PeptiLine: An Interactive Platform for Customizable Functional Peptidomic Visualization and Analysis

Abstract Functional peptidomic studies produce data sets of thousands of peptides, which are assigned bioactivities through curated databases and prediction tools. Annotation, data preparation, and visualization are handled in different tools, fragmenting the workflow. Because peptides often have multiple bioactivities, grouping by function can double-count peptides and overstate total functional abundance within each sample. We developed PeptiLine, a browser-based platform for functional peptidomic analysis, whose integrated annotation tool searches bioactive databases. Automated column mapping and multifile merging accommodate diverse proteomic software exports, and analysis extends to noncanonical protein sequences. The Data Transformation module organizes data through an auditable workflow spanning functional annotation, column renaming, replicate and group assignment, and peptide-to-protein mapping. The Descriptive Analysis and Heatmap Visualization modules generate sequence heatmaps, correlation plots, categorical charts, and scaled abundance plots of bioactivity, protein origin, abundance, and peptide counts, with optional group-comparison statistics. Our scaled bar plots resolve double counting: bar heights derive from unique-peptide summation and stay comparable between samples, while a sample’s functional composition is proportionate to the unique-peptide summation within each sample. Case studies from food, clinical, and comparative-physiology peptidomes demonstrate the broad applicability of PeptiLine. PeptiLine is freely available at https://peptiline.nws.oregonstate.edu/ and on GitHub (https://github.com/kuhfeldrf/peptiline/) under an MIT license.