iSwathX 2.0 for Processing DDA Spectral Libraries for DIA Data Analysis

Q1 Biochemistry, Genetics and Molecular Biology

Current protocols in bioinformatics Pub Date : 2020-06-01 DOI:10.1002/cpbi.101

Zainab Noor, Abidali Mohamedali, Shoba Ranganathan

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引用次数: 2

Abstract

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

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iSwathX 2.0用于DIA数据分析的DDA谱库处理

iSwathX web应用程序处理并规范化了数据依赖采集(DDA)方法中生成的基于质谱的蛋白质组学谱库。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，并为数据独立采集(DIA)目标数据提取和分析提供参考数据。iSwathX 2.0可以有效地规范化来自不同仪器、不同实例采集的DDA数据，并使其与特定的DIA实验兼容。iSwathX 2.0中提供了用于并行处理DDA库和DIA报告文件以及各种数据可视化的新功能。这里提供的分步协议描述了如何使用应用程序的各个模块上传、处理、可视化和下载库。它们还提供了使用DIA报告文件进行数据分析和可视化的详细指南。©2020 Wiley Periodicals llc .基本协议1:两个DDA库的处理、组合和可视化基本协议2:多个DDA库的并行处理和组合基本协议3:DIA报告文件的下游处理、比较和可视化

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Current protocols in bioinformatics Biochemistry, Genetics and Molecular Biology-Biochemistry

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