Dataset and Source Code of Manuscript Plasma and Platelet Lipidome Changes in Fabry Disease

SUMMARY

This repository contains mass-spectrometry (MS) raw data files and R scripts used in the manuscript “Plasma and Platelet Lipidome Changes in Fabry Disease” by Bo Burla, Jeongah Oh, Nathalie Piraud, Eduardo Meyer, Ding Mei, Anne K Bendt, Jan-Dirk Studt, Beat M Frey, Federico Torta, Albina Nowak, Markus R Wenk, and Pierre-Alexandre Krayenbuhl,

DATA STRUCTURE

(1) Mass-spectrometry raw data files in "FabryLipidomics_Burla2023_RawDataMS_V3.zip": This zip file contains folders for each measured lipid panel comprising of LC-MS-MRM (Agilent QQQ MS) raw data. Each raw data subfolder (.d) in these folders corresponds to the raw data of one analysis/sample. The subfolders “QuantResults” contain Agilent MassHunter Quant batch files (*.batch.bin) used for the peak picking and peak integration of the corresponding panel. 

(2) RStudio project in "GitHub_PUB_Burla2023_FabryLipidomics-main-v0.4.0.zip"(download from GitHub) containing pre-processed raw data (i.e peak areas and other information from peak integration), experimental metadata, and the R script pipeline used to postprocess, analyze and visualize the data.

VIEWING THE DATA

- Raw data files (.d) can be viewed and analysed using Agilent software (Agilent MassHunter QUAL or MassHunter QUANT)

- Raw data files (.d) can also be converted to the open *.mzML format using msconvert (https://proteowizard.sourceforge.io/tools/msconvert.html) and then viewed in e.g. Skyline (https://skyline.ms) or other open-source tools and R/Python scripts supporting this format.

- The MassHunter QUANT batch file  (*.batch.bin)  containing the peak picking and integration definitions can only be viewed using Agilent MassHunter QUANT (version 10 or higher)

- The pre-processed data (peak areas) and corresponding experimental metadata are within the folder "data" of the RStudio project folder (GitHub_PUB_Burla2023_FabryLipidomics-main-v0.4.0.zip)

- The R data analysis scripts can be opened in R/RStudio. For further information please refer to README.html within this RStudio project. 

CONTACT

Bo Johannes Burla, PhD,  Singapore Lipidomics Incubator, National University of Singapore, [e-mail]