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bioRxiv · 10.1101/2025.10.23.684139

PeptiLine: an interactive platform for customizable functional peptidomic analysis

Kuhfeld, R. F.·Nielsen, S. D.-H.·Dallas, D. C.
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Abstract

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. Author summaryBioactive peptides in food have health benefits ranging from antimicrobial activity to blood pressure regulation. We use mass spectrometry to identify these peptides, but analyzing the resulting datasets is challenging. The data comes out as massive spreadsheets that are difficult to interpret, and existing tools either require advanced programming skills, lack key analytical features, or are no longer maintained. We built PeptiLine to address these problems. Its a user-friendly platform that transforms peptidomic data into interactive visualizations and statistical summaries. The key challenge we solved was handling peptides with multiple overlapping functions, for instance, a peptide thats both antimicrobial and antihypertensive. Most tools would double-count such peptides, inflating the totals. We figured out how to accurately display both individual functional categories and true abundance totals without this double-counting bias. We demonstrated PeptiLines capabilities by analyzing bitter peptides in aged Cheddar cheese, successfully identifying specific protein regions responsible for bitterness and novel insight into Cheddars bioactive potential. The software is freely available as both a web application and for local installation, requiring no programming expertise.

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Kuhfeld, R. F., Nielsen, S. D.-H., Dallas, D. C.. 2025-10-26. PeptiLine: an interactive platform for customizable functional peptidomic analysis. https://doi.org/10.1101/2025.10.23.684139

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