I do not understand your question but if you send us your Skyline documents we might 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 extracted chromatograms.

If those .zip files are less than 50MB you can attach them to this support request.
You can upload larger files here:
https://skyline.ms/files.url
-- Nick

Thank you Nick!I have uploaded the file (desmin peptides_SS). the peptides from the first 50 AA of my interest protein that were shown previously on my peptide selection are no longer coming up in my peptide selection and I can't figure out why :)
this is an example of one of thoe peptides that is not coming up ! "TFGGAPGFPLGSPLSSPVFPR"

See attached image. What do you have in this setting?
-Mike

same as the yours, 25

Sogol,

The "Exclude N-terminal AAs" setting that you have at "Settings > Peptide Settings > Filter" is causing all of the peptides which are within 25 amino acids of the start of the protein sequence to be excluded from your document.
You should change that setting to a lower number such as "0".
-- Nick

Thank you Nick , It worked :)