Running the data analysis 100% automated is powerful for a quick screening of data, e.g. for evaluating data during or right after acquisition by the instrument, or as the first step in the following analysis.

The auto-analysis runs all steps in the data analysis using the current settings of the session. Some steps are optionally included which is defined in 'Settings->Autorun settings'. Since the processed data depends on threshold settings and methods used, the settings must be optimized manually to your setup before the auto-analysis is put properly into operation.