Thank you for sending that file.
It appears that your .skyd file only contains MS1 chromatograms. You cannot see these MS1 chromatograms because your Targets tree does not contain any precursor transitions.
You can make the precursor transitions show up by going to:
Settings > Transition Settings > Filter
and change "Ion Types" to something that included "p", for instance "y, p".
The question is, why are there no MS2 chromatograms in your .skyd file?
I can think of several reasons. One might be that at the time that you extracted chromatograms from your .raw files, you did not have any MS2 transitions in your Targets tree, or your settings at Settings > Transitions Settings > Full Scan were different than they are now.
If you change the set of Targets, or the Transition Settings, you usually need to tell Skyline to extract the chromatograms again. You can do this by going to:
Edit > Manage Results > Reimport
I imagine that this in not the reason that you do not have MS2 chromatograms.
It might be that Skyline did not think that any of the MS2 scans in your .raw file matched either your DIA isolation scheme, or matched any of the transitions in your document.
If you send me one of your .raw files (e.g. "CB20191015_P100_Plate92_iPSC_LINCS_CommonProject_P-0092_A01_acq_01.raw") I can figure out whether something like that happened.