CasanovoGUI: a cross-platform desktop application for deep learning-based de novo peptide sequencing with Casanovo
- 1University of Washington
Abstract
De novo peptide sequencing detects peptides directly from tandem mass spectra without a protein sequence database, and deep learning has substantially advanced its performance. Casanovo, one such widely used model, is distributed as a Python command-line program. Consequently, installation, GPU and dependency configuration, and manual parameterization can be challenging for many bench scientists and are a recurring source of errors. Interpreting and validating the resulting predictions poses a further challenge. We present CasanovoGUI, an open-source Java-based desktop application that makes all of Casanovo's main analysis functions available through a point-and-click interface on Windows, macOS, and Linux. On first use, CasanovoGUI automatically installs a private Python environment and Casanovo with a GPU-matched build, requiring no prior software setup. The GUI provides access to Casanovo's analysis functions and configuration parameters, streams live progress, and integrates results interpretation: annotated spectra with per-residue confidence scores in the PDV viewer, and mismatch-tolerant mapping of de novo peptides back to a reference proteome. CasanovoGUI is available at https://github.com/Noble-Lab/CasanovoGUI.
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BibTeX
@misc{wen2026casanovogui,
title = {{CasanovoGUI: a cross-platform desktop application for deep learning-based de novo peptide sequencing with Casanovo}},
author = {B. Wen and K. Li and M. Riffle and M. J. MacCoss and W. Bittremieux and W. S. Noble},
howpublished = {bioRxiv},
year = {2026},
month = jul,
doi = {10.64898/2026.07.11.737889},
url = {https://www.biorxiv.org/content/10.64898/2026.07.11.737889v2},
note = {CC BY},
}
RIS
TY - UNPB
TI - CasanovoGUI: a cross-platform desktop application for deep learning-based de novo peptide sequencing with Casanovo
AU - B. Wen
AU - K. Li
AU - M. Riffle
AU - M. J. MacCoss
AU - W. Bittremieux
AU - W. S. Noble
PY - 2026
DA - 2026/07/11
PB - bioRxiv
DO - 10.64898/2026.07.11.737889
UR - https://www.biorxiv.org/content/10.64898/2026.07.11.737889v2
AB - De novo peptide sequencing detects peptides directly from tandem mass spectra without a protein sequence database, and deep learning has substantially advanced its performance. Casanovo, one such widely used model, is distributed as a Python command-line program. Consequently, installation, GPU and dependency configuration, and manual parameterization can be challenging for many bench scientists and are a recurring source of errors. Interpreting and validating the resulting predictions poses a further challenge. We present CasanovoGUI, an open-source Java-based desktop application that makes all of Casanovo's main analysis functions available through a point-and-click interface on Windows, macOS, and Linux. On first use, CasanovoGUI automatically installs a private Python environment and Casanovo with a GPU-matched build, requiring no prior software setup. The GUI provides access to Casanovo's analysis functions and configuration parameters, streams live progress, and integrates results interpretation: annotated spectra with per-residue confidence scores in the PDV viewer, and mismatch-tolerant mapping of de novo peptides back to a reference proteome. CasanovoGUI is available at https://github.com/Noble-Lab/CasanovoGUI.
ER -