The study holds the study factors, raw data files, quantification methods, and links to all search results for analyses performed on those data files within the study.


  1. Select the Start Page tab in the Proteome Discoverer application.
  2. Under Start, select New Study/Analysis.
  3. The New Study and Analysis dialog box opens.
  4. In the Study Name text box, enter a study name (for example, Triple Knockout Example).
  5. (Optional) For Study Root Directory, change the folder for storing the study.
  6. Select the following Processing workflow:
  7. ProcessingWF_Tribrid\ PWF_Tribrid_TMT_Quan_SPS_MS3_SequestHT_Percolator.pdProcessingWF
  8. Select the following Consensus workflow:
  9. ConsensusWF\CWF_Comprehensive_Enhanced Annotation_Reporter_Quan_MS3.pdConsensusWF
  10. Select OK.
  11. In the Quantification Methods area on the Study Definition page, select the Add dropdown menu and select TMT 11plex SG253828.
  12. This is the method you created in Configure the quantification method.
  13. Define the study factors, and associate them with the quantification channels.
  14. In the Study Factors area on the Study Definition pane, select the Add dropdown menu and select Categorical Factor.
  15. For the title of the factor, enter Yeast Strain, and select Apply.
  16. In the New Factor dialog box, select Edit.
  17. Add the following items to the new study factor: Met6, His4, Ura2, and Parental.
  18. Select the Input Files tab, and then select Add Files.
  19. In the Quan Method column next to the file name, select TMT 11plex SG253828.
  20. Select and drag the file from the Input Files tab to the Files for Analysis section of the Analysis.
  21. Select the Samples tab.
  22. In the Yeast Strain column, make the following changes in the quantification:
  23. Change the 126, 127N, and 127C quan channels to Met6.
  24. Change the 128N, 128C, and 129N quan channels to His4.
  25. Change the 129C, 130N, and 130C quan channels to Ura2.
  26. Change the 131N and 131C columns to Parental.
  27. TIP

    You can enter these changes one row at a time using the dropdown menu, or by selecting multiple rows. Right-click in the dropdown menu and select Set Yeast Strain to.