These instructions apply to creating processing workflows and consensus workflows.

Procedure

  1. On the Start page, open a study by doing one of the following:
  2. Select Open Study.
  3. Select File > Open Study.
  4. The Open Study dialog box opens.
  5. Locate the study.
  6. Select Open.
  7. The study opens as a separate page in the Proteome Discoverer application.

  8. TIP

    You can also open a study by selecting a recent study from the Recent Studies column on the Start page.

  9. If an analysis is not already open, select New Analysis.
  10. On the Study page, select the Workflows tab.
  11. Do one of the following:
  12. Select the title bar of the Consensus Step area of the Analysis pane.
  13. A blue border highlights the Consensus Step area in the Analysis pane.
  14. Select the title bar of the Processing Step area of the Analysis pane.
  15. A blue border highlights the Processing Step area in the Analysis pane.
  16. On the Workflow Editor page, do one of the following:
  17. Select Open Common to open a workflow file that you choose.
  18. Select Open to open the most recent file path that you opened.
  19. If you clicked the Processing Step bar, the Open Workflow dialog box displays .pdProcessingWF files in the Common Templates folder.
  20. If you clicked the Consensus Step bar, the Open Workflow dialog box displays .pdConsensusWF files in the Common Templates folder.
  21. Select the workflow file, and select Open.
  22. The workflow opens in the Workflow Tree pane. If you must update the template, see Correct workflow errors.
  23. Configure the search node.
  24. Make any other changes required.
  25. Save the workflow as follows:
  26. In the Workflow box, enter a name for the workflow.
  27. (Optional) In the Description box above the Workflow Tree pane, enter a brief description of the workflow.
  28. Do one of the following:
    - Select Save to save the current workflow as a template file.
    - Select Save Common to save the current workflow as a template to the common templates folder.
  29. The Save Workflow dialog box opens.
  30. In the Save Workflow dialog box, do the following:
    - Navigate to the folder that you want to save the file to.
    - Enter a name for the file.
  31. Select Save.
  32. The application saves processing workflows as .pdProcessingWF files and saves consensus workflows as .pdConsensusWF files.