readme file associated with research data archive for the publication:

Title: Breath response following a nutritional challenge monitored by secondary electrospray ionization high-resolution mass spectrometry
Authors: Cedric Wüthrich, Miguel de Figueiredo, Kathryn Jane Burton-Pimentel, Guy Vergères, Fabian Wahl, Renato Zenobi, Stamatios Giannoukos
Year: 2022

Information from the manuscript's main text:
The mass spectrometer used in this study was an Orbitrap Q-Exactive Plus (Thermo Scientific) operated with the manufacturer’s standard control software (ExactiveTune, version 2.9, Thermo Scientific) and Xcalibur (version 4.1.31.9, Thermo Scientific). Mass calibration was done according to the instrument manual and was always more recent than seven days according to specifications.
Spectra were recorded with Xcalibur (version 4.1.31.9, Thermo Scientific). The acquired .RAW data was converted to .mzML files using ProteoWizard (version 3.0.20248-44f73ac78).

Main data processing:
The .mzML-files were then processed with a custom written Python script (version 3.9.1) in the folder DataProcessing. For the script to work, the pymzml library has to be installed (2.5.0, https://doi.org/10.1093/bioinformatics/bty046), as well as the Anaconda distribution.
The file main_multicore.py has to be run with the correct path to be set for the mzML-data folder, each time for the intervention data and the control data.
After the files have been processed, the control intensity matrix has to be processed with the file shakevsfasting.py The intensity matrix of the intervention data has to be processed with the ASCA Matlab-script.

Plots:
After the processing of the intensity matrices, the script PublicationPlots.py has to be run with the correct pathways pointing to the diverse input files to obtain all data plots found in the publication. The code is divided into cells and each cell corresponds to one plot. The cells are ordered in the order of the Figures they create. The preprocessed data is found in the StatisticData.zip and can be directly used, skipping the preprocessing.

MS2-experiments:
The script iqaros_main.py has to be run on them mgf-files to obtain the reconstructed mass spectra.