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

Phosphoproteomicsis nowadays the method of choice to comprehensivelyidentify and quantify thousands of phosphorylated peptides and theirassociated proteins with the goal of interrogating changes in signaltransduction pathways and other cellular processes. One of the mostpopular software suites to analyze phosphoproteomic data sets is MaxQuant,which converts mass spectrometric raw data into quantitative informationon phosphopeptides and proteins. However, despite the increased utilizationof phosphoproteomics in biomedical research, simple and user-friendlytools supporting downstream statistical analysis and interpretationof these highly complex outputs are still lacking. We have thereforedeveloped Phospho-Analyst, which similar to its sibling LFQ-Analyst isan easy-to-use, interactive web application specifically designedto reproducibly perform differential expression analyses with oneclick and to visualize phosphoproteomic results in a meaningfuland practical manner. Furthermore, if quantitative total proteomicinformation is available for the same samples, Phospho-Analyst automaticallynormalizes all phosphoproteomic results to underlying protein abundancelevels, thereby ensuring that only genuine changes in phosphorylationevents are considered. As such, Phospho-Analyst can not only be usedby experienced proteomic veterans but also by researchers withoutany prior knowledge in (phospho)proteomics, statistics, or bioinformatics.Phospho-Analyst, including a detailed manual, is freely availableat https://analyst-suites.org/apps/phospho-analyst/.

Automated summary

Phosphoproteomics is a comprehensive method for identifying and quantifying phosphorylated peptides and their associated proteins. Phospho-Analyst is an easy-to-use web application that simplifies the statistical analysis and interpretation of phosphoproteomic data. It also automatically normalizes the results to protein abundance levels, ensuring the consideration of genuine phosphorylation changes.