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SSL format for cross-links

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SSL format for cross-links julian bender  2025-07-16 05:45
 

As described on GitHub in more detail, I was trying to use an SSL-file generated by the xiview server for spectral library generation in Skyline. However, there seems to be an issue with either the format generated by xiview (which I think is in accordance with a Skyline presentation describing the format) or the way BiblioSpec is interpreting the file.

I have attached a minimal ssl file and the corresponding mgf file for testing. Please let me know if you need any further details.
Thanks
Julian
 
 
Nick Shulman responded:  2025-07-16 07:01
I am not sure I understand your question.
The peptide sequence in the attached .ssl file is:
SLGK[+1.007825]VGTRE[+25.020401]C[+57.021460]C[+57.021460]TK[+1.007825]PESERM[+15.994910]PC[+57.021460]TEDYLSLILNR

That is an ordinary flat peptide sequence, not a crosslinked peptide sequence.
A crosslinked peptide sequence would have hyphens in between each of the individual peptide sequences, and then at the end there is another hyphen followed by the crosslinked description in square brackets.

Something like the following would be a crosslinked sequence:
SLGK[+1.007825]VGTRE[+25.020401]C[+57.021460]C[+57.021460]TK[+1.007825]-PESERM[+15.994910]PC[+57.021460]TEDYLSLILNR-[+138.1@6,4]

Did you attach the correct .ssl file?
Are you seeing some sort of error message?
-- Nick
 
julian bender responded:  2025-07-16 09:46

Hi Nick, sorry for the mistake, I did indeed attach the wrong file (correct one attached now).

My issue is that my ssl file follows the format you described for cross-links but the resulting annotated spectrum from the Spectral Library Viewer is incomplete (see picture). In contrast, using the old linearised syntax does results in annotations for both cross-linked peptides in the spectrum (also attached). The library builder does not throw an error with either ssl file.
 
Nick Shulman responded:  2025-07-16 12:37
My Library Explorer doesn't look anything like that (see attached picture)
Are you maybe using a very old version of Skyline?
Can you send me your Skyline document?

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including the spectral library with that crosslinked peptide sequence.

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
 
julian bender responded:  2025-07-21 01:18
Hi Nick,
Thanks again for looking into this.
The Skyline document you sent opens fine on my end as well and spectra look good (I'm using the skyline-daily version, by the way). This morning, I started fresh with a new Skyline document after rebooting my VM and built a new library directly from the SSL file with the cross-linker syntax (i.e. the non-linearised one). Everything worked smoothly, and the spectra look good too.

Although I am sure I did the same thing on Thursday, there seems to be no issue with Skyline in general, at least not a reproducible one. Feel free to consider this resolved. I appreciate your support!

Cheers
Julian