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.

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

I am not sure why those values are #N/A, but after we see your Skyline document we will probably be able to figure out what is going on.
-- Nick

File attached. I enabled FAIMS filter for the last peptide, as circled in the screen shot.

Thanks,
Qing

Thank you for sending that Skyline document.

I see that you are using the relatively new "Spectrum Filter" to tell Skyline to only extract the chromatogram from spectra with a particular compensation voltage value.
The Spectrum Filter feature is relatively new, and is not the recommended way to do this sort of filtering.
A different way to achieve the same result would be to set the "Explicit Compensation Voltage" value on these precursors.
The "Explicit Compensation Voltage" is a column that you can display in the Document Grid if you create a custom report.
You can learn about custom reports in the Custom Reports tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports

Currently, precursors that have a Spectrum Filter do not participate in the calculation of the "Ratio to Standard" value. This is probably a bug, but I will need to investigate further in order to be sure.

There is a different column "Total Area Ratio" which will display the ratio that you are looking for. If you add the "Total Area Ratio" column to your report then you will get one row for each light and each heavy precursor. You would probably want to filter out the rows where the "Isotope Label Type" column is "heavy" since those rows will have "#N/A" in the "Total Area Ratio" column.
-- Nick