A web‐tool for visualizing quantitative protein–protein interaction data

Quantitative interaction proteomics data can be a challenge to efficiently analyze and subsequently present to an audience in a simple and easy to understand format that still conveys sufficient levels of information. Here we present freely accessible and open‐source web tools for displaying multiple parameters from quantitative protein–protein interaction data sets in a visually intuitive format. Given a set of “bait” proteins with detected “prey” interactions, dot plots can be generated to display absolute spectral counts for the preys, relative spectral counts between baits and confidence levels for the interactions (e.g. as determined by SAINTexpress). Additional tools are available for displaying fold change results between numerous baits with their associated confidence level (e.g. resulting from intensity measurements) and pairwise bait analyses displaying spectral counts, confidence score and fold change differences in a scatter plot format. These tools make it easy for the user to identify important interaction changes, interpret their data, and present this information to others in an intuitive way.