You can modify the way chromatograms are displayed.
Select [View] in the menu bar and then select [Chromatogram Filter] from the drop down menu.
Select one of the three options.
Chromatograms containing spectra from all MS stages will be displayed.
Chromatograms containing only spectra from MS stage 1 will be displayed.
Chromatograms containing spectra from all MS stages except MS stage 1 will be displayed.