Dataset for 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_V1.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-v0.2.0.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-v0.1.0.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]

摘要
本仓库包含发表于论文《法布里病患者血浆与血小板脂质组变化（Plasma and Platelet Lipidome Changes in Fabry Disease）》的质谱（mass-spectrometry, MS）原始数据文件及R脚本，论文作者为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及Pierre-Alexandre Krayenbuhl。
数据结构
(1) 质谱原始数据文件存于"FabryLipidomics_Burla2023_RawDataMS_V1.zip"：该压缩包包含每个被测脂质组的文件夹，其中存储采用液相色谱-质谱多反应监测（LC-MS-MRM，安捷伦QQQ质谱（Agilent QQQ MS））采集的原始数据。这些文件夹中的每个原始数据子文件夹（.d）对应一次分析/单个样本的原始数据。名为"QuantResults"的子文件夹中包含安捷伦MassHunter定量批量处理文件（*.batch.bin），用于对应脂质组的峰识别与峰积分。
(2) RStudio项目存于"GitHub_PUB_Burla2023_FabryLipidomics-main-v0.2.0.zip"（可从GitHub下载），其中包含预处理后的原始数据（即峰面积及其他峰积分相关信息）、实验元数据，以及用于数据后处理、分析和可视化的R脚本流程。
数据查看方法
- 原始数据文件（.d）可使用安捷伦软件（Agilent MassHunter QUAL或MassHunter QUANT）进行查看与分析。
- 原始数据文件（.d）也可通过msconvert工具（https://proteowizard.sourceforge.io/tools/msconvert.html）转换为开放格式*.mzML，随后可在Skyline（https://skyline.ms）或其他支持该格式的开源工具及R/Python脚本中查看。
- 包含峰识别与积分定义的MassHunter QUANT批量处理文件（*.batch.bin）仅可通过安捷伦MassHunter QUANT软件（10及以上版本）查看。
- 预处理后的数据（峰面积）及对应的实验元数据存于RStudio项目文件夹（GitHub_PUB_Burla2023_FabryLipidomics-main-v0.1.0.zip）的"data"文件夹中。
- R数据分析脚本可在R/RStudio中打开。如需更多信息，请参阅该RStudio项目内的README.html文件。
联系方式
Bo Johannes Burla博士，新加坡脂质组学孵化器（Singapore Lipidomics Incubator），新加坡国立大学，邮箱：[e-mail]