Hi Abla,

I would be happy to look at this for you. Can you please do this:

Open Skyline
Save an empty document using any name you like
Use the File | Share menu item to create a shareable .sky.zip file
Upload that .zip and the peptide list you are trying to paste to https://skyline.ms/filecontent/home/support/file%20sharing/begin.view?

With those two items we can probably figure this out quickly.

Thanks for using the Skyline support board!

Brian Pratt

Hi Abla,
This is definitely a settings issue. So, you want to look to your settings.

Are you really saying that you create a Skyline document in 3.7 release and you can paste peptides and FASTA into it with expected results. You then undo that paste and save the document. When you open the saved document in Skyline-daily and paste the same FASTA or peptide list you don't get any transitions?

This would really surprise me. More likely there is some difference you are missing between your settings in 3.7 and Skyline-daily. But, if the steps above truly produce different results with exactly the same Skyline document between 3.7 and Skyline-daily, then we may have changed something I have not yet realized. Certainly, it is something very specific to you, because of the number of automated tests that still pass on Skyline-daily, and I am myself working with Skyline-daily and importing FASTA a lot with no such problem.

Let us know. If you post your file, as Brian suggests, I am sure we can figure it out also.

--Brendan

Hi Brendan and Brian,
Brendan is right and sorry about the confusion. Apparently, somehow I unchecked autoselect matching transitions inadvertently (which is something I normally never do). I forgot to double check that one particular setting.
It is working now.
Sorry again about that and thank you for your responses.
Abla