How to use CIRT to predict retention time?

How to use CIRT to predict retention time? caixue  2020-05-20

I am trying to use the peptides selected by myself as CiRT to predict the retention time. The irt value of each CiRT peptide has been calculated and saved as a new Retention time predictor. Please see the attachment. However, when I chose the predictor, the document could not import the cirt peptides I selected, so I could not import the result. What should I do?
Looking forward to a reply. Thanks!

Nick Shulman responded:  2020-05-20
You need to add those peptides to your Skyline document. Skyline does not know how to add them for you.

In order for Skyline to add those peptides to your document, Skyline would need to know which charge states and transitions are supposed to be measured. For the built-in iRT standards that Skyline knows about, Skyline knows which charge states and transitions.

If you have measured these peptides before, you probably have a Skyline document that already has those peptides in it. You could start by copying those peptides out of that document (you can select the peptides in the Targets tree, and do "Edit > Copy", and then paste them into a different Skyline document).

You can always add peptides to your document using the menu item:
Edit > Insert > Peptides
and Skyline will give you precursors and transitions based on your settings at Settings > Transition Settings

It might be helpful if you look at the iRT tutorial:

-- Nick
Brendan MacLean responded:  2020-05-20
Are all of the peptides in your iRT standards list from the CiRT set published in this paper?

If so, we should be able to do a better job of offering to add these to your document, as we do for the other standards built into Skyline. It looks like we missed doing this for the larger list and only did it for the subset listed under "CiRT (IRT-C18)".

Until we do that, however, as Nick suggests, you would need to work out the details yourself by figuring out which precursors and fragment ions to measure and ideally to get library spectra for them into Skyline.

We will see if we can get a workaround transition list posted here soon, which you could import through File > Import > Transition List.

Thanks for posting to the Skyline support board.

caixue responded:  2020-05-20
Thanks for your reply. These CiRT peptides were selected from our samples and have not been published. At present, I am trying the method you introduced and will reply to the details later.
16622080827 responded:  2021-02-15

Have you fixed this problem? I met the same problem but I have tried this but failed.
Looking foward to your reply!

Brendan MacLean responded:  2021-02-24
We have made a lot of improvements to iRT and CiRT support since this request. Can you please be more specific about what you are seeing?

In this case, we didn't end up feeling like we had anything to fix. The user was missing the iRT standard peptides in their Skyline document. You are required to add the standard peptides to your document as targets. Do your iRT standards appear in the Targets view?

Please add screenshots illustrating what you are seeing if you still require help.