[Psidev-ms-dev] Pending points in Nov 29th PSI MSS WG teleconference: MIAPE-MS related c.v. terms

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

Dear community,

Following the issues explained in Nov 29th previous mail, in order to 
validate some concepts covered by MIAPE-MS, some new terms maybe should 
be added to the controlled vocabulary.
A phone conference started to take into the consideration these points. 
Some were not taken into consideration because we ran out of time. 
Here's a list of the remaining points and at the end of this email, a 
list of hypothetical controlled vocabulary terms that could improve the 
mapping between the controlled vocabulary and the concepts covered by 
the MIAPE-MS (always Version 2.24 cited in this mail, last publicly 
available).

Pending points:

Discussion point 1: Difference between a “source interface” and “inlet type”
===============================================
In MIAPE-MS, having the ion source as "Electrospray Ionisation (ESI)", 
the "Interface manufacturer, model and catalog number (where available)" 
are required.
Is the "inlet" the same concept than "source interface"?
- If it is the same, maybe the MIAPE documentation should use the c.v. 
term (inlet type, MS:1000007) or we should add “source interface” as 
exact synonym to "inlet type"
- If they are different, a new “source interface” (MS:XXXXXX2) term 
should be added to the controlled vocabulary
In both cases, explicitly asking the "manufacturer" and "model" in the 
MIAPE-MS guidelines makes necessary the addition of these concepts in 
the controlled vocabulary, under "souce attribute"?

Discussion point 2: Sprayer type, coating, manufacturer, model
===============================================
In MIAPE-MS, having the ion source as "Electrospray Ionisation (ESI)", 
the "Sprayer type, coating, manufacturer, model" are required.
To cover this concept, a term called "source sprayer" (MS:XXXXXX3) was 
proposed (as part_of source), and several children to it: "source 
sprayer type", "source sprayer manufacturer", "source sprayer model".
As before, explicitly asking the "manufacturer" and "model" in the 
MIAPE-MS guidelines makes necessary the addition of these concepts in 
the controlled vocabulary, under the hypothetical "source sprayer"?

Discussion point 3: Sample plate
===============================================
In MIAPE-MS, having the ion source as "MALDI", the "Plate composition 
(or type)" is required.
We can cover this concept by creating a new term called "sample plate" 
(MS:XXXXXX4) under source, another called "sample plate type" 
(MS:XXXXXX5) under "sample plate" and as children to the last, the 
several types of sample plate types (to this moment, two are proposed as 
new types of plate: "stainless steel plate" and "coated glass plate"; 
the "precoated plate", already present in the C.V., in addition to be a 
"MS:1000833 ! matrix application type" should have also a relationship 
"is_a" to the hypothetical "sample plate type" ).

Discussion point 4: Hexapole
===============================================
Listed in the MIAPE-MS as a type of analyzer, we find the "hexapole".
There was a proposal to introduce and "hexapole" term under "mass 
analyzer type".
The hexapoles (and sometimes octupoles, and in some modern instruments, 
lens stacks) can be usually found in the triple quadrupole analyzers, as 
"collision cells". In "mass analyzer type" (MS:1000443), we have a 
general description of the analyzer (like "cyclotron", "ion trap", 
"orbitrap", "quadrupole"...). The hybrid mass analyzers are not
directly covered here (a Q-TOF, a triple-quadrupole...).
In my opinion: introducing "hexapole" as a description for a "mass 
analyzer type" would only be meaningful if we find some instrument based 
only in a hexapole as analyzer.
Does anybody know an instrument analyzer based in a "hexapole"? Do we 
need to add this in the Controlled vocabulary under "mass analyzer type" 
(MS:1000443).


We have a couple more of pending details left... but I think that having 
the previous 4 discussion points clear would be a clear improvement to 
move further in the validation of the MIAPE-MS requirements using the MS 
controlled vocabulary.
Please: follow this thread with your comments, suggestions, 
corrections... and thanks a lot in advance.

Best,
David


Listing of the additions and proposed change in the controlled vocabulary:

ADDITIONS
========

[Term]
id: MS:XXXXXX2
name: source interface
def: "The source interface." [PSI:MS]
relationship: part_of MS:1000458 ! source

[Term]
id: MS:XXXXXXX
name: source interface manufacturer
def: "The source interface manufacturer." [PSI:MS]
relationship: part_of MS:XXXXXX2 ! source interface

[Term]
id: MS:XXXXXXX
name: source interface model
def: "The source interface model." [PSI:MS]
relationship: part_of MS:XXXXXX2 ! source interface

[Term]
id: MS:XXXXXX3
name: source sprayer
def: "The source sprayer." [PSI:MS]
relationship: part_of MS:1000458 ! source

[Term]
id: MS:XXXXXXX
name: source sprayer type
def: "The source sprayer type." [PSI:MS]
relationship: part_of MS:XXXXXX3 ! source sprayer

[Term]
id: MS:XXXXXXX
name: source sprayer manufacturer
def: "The source sprayer manufacturer." [PSI:MS]
relationship: part_of MS:XXXXXX3 ! source sprayer

[Term]
id: MS:XXXXXXX
name: source sprayer model
def: "The source sprayer model." [PSI:MS]
relationship: part_of MS:XXXXXX3 ! source sprayer

[Term]
id: MS:XXXXXX4
name: sample plate
def: "Plate where the sample solution is spotted in a MALDI or similar
instrument." [PSI:MS]
relationship: part_of MS:1000458 ! source

[Term]
id: MS:XXXXXX5
name: sample plate type
def: "The sample plate type." [PSI:MS]
relationship: part_of MS:XXXXXX4 ! sample plate

[Term]
id: MS:XXXXXXX
name: stainless steel plate
def: "Stainless steel plate." [PSI:MS]
is_a: MS:XXXXXX5 ! sample plate type

[Term]
id: MS:XXXXXXX
name: coated glass plate
def: "Coated glass plate." [PSI:MS]
is_a: MS:XXXXXX5 ! sample plate type


One existent term changed
================
A new relation in "precolated plate", now also a "sample plate type"

[Term]
id: MS:1000839
name: precoated plate
def: "Precoated plate." [PSI:MS]
is_a: MS:1000833 ! matrix application type
is_a: MS:XXXXXX5 ! sample plate type





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