Can you send us your Skyline document and maybe your raw file too?

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 gives you the option of including 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

I am not sure what might be going wrong for you but after we see your Skyline document we will probably be able to figure it out.
-- Nick

Hi Nick,

Thank you for your response.
I uploaded my skyline.zip through https://skyline.ms/files.url.
Its name is "ForSupport_TY_20250120_MS1XIC_FullMS.sky.zip".
Please see the file and give your advice.

Best,
TY

Thank you for sending that Skyline document.
You should tell Skyline that you are interesting in extracting chromatograms for the precursor from MS1 spectra.

The way to do that is:
1. Go to the "Filter" tab at "Settings > Transition Settings" and set "Ion Types" to "p".
2. Go to the "Full Scan" tab at "Settings > Transition Settings" and set "Isotope peaks included" to something. In the attached screenshot I set it to "Count" but "Percent" will also work. You should also set the MS/MS Filtering Acquisition Method to "None" because you are not interested in extracting chromatograms from MS2 spectra.

After you have done that you will need to tell Skyline to extract chromatograms again. You can do that with the "Reimport" button at "Edit > Manage Results" or you can use the "File > Import > Results" menu item.

-- Nick

Hi Nick,

Thanks for your advise, I finally do what I want to!
Thank you very much.

Best,
Tomoki