PeptideVisualizer : a novel software solution for PROTOMAP analysis

Kolarič, Matej (author), Ivanovski, Sara (author), Sever, Tilen (author), Turk, Boris (author), Fonović, Marko (author)

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.

• Language: English
• Keywords: proteolysis, proteases, PeptideVisualizer, mass spectrometry, PROTOMAP, open-source software, MaxQuant
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: FKKT - Faculty of Chemistry and Chemical Technology
• Publication status: Published
• Publication version: Version of Record
• Year: 2026
• Number of pages: Str. 2591-2597
• Numbering: Vol. 25, iss. 5
• PID: 20.500.12556/RUL-189586
• UDC: 577
• ISSN on article: 1535-3907
• DOI: 10.1021/acs.jproteome.5c01209
• COBISS.SI-ID: 281770243
• Publication date in RUL: 09.10.2026

Record is a part of a journal

• Title: Journal of proteome research
• Shortened title: J. proteome res.
• Publisher: American Chemical Society
• ISSN: 1535-3907
• COBISS.SI-ID: 513576473

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

• Language: Slovenian
• Keywords: proteoliza, proteaze, PeptideVisualizer, peptidi, masna spektrometrija, odprtokodna programska oprema

Projects

• Funder: ARIS - Slovenian Research and Innovation Agency
• Project number: J1-3022
• Name: Sistemska določitev fizioloških vlog legumaina

• Funder: ARIS - Slovenian Research and Innovation Agency
• Project number: P1-0140
• Name: Proteoliza in njena regulacija pri zdravju in boleznih