I can't think of any reason this might be happening but if you send us your Skyline document and one or more of your raw files we will probably be able to figure it out.

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

Files which are less than 50MB can be attached to this support request, but that .zip file and your raw file will probably be too large so you can zip them up together and upload them here:
https://skyline.ms/files.url
-- Nick

Hi Nick,
Thanks for the quick response. I used an old computer from my work (after using the one I'm currently having issues with) and imported the same files on the old version of Skyline and everything worked just fine. Then, on that same computer, I downloaded version 23.1 and tried to import the same exact files and they no longer worked. I have hundreds of raw files on these computers and not a single one is working. So I don't believe its the files.
I uninstalled and reinstalled Skyline twice.
I restarted my computer both times.
I tried several different files.
I tried the old settings I use every day, as well as new settings.
Do you have any trouble shooting suggestions? I have asked my coworkers to do the same thing and the same thing happened to them- the chromatograms disappeared after updating Skyline.

No other users have reported an issue like this, so it is very likely that this is something unique to your data or the way that you are using Skyline.

Are you working with small molecules or with peptides? Are the chromatograms that are missing MS1 or MS2 or both?
Have you specified the "Explicit Retention Time" for any of the items in your document?

Typically, when behavior like this happens to a particular person ends up being caused by an obscure difference that would never seem like it should matter such as spaces in the middle of a chemical formula.

If you send me your Skyline document and one of your raw files I will probably be able to tell you what is going on in a few minutes.
Is there a reason that you cannot send me any of your files?
I will send you an email directly in case the problem is that you do not want to upload your files to the page that I mentioned before.
-- Nick

Hi I am having the same issue when I import my DDA search results. I have also installed and uninstalled skyline to see if the issue was from my computer. This is happening for all my files as well.

If you can provide the necessary files to demonstrate the problem, I'd be happy to have a look.

Thanks for using the Skyline support board,

Brian Pratt