ProteoPlotter: an executable proteomics visualization tool compatible with Perseus

Abstract

Mass spectrometry-based proteomics experiments produce complex datasets requiring robust statistical testing and effective visualization tools to ensure meaningful conclusions are drawn. The publicly-available proteomics data analysis platform, Perseus, is extensively used to perform such tasks, but opportunities to enhance visualization tools and promote accessibility of the data exist. In this study, we developed ProteoPlotter, a user-friendly, executable tool to complement Perseus for visualization of proteomics datasets. ProteoPlotter is built on the Shiny framework for R programming and enables illustration of multi-dimensional proteomics data. ProteoPlotter provides mapping of one-dimensional enrichment analyses, enhanced adaptability of volcano plots through incorporation of Gene Ontology terminology, visualization of 95% confidence intervals in principal component analysis plots using data ellipses, and customizable features. ProteoPlotter is designed for intuitive use by biological and computational researchers alike, providing descriptive instructions (i.e., Help Guide) for preparing and uploading Perseus output files. Herein, we demonstrate the application of ProteoPlotter towards microbial proteome remodeling under altered nutrient conditions and highlight the diversity of visualizations enabled with the platform for improved biological characterization. Through its comprehensive data visualization capabilities, linked to the power of Perseus data handling and statistical analyses, ProteoPlotter facilitates a deeper understanding of proteomics data to drive new biological discoveries.