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importing multiple complex crosslinked peptides

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importing multiple complex crosslinked peptides sri ramarathinam  2024-10-02 21:49
 
Hi
Thanks again for making such a fantastic tool as Skyline!
I might be missing something, but I was unable to import crosslinked peptides. I was trying to replicate what was done in following ASMS presentation https://skyline.ms/wiki/home/software/Skyline/page.view?name=Crosslinking#:~:text=Support%20for%20crosslinked%20peptides%20was%20first%20added%20to%20Skyline%20version

In this poster there is a dialogue box that says add crosslinked peptides (screenshot attached)- I am not sure how to get to this screen and specifically how to add multiple peptides using the String based representation. If I try via Edit>insert Peptides it recognises "-" as invalid character so I am assuming this is someplace else.

If I have over 100 crosslinked peptide combinations (2 or 3 possible links) and can generate a text output, would be nice if I could import them into Skyline all at once in format that was demonstrated in the poster:
PKEPTIKDEA-PEKPTIDKEB-PEPKTIDEKC[+57.021464]-[+138.06808@2,3,*][+138.06808@7,*,4]

Many thanks again
Sri
 
 
Nick Shulman responded:  2024-10-02 22:10
That crosslinked sequence works for me when I use it in "Edit > Insert > Peptides".
If you have not yet defined the crosslinker then you would get the error "Unable to interpret peptide modifications"

I am thinking that the sequence that you are having trouble with is slightly different.

The "-" between the end of the last peptide sequence and the first crosslinker is very important.
That is, the following sequence works:
PKEPTIKDEA-PEKPTIDKEB-PEPKTIDEKC[+57.021464]-[+138.06808@2,3,*][+138.06808@7,*,4]
but the following, which is missing one hyphen would not work at all:
PKEPTIKDEA-PEKPTIDKEB-PEPKTIDEKC[+57.021464][+138.06808@2,3,*][+138.06808@7,*,4]

If you are still having troubles you should send us your Skyline document and the list of crosslinked peptides that you are trying to insert.

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 and spectral library.

Files which are less than 50MB can be attached to these support requests.
You can always upload larger files here:
https://skyline.ms/files.url
-- Nick
 
Nick Shulman responded:  2024-10-02 22:20
I might have misunderstood your question.
The "Insert Crosslinked Peptides" form that appears on the poster does not exist in the current version of Skyline.
If you want to insert many crosslinked peptides, you would do that with the Edit > Insert > Peptides window.

If you already have crosslinked peptides in your Skyline document, you can see what the string representation of them is by looking at the "Peptide Modified Sequence" column of the "Peptide" report in the Document Grid.
You can learn more about the Document Grid in the Custom Reports tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports

-- Nick
 
sri ramarathinam responded:  2024-10-03 01:20
Hi Nick
Thanks for your quick response. I think you have solved my issue - it was the second hyphen causing issues and as I was looking for the window shown in poster I was wondering if I was importing them from the wrong screen.
But this makes sense and a whole lot easier to just copy and paste these crosslinked peptides rather than manually linking them together after importing.
Kind regards
Sri