Monash Proteomics & Metabolomics Platform, Monash Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.
Monash Genomics & Bioinformatics Platform, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.
J Proteome Res. 2023 Sep 1;22(9):2890-2899. doi: 10.1021/acs.jproteome.3c00186. Epub 2023 Aug 16.
Phosphoproteomics is nowadays the method of choice to comprehensively identify and quantify thousands of phosphorylated peptides and their associated proteins with the goal of interrogating changes in signal transduction pathways and other cellular processes. One of the most popular software suites to analyze phosphoproteomic data sets is MaxQuant, which converts mass spectrometric raw data into quantitative information on phosphopeptides and proteins. However, despite the increased utilization of phosphoproteomics in biomedical research, simple and user-friendly tools supporting downstream statistical analysis and interpretation of these highly complex outputs are still lacking. We have therefore developed Phospho-Analyst, which─similar to its sibling LFQ-Analyst─is an easy-to-use, interactive web application specifically designed to reproducibly perform differential expression analyses with "one click" and to visualize phosphoproteomic results in a meaningful and practical manner. Furthermore, if quantitative total proteomic information is available for the same samples, Phospho-Analyst automatically normalizes all phosphoproteomic results to underlying protein abundance levels, thereby ensuring that only genuine changes in phosphorylation events are considered. As such, Phospho-Analyst can not only be used by experienced proteomic veterans but also by researchers without any prior knowledge in (phospho)proteomics, statistics, or bioinformatics. Phospho-Analyst, including a detailed manual, is freely available at https://analyst-suites.org/apps/phospho-analyst/.
磷酸化蛋白质组学是目前全面鉴定和定量数千种磷酸化肽及其相关蛋白质的首选方法，其目的是研究信号转导途径和其他细胞过程的变化。分析磷酸蛋白质组学数据集最流行的软件套件之一是 MaxQuant，它将质谱原始数据转换为关于磷酸肽和蛋白质的定量信息。然而，尽管磷酸蛋白质组学在生物医学研究中的应用日益增加，但仍然缺乏简单易用的工具来支持这些高度复杂输出的下游统计分析和解释。因此，我们开发了 Phospho-Analyst，它与 LFQ-Analyst 类似，是一种易于使用的交互式网络应用程序，专门设计用于通过“一键”进行差异表达分析，并以有意义和实用的方式可视化磷酸蛋白质组学结果。此外，如果相同样本有定量的总蛋白质组学信息，Phospho-Analyst 会自动将所有磷酸蛋白质组学结果归一化为潜在的蛋白质丰度水平，从而确保只考虑真正的磷酸化事件变化。因此，Phospho-Analyst 不仅可以供有经验的蛋白质组学专家使用，也可以供没有任何（磷酸）蛋白质组学、统计学或生物信息学知识的研究人员使用。Phospho-Analyst 及其详细手册可在 https://analyst-suites.org/apps/phospho-analyst/ 免费获得。
