Re: [Psidev-ms-dev] new instrument CV terms

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

Dear Hans, Matt and PSI community,

I've updated the psi-ms c.v. with the 32 new Waters instruments list.
I'll also add, in a couple of days, the next 4 c.v. terms. Please, check 
them and if you see anything wrong, write an email....

[Term]
id: MS:XXXXXXX
name: MassLynx
def: "Waters software for Mass spectrometry acquisition, processing and 
data analysis." [PSI:MS]
is_a: MS:1000694 ! Waters software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:XXXXXXX
name: Empower
def: "Waters software for liquid chromatography acquisition, processing, 
data analysis and data management." [PSI:MS]
is_a: MS:1000694 ! Waters software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:XXXXXXX
name: Unify
def: "Waters software for liquid chromatography and mass spectrometry 
acquisition, processing, data analysis and data management." [PSI:MS]
is_a: MS:1000694 ! Waters software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software


********************************** New type of mass spectrometer, TWIMS 
,son of IMS


id: MS:XXXXXXX
name: Travelling wave ion mobility mass spectrometer
def: "An ion mobility mass spectrometry technique based on the 
superimposition of travelling voltage waves on a radially-confining RF 
voltage in a gas-filled, stacked-ring ion guide." [PSI:MS]
synonym: "TWIMS" EXACT []
is_a: MS:1000261 ! ion mobility spectrometry


By the way... the "mass spectrometer" term (MS:1000293), is inside the 
purgatory...  Do you (community) really think this is the place for this 
term? Maybe is not used in the cv mappings for mzML, but, anyway.... is 
strange, at least for me, finding the "mass spectrometer" in the 
purgatory...

Best,
David















On 11/07/2011 07:28, Han...@wa... wrote:
>
> Dear David and Matt,
>
> I have provided answers 'in line' in red.
>
> I will try to find out, with regard to Matt's question, if the 
> instrument type can be retrieved from the header.txt file. The serial 
> number, i.e. JAA143, refers to a specific type and configuration so 
> this may be the easiest way forward. If an overview 'lookup type' 
> table exists, I will forward it.
>
> Would you happen to know who could be contacted for column liquid 
> chromatography and sample preparation CV terms? We are trying to 
> integrate those as well into sample forms and a repository like 
> system, but finding them is not that straightforward.
>
> Thanks and best regards,
> Hans
>
>
>
>
> Inactive hide details for "David Ovelleiro" ---08/07/2011 
> 16:45:04---Dear Hans, Thanks for sending us that intensive list of 
> te"David Ovelleiro" ---08/07/2011 16:45:04---Dear Hans, Thanks for 
> sending us that intensive list of terms.
>
> From: "David Ovelleiro" <do...@eb...>
> To: "Mass spectrometry standard development" 
> <psi...@li...>
> Cc: Han...@wa...
> Date: 08/07/2011 16:45
> Subject: Re: [Psidev-ms-dev] new instrument CV terms
>
> ------------------------------------------------------------------------
>
>
>
> Dear Hans,
>
> Thanks for sending us that intensive list of terms.
>
> Some comments addressed to you and the rest of the community:
>
> 1. Instrument list
> ===============
> You’ve provided a list of 32 new instruments to be added.
> a/ I’ll ad them under “Waters instrument model” (MS:1000126). Every 
> new term will be like:
> id: MS:XXXXXXX
> name: Xevo TQ-S
> def: "Waters quadrupole based instrument." [PSI:MS]
> is_a: MS:1000126 ! Waters instrument model
>
> The terms “quadrupole”, “oa-ToF” and “LC-systems” will be applied 
> correctly in each case. Is this OK?
>
> b/ Some of the new proposed instruments maybe overlap with some of the 
> old ones. I list below the four “suspects” (old terms below “Waters 
> instrument model” MS:1000126):
> Acquity UPLC FLR
> Acquity UPLC PDA
> GCT
> quattro micro
> Please Hans, check if your new terms can safely be included without 
> repeating some of the four previous members.
>
> [HV]:
>
> 'Acquity UPLC FLR' and 'Acquity UPLC PDA' are respectively a 
> fluorescence and PDA detector for 'ACQUITY UPLC' liquid chromatography 
> systems.
>
> 'GCT' and 'quattro micro' have superseded by 'GCT premier' and 'Xevo 
> TQD' mass spectrometers
>
> I therefore do not believe that there is CR term overlap/conflicts
>
>
>
> 2. Mass spectrometer
> ==================
> You propose a new “mass spectrometer type” called “Travelling wave 
> mobility separator”.
> a/ Can this be correctly included under “mass spectrometer” (MS:1000293)?
> b/ Is not more appropriate to use “Travelling wave ion mobility mass 
> spectrometer” as the name of the new cv term?
> c/ Can we use Synonym: TWIMS?
> d/ We would need a short description of the new kind of mass 
> spectrometer. I’ve found this: “An ion mobilitymass spectrometry 
> technique based on the superimposition of travelling voltage waves on 
> a radially-confining RF voltage in agas-filled,stacked-ring ion 
> guide”. Any better suggestion?
>
> [HV]:
>
> a/b/c/ - please see Matt's reply (TWIMS is an IMS variant)
> d/ see suggestion above
>
>
> 3. Software
> ===========
> Three new “software” terms to be included: MassLynx, Empower and 
> Unify. All three under “Waters software” (MS:1000694).
> a/ Please, Hans, we would need a short description of what these 
> software do (one line each is enough).
>
> [HV]:
>
> MassLynx:
> "Mass spectrometry acquisition, processing and data analysis software"
>
>
> Empower:
> "Liquid chromatography acquisition, processing, data analysis and data 
> management software"
>
> If believe that most vendors would call this CDS (chromatography data 
> software). Would there be a specific PSI-MS CV term for this?
>
>
> Unify:
> "Liquid chromatography and mass spectrometry acquisition, processing, 
> data analysis and data management software"
>
>
>
> I’ll be waiting for your comments, suggestions, changes, corrections…
>
> Best
> david ovelleiro
>
>
>
> On 07/07/2011 09:05, _Ha...@wa..._ 
> <mailto:Han...@wa...>wrote:
>
>
>     Dear all,
>
>     Can the following instruments be added to the CV:
>
>     quadrupole based:
>
>     Xevo TQ-S
>     Xevo TQ MS
>     Xevo TQD
>     Acquity TQD
>     Acquity SQD
>     3100
>     Quattro micro GC
>
>     oa-ToF based:
>
>     Synapt G2-S HDMS
>     Synapt G2 HDMS
>     Synapt HDMS
>     Synapt G2-S MS
>     Synapt G2 MS
>     Synapt MS
>     MALDI Synapt G2-S HDMS
>     MALDI Synapt G2 HDMS
>     MALDI Synapt HDMS
>     MALDI Synapt G2-S MS
>     MALDI Synapt G2 MS
>     MALDI Synapt MS
>     Xevo G2 Q-Tof
>     Xevo Q-Tof
>     Xevo G2 Tof
>     GCT Premier
>
>     LC-systems:
>
>     ACQUITY UPLC I-Class
>     ACQUITY UPLC
>     ACQUITY UPLC H-Class
>     ACQUITY UPLC H-Class Bio
>     ACQUITY UPLC Systems with 2D Technology
>     nanoACQUITY UPLC
>     nanoACQUITY UPLC System with Technology
>     nanoACQUITY UPLC with HDX Technology
>     TRIZAIC UPLC nanoTile
>
>     software:
>
>     MassLynx
>     Empower
>     Unify
>
>     mass spectrometer type:
>
>     travelling wave mobility separator
>
>
>     The vendor or brand should be listed as "Waters Corporation".
>     Would any more information be required?
>
>     Thanks and best regards,
>
>     Hans
>
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> -- 
> David Ovelleiro
> Bioinformatician
> PRIDE Group
> Proteomics Services Team, PANDA Group
> EMBL European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton, Cambridge, UK
> CB10 1SD
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-- 
David Ovelleiro
Bioinformatician
PRIDE Group
Proteomics Services Team, PANDA Group
EMBL European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, UK
CB10 1SD