[Psidev-ms-dev] Proposal of changes in the controlled vocabulary related to MIAPE validation (psi-ms C.V release candidate 3.17.0)

[David O. <do...@eb...>]

Dear community,

After Tuesday's PSI MSS WG teleconference and following the notes sent 
by Eric on 29th, we agreed some concrete points (if I'm wrong in any of 
them, please, correct me):

- Adding three new terms: "electrospray supply type", "static supply 
electrospray" and "fed supply electrospray", descending from source.
- Making obsolete the term "paul ion trap" (MS:1000297).
- Put axial and redial ejection linear ion traps under linear ion traps
A detailed description of the changes is at the end of this message.

Related tasks to this changes are:
- Pierre-Alain will find an MS guru at Bruker to clarify
- Need to update mapping files to accommodate "electrospray supply 
type", "static supply electrospray" and "fed supply electrospray"

If you think this is correct, or not incorrect, I'll update the 
controlled vocabulary in three working days: (Tuesday).

In a couple of hours I'll send another email collecting the remaining 
discussion points related to the controlled vocabulary.


ADDITIONS
================
Add three terms to accommodate de MIAPE concept of "Supply type".

[Term]
id: MS:1001914
name: electrospray supply type
def: "Whether the sprayer is fed or is loaded with sample once." [PSI:MS]
relationship: part_of MS:1000458 ! source

[Term]
id: MS:1001915
name: static supply electrospray
def: "The sprayer is loaded with sample once." [PSI:MS]
is_a: MS:1001914 ! electrospray supply type

[Term]
id: MS:1001916
name: fed supply electrospray
def: "The sprayer is continuously fed with sample." [PSI:MS]
is_a: MS:1001914 ! electrospray supply type



CHANGES
================
CHANGE 1-> Paul ion trap is now obsolete, because redundant to 
quadrupole ion trap

[Term]
id: MS:1000297
name: paul ion trap
def: "OBSOLETE A device that permits the trapping of ions by means of an 
alternating current voltage. The ejection of ions with a m/z less than a 
prescribed value and retention of those with higher mass depends on the 
application of radio frequency voltages between a ring electrode and two 
end-cap electrodes to confine the ions in a circular path. The choice of 
these voltages determines the m/z below which ions are ejected." [PSI:MS]
comment: This term was made obsolete because it is redundant to 
quadrupole ion trap
synonym: "quadrupole ion trap" RELATED []
is_a: MS:1000479 ! purgatory
is_obsolete: true

CHANGE 2-> Axial and redial ejection linear ion traps under linear ion traps

[Term]
id: MS:1000078
name: axial ejection linear ion trap
def: "A linear ion trap mass spectrometer where ions are ejected along 
the axis of the analyzer." [PSI:MS]
is_a: MS:1000291 ! linear ion trap

[Term]
id: MS:1000083
name: radial ejection linear ion trap
def: "A linear ion trap mass spectrometer where ions are ejected along 
the radius of the analyzer." [PSI:MS]
is_a: MS:1000291 ! linear ion trap


-- 
David Ovelleiro
Bioinformatician
PRIDE Group
Proteomics Services Team, PANDA Group
EMBL European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, UK
CB10 1SD