two peptide bridges on the same amino acid

two peptide bridges on the same amino acid vonroep  2024-04-17 01:41

Dear support team,

I used Skyline to design peptide transitions for our QTRAP6500+ System (Sciex). I could use the software to develop peptide transitions containing a NOS bridge . However I am not able to design a crosslinking modification involving two crosslinking events to the same amino acid (SONOS bridge). I always get an error message (see attached file). Is there a way around the problem?

Thanks for the support.
Kind regards
Edda von Roepenack-Lahaye

Nick Shulman responded:  2024-04-17 07:14
Even though you are not able to achieve that crosslinked structure using the "Edit Modifications" dialog, you can get it into your document by using the "Edit > Insert > Peptides" dialog.

In the Insert Peptides dialog, type the following into the "Peptide Sequence" column:

There is a little more information about that "[crosslinker@residue1,residue2]" syntax on page 9 of "CrosslinkingInSkyline.pdf":

The Edit Modifications dialog has the limitation that it never allows you to apply more than one modification to the same residue.

I am not sure how much testing we have done of crosslinked peptides with that sort of structure so let me know if anything seems to be misbehaving.
-- Nick