Once a TIMS TOF MS/MS data set has been collected in the data dependent acquisition, or DDA, passive mode, run the data-independent acquisition, or DIA, on the ion mobility software application. To do so, first load the previously saved DDA method. Change the mass spectrometry to DIA passive fragmentation.
Leave all other settings the same. Under the MS/MS tab, select edit windows, then use the open analysis button located at the top of the DIA pop-up window and load the previously saved DDA data set. When a heat map appears at the bottom left, displaying a polygon of windows running diagonally across the graph, click and drag to resize the polygon so that it fits the data in the heat map.
Set the number of mobility windows in the per mass width and the overlap. Click calculate windows on the bottom right of the pop-up to see the windows displayed with the new settings. Once suitable, click on apply.