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Rappsilber-Laboratory / XiSearch

XiSearch
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Define CDI cleavable crosslinker in xiSEARCH #58

Open GianArauz opened 3 years ago

GianArauz commented 3 years ago

The cleavable crosslinker 1,1'-carbonyldiimidazole (CDI) is not currently defined in xiSEARCH v1.7.6.3. This linker is somewhat analogous to the disuccinimidyl dibutyric urea (DSBU) linker, but with many subtleties. (check the corresponding paper for details).

I tried to define CDI starting from the DSBU definition already present in xiSEARCH: crosslinker:SymetricSingleAminoAcidRestrictedCrossLinker:Name:DSBU;MASS:196.08479231;LINKEDAMINOACIDS:K(0),S(0.2),T(0.2),Y(0.2),nterm(0);MODIFICATIONS:NH2,17.026549105,OH,18.0105647,loop,0;STUBS:Bu,85.052763875,BuUr,111.032028435

My try was: crosslinker:AsymetricSingleAminoAcidRestrictedCrossLinker:Name:CDI-KK;MASS:25.97926456;FIRSTLINKEDAMINOACIDS:K,nterm;SECONDLINKEDAMINOACIDS:K,S,T,Y,nterm;STUBS:Left,0,Right,25.97926456

I'm not sure if the above linker definition is correct or not.

  1. Is correct my CDI definition?
  2. Is there a neater way to define CDI in xiSEARCH?

Many thanks in advance.

lutzfischer commented 3 years ago

At least to me the definition looks right (I calculate the same mass - but I am not much of a chemist). And at least at the moment there is no neater way to define the crosslinker (if you have an idea let me know).