In the Daemon utility, you can create a parameter file that you can use to call the Daemon application from the Xcalibur data system. The application automatically translates the options that you set on the utility interface and in the workflow used for the search into text commands in the parameter file.

Procedure

  1. Set up the search according to the instructions in Run the Daemon utility from the window. You do not need to have files loaded to create a parameter file.
  2. Select the Export Parameter File tab on the Start Jobs page.
  3. Export Parameter File page
  4. In the Number of Rawfiles box for a MudPIT search, select the number of files that will appear in the Xcalibur Sequence Setup dialog box.
  5. Select Export.
  6. The Save a Parameter File dialog box opens.
  7. Specify the path and name of the parameter file, and select Save.
  8. The Proteome Discoverer Daemon application writes the parameter file in XML format to the specified directory.

To call the utility through the parameter file, see Running the Daemon utility from the Xcalibur data system.