You can process MudPIT samples by using a processing method.

Procedure

  1. Start the Daemon utility and export a parameter file for MudPIT processing. For information about exporting a parameter file, see Run the Daemon utility from a parameter file.
  2. The following figure shows how to configure the Export Parameter File page in the utility to export a parameter file. In this example, the parameter file is saved in C:\Xcalibur\methods.
  3. Selecting MudPIT processing in the Start Jobs page
  4. This example features two MudPIT samples. Each one consists of two raw data files (for a total of four raw data files).
  5. Define a processing method (see Create a processing method that calls the Daemon utility from the Xcalibur data system) using the parameter file exported in step 1, and select the method as the processing method in the Proc Meth column.
  6. Sequence used for MudPIT processing
  7. Start processing the MudPIT samples in the Run Sequence dialog box.
  8. Starting the processing of the MudPIT samples
    Starting the processing of the MudPIT samples
  9. The utility processes the two samples as MudPIT.
  10. Two MudPIT samples processed in the Daemon utility
  11. The Proteome Discoverer application saves the data in the two MudPIT samples in two directories, each one containing the raw data files of one MudPIT sample (in this example, two raw data files).
  12. Two directories where the raw data files of each MudPIT group are saved