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. In the Start window, select New Study/Analysis.
  3. The New Study and Analysis dialog box opens.
  4. In the New Study and Analysis dialog box, do the following:
  5. In the Study Name text field, enter a name (for example, Triple Knockout Two Replicates).
  6. (Optional) For Study Root Directory, change the folder for storing the study.
  7. Keep the study on a local drive.
  8. Select the Processing workflow:
  9. ProcessingWF_Tribrid\ PWF_Tribrid_TMT_Quan_SPS_MS3_SequestHT_Percolator.pdProcessingWF
  10. Select the Consensus workflow:
  11. ConsensusWF\CWF_Comprehensive_Enhanced Annotation_Reporter_Quan.pdConsensusWF
  12. Select OK.
  13. In the Quantification Methods section of the Study Definition page, select Add, and select TMT 11plex SG253828.
  14. This is the method you created in Configure the quantification method.
  15. Define the study factors, and associate them with the quantification channels.
  16. In the Study Factors section of the Study Definition pane, select Add > Categorical Factor.
  17. For the title of the factor, enter Yeast Strain, and select Apply.
  18. In the New Factor dialog box, select Edit.
  19. Add the following items to the new study factor: Met6, His4, Ura2, and Parental.
  20. Select Apply.
  21. Select the Input Files tab, and then the select Add Files.
  22. The Add Files dialog box opens.
  23. Select both of the TMT 11plex data files (TKOTT11_1ms3_1 and TKOTT11_1ms3_2), and then select Open.
  24. In the Quan Method column next to the file name, select the TMT 11plex SG253828 quan method for both data files.
  25. Press Shift and select both files, and then drag them from the Input Files tab to the Files for Analysis section of the Analysis.
  26. The files are now part of the analysis.
  27. Select the Samples tab.
  28. In the Yeast Strain column, make the following changes in the quantification for both data files:
  29. Change the 126, 127N, and 127C quan channels to Met6.
  30. Change the 128N, 128C, and 129N quan channels to His4.
  31. Change the 129C, 130N, and 130C quan channels to Ura2.
  32. Change the 131N and 131C columns to Parental.
  33. TIP

    You can enter these changes one row at a time using the dropdown list, or by selecting multiple rows, right-clicking, and in the dropdown list selecting Set Yeast Strain to.

  34. For the four parental channels, change the Sample Type column from Sample to Control.