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.
- Is correct my CDI definition?
- Is there a neater way to define CDI in xiSEARCH?
Many thanks in advance.
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,111.032028435My try was:
crosslinker:AsymetricSingleAminoAcidRestrictedCrossLinker:Name:CDI-KK;MASS:25.97926456;FIRSTLINKEDAMINOACIDS:K,nterm;SECONDLINKEDAMINOACIDS:K,S,T,Y,nterm;STUBS:Left,0,Right,25.97926456I'm not sure if the above linker definition is correct or not.
Many thanks in advance.