Phospho-Analyst: An Interactive, Easy-to-Use Web Platform To Analyze Quantitative Phosphoproteomics Data.

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/.

Analysis and visualization of quantitative proteomics data using FragPipe-Analyst.

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.