The following procedure describes how to create a processing method that calls the Daemon utility from the Xcalibur data system. Process method files have a .pmd file extension.

Procedure

  1. Open Xcalibur to start the Xcalibur data system.
  2. Select Processing Setup, .
  3. The Processing Setup window opens.
  4. Open the processing method that you want to modify as follows:
  5. Select File > Open.
  6. Locate the processing method file and select the file.
  7. Select Open.
  8. Open the Programs view of the Processing Setup window as follows:
  9. Select View > Programs.
  10. The Programs view of the Processing Setup window opens.
  11. Programs view with an empty table
    Programs view with an empty table
  12. If the Programs view has an empty table, right-click the table and select Insert Row.
  13. A new row appears above the placeholder row. An asterisk to the left side of a table row defines it as a placeholder row.
  14. Programs view with an unedited table row
    Programs view with an unedited table row
  15. In the added table row, specify the name and location of the parameter file as follows.
  16. In the Enable column, select the checkbox.
  17. Right-click the Program or Macro Name column and select Browse.
  18. Programs view with the shortcut menu displayed
    Programs view with the shortcut menu displayed
  19. Locate the following executable, and select Open:
  20. C:\Program Files\Thermo\Proteome Discoverer 3.1\Proteome Discoverer Daemon 3.1\System\Release
  21. If the following warning appears, “The file ‘DiscovererDaemon’ does not exist on this computer,” select OK.
  22. In the Parameters column, enter the location of the parameter file containing the commands that will execute the utility:
  23. -p path_to_parameter_file\parameter_filename %R

  24. NOTE

    Do not copy/paste from this PDF. To ensure the location is correct, enter the name of the parameter file. If the name of the parameter file contains a space, you must enclose the name in quotation marks, as in this example:
    -p “C:\Xcalibur\methods\batch processing.param” %R

  25. In the Std, QC, Unk, Other, and Sync columns, accept the default settings or modify them according to your requirements. For information about setting the sample types to be sent, see Specify the sample types to be sent to Proteome Discoverer Daemon.
  26. To send all sample types to the Daemon utility, make sure that all of the sample type columns are set to Yes.
  27. Program table with a call to the Daemon utility
    Program table with a call to the Daemon utility
  28. Select OK to save the changes to the processing method.
  29. Select File > Save.