Unipept Desktop - Project management

Projects are a central concept to the Unipept Desktop Application and aid to organize a collection of samples.

Project structure


A project is a collection of studies, and every study is a collection of assays. This terminology adheres to the definitions found in the ISA-tab standard.


A study is a collection of assays that are somehow related. They, for example, all originate from the same object under study. Every study needs to be uniquely named, no two studies with the same name in the same project can exist! The application will inform you of a conflict, should one arise.


An assay corresponds directly to a list of peptides and the configuration of search settings for this assay. Note that a project can thus contain multiple assays with the same peptide content, but with a different search configuration. Every assay should be uniquely named within a study. Assays with the same name can only occur within one project, if they belong to different studies.

Physical structure

A project corresponds to a folder on your local hard drive and contains the following files / folders:
  • metadata.sqlite: This file is a SQLite-database that keeps track of the analysis results and metadata that belongs to this project.
  • subfolder per study: One folder per study is present. A study's name is derived from the folder's name. The study's name in the application will change if you change the name of this folder.
    • file per assay: The study folder also contains one file per assay that belongs to this study. These files end in the ".pep" extension and contain one peptide per line.

External modifications

Please note that the Unipept Desktop Application keeps track of changes made to the physical structure of a project. This means that you can edit projects with external applications after which the application will automatically adjust. You can copy and paste items to and from the project folder, rename folder and files to respectively update study and assay names, update assay files, etc.