PeptiLine: an interactive platform for customizable functional peptidomic analysis

The PeptiLine peptidomics pipeline is a comprehensive software platform designed to transform peptidomic mass spectrometry output data into interactive, intuitive visualizations and statistical summaries. By integrating peptide-to-protein mapping, quantitative comparisons, bioactive annotations and descriptive and inferential analyses into a single user-friendly interface, PeptiLine addresses the bottleneck of timely and complex data exploration and visualization in bioactive peptide research. It enables visualization of peptidomic data through a series of modules allowing the user to create peptide sequence heatmaps, correlation plots and a series of categorical bar plots and pie plots to explore the absolute and relative bioactivity, protein origin, summed abundance and total peptide count. Here, we provide example uses of our Data Transformation, Descriptive Analysis and Heatmap Visualization tools to pinpoint functional peptide hotspots across protein sequences and compare samples across different protein variants. PeptiLine is freely available at https://mbpdb.nws.oregonstate.edu/peptiline/ and on GitHub (https://github.com/Kuhfeldrf/peptiline/) under an MIT license. The software runs on Windows, macOS, and Linux systems with Python ≥3.10. Support and bug reports: contact-mbpdb@oregonstate.edu.