Fig. 1

Flowchart that outlines the workflow of PTMViz. The tool has two separate sections that work independently from one another. a Protein data analysis includes the user loading in protein intensity data matrix and defining the sample metadata used for the analysis. The data distribution is visualized by various plots including histogram, boxplot, PCA, and MDS presented in the Protein Preliminary Shiny dashboard tab. Limma is used for the differential analysis and results are displayed as interactive data tables and plots in the Protein Data Shiny dashboard tab. b PTM data analysis begins with user loaded peptide intensity data and the defining of sample metadata. The data is then organized into interactive data tables and plots, which are displayed in the Post Translational Modification tab of the Shiny dashboard. The significance thresholds for the plots can be modified and the tables can be filtered to search for data of interest interactively