This sounds like it could be a bug in Skyline.
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 and spectral libraries.

If that .zip file is less than 50MB you can attach it to this support request. Larger files can always be uploaded here:
https://skyline.ms/files.url
-- Nick

Hi Nick,

I just uploaded the file named "20240801batch_tjiang" using the link. I also have another question: the product ions under the library peptide lists in the left panel are a lot more than defined in the transition setting, as show in the attached. Could you please also look into this while you check out the file?

Thank you!
Ting

Thank you for sending that Skyline document.
It looks like the m/z value is only incorrect in that tooltip in your screenshot. There is a wrench button in the Spectral Library Explorer which you can use to show the property sheet for the spectrum, and that says the correct value m/z value.

I will certainly try to fix that tooltip, but I do not think the tooltip would cause you any real problems. Let me know if something else seems to be going wrong because that probably has a completely different cause.

For crosslinked peptides, the "Product ion selection" rules that you may specify on the "Filter" tab at "Settings > Transition Settings" do not actually have any impact. Part of the reason is that I was not sure exactly how to make them work for crosslinked peptides.

In your document, the peptides which do not match anything in the spectral library are the ones that have a huge number of transitions in the Skyline document. These are seem to be peptides where the thing in the Skyline document is missing the Carbamidomethyl modification on one or more Cysteines. All of the spectra in your spectral library have modified Cysteines.
For the peptides that could be found in the spectral library, Skyline has given you 6 transitions based on the settings on the "Library" tab at "Settings > Transition Settings".

Is it your intention to have crosslinked peptides in your Skyline document with different modifications than what can be found in the library? If so, how would you like Skyline to decide which transitions to give you? Part of the reason that the rules on the "Filter" tab of the transition settings have not been implemented is that no one has asked for it, and I was not sure how exactly people would want it to work, but if you knew what you wanted, I might be able to implement it.

I hope this helps.
-- Nick

Thank you, Nick, for your time and information!

That helps and I don't intend to look at different modifications other than those in the library.

Cheers,
Ting