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add modification by specify the position #77

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ShadoWyyyy opened this issue Mar 8, 2023 · 1 comment
Closed

add modification by specify the position #77

ShadoWyyyy opened this issue Mar 8, 2023 · 1 comment

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@ShadoWyyyy
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hello, I know the modifications are represent as follow:
modification:(fixed|variable|known)::SYMBOL:(how is the modification represented);MODIFIED:[amino acid];MASS:[mass of the modified amino acid]
for example Carbamidomethylation on cysteine are
modification:fixed::SYMBOLEXT:cm;MODIFIED:C;DELTAMASS:57.021464

if I have a modification on protein N term or peptide N term, regardless of what amino acids it is, what should i fill in the MODIFIED[amino acid], I can't just fill in all amino acids, because the main point is to show it's a modification on N term, appreciate any help.

@lutzfischer
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I know it's a closed issue but just in case somebody else stumbles over this -
peptide nterminal modification:

modification:fixed::SYMBOLEXT:cm;MODIFIED:X;DELTAMASS:57.021464;PEPTIDEPOSITION:nterm

Protein nterminal modification:

modification:fixed::SYMBOLEXT:cm;MODIFIED:X;DELTAMASS:57.021464;PROTEINPOSITION:nterm

if the X is replaced with a list of residues, only these will be modified if nterminal.

newer versions of xisearch also permit

modification:fixed::SYMBOLEXT:cm;MODIFIED:C,nterm;DELTAMASS:57.021464

meaning C anywhere and anything on a protein nterminal (peptide would be pepnterm)

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