CasanovoGUI

CasanovoGUI is a cross-platform desktop application for Casanovo — de novo peptide sequencing from MS/MS spectra with a transformer model. Configure your inputs and parameters in a simple form, click Run Casanovo, and watch the output stream live in the console. The GUI wraps Casanovo's command-line sub-commands — de novo sequencing, database search, evaluation, training, and config generation — each as its own tab, and can open your results in PDV for annotated-spectrum visualization.

Installation

Download the installer for your platform from the Releases page:

OS	Download	How to run
Windows	CasanovoGUI-<version>-windows-x64.zip	Unzip and run CasanovoGUI.exe
macOS (Apple Silicon)	CasanovoGUI-<version>-macos-arm64.dmg	Open and drag to Applications
Linux	CasanovoGUI-<version>-linux-x86_64.deb or …-linux-x86_64.tar.gz	Install the .deb, or just extract the .tar.gz (no root) and run

No manual tool installation is needed. The installers bundle their own Java runtime, so you do not have to install Java. And the first time you start an analysis, if Casanovo isn't already on your machine the GUI offers to install it for you — it downloads a private Python and Casanovo automatically (no Python or pip setup required). Just download, launch, and run.

Intel Macs: use the cross-platform CasanovoGUI-<version>.jar from the Releases page instead (it needs a Java 23+ runtime installed).

The De novo panel

The De novo tab runs casanovo sequence to predict peptide sequences directly from your spectra. Its main input settings are:

• Spectrum file(s) (required) — one or more mzML, mzXML, or MGF files to sequence. You can select several at once.
• Model weights (--model) (optional) — a .ckpt model file. Leave it blank to use Casanovo's cached default weights, which the GUI detects and shows for you.
• Config file (--config) (optional) — a YAML file that overrides parameters. Leave it blank to use the values from the Parameters dialog instead.
• Output directory and output root name — where the result .mztab and log are written, and the base name used for them.
• Verbosity and Overwrite existing output files — the logging level and whether to overwrite a previous run in the same folder (on by default).

Click Parameters to fine-tune any Casanovo setting (precursor m/z tolerance, peptide length, number of beams, batch size, accelerator, and more) without editing YAML by hand, and the live command preview shows the exact casanovo … command that will run.