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Addition of a deamination modification on an N-ter cysteine

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Addition of a deamination modification on an N-ter cysteine laurie josset  2022-09-30 00:32
 
Hello to all,

I am working on the quantification of desmopressin, when I add the peptide sequence in skyline I end up with arginine vasopressin (that is normal). I tried to manually create the deamination modification to apply on the N-ter cysteine, only I don't end up with the right m/z for the precursors (I want 535.35 ++ and Skyline predicts me 545.7196 ++). For the chemical formula I indicated "O-HC", maybe this is not correct. Would it be possible to help me?

Thanks in advance,

Sincerely,

Laurie Josset

Translated with www.DeepL.com/Translator (free version)
 
 
Nick Shulman responded:  2022-09-30 13:39
If you want to see the chemical formula that Skyline has assigned to your peptide, the following columns in the Document Grid might be helpful:
Molecule Formula: Molecular formula of the peptide
Precursor Neutral Formula: Molecule formula plus any heavy isotope modifications
Precursor Ion Formula: Molecular formula plus hydrogens equal to the charge on the precursor ion.

It sounds like you know what chemical formula your molecule is supposed to have, so you will probably be able to look at these columns in the Document Grid and figure out what Modification you need to apply to the peptide to get the correct result formula.

If you would like to learn more about the Document Grid you can look at the Custom Reports tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports
-- Nick