AbstractMotivationSingle-cell proteomics provide unprecedented resolution to examine biological processes. Customized data analysis and facile data visualization are crucial for scientific discovery. Further, user-friendly data analysis and visualization software that is easily accessible for the general scientific community is essential.ResultsWe have created a web server,IsoAnalytics, that gives users without computational or bioinformatics background the ability to directly analyze and interactively visualize data obtained from the Isoplexis single cell technology platform. We envision this open-sourced web server will increase research productivity and serve as a free, competitive alternative for single-cell proteomics research.Availability and implementationIsoAnalytics is free and available at:https://cdc.biohpc.swmed.edu/isoplexis/and is implemented in Python, with all major browsers supported. Code for IsoAnalytics is free and available at:https://github.com/zhanxw/Isoplexis_Data_Analysis.Supplementary informationSupplementary dataare available atBioinformatics Advancesonline.