CasanovoGUI: a cross-platform desktop application for deep learning-based de novo peptide sequencing with Casanovo
preprint · bioRxiv · 2026
| Date | 2026-07-11 |
| Type | preprint |
| Venue | bioRxiv |
| Publisher | Cold Spring Harbor Laboratory |
| Contribution | adjacent |
| DOI | 10.64898/2026.07.11.737889 |
| Citations (OpenAlex) | 0 |
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 Casanovos 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 Casanovos 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.
Methods and tools
- CasanovoGUI: Cross-platform desktop application that wraps the Casanovo Transformer de novo peptide sequencer with a graphical front-end, lowering the barrier to entry for lab-facing MS users who would otherwise need to run Casanovo from the command line.
Methods it uses
- Casanovo: First Transformer
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