I do not know the answer to your question but if you send us your Skyline document and one or more of your .raw files 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.
The "Share Document" dialog also gives you the option to include the .raw files or you could send those to us separately.

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

Here is the file. This is an example of a protein with two peptides and I have several of these proteins with such a situtation where one ppetide responds good and the other not. And they were selected from Unscheduled runs so we could identify them .

Here is the file. This is an example of a protein with two peptides and I have several of these proteins with such a situtation where one ppetide responds good and the other not. And they were selected from Unscheduled runs so we could identify them .

Thank you for uploading that Skyline document.
It looks like there really are no MS2 spectra which match that precursor.
Can you upload one of your .raw files?
-- Nick

Here is the raw file.