If you want to tell Skyline to look for a fragment which is not attached to any of the amino acids from the original peptide, then you should go to:
Settings > Transition Settings > Filter
and add the fragment to the "Special ions" list and make sure that it has some sort of checkbox next to it.
The solid checkbox indicates that the special ion transition will be added to precursors by default and the greyed out checkbox indicates that the special ion transition will only be included if you explicitly add it to the precursor using the "Add Children" right-click menu item in the Targets tree.

On the other hand, if you want Skyline to look for the other half of the molecule that the special ion fell off of, then that is a "Neutral Loss", which you can define in the "Edit Structural Modification" dialog box.
-- Nick

Hi!
Thanks for your answer. They are useful! Now I can check the specific ions. And there are some new problems.
When I tried to check the intensity of these ions, I found that I couldn't find a place to check. Because there are no green dots before the children ions(all the children ions).
I imported these data from fragpipe.

Thanks.

sunxinyi

I do not understand your new question. Could you post a picture of what you are seeing?

It might be helpful if you could 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.
If that .zip file is less than 50MB you can attach it to this support request. You can upload larger files here:
https://skyline.ms/files.url

-- Nick

Hi Nick,

I have similar needs, in that I want to check the ion current of TMT tag. However after following the above procedure, the special ion transition is not added to the precursor. I have my file in the attachment. Could you help check?

--Li

Li,

Thank you for attaching your Skyline document.
I think you need to go to:
Settings > Transition Settings > Instrument
and change "Min m/z" to a lower number.
It is currently set to "300" which is too high for TMT transitions such as "126" to be added to your document.
-- Nick