update versions and added terms #3
Conversation
| synonym: "C2-Urea-NHS-crosslinker" EXACT [] | ||
| synonym: "Urea-crosslinker C2-succinimide" EXACT [] | ||
| synonym: "DSAU" EXACT [] | ||
| property_value: deadEndFormula: "C 13 H 14 N 4 O 9" xsd:string |
There was a problem hiding this comment.
dead end formula makes no sense here. That is only for the hydrolised or otherwise quenched.
There was a problem hiding this comment.
| property_value: deadEndFormula: "C 13 H 14 N 4 O 9" xsd:string | |
| property_value: bridgeFormula: "C5 H4 N2 O3" xsd:string | |
| property_value: reactionSites: "2" xsd:nonNegativeInteger | |
| property_value: spacerLength: "7.7" xsd:float |
| property_value: monoIsotopicMass: "140.02219198" xsd:double | ||
| is_a: XLMOD:00005 ! homofunctional cross-linker | ||
| relationship: has_reactive_group XLMOD:00101 ! NHS ester | ||
| relationship: is_cleavable XLMOD:00067 ! CID cleavable C-S bond |
There was a problem hiding this comment.
XLMOD:00067 is also the wrong term here - need to check for the right one
There was a problem hiding this comment.
Most simple would be XLMOD:00018 ! cleavable by MS2 labile bond
There was a problem hiding this comment.
the only terms that look like they would be accurate are XLMOD:00018 ! cleavable by MS2 labile bond as the most general term or XLMOD:00035 ! CID cleavable (assuming it cleaves in in CID as well).
I don't think we have a term for CO-NH bond cleavable /peptide like cleavage (I assume that is where it cleaves) - we could add a term for that as well (copied from the C-S bond term)
[Term]
id: XLMOD:000174
name: CID cleavable CO-NH bond
def: "Indicates that a cross-linker contains a CID (Collision Induced Dissociation) cleavable peptide bond." [PSI:XL]
is_a: XLMOD:00035 ! CID cleavable
relationship: is_cleavable XLMOD:00018 ! cleavable by MS2 labile bond
But somebody with a better authority on chemical/MS nomenclature would need to decide what name/description to use
No description provided.