Hi Steffen,
Wouldn't it do to add a
MAY supply term MS:1000792 (isolation window attribute) (without
restrictions on number of occurencies)
in addition to the existing rules?
Then isolation target m/z is still required, and the other terms can be
added in when needed.
Fredrik
Steffen Neumann skrev:
> Hi,
>
> we currently have for <Precursor> the cvParam Mapping Rules:
>
> Path /TraML/TransitionList/Transition/Precursor
> MUST supply term MS:1000827 (isolation window target m/z) only once
> MAY supply term MS:1000041 (charge state) only once
> Path /TraML/TargetList/TargetIncludeList/Target/Precursor
> MUST supply term MS:1000827 (isolation window target m/z) only once
> MAY supply term MS:1000041 (charge state) only once
> Path /TraML/TargetList/TargetExcludeList/Target/Precursor
> MUST supply term MS:1000827 (isolation window target m/z) only once
> MAY supply term MS:1000041 (charge state) only once
>
> 1) We could just require one or more "isolation window attribute"s
> http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MS&termId=MS%3A1000792
> which would also allow to put the lower/upper offset here.
> Those offsets can be important if a too narrow window
> looses too much transmission, leading to poor ion intensities.
>
> We'd lose the validation that someone might supply
> only those lower/upper offsets, and forget the actual "target m/z".
>
> How'd we handle the "part_of MS:1000441 ! scan" in that case ?
> Would that be a problem ?
>
>
> [Term]
> id: MS:1000792
> name: isolation window attribute
> def: "Isolation window parameter." [PSI:MS]
> is_a: MS:1000547 ! object attribute
> relationship: part_of MS:1000441 ! scan
>
> [Term]
> id: MS:1000455
> name: ion selection attribute
> def: "Ion selection properties that are associated with a value." [PSI:MS]
> is_a: MS:1000547 ! object attribute
> relationship: part_of MS:1000442 ! spectrum
>
>
>
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