Once you have ZNova-ized your Xcalibur sequence and have acquired your data, then you are ready to process your data automatically using ProMass.
Batch Reprocessing:
You batch reprocess a sequence if you have already acquired the data and want to process it post-acquisition. Use the mouse to select the rows in the sequence that you want to process. Click on the Batch Reprocess 
button in the Xcalibur Sequence Setup or access this function from the menu under Actions | Batch Reprocess... You should see the dialog
box shown below. Make sure that the same options checked below are checked in
your dialog. The rows that you selected should appear in the Process Rows box.
Make sure that only the following options are checked:
Qual - Peak detection and integration
Qual - Spectrum
Enhancement (Optional, select this option if your processing
method is configured for background
subtraction).
Programs
Replace Sample Info
Click on OK.
If processing proceeds correctly, then a console window will pop-up similar to the one shown below. This indicates that the Xcalibur processing method has found chromatographic peaks and ProMass has passed spectra to ZNova for deconvolution. Do not dismiss the console window, or processing will terminate for the sample being processed. Also note, if you inadvertently click in the console window, processing will pause until you hit the Enter key. The ProMass console can be configured to run in a minimized state if desired.
Processing data immediately after acquisition:
If you want to process your spectra automatically immediately after acquisition, then select the Qual and Programs options in the Processing Actions area of the Xcalibur Run Sequence dialog as shown below. Note that processing will not occur until all samples in the list are acquired.
Reprocessing previously processed samples:
If you need to change a ZNova parameter and reprocess a data file in the sample list, ProMass will automatically replace the results for the reprocessed sample in the summary report. This prevents you from having to reprocess the entire list when you only need to reprocess one or a few samples. In order for ProMass to update previously processed sample results, the summary report and other results files must be in their original location. Also note that ProMass does not use Xcalibur's file versioning information. Therefore, if you acquired more than one version of the same raw data file in the Xcalibur sample list, be sure that the sample list is updated with the correct data file name to ensure that your desired file gets processed.