Disulfide Bond as modification

Disulfide Bond as modification thcsam  2024-05-21 06:51

Dear Skyline,

I currently would like to analysis the disulfide bond pattern for one single protein.
I originally though if i added disulfide bond as crosslinker as indicate in (https://skyline.ms/wiki/home/software/Skyline/download.view?entityId=ac4c6cc4-97c6-1038-8aae-e465a393ee52&name=NicholasShulman2020ASMSPoster.pdf) then all possible linkage of disulfide bond within the same protein will be listed. It turned out I have to add the linked peptide one by one. Since it have only 2 Cys in the protein, the first segment contain 3 variable modification which generate a total of 8 possible peptide, where second segment contain no modification. Considering these two cysteine containing peptide, it will have 88 (1st segment disulfide link to 1st segment) plus 18 (1st segment disulfide link to 2nd segment) plus 1 (2nd segment disulfide link to 2nd segment), 73 possible disulfide peptide is generated.(assume no misscleavage). 73 is still reasonable for me to add it one by one.
I have few question.

  1. Did i miss some feature of skyline that do the above automatically instead of adding one by one?
  2. If I do not miss feature of skyline, would this feature be added? As if No. of cysteine and no. of modification of cysteine containing peptide
    increase, then the manual addition of crosslink peptide seem to be impossible.
    Really appreciate and looking forward for your response.

Best regards,

Nick Shulman responded:  2024-05-21 08:29
I do not think that Skyline will be able to permute the set of variable modifications on the crosslinked peptides and add them to the document the way that Skyline does with ordinary peptides.

The easiest way to insert a large number of crosslinked peptides is to use the "Edit > Insert > Peptides" menu item.
There is a description of how to specify a crosslinked peptide sequence using the "-[crosslinkername@position1,position2]" on pages 9 and 10 of the "CrosslinkingInSkyline.pdf" file here:

The column "Peptide Modified Sequence Full Names" in the Document Grid will show you what the modified sequence for the peptides in your document which might be helpful for you when you need to compose the crosslinked sequences for the peptides that are missing from your document.
-- Nick
thcsam responded:  2024-05-21 20:11
I think i can write a python code to permute all the set as list using the naming pattern you provided and then directly insert as a peptide.
That a valuable advise, thanks a lot.