Division of Molecular Biology and Human Genetics, Department of Biomedical Science, DST/NRF Centre of Excellence in Biomedical TB Research, SA MRC Centre for Tuberculosis Research, Faculty of Medicine and Health Science, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa.
Section Molecular Microbiology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam 1081 HZ, The Netherlands.
Bioinformatics. 2020 Dec 8;36(19):4965-4967. doi: 10.1093/bioinformatics/btaa620.
Proteomics is a powerful tool for protein expression analysis and is becoming more readily available to researchers through core facilities or specialized collaborations. However, one major bottleneck for routine implementation and accessibility of this technology to the wider scientific community is the complexity of data analysis. To this end, we have created ProVision, a free open-source web-based analytics platform that allows users to analyze data from two common proteomics relative quantification workflows, namely label-free and tandem mass tag-based experiments. Furthermore, ProVision allows the freedom to interface with the data analysis pipeline while maintaining a user-friendly environment and providing default parameters for fast statistical and exploratory data analysis. Finally, multiple customizable quality control, differential expression plots as well as enrichments and protein-protein interaction prediction can be generated online in one platform.
Quick start and step-by-step tutorials as well as tutorial data are fully incorporated in the web application. This application is available online at https://provision.shinyapps.io/provision/ for free use. The source code is available at https://github.com/JamesGallant/ProVision under the GPL version 3.0 license.
蛋白质组学是一种强大的蛋白质表达分析工具，通过核心设施或专门的合作，越来越容易为研究人员所获得。然而，将这项技术常规应用于更广泛的科学界的一个主要瓶颈是数据分析的复杂性。为此，我们创建了 ProVision，这是一个免费的开源基于网络的分析平台，允许用户分析两种常见的蛋白质组学相对定量工作流程的数据，即无标记和串联质量标签实验。此外，ProVision 允许在保持用户友好环境的同时，自由地与数据分析管道接口，并提供默认参数，用于快速的统计和探索性数据分析。最后，可以在一个平台上在线生成多个可定制的质量控制、差异表达图以及富集和蛋白质-蛋白质相互作用预测。
快速入门和逐步教程以及教程数据都完全包含在网络应用程序中。该应用程序可在 https://provision.shinyapps.io/provision/ 上免费使用。源代码可在 https://github.com/JamesGallant/ProVision 下根据 GPL 版本 3.0 许可证获得。
