSL. IPA characterizes the organic chemical space in untargeted LC/HRMS datasets. Journal of proteome research, 2022, 21(6), 1485-1494.