Analysis and visualization of quantitative proteomics data using FragPipe-Analyst.
Analysis and visualization of quantitative proteomics data using FragPipe-Analyst.
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使用 FragPipe-Analyst 分析和可视化定量蛋白质组数据。
DOI：
10.1101/2024.03.05.583643
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发表时间：
2024
期刊：
影响因子：
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通讯作者：
Nesvizhskii,AlexeyI
中科院分区：
文献类型：
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作者：
Hsiao,Yi;Zhang,Haijian;Li,GinnyXiaohe;Deng,Yamei;Yu,Fengchao;Kahrood,HosseinValipour;Steele,JoelR;Schittenhelm,RalfB;Nesvizhskii,AlexeyI
FragPipe 计算蛋白质组学平台因其快速的处理速度和用户友好的图形界面而在蛋白质组学研究界获得广泛欢迎。尽管 FragPipe 生成可供分析的格式良好的输出表，但仍然需要一种易于使用且用户友好的下游统计分析和可视化工具。 FragPipe-Analyst 通过提供 R 闪亮的 Web 服务器来帮助 FragPipe 用户对生成的定量蛋白质组数据进行下游分析，从而满足了这一需求。它支持主要的定量工作流程，包括无标记定量、串联质量标签和数据独立采集。 FragPipe-Analyst 提供了一系列有用的功能，例如各种缺失值插补选项、数据质量控制、无监督聚类、使用 Limma 的差异表达 (DE) 分析以及使用 Enrichr 的基因本体和通路富集分析。为了支持高级分析和定制可视化，我们还开发了 FragPipeAnalystR，这是一个包含所有 FragPipe-Analyst 功能的 R 包，经过扩展可支持翻译后修饰 (PTM) 的位点特定分析。 FragPipe-Analyst 和 FragPipeAnalystR 都是开源且免费提供的。
The FragPipe computational proteomics platform is gaining widespread popularity among the proteomics research community because of its fast processing speed and user-friendly graphical interface. Although FragPipe produces well-formatted output tables that are ready for analysis, there is still a need for an easy-to-use and user-friendly downstream statistical analysis and visualization tool. FragPipe-Analyst addresses this need by providing an R shiny web server to assist FragPipe users in conducting downstream analyses of the resulting quantitative proteomics data. It supports major quantification workflows, including label-free quantification, tandem mass tags, and data-independent acquisition. FragPipe-Analyst offers a range of useful functionalities, such as various missing value imputation options, data quality control, unsupervised clustering, differential expression (DE) analysis using Limma, and gene ontology and pathway enrichment analysis using Enrichr. To support advanced analysis and customized visualizations, we also developed FragPipeAnalystR, an R package encompassing all FragPipe-Analyst functionalities that is extended to support site-specific analysis of post-translational modifications (PTMs). FragPipe-Analyst and FragPipeAnalystR are both open-source and freely available.