Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.
Curr Protoc Bioinformatics. 2020 Jun;70(1):e101. doi: 10.1002/cpbi.101.
The iSwathX web application processes and normalizes mass spectrometry-based proteomics spectral libraries generated in the data-dependent acquisition (DDA) approach. These libraries are stored in various proteomics repositories such as PeptideAtlas and NIST, or are user-generated and provide reference data for data-independent acquisition (DIA) targeted data extraction and analysis. iSwathX 2.0 can efficiently normalize DDA data from different instruments, gathered at different instances, and make it compatible with specific DIA experiments. Novel functions for parallel processing of DDA libraries and DIA report files, along with various data visualizations, are available in iSwathX 2.0. The step-by-step protocols provided here describe how the libraries are uploaded, processed, visualized, and downloaded using various modules of the application. They also provide detailed guidelines on the use of DIA report files for data analysis and visualization. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Processing, combining, and visualizing two DDA libraries Basic Protocol 2: Parallel processing and combination of multiple DDA libraries Basic Protocol 3: Downstream processing, comparison, and visualization of DIA report files.
iSwathX 网络应用程序处理和标准化基于质谱的蛋白质组学光谱库，这些库是在数据依赖采集（DDA）方法中生成的。这些库存储在各种蛋白质组学存储库中，如 PeptideAtlas 和 NIST，或者是用户生成的，为数据独立采集（DIA）靶向数据提取和分析提供参考数据。iSwathX 2.0 可以有效地归一化来自不同仪器、不同时间收集的 DDA 数据，并使其与特定的 DIA 实验兼容。iSwathX 2.0 提供了用于并行处理 DDA 库和 DIA 报告文件的新功能，以及各种数据可视化功能。这里提供的逐步协议描述了如何使用应用程序的各种模块上传、处理、可视化和下载库。它们还提供了有关如何使用 DIA 报告文件进行数据分析和可视化的详细指南。©2020WileyPeriodicalsLLC.基本方案 1：处理、组合和可视化两个 DDA 库基本方案 2：并行处理和多个 DDA 库的组合基本方案 3：DIA 报告文件的下游处理、比较和可视化。
