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Transitions for cyclic dipeptides

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Transitions for cyclic dipeptides ge78faz  2025-11-11 06:05
 

Hi everybody,

I am using Skyline for identification of tri and oligo peptides. That is working perfectly.
I was wondering if there is a way to predict the transitions of cyclic dipeptides (diketopiperazines) for LC-MS as well. I used the modification option to subtract one water molecule from the dipeptide but unfortunately that didn't work properly.

I am looking forward to your responses.

Best regards,
Mike

I am using Skyline (64-bit) version 25.1.0.237 on Windows 11
 
 
Nick Shulman responded:  2025-11-11 14:32
Are you familiar with crosslinking support in Skyline?
https://skyline.ms/home/software/Skyline/wiki-page.view?name=Crosslinking

In theory, a cyclic peptide would be two peptides joined together by two crosslinkers whose chemical formula is "-H2O".
Does this help?
-- Nick
 
ge78faz responded:  2025-11-12 00:53
Hi Nick,

thank you, this helps a lot.
Is it possible to create a spectral library from crosslinked peptide search results for cyclic dipeptides? Kojak does not seem to be able to output search results for dipeptides. Or is there another way to get a transition list for these molecules?

Best regards,
Mike