Unipept Desktop documentation v1.2.4

The Unipept Desktop application allows, in contrast to the web application, to analyse much larger samples, to store analysis results offline, to extensively compare assays with each other and to better manage samples.

Unipept's web application provides users with the ability to analyze a metaproteomics sample and extract taxonomic and functional information from environmental samples. Our web app provides interactive visualizations to researchers and allows them to, for example, filter out all functions that are associated with a specific taxon. Due to its inherent web-based nature, the size and amount of samples that can be analysed are rather limited.

The Unipept Desktop application, however, is not limited in the amount of memory and storage that it can consume, allowing us to process datasets with much more peptides than before. All analysis results in the desktop app are stored as part of a project directory. Once an analysis has been performed, the computed results can easily be restored without the need to analyse the assay again. Projects can be easily shared with other researchers and analysis can be performed offline, if required. Another advantage of the desktop application is the ability to better compare multiple datasets (assays) with each other. This allows you to gain a deeper understanding of the interactions that are taking place in a complex environment.

Our desktop application is open source under the MIT License and all code is available on GitHub. Changes between releases are listed in the changelog . In case you have encountered an issue using these tools, have feature requests or found a bug, don't hesitate to contact us by email (unipept@ugent.be), or create an issue on Github.


In order to use the Unipept Desktop Application, it needs to be installed first. You can always download the most recent version for your operating system from the releases on GitHub. Direct links for the different operating systems are also available (these links will always point to the most recent version):

All required dependencies will automatically be installed using the installation packages provided above. If a specific installer is not suitable for your current operating system (e.g. specific flavours of Linux that do not support AppImage's), you can always clone the repository and build the project yourselves.

Installation on Windows

1. Start the installer package

Double-click the installer package to start the installation. You will be greeted by a window that asks for your explicit approval to install our application. Click "More info".

2. Proceed with security checks

A new button appears "Run anyway". Click this button to start the installation process. Windows shows this warning as part of the "SmartScreen Security" system. This system protects your computer from running potentially unsafe apps. Windows displays this message for our application since it's very new, without a large userbase yet. The more people start to use this app, the faster it will be trusted by Microsoft.

3. Installation process is started

The installation process is now started, and a progress bar should be visible. This process should not take longer than one minute on most modern systems. Please wait for the installer to disappear (without any errors). Once it's gone, the installation process is fully finished.

4. Installation process is done

You can now start the application, by double clicking it's shortcut on your desktop or by selecting it from the applications list in Windows.

Installation on macOS

1. Mount the installer image

Double-click the downloaded "Unipept.dmg" file to mount the installer image. A new window pops up in which you need to drag the Unipept Desktop logo into your applications folder.

2. Installation process is done

Look for the installed application in Launchpad and start Unipept Desktop.

Installation on Linux (Ubuntu)

1. Open AppImage properties

Right-click the downloaded "Unipept.AppImage" file and select "properties". A properties window will pop up.

2. Enable executable permissions

Click the "permissions" tab and check the box before "Allow executing file as program". Close the window.

3. Open the application

Double-click the downloaded AppImage-file to start the application.


The Unipept Desktop Application will check for updates automatically. Once an update is found, the new version of the application will automatically be downloaded and a progress bar at the bottom of the application appears.Once the application is done downloading the new application, the update is installed in the background. After the installation finishes, a notification pops up and requests the user to restart the application to complete the update.

It's not mandatory to restart the application immediately after an update is installed. Note, however, that the new version will only take effect after restarting the app.