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

-- Nick

Thank you, Nick,
I have shared the files through skyline line and also added to the skyline.ms/files.
Peptide 9 scouting. For this one, for CE optimization there are 242 transitions.
Thanks,

Thank you for sending that Skyline document.
I believe the behavior that you are seeing is the same as it was in Skyline 23.1.

The "Max transitions per sample injection" value is the maximum number of rows in each exported transition list file.
If you are doing collision energy optimization with 5 optimization steps, then each transition is going to require 11 rows in the transition list (since the optimization step values go from -5 to +5).
Skyline insists that all transitions for a given precursor must be able to fit in the same method.
One of the precursors in your document has 31 transitions.
If you set "Max transitions per sample injection" to a high enough number (i.e. 341 which is 31 times 11) then you will be able to export a CE optimization method with 5 optimization steps.

If there is any precursor that has more transitions that will fit in a single method then Skyline will not tell you the number of methods, and will refuse to export a transition list until you set "Max transitions per sample injection" to a higher number.
-- Nick

Thank you very much, Nick!
I will review and execute in agreement with your explanation.