The error is telling you to use the menu item:
Settings > Transition Settings
and then click on the "Full Scan" tab.

On the Full Scan tab, if you choose something in the "Isotope Peaks Included" dropdown then Skyline will extract chromatograms from MS1 spectra.
To tell Skyline to extract chromatograms from MS2 spectra you would usually choose "DIA" in the "Acquisition Method" dropdown in the "MS/MS filtering" section on that dropdown. After you choose "DIA" you would probably choose "Results Only" in the "Isolation Scheme" dropdown.

After you make those settings changes you will probably be able to use the menu item:
File > Import > Results
to tell Skyline to extract chromatograms from your .wiff or .wiff2 files.

If you go to the Skyline tutorials page there are several tutorials in the "Introduction to full-scan acquisition data" section which will help you get started:
https://skyline.ms/home/software/Skyline/wiki-page.view?name=tutorials

If you get stuck you can send us your files and we can figure out what you need to do.

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 you want to send us your .wiff or .wiff2 files, you should also send us the .wiff.scan file which goes with it because we cannot read .wiff or .wiff2 files without the accompanying .wiff.scan.

Files which are less than 50MB can be attached to these support requests. You can always upload larger files here:
https://skyline.ms/files.url
-- Nick

I've uploaded the files under a folder Jiny- ZenoTOF8600 I am able to import the files which were run as MRM but the results I am able to view are only spectral, I'm unsure what I've done incorrectly.

The issue I am having is that the run was not a full-scan run, this was a standard MRM method, just run on the ZenoTOF for background reduction, but because of the instrument type I think reading the data is being impacted and I cannot find how to fix the issue, changing to the settings recommended above gives me unusable data.

Sorry for the slow response.

I believe there might be some issues with Skyline reading data files from newer SCIEX instruments because Skyline is using old versions of the SCIEX data files readers. We hope to fix this in a few weeks.

I will take a look at your files and figure out whether upgrading our data readers is what will fix the problem or whether there might be something else going wrong.
-- Nick

Hi Jiny,

I don't think this kind of data is accessible as MRM chromatograms which is how Skyline usually processes MRM data. Instead, it looks like full scan data but with narrow scan windows (20m/z). Skyline would build its own chromatograms while enumerating the spectra. But I also have tried to import your data after switching to full scan settings, and that doesn't look good either. Looking at the data on a spectrum-by-spectrum basis, the transitions don't seem to line up with what's in the spectra. Mostly for the product m/zs: the precursor m/zs match. What are some transitions that you get good chromatograms for in the Sciex software so I can focus on those?

Hi Jiny,

Can you try the custom Skyline-daily build at https://mc-tca-01.s3.us-west-2.amazonaws.com/ProteoWizard/bt209/3875132/SkylineTester.zip and let me know if that fixes the issues with reading your data (set up as TOF/PRM, not SRM). Import the WIFF2 file. The new build has a bug fixed where multi-sample WIFF2 files were not supported properly (now it will prompt you for what samples you want to import).