You can use the Daemon utility to run processing and consensus workflows on a remote server. These workflows are saved in templates that you created in the Workflow Editor of the Proteome Discoverer application on the remoter server computer. You must set the values of the required parameters for the workflow templates before you run the utility. The specified values—for example, FASTA databases—must be available on the server where they will be processed. You cannot change the workflows by using the Proteome Discoverer Daemon interface.

You can choose quantification methods from predefined quantification methods on the server or from a method file that you load with the Browse button.

Procedure

  1. Select the Start Jobs tab.
  2. The Start Jobs page opens.
  3. Start Jobs page of the Daemon utility
  4. Select the By File radio button if it is not already selected. For MudPIT, select the MudPIT radio button. If you want to export the parameter file to the remote Magellan server, continue with steps 3 through 8. Otherwise, continue to step 9.
  5. For MudPIT only, select the Export Parameter File tab and change the Number of Rawfiles to at least 2. This example features two MudPIT samples. Each one consists of two raw data files (for a total of four raw data files).
  6. Export Parameter File tab for MudPIT
  7. In the Workflows and Quan Method area, choose the Processing and Consensus workflows from the list or browse by selecting the browse button.
  8. In the Server Output Directory area, the folder name is automatically filled with the Processing workflow.
  9. In the Output Filename area, type a file name.
  10. Select Export.
  11. The Save a parameter file dialog box opens.
  12. Type the name of the parameter file and select Save.
  13. Select the Load Files tab and select Add.
  14. In the Open dialog box, locate the folder that contains the raw data files, select the spectrum (RAW) files that you want to load, and select Open.
  15. The selected spectrum files appear on the Load Files page.
  16. To remove a file from the Load Files page, select the file and select Remove.
  17. To specify the type of processing, select the By File or MudPIT option.
  18. File processing (the default): Executes the workflow once for each spectrum file.
  19. MudPIT: Feeds all spectrum files into one workflow.
  20. When you select the MudPIT option, the Treat as Replicates checkbox and the Output Filename box become available.
  21. (Optional) For the MudPIT option, select the Treat as Replicates check box to group the samples by quantification channel and to average the abundance values for each channel across files.
  22. This option is only available when you select the MudPIT option.
  23. If you do not select the Treat as Replicates option, the application groups the samples by quantification channel and by file. It creates the sample groups and ratios only within files, not across files.
  24. Select a processing template from template files located on the Daemon server.
  25. In the Workflows and Quan Method area of the Start Jobs page, do one of the following:
  26. Select the Browse button (...), select the processing template from the Open dialog box, and select Open.
  27. –or–
  28. Select a processing workflow template from the Processing menu.
  29. The menu box lists only the templates that you selected in the current run. When you restart the application, the menu box does not list any templates. When you connect the application to another server, the application verifies that the templates are still valid and can be run by the connected server.
  30. The template files for processing workflows have a .pdProcessingWF extension.
  31. Select a consensus template.
  32. In the Workflows and Quan Method area of the Start Jobs page, do one of the following:
  33. Select the Browse button, select a consensus workflow template from the Open dialog box, and select Open.
  34. –or–
  35. Select a consensus workflow template from the Consensus menu.
  36. The menu box lists only the templates that you selected in the current run. When you restart the application, the menu box does not list any templates. When you connect the application to another server, the application verifies that the templates are still valid and can be run by the connected server.
  37. The template files for consensus workflows have a .pdConsensusWF extension.
  38. To obtain quantification results, select a quantification method from the Quan Method menu in the Workflows and Quan Method area of the Start Jobs page.
  39. (Optional) To specify the control channel to use in creating ratios when you process quantification samples, select the control channel from the Control Channel list.
  40. If you selected the MudPIT option, in the Output Filename box, enter the name of the output file where you want to store the results of the search.
  41. The Start Jobs page should now resemble the following figures for batch processing or for MudPIT processing, respectively.
  42. Select Start to execute the job.
  43. Start Jobs page of the Daemon utility for By File
  44. Start Jobs page of the Daemon utility for MudPIT processing