The study holds information necessary to run data analysis.


  1. Select the Start Page tab in Proteome Discoverer.
  2. On the Start Page, 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, TMT Phosphopeptide Example.
  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_MS3.pdConsensusWF.
  12. Select OK.
  13. The page for your study opens.
  14. Define the study factors by doing the following:
  15. In the Study Definition page, in the Study Factors section, select Add, and select Categorical Factor.
  16. Select Stimulation as the title of the factor.
  17. Add the following items to the new study factor: Control, IGF-1, Insulin, and Pool.
  18. Select Apply.
  19. The updated study factors appear.
  20. Add the quantification method to the study.
  21. In the Quantification Methods section, select Add.
  22. Select TMT 10plex phosphopeptide.
  23. The method now appears in the Quantification Methods section.
  24. Add the raw file to the study:
  25. Select the Input Files tab.
  26. Select Add Files.
  27. In File Explorer, select 20160307_A549_Phospho_1ug_CID_NL_trigger_top1_Lumos_01.raw, and then select OK.
  28. In the Quan Method column for the raw file, select TMT 10plex phosphopeptide.
  29. Select OK.
  30. Drag the file from Input Files to the Files for Analysis area in the Analysis pane.
  31. Associate the study factors with the quan channels, by doing the following:
  32. Select the Samples tab.
  33. In the Stimulation column, make the following changes:
  34. Change the 126, 127N, and 127C quan channels to Control.
  35. Change the 128N, 128C, and 129N quan channels to Insulin.
  36. Change the 129C, 130N, and 130C quan channels to IGF-1.
  37. Change the 131 quan channel to Pool.
  38. TIP

    You can change the value:

    • One row at a time by using the dropdown menu.
    • Multiple rows at a time by holding down SHIFT or CTRL, right-clicking, and selecting the Set Stimulation option in the menu.