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BS3: how to insert in two peptides, which are probably cross-linked, two different site of BS3 modification?

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BS3: how to insert in two peptides, which are probably cross-linked, two different site of BS3 modification? francesca grassiscalvini  2022-11-30
 

Hi,

I would like to verify an option of cross linking between two peptides:

ATAQDNPKSATEQSGTGI (with BS3 linked on K) and SYCR (with BS3 linked on S which is the amino-term)

Is it possible in the panel modify, clicking on the sequence of one of the two peptide, insert two different site of modification for the two peptides?

or is it possible to insert my modification with K as a position and also C term, in the same modification? I know that is possible but then the program search for K only in the position C term and in the peptide ATAQDNPKSATEQSGTGI it's not on the c term

many thanks
 
 
Nick Shulman responded:  2022-11-30
Are you asking whether you can define a crosslinker where the type of amino acid that the two ends attach to are different?
If the crosslinker needs to be able to attach to more than one type of amino acid then you set to blank the "Amino Acid" dropdown in the Edit Structural Modification dialog.

If your question was something different, then I am not sure I understand your question. It would be helpful if you could 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 extracted chromatograms and spectral libraries.
If that .zip file is less than 50MB you can attach it to this support request. You can upload larger files here:
https://skyline.ms/files.url

-- Nick