[Psidev-ms-dev] Mappings for <Precursor>

[Steffen N. <sne...@ip...>]

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 ?

2) While I'm at it, we could allow "ion selection attribute"s
   instead of only "charge state", because that would also allow 
   the (somewhat obscure) term "possible charge state":
   http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MS&termId=MS%3A1000455

I'd opt in favor of 1) and against 2).

Yours,
Steffen

[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


-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409