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Inter-Peptide Disulfide Bridge Settings

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Inter-Peptide Disulfide Bridge Settings david schmidt  2023-03-29 06:38
 

Hi,

I wanted to analyze inter-peptide disulfide bond formation, which could be treated as a CID cleavable cross-link. Could you please tell me the settings for long- and short-arm mass as well as modification A and -B for the disulfide-linked form?

Thank you and best wishes,
David
 
 
engj responded:  2023-03-29 15:33

David,

As far as I'm aware (and take this with a grain of salt coming from a software engineer), peptides connected via disulfide bond should be treated as non-cleavable crosslinks. Here's an example:

  • example disulfide linked peptides ILCSK and ARLECEINTYR
  • precursor charge of 4
  • ILCSK has a neutral mass of 562.3149. Subtract two protons (-2.0146) for the disulfide bond to get 560.3003. This is effectively the mass modification applied to the cysteine on peptide ARLECEINTYR.
  • ARLECEINTYR has a neutral mass of 1366.6663 - 2.0146 = 1364.6508. This is effectively the mass modification applied to the cysteine on peptide ILCSK.
  • There are many peptide mass calculators online but I used my peptide fragmentation calculator here to paste in each sequence to calculate their neutral mass (and then subtract the mass of two protons).
  • The @3 denotes the third residue (the cysteine) is the crosslinked residue of the first peptide and the @5 denotes the fifth residue (also the cysteine) is the crosslinked residue of the second peptide.
  • There are no long arm/short arm masses for the non-cleavable crosslink hence the "0.0" in the first line.

Thus the input would be:

0.0 0.0
ILCSK ARLECEINTYR 1364.6508@3 560.3003@5 4