Reprocessed dataset with Skyline Batch: Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen treated 3D liver microtissues

The data set represents a fair comparison of shotgun proteomics with HRM (swath type DIA). Additionally, a human liver microtissue was profiled with HRM. REPROCESSING METHODS: Skyline Batch is a newly developed Windows forms application that enables easy and consistent reprocessing of data with Skyline. Skyline has made previous advances in this direction; however, none enable seamless automated reprocessing of local and remote files. Skyline keeps a log of all the steps that were taken in the document; however, reproducing these steps takes time and allows room for human error. Skyline also has a command-line interface, enabling it to be run from a batch script, but using the program in this way requires expertise in editing these scripts. By formalizing the workflow of a highly used set of batch scripts into an intuitive and powerful user interface, Skyline Batch can reprocess data stored in remote repositories just by opening and running a Skyline Batch configuration file. When run, a Skyline Batch configuration downloads all necessary remote files and then runs a four-step Skyline workflow. By condensing the steps needed to reprocess the data into one file, Skyline Batch gives researchers the opportunity to publish their processing along with their data and other analysis files. These easily run configuration files will greatly increase the transparency and reproducibility of published work. Skyline Batch is freely available at https://skyline.ms/batch.url.

本数据集旨在实现鸟枪法蛋白质组学（shotgun proteomics）与采用swath型数据非依赖采集（DIA）的高分辨质谱（HRM）之间的公平对比。此外，研究团队还采用HRM对人类肝脏微组织进行了表征分析。
后处理方法：
Skyline Batch是一款全新开发的Windows窗体应用程序，可实现依托Skyline对数据进行便捷且标准化的后处理。Skyline此前已在该领域取得进展，但尚未有方案能够实现本地与远程文件的无缝自动化后处理。Skyline会记录文档中执行的所有操作步骤，但复刻这些步骤既耗时，又存在人为操作误差的风险。Skyline同样提供命令行界面，支持通过批处理脚本运行，但该使用方式需要用户具备脚本编辑的专业技能。
研究团队将一套常用批处理脚本的工作流封装为直观且功能强大的用户界面，Skyline Batch仅需打开并运行其配置文件，即可对远程存储库中存储的数据执行后处理。运行该配置文件时，Skyline Batch会先下载所有所需的远程文件，随后执行四步式Skyline工作流。通过将数据后处理所需的全部步骤浓缩至单个配置文件中，Skyline Batch可让研究人员将数据处理流程与原始数据及其他分析文件一同发表。这类易于部署运行的配置文件，将大幅提升已发表研究成果的透明度与可重复性。Skyline Batch可通过https://skyline.ms/batch.url免费获取。