You can manually define the study factors for each sample file or sample fraction in the Proteome Discoverer user interface. However, if you have many files or many factors, you may find it quicker to define the study factors in an Excel file or a text file and import that file when you define the new study. When you import the study factors in a file, you do not need to add them through the Proteome Discoverer interface.


  1. In Windows Explorer, open the Proteome Discoverer application folder structure, and open the Example RAW Files folder.
  2. Copy the LFQ Example.txt file to a local directory.
  3. Open LFQ Example.txt in a text editor, such as Notepad or WordPad.
  4. Regarding the abbreviations in the file heading:
  5. NF refers to numerical factor.
  6. CF refers to categorical factor (if used).
  7. Change the paths given for the 12 raw files to match the folders on the local computer.
  8. The paths in the example text file must match the actual paths of the raw files or the import will fail. You can change the paths in the file or put the raw files in the folder specified in the file.