PeptideVisualizer: A Novel Software Solution for PROTOMAP Analysis

PeptideVisualizer is an open-source software for PROTOMAP analysis, offering an intuitive graphical user interface and command-line compatibility. The software processes mass spectrometry data output from MaxQuant to visualize protein migration in polyacrylamide gel electrophoresis and sequence coverage. In addition, it integrates information regarding protein secondary structure and features from the UniProt database to visualize them within comprehensive peptographs. These features allow us to assess the occurrence of a proteolytic event based on sequence context and peptides abundance. The key advantages of PeptideVisualizer include the integration of quantitative information, handling of multiple experiments with biological replicates, and the introduction of a novel mismatch factor─a metric designed to rapidly identify proteolytic events. Herein, the software was validated in an apoptosis-related data set, demonstrating its effectiveness and usefulness in large-scale proteomic data analysis.