To inject samples and to acquire and process data files with the Xcalibur data system, you must create one or more instrument methods, one or more processing methods, and a sequence that defines the sample injection set.

For information about creating an instrument method for your LC/MS system, refer to the Help for the LC devices and the Help for the mass spectrometer. For information about creating processing methods and sequences, refer to the Xcalibur Help.

TIP

For a typical LC/MS experiment, an autosampler automates the sample injection process, and the position nomenclature depends on the autosampler tray type.

For information about specifying the autosampler tray type and the position nomenclature for the specified tray type, refer to the Help for the autosampler.

For some autosamplers, you can change the tray type from the Sequence Setup view by selecting Change > Tray Name and then selecting a different tray type.

To start the utility from the Xcalibur data system version 2.10 or later, you must add a processing method that calls the application to the sequence.

Procedure

  1. From the Home Page window of the Xcalibur data system, select Sequence View in the toolbar.
  2. The Sequence Setup view opens with an empty sequence table. Refer to the Xcalibur – Sequence Setup view Help for information about filling out the sequence table.
  3. In the Proc Meth column, select a processing method with a parameter file that calls the utility as follows:
  4. Enter the file location and name of the processing method.
  5. –or–
  6. Double-click the column to open the Select Processing Method dialog box, where you can locate and select the processing method.
  7. You can now start the sequence without first saving it, or you can save the sequence for later use.
  8. In the sequence table, select the row or rows that you want to run.
  9. Select Actions > Run Sequence or select Run Sequence .
  10. If you have changed the instrument configuration in Foundation platform after the previous sequence run, the Change Instruments In Use dialog box opens. Otherwise, the Run Sequence dialog box opens.
  11. For an LC/MS system, the autosampler (or device with an autosampler) is specified as the start instrument. When the autosampler makes an injection, it triggers the mass spectrometer to begin data acquisition.
  12. Run Sequence dialog box
    Run Sequence dialog box
  13. Select the Programs checkbox if it is not already selected.
  14. You must select this checkbox to start the utility.
  15. Select OK.
  16. If you did not save the sequence, the File Summary Information dialog box opens.
  17. Save the sequence as follows:
  18. In the File Summary Information box, select OK.
  19. In the File Name box, enter a unique name for the sequence.
  20. In the Save In list, select the appropriate folder location for the sequence.
  21. Select Save.
  22. The Xcalibur data system adds the sequence to the acquisition queue.

For each sequence row, after the data system acquires a raw data file, it sends the processing method and the raw data file to the Proteome Discoverer application, which stores the raw data file and the result file in the server output directory specified in the Server Output Directory box of the Export Parameter File page of the Start Jobs page. All the search results of the batch processing are stored in the same directory. If the same directory name is used for the results of another batch process, the application appends the date and an incremental index number to the folder name.