Analytical methods and tools for processing mass spectrometry-based proteomics data are still in early stages of development compared to other ‘omics fields. For this reason, we sought to develop an accessible online application to facilitate normalization, basic statistical testing, and biological interpretation of mass-spec based proteomics data. GiaPrOnto (Graphical Interpretation and Analysis of Proteins and their Ontologies) is an R-Shiny application written to fill this void (Weiner, et al, Mol. Cell. Proteom. 2018). Input to GiaPrOnto can be the direct output of MaxQuant protein or PTM (commonly used protein quantification software), or any properly formatted text file. GiaPrOnto performs normalization, basic statistical tests (e.g. t-test), gene ontology (GO) evaluation, and provides visualization of sample features and results. Each figure can be exported in high resolution (right click) and includes a comprehensive legend to assist in its interpretation. Currently, supported Gene Ontology includes human, mouse, worm, fly, yeast and Arabidopsis. For questions, suggestions or bug reports, please contact Amber K. Weiner (email@example.com).