Unipept Desktop - Overview

Read this document to quickly get started to use our application.

First time use

A few things are automatically set up the first time you start this application. You will directly notice a dialog popping up that downloads a small SQLite-database. This database contains static information about taxa and functional annotations. Every month, a new release of this database is automatically generated. Unipept Desktop will regularly check for a new version of this database and update it in the background.
Installation for this static database can take up to a few minutes, depending on the downlink of your internet connection. The application will continue to work if the installation fails for some reason, it will only take longer before analysis results are available. A new attempt to install the database will be made when you restart the application.

Figure 1 Overview of the Unipept Desktop Application. The application window consists of three distinct main parts: the sidebar (to the left), the project explorer (directly right of the sidebar) and the content view (remainder of the application).

See Figure 1 for a full overview of the application's main window. The application consists of three main parts: the sidebar, the project explorer and the content view. The sidebar provides access to the distinct functions and analysis pipelines that are supported by the Unipept Desktop Application:


Use the Home button to return to the application's starting point (e.g. if you want to switch between projects).

Single Assay Analysis

The single assay analysis is designed to provide all available information related to a single assay.

Comparative Analysis

The comparative analysis allows you to compare multiple assays with each other. You can select items from different data sources that should be compared across assays after which a heatmap visualization will be generated.

Tryptic Peptide Analysis

The tryptic peptide analysis pipeline generates a summary with all information that is known for a single tryptic peptide. This includes a list of all proteins in which a given peptide is contained, all functional annotations related with these proteins, as well as the lowest common ancestor for this peptide.


This button brings you to the settings page, which allows you to configure the application (e.g. how many CPU cores can be used, which endpoint should be used, ...).