Can you send us your Skyline document?

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

If that .zip file is less than 50MB you can attach it to this support request.

Otherwise, you can upload it here:
https://skyline.ms/files.url

-- Nick

Skyline document

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.
-- Nick

raw file

We have not actually received a .raw file from you.

The file was probably too large to attach to this support request.

You can upload larger files here:
https://skyline.ms/files.url

I'll also send you an email in case that makes sending the file easier.
-- Nick

Thank you for sending us that .raw file.

The DIA isolation scheme that you have specified at:
Settings > Transition Settings > Full Scan
is configured to use the "Overlap Deconvolution".

It appears that I completely broke the deconvolution that Skyline-Daily does in the Sept 5 update.
I will fix this in the next update of Skyline-Daily. Thank you for reporting this bug.

We actually do not recommend that you use the Deconvolution settings in Skyline at all. The deconvolution algorithm in Skyline is something from six years ago. The amount of time that this algorithm takes to run is proportional to the number of transitions that you have in your Skyline document.

The thing that we do recommend that you use is the deconvolution in MSConvert. This deconvolution algorithm looks at the entire spectra and deconvolutes the spectra in a way that is independent of the transitions that you are going to be extracting chromatograms for. We recommend that you use MSConvert to create deconvoluted .mzML files.

-- Nick