psidev-ms-dev — Mass spectroscopy standard development

[Psidev-ms-dev] TraML: Proposing to use EDAM ontology for <Compound>

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

Hi,

I am currently preparing a set of MRM Transitions 
as showcase for TraML in Metabolomics.

I'll need to specify for which <Compound> a transition 
was obtained. Currently, we only have cvParams 
for "predicted isoelectric point", "theoretical mass"
and children of "chemical compound formula":
http://www.peptideatlas.org/schemas/TraML/1.0.0/TraML1.0.0.html#Compound

This is a) far from complete, and b) underspecified, 
because MS:1000867 "structural formula" does not specify 
whether the value shall be SMILES, InChI or whatever.

Is there a way to embrace (pun intended :-) 
the EDAM (EMBRACE Data and Methods) ontology of [...] identifiers
for <Compound> ? Then we'd have something like this:

<TraML>
  <cv URI="http://edamontology.org/ontology?format=obo"
      fullName="EDAM (EMBRACE Data And Methods)" id="EDAM" version="unknown" />
  ...
  <Compound>
  <cvParam accession="EDAM_data:1172" cvRef="EDAM" name="PubChem CID" value="932" />
  </Compound>

EDAM has entries for a gazillion different compound identifiers:
http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=EDAM&termId=EDAM_data:1086&termName=Compound%20identifier

and InChI, SMILES, molecular formula:
http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=EDAM&termId=EDAM_format%3A2035&termName=Chemical%20formula%20format

The only downside I can see is that the converters and validators 
need to slurp in another ontology of respectable size.

Thoughts ?

Yours,
Steffen


-- 
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

Re: [Psidev-ms-dev] RFC: Collision cell exit potential in CV ?

[Eric D. <ede...@sy...>]

Yes, let's plan on a call this coming Tuesday at the usual time.

Thanks,
Eric


> -----Original Message-----
> From: Steffen Neumann [mailto:sne...@ip...]
> Sent: Wednesday, January 25, 2012 1:01 AM
> To: Mass spectrometry standard development
> Subject: Re: [Psidev-ms-dev] RFC: Collision cell exit potential in CV ?
>
> Hi,
>
> can we add this to the agenda of the next call ?
>
> Yours,
> Steffen
>
> On Wed, 2011-12-21 at 10:21 +0100, Steffen Neumann wrote:
> > Hi,
> >
> > we're generating some examples of TraML files from methods
> > that were developed on a QTrap 3200.
> >
> > One of the parameters is the "CXP, Collision Cell Exit Potential".
> > We couldn't find a corresponding CV term for that.
> >
> > Question: Did we miss anything ? Should one be created ?
> >
> > I have almost no experience with Traps, but I could imagine
> > this should be a child of MS:1000510 (precursor activation
> attribute).
> > Does the following make sense:
> >
> > 	[Term]
> > 	id: MS:1000876
> > 	name: Collision cell exit potential
> > 	def: "Potential difference between Q2 and Q3 in a triple
> quadrupole instrument in volts." [PSI:MS]
> > 	xref: value-type:xsd\:float "The allowed value-type for this CV
> term."
> > 	is_a: MS:1000510 ! precursor activation attribute
> > 	relationship: has_units UO:0000218 ! volt
> > 	synonym: "CXP" EXACT []
> >
> > Is this restricted to triple quads / linear ion traps ?
> > Or is there something equivalent for QqTOF ? Then the def:
> > above should be modified "between Q2 and the following instrument
> compartment..."
> >
> > There is an issue in the tracker for skyline:
> > https://brendanx-
> uw1.gs.washington.edu/labkey/issues/home/issues/details.view?issueId=12
> 2
> >
> > Yours,
> > Steffen
> >
> >
> >
>
> --
> 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
>
>
>
> -----------------------------------------------------------------------
> -------
> Keep Your Developer Skills Current with LearnDevNow!
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> MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
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Re: [Psidev-ms-dev] RFC: Collision cell exit potential in CV ?

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

Hi,

can we add this to the agenda of the next call ?

Yours,
Steffen

On Wed, 2011-12-21 at 10:21 +0100, Steffen Neumann wrote:
> Hi,
> 
> we're generating some examples of TraML files from methods
> that were developed on a QTrap 3200.
> 
> One of the parameters is the "CXP, Collision Cell Exit Potential".
> We couldn't find a corresponding CV term for that.
> 
> Question: Did we miss anything ? Should one be created ?
> 
> I have almost no experience with Traps, but I could imagine
> this should be a child of MS:1000510 (precursor activation attribute).
> Does the following make sense:
> 
> 	[Term]
> 	id: MS:1000876
> 	name: Collision cell exit potential
> 	def: "Potential difference between Q2 and Q3 in a triple quadrupole instrument in volts." [PSI:MS]	
> 	xref: value-type:xsd\:float "The allowed value-type for this CV term."
> 	is_a: MS:1000510 ! precursor activation attribute
> 	relationship: has_units UO:0000218 ! volt
> 	synonym: "CXP" EXACT []
> 
> Is this restricted to triple quads / linear ion traps ? 
> Or is there something equivalent for QqTOF ? Then the def:
> above should be modified "between Q2 and the following instrument compartment..."
> 
> There is an issue in the tracker for skyline:
> https://brendanx-uw1.gs.washington.edu/labkey/issues/home/issues/details.view?issueId=122
> 
> Yours,
> Steffen
> 
> 
> 

-- 
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

Re: [Psidev-ms-dev] [Psidev-pi-dev] ProteomeXchange related terms ideally to be added to the PSI MS CV

[pierre-alain b. <pie...@is...>]

Hi Juan,
In general, fine for me also. Just some definition details:

1) Keyword however is a generic term that need more precise definition: 
I would prefer External reference keyword.
I assume that a curator keyword is used to characterize an external 
reference here.

In that case it also differentiates from a keyword that would be 
associated with something else (another meta-data information, or a 
specific dataset), even if we do not use keywords for those at the moment.

2) ProteomeXchange accession number: will it be a number? if not, 
ProteomeXchange primary accession code (or identifier) is better
3) ProteomeXchange identifier: for the sake of consistency, use 
ProteomeXchange secondary accession code (or identifier)
4) ProteomeXchange accession version number: will it be a number? for 
consistency : ProteomeXchange primary accession code (or identifier) version
5) No version for the secondary identifier?

Cheers


Pierre-Alain


On 22.01.2012 23:14, Eric Deutsch wrote:
>
> Hi Juan Antonio, this all seems good to me. I suppose all these terms 
> will need datatypes added to them, though. As for the manuscript 
> status, can't it go as a sibling of PubMed ID along with the other 
> publication attributes?
>
> Thanks,
>
> Eric
>
> *From:*Juan Antonio Vizcaino [mailto:ju...@eb... 
> <mailto:ju...@eb...>]
> *Sent:* Friday, January 20, 2012 3:23 AM
> *To:* psi...@li... 
> <mailto:psi...@li...>; Mass spectrometry 
> standard development; psi...@li... 
> <mailto:psi...@li...>
> *Subject:* [Psidev-ms-dev] ProteomeXchange related terms ideally to be 
> added to the PSI MS CV
>
> Dear all,
>
> I would like to propose the following terms related to the 
> ProteomeXchange submission pipeline. Ideally, we would like to have 
> them included here since we need them not only for PRIDE purposes, but 
> not be integrated with the other resources such as PeptideAtlas, 
> UniProt or Tranche.
>
> Any feedback is welcome.
>
> Best regards,
>
> Juan Antonio
>
> [Term]
>
> id: MS: ?
>
> name: ProteomeXchange accession number
>
> def: Main identifier of a ProteomeXchange dataset
>
> is_a: MS: 1000878 ! External reference identifier
>
> [Term]
>
> id: MS: ?
>
> name: ProteomeXchange  identifier
>
> def: Secondary identifier of a ProteomeXchange dataset
>
> is_a: MS: 1000878 ! External reference identifier
>
> [Term]
>
> id: MS: ?
>
> name: ProteomeXchange accession version number
>
> def: version number of a ProteomeXchange accession number
>
> is_a: MS: 1000878 ! External reference identifier
>
> [Term]
>
> id: MS: ?
>
> name: Digital Object Identifier (DOI)
>
> def: DOI unique identifier
>
> is_a: MS: 1000878 ! External reference identifier
>
> [Term]
>
> id: MS: ?
>
> name: Keyword
>
> def: Free text attribute that can enrich the information about an entity
>
> is_a: MS: 1000878 ! External reference identifier
>
> We also need children terms for this under the previous term:
>
> [Term]
>
> id: MS: ?
>
> name: Journal article keyword
>
> def: Keyword present in a scientific publication
>
> is_a: MS: ? ! Keyword
>
> [Term]
>
> id: MS: ?
>
> name: Submitter keyword
>
> def: Keyword assigned by the data submitter
>
> is_a: MS: ? ! Keyword
>
> [Term]
>
> id: MS: ?
>
> name: Curator keyword
>
> def: Keyword assigned by a data curator
>
> is_a: MS: ? ! Keyword
>
> [Term]
>
> id: MS: ?
>
> name: Tranche file hash
>
> def: Hash assigned by the Tranche resource to an individual file
>
> is_a: MS: 1000878 ! External reference identifier
>
> [Term]
>
> id: MS: ?
>
> name: Tranche project hash
>
> def: Hash  assigned by the Tranche resource to a whole project
>
> is_a: MS: 1000878 ! External reference identifier
>
> [Term]
>
> id: MS: ?
>
> name: PRIDE experiment URI
>
> def: URI that allows the access to one experiment in the PRIDE database.
>
> is_a: MS: 1000878 ! External reference identifier
>
> [Term]
>
> id: MS: ?
>
> name: PRIDE project URI
>
> def: URI that allows the access to one project in the PRIDE database.
>
> is_a: MS: 1000878 ! External reference identifier
>
> We also need three more terms to represent:
>
> - 'Accepted manuscript'. We will use this when the data is published 
> but the reference (PubMed ID) is not yet public.
>
> - 'Data derived from previous dataset'. We need this term to flag is 
> new data has been obtained by reanalysing a previous dataset.
>
> - 'No PTMs are included in the dataset'. This may be included under 
> the term MS:1001055 ('Modification parameters for the search engine 
> run'), but it does not really fit there.
>
>  I am not sure it these terms should be included here. We could just 
> use the PRIDE CV for this.
>
>
>
> ------------------------------------------------------------------------------
> Try before you buy = See our experts in action!
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Re: [Psidev-ms-dev] pymzML

[Eric D. <ede...@sy...>]

Looks good, thanks David!


> -----Original Message-----
> From: David Ovelleiro [mailto:do...@eb...]
> Sent: Thursday, January 19, 2012 2:38 AM
> To: Mass spectrometry standard development
> Subject: Re: [Psidev-ms-dev] pymzML
>
> Hi Christian and community,
>
> Thanks for contacting us. Here is my suggestion anout your suggested
> c.v. Please, check it (both the name and definition) and send an email
> if you have a different suggestion (there's more than one way to do it
> ;)).
>
> [Term]
> id: MS:1001914
> name: pymzML
> def: "Python module to interface mzML Data." [PSI:MS]
> is_a: MS:1001457 ! data processing software
>
> If nobody objects to this new term, I'll add it to a new version of the
> controlled vocabulary between three and four working days (let's say,
> on
> Tuesday).
>
> Best,
> David Ovelleiro
>
>
>
> On 16/01/12 19:15, Christian Fufezan wrote:
> > Hi,
> >
> > we are in the process of publishing a Python module to interface mzML
> Data in Bioinformatics. Although we planned to offer a read only
> interface, the reviewer pointed out that writing mzML would be a great
> feature and we are about to implement it.
> > As such we have already implemented a "crude" version of the
> pymzml.run.Writer but we will need a software related cvParam for
> pymzML in the future. The reviewer suggested that we could apply for
> such a cvparam. Thanks for your help.
> >
> > In addition we would like to invite all Python enthusiasts to join
> the project on pymzml.github.com
> >
> > Kind regards,
> >
> > Christian Fufezan
> >
> >
> > Dr. Christian Fufezan
> > Westfälische Wilhelms-Universität Münster
> >
> > Institut für Biologie und Biotechnologie der Pflanzen
> >
> > Hindenburgplatz 55
> > 48143 Münster - Germany
> >
> > Tel:  ++49 251 83 24861
> > Fax: ++49 251 83 28371
> > Web: http://www.uni-muenster.de/Biologie.IBBP.AGFufezan
> >
> >
> > ---------------------------------------------------------------------
> ---------
> > Keep Your Developer Skills Current with LearnDevNow!
> > The most comprehensive online learning library for Microsoft
> developers
> > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3,
> MVC3,
> > Metro Style Apps, more. Free future releases when you subscribe now!
> > http://p.sf.net/sfu/learndevnow-d2d
> > _______________________________________________
> > Psidev-ms-dev mailing list
> > Psi...@li...
> > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>
>
> --
> David Ovelleiro
> Bioinformatician
> PRIDE Group
> Proteomics Services Team, PANDA Group
> EMBL European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton, Cambridge, UK
> CB10 1SD
>
>
> -----------------------------------------------------------------------
> -------
> Keep Your Developer Skills Current with LearnDevNow!
> The most comprehensive online learning library for Microsoft developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3,
> MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-d2d
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] ProteomeXchange related terms ideally to be added to the PSI MS CV

[Eric D. <ede...@sy...>]

Hi Juan Antonio, this all seems good to me. I suppose all these terms will
need datatypes added to them, though. As for the manuscript status, can’t
it go as a sibling of PubMed ID along with the other publication attributes?



Thanks,

Eric





*From:* Juan Antonio Vizcaino [mailto:ju...@eb...]
*Sent:* Friday, January 20, 2012 3:23 AM
*To:* psi...@li...; Mass spectrometry standard
development; psi...@li...
*Subject:* [Psidev-ms-dev] ProteomeXchange related terms ideally to be
added to the PSI MS CV



Dear all,



I would like to propose the following terms related to the ProteomeXchange
submission pipeline. Ideally, we would like to have them included here
since we need them not only for PRIDE purposes, but not be integrated with
the other resources such as PeptideAtlas, UniProt or Tranche.





Any feedback is welcome.



Best regards,



Juan Antonio







[Term]

id: MS: ?

name: ProteomeXchange accession number

def: Main identifier of a ProteomeXchange dataset

is_a: MS: 1000878 ! External reference identifier



[Term]

id: MS: ?

name: ProteomeXchange  identifier

def: Secondary identifier of a ProteomeXchange dataset

is_a: MS: 1000878 ! External reference identifier



[Term]

id: MS: ?

name: ProteomeXchange accession version number

def: version number of a ProteomeXchange accession number

is_a: MS: 1000878 ! External reference identifier



[Term]

id: MS: ?

name: Digital Object Identifier (DOI)

def: DOI unique identifier

is_a: MS: 1000878 ! External reference identifier



[Term]

id: MS: ?

name: Keyword

def: Free text attribute that can enrich the information about an entity

is_a: MS: 1000878 ! External reference identifier



We also need children terms for this under the previous term:



[Term]

id: MS: ?

name: Journal article keyword

def: Keyword present in a scientific publication

is_a: MS: ? ! Keyword



[Term]

id: MS: ?

name: Submitter keyword

def: Keyword assigned by the data submitter

is_a: MS: ? ! Keyword



[Term]

id: MS: ?

name: Curator keyword

def: Keyword assigned by a data curator

is_a: MS: ? ! Keyword



[Term]

id: MS: ?

name: Tranche file hash

def: Hash assigned by the Tranche resource to an individual file

is_a: MS: 1000878 ! External reference identifier



[Term]

id: MS: ?

name: Tranche project hash

def: Hash  assigned by the Tranche resource to a whole project

is_a: MS: 1000878 ! External reference identifier



[Term]

id: MS: ?

name: PRIDE experiment URI

def: URI that allows the access to one experiment in the PRIDE database.

is_a: MS: 1000878 ! External reference identifier



[Term]

id: MS: ?

name: PRIDE project URI

def: URI that allows the access to one project in the PRIDE database.

is_a: MS: 1000878 ! External reference identifier





We also need three more terms to represent:



- 'Accepted manuscript'. We will use this when the data is published but
the reference (PubMed ID) is not yet public.



- 'Data derived from previous dataset'. We need this term to flag is new
data has been obtained by reanalysing a previous dataset.



- 'No PTMs are included in the dataset'. This may be included under the
term MS:1001055 ('Modification parameters for the search engine run'), but
it does not really fit there.







 I am not sure it these terms should be included here. We could just use
the PRIDE CV for this.

[Psidev-ms-dev] ProteomeXchange related terms ideally to be added to the PSI MS CV

[Juan A. V. <ju...@eb...>]

Dear all,

I would like to propose the following terms related to the ProteomeXchange submission pipeline. Ideally, we would like to have them included here since we need them not only for PRIDE purposes, but not be integrated with the other resources such as PeptideAtlas, UniProt or Tranche. 


Any feedback is welcome.

Best regards,

Juan Antonio



[Term]
id: MS: ?
name: ProteomeXchange accession number
def: Main identifier of a ProteomeXchange dataset
is_a: MS: 1000878 ! External reference identifier

[Term]
id: MS: ?
name: ProteomeXchange  identifier
def: Secondary identifier of a ProteomeXchange dataset
is_a: MS: 1000878 ! External reference identifier

[Term]
id: MS: ?
name: ProteomeXchange accession version number
def: version number of a ProteomeXchange accession number
is_a: MS: 1000878 ! External reference identifier

[Term]
id: MS: ?
name: Digital Object Identifier (DOI)
def: DOI unique identifier
is_a: MS: 1000878 ! External reference identifier

[Term]
id: MS: ?
name: Keyword
def: Free text attribute that can enrich the information about an entity
is_a: MS: 1000878 ! External reference identifier

We also need children terms for this under the previous term:

[Term]
id: MS: ?
name: Journal article keyword
def: Keyword present in a scientific publication
is_a: MS: ? ! Keyword

[Term]
id: MS: ?
name: Submitter keyword
def: Keyword assigned by the data submitter
is_a: MS: ? ! Keyword

[Term]
id: MS: ?
name: Curator keyword
def: Keyword assigned by a data curator
is_a: MS: ? ! Keyword

[Term]
id: MS: ?
name: Tranche file hash
def: Hash assigned by the Tranche resource to an individual file  
is_a: MS: 1000878 ! External reference identifier

[Term]
id: MS: ?
name: Tranche project hash
def: Hash  assigned by the Tranche resource to a whole project
is_a: MS: 1000878 ! External reference identifier

[Term]
id: MS: ?
name: PRIDE experiment URI
def: URI that allows the access to one experiment in the PRIDE database.
is_a: MS: 1000878 ! External reference identifier

[Term]
id: MS: ?
name: PRIDE project URI
def: URI that allows the access to one project in the PRIDE database.
is_a: MS: 1000878 ! External reference identifier


We also need three more terms to represent:

- 'Accepted manuscript'. We will use this when the data is published but the reference (PubMed ID) is not yet public.

- 'Data derived from previous dataset'. We need this term to flag is new data has been obtained by reanalysing a previous dataset.

- 'No PTMs are included in the dataset'. This may be included under the term MS:1001055 ('Modification parameters for the search engine run'), but it does not really fit there.



 I am not sure it these terms should be included here. We could just use the PRIDE CV for this.

Re: [Psidev-ms-dev] pymzML

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

Hi Christian and community,

Thanks for contacting us. Here is my suggestion anout your suggested 
c.v. Please, check it (both the name and definition) and send an email 
if you have a different suggestion (there's more than one way to do it ;)).

[Term]
id: MS:1001914
name: pymzML
def: "Python module to interface mzML Data." [PSI:MS]
is_a: MS:1001457 ! data processing software

If nobody objects to this new term, I'll add it to a new version of the 
controlled vocabulary between three and four working days (let's say, on 
Tuesday).

Best,
David Ovelleiro



On 16/01/12 19:15, Christian Fufezan wrote:
> Hi,
>
> we are in the process of publishing a Python module to interface mzML Data in Bioinformatics. Although we planned to offer a read only interface, the reviewer pointed out that writing mzML would be a great feature and we are about to implement it.
> As such we have already implemented a "crude" version of the pymzml.run.Writer but we will need a software related cvParam for pymzML in the future. The reviewer suggested that we could apply for such a cvparam. Thanks for your help.
>
> In addition we would like to invite all Python enthusiasts to join the project on pymzml.github.com
>
> Kind regards,
>
> Christian Fufezan
>
>
> Dr. Christian Fufezan
> Westfälische Wilhelms-Universität Münster
>
> Institut für Biologie und Biotechnologie der Pflanzen
>
> Hindenburgplatz 55
> 48143 Münster - Germany
>
> Tel:  ++49 251 83 24861
> Fax: ++49 251 83 28371
> Web: http://www.uni-muenster.de/Biologie.IBBP.AGFufezan
>
>
> ------------------------------------------------------------------------------
> Keep Your Developer Skills Current with LearnDevNow!
> The most comprehensive online learning library for Microsoft developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-d2d
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev


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

[Psidev-ms-dev] pymzML

[Christian F. <chr...@fu...>]

Hi,

we are in the process of publishing a Python module to interface mzML Data in Bioinformatics. Although we planned to offer a read only interface, the reviewer pointed out that writing mzML would be a great feature and we are about to implement it. 
As such we have already implemented a "crude" version of the pymzml.run.Writer but we will need a software related cvParam for pymzML in the future. The reviewer suggested that we could apply for such a cvparam. Thanks for your help.

In addition we would like to invite all Python enthusiasts to join the project on pymzml.github.com

Kind regards,

Christian Fufezan


Dr. Christian Fufezan
Westfälische Wilhelms-Universität Münster

Institut für Biologie und Biotechnologie der Pflanzen

Hindenburgplatz 55
48143 Münster - Germany

Tel:  ++49 251 83 24861
Fax: ++49 251 83 28371
Web: http://www.uni-muenster.de/Biologie.IBBP.AGFufezan

[Psidev-ms-dev] PSI MSS WG call postponed

[Eric D. <ede...@sy...>]

Hi everyone, since the phone conferencing system will not be available to
us tomorrow, let’s defer until next week. No phone conference this week,
but we will meet next Tuesday.



Thanks,

Eric





*From:* Juan Antonio Vizcaino [mailto:ju...@eb...]
*Sent:* Monday, January 09, 2012 11:59 AM
*To:* Mass spectrometry standard development
*Subject:* Re: [Psidev-ms-dev] PSI MSS WG call reminder



Hi Eric,



I am afraid tomorrow there will not be anyone at the office to be able to
start the phone conference.

We have a retreat of both the PRIDE and Intact groups together at a
different place.



Sorry about that,



Juanan







On 9 Jan 2012, at 19:19, Eric Deutsch wrote:



Hi everyone, this is a reminder about the PSI MSS WG teleconference call
tomorrow, Tuesday, at the usual time.



08:00 San Francisco

11:00 New York

16:00 London

17:00 Geneva



+ Germany: 08001012079

+ Switzerland: 0800000860

+ Finland: 080011569

+ UK: 08081095644

+ USA: 1-866-832-8490

Generic international: +44 2083222500 (UK number)



access code: 297427 #





Agenda:

1) Plans and agenda for spring PSI workshop in San Diego March 12-14

2) mzML status

3) TraML status

4) Discuss controlled vocabulary items:

  - CXP

  - cleavage agents

  - others?

5) MIAPE – MS

6) MIAPE – Quant



Next meeting:

- Jan 31 8am Seattle Time?





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Re: [Psidev-ms-dev] PSI MSS WG call reminder

[Juan A. V. <ju...@eb...>]

Hi Eric,

I am afraid tomorrow there will not be anyone at the office to be able to start the phone conference.
We have a retreat of both the PRIDE and Intact groups together at a different place.

Sorry about that,

Juanan



On 9 Jan 2012, at 19:19, Eric Deutsch wrote:

> Hi everyone, this is a reminder about the PSI MSS WG teleconference call tomorrow, Tuesday, at the usual time.
>  
> 08:00 San Francisco
> 11:00 New York
> 16:00 London
> 17:00 Geneva
>  
> + Germany: 08001012079
> + Switzerland: 0800000860
> + Finland: 080011569
> + UK: 08081095644
> + USA: 1-866-832-8490
> Generic international: +44 2083222500 (UK number)
>  
> access code: 297427 #
>  
>  
> Agenda:
> 1) Plans and agenda for spring PSI workshop in San Diego March 12-14
> 2) mzML status
> 3) TraML status
> 4) Discuss controlled vocabulary items:
>   - CXP
>   - cleavage agents
>   - others?
> 5) MIAPE – MS
> 6) MIAPE – Quant
>  
> Next meeting:
> - Jan 31 8am Seattle Time?
>  
>  
> ------------------------------------------------------------------------------
> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
> infrastructure or vast IT resources to deliver seamless, secure access to
> virtual desktops. With this all-in-one solution, easily deploy virtual 
> desktops for less than the cost of PCs and save 60% on VDI infrastructure 
> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox_______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

[Psidev-ms-dev] PSI MSS WG call reminder

[Eric D. <ede...@sy...>]

Hi everyone, this is a reminder about the PSI MSS WG teleconference call
tomorrow, Tuesday, at the usual time.



08:00 San Francisco

11:00 New York

16:00 London

17:00 Geneva



+ Germany: 08001012079

+ Switzerland: 0800000860

+ Finland: 080011569

+ UK: 08081095644

+ USA: 1-866-832-8490

Generic international: +44 2083222500 (UK number)



access code: 297427 #





Agenda:

1) Plans and agenda for spring PSI workshop in San Diego March 12-14

2) mzML status

3) TraML status

4) Discuss controlled vocabulary items:

  - CXP

  - cleavage agents

  - others?

5) MIAPE – MS

6) MIAPE – Quant



Next meeting:

- Jan 31 8am Seattle Time?

[Psidev-ms-dev] RFC: Collision cell exit potential in CV ?

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

Hi,

we're generating some examples of TraML files from methods
that were developed on a QTrap 3200.

One of the parameters is the "CXP, Collision Cell Exit Potential".
We couldn't find a corresponding CV term for that.

Question: Did we miss anything ? Should one be created ?

I have almost no experience with Traps, but I could imagine
this should be a child of MS:1000510 (precursor activation attribute).
Does the following make sense:

	[Term]
	id: MS:1000876
	name: Collision cell exit potential
	def: "Potential difference between Q2 and Q3 in a triple quadrupole instrument in volts." [PSI:MS]	
	xref: value-type:xsd\:float "The allowed value-type for this CV term."
	is_a: MS:1000510 ! precursor activation attribute
	relationship: has_units UO:0000218 ! volt
	synonym: "CXP" EXACT []

Is this restricted to triple quads / linear ion traps ? 
Or is there something equivalent for QqTOF ? Then the def:
above should be modified "between Q2 and the following instrument compartment..."

There is an issue in the tracker for skyline:
https://brendanx-uw1.gs.washington.edu/labkey/issues/home/issues/details.view?issueId=122

Yours,
Steffen



-- 
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

[Psidev-ms-dev] No MSS WG call Tuesday

[Eric D. <Eri...@sy...>]

Hi everyone, I haven’t received any topics for a call tomorrow and I
imagine that many of you have entered a holiday mode already, or finishing
up things before you do. So since there is nothing pressing, let’s just
defer until next year. Let’s set the next call for Tuesday Jan 10. I’ll
send out a reminder in January.



Happy holidays everyone!

Eric





*From:* Eric Deutsch [mailto:Eri...@sy...]
*Sent:* Tuesday, December 13, 2011 12:32 AM
*To:* Mass spectrometry standard development
*Cc:* Eric Deutsch
*Subject:* No MSS WG call Tuesday



Hi everyone, let’s skip the call this Tuesday. There doesn’t seem to be
much very pressing that we can’t deal with via email. Let me know if you
have topics or next week or else we’ll resume in the new year.



The good news is that the TraML manuscript has been accepted, and we have
the green light to release TraML 1.0.0. So here it is:



http://mcponline.org/content/early/2011/12/12/mcp.R111.015040.abstract



http://psidev.info/traml



Many thanks for all who helped the development of TraML.



Regards,

Eric

[Psidev-ms-dev] No MSS WG call Tuesday

[Eric D. <Eri...@sy...>]

Hi everyone, let’s skip the call this Tuesday. There doesn’t seem to be
much very pressing that we can’t deal with via email. Let me know if you
have topics or next week or else we’ll resume in the new year.



The good news is that the TraML manuscript has been accepted, and we have
the green light to release TraML 1.0.0. So here it is:



http://mcponline.org/content/early/2011/12/12/mcp.R111.015040.abstract



http://psidev.info/traml



Many thanks for all who helped the development of TraML.



Regards,

Eric

Re: [Psidev-ms-dev] item Paul ion trap

[David S. <osp...@pa...>]

I need to make a comment on this.

I do not think that the original (classical) ion trap describe by Paul should be called the Paul Ion Trap or the Classical Ion Trap.  The name should have the word quadrupole (which describes the field used to store the ions).  The best description is the three-dimensional quadrupole ion trap, abbreviated 3D QIT.  The 3d QIT is composed of a ring electrode and two end-cap electrodes.  The cross-sectional view of the 3D QIT is two orthogonally opposed hyperbola, just as the cross section of a transmission quadrupole is, even when it is constructed using round rods.

 

The linear ion trap (abbreviated LIT) is different than the 3D QIT.  The LTQ (ThermoFisher) and the QTrap (AB/Sciex) are trade names just as the name Orbitrap is a trade name for the device that may best be call an electrostatic ion trap or Kingdon trap; although, the word orbitrap (without a capital O) is now being used as the device type.  The term Kingdon trap is just as non-descriptive as the term Paul trap.



Regards;
David

O. David Sparkman
Adjunct Professor of Chemistry
Pacific Mass Spectrometry Facility
Chemistry Department
College of the Pacific
University of the Pacific
3601 Pacific Ave.
Stockton, CA USA 95211
1-209-483-5740
Web Page: http://www1.pacific.edu/~osparkma/

  ----- Original Message ----- 
  From: pierre-alain binz 
  To: psi...@li... ; PSI MS Dev 
  Cc: mm...@bd... 
  Sent: Friday, December 02, 2011 7:40 AM
  Subject: [Psidev-ms-dev] item Paul ion trap


  Hi all,

  one action item was to clarify the existence, relevance and position of the Paul ion trap term.

  Marcus Macht from Bruker did help in this, and here is the explanation and proposal:


  We have the following terms discussed here:
  -    Quadrupole ion trap
  -    Paul ion trap
  -    Linear trap
  -    Ion trap


  -    The term "quadrupole ion trap" refers to the nature of the fields inside an ion trap and NOT to the geometry of the analyzer.
  -    A quadrupole ion trap, in its classical design, and as described by Paul is made of a circular electrode and 2 end-caps electrodes. It is NOT constituted by a quadrupole (i.e. 4  linear or curved rods) with 2 end caps electrodes.
  -    The Paul ion trap is synonym to the classical quadrupole ion trap.
  -    The linear trap (as in LTQ or Qtrap for instance) has the geometry of a quadrupole + end caps electrodes and generates quadrupolar ion trap fields. It is a quadrupole ion trap.
  -    Both Paul ion trap an linear trap are quadrupole ion traps.

  We should therefore have in the PSI-MS CV:
    +-quadrupole ion trap
       +-Paul ion trap (classical quadrupole ion trap with circular electrode such as in : Bruker Esquire, HCT, amaZon; Thermo LCQ; Shimadzu LC-IT-TOF and Axima Resonance (MALDI), Agilent/Varian 500-MS)
       +-Linear quadrupole ion trap (such as in ABSCIEX QTRAPs, Thermo LTQs)


  Now about the term ion trap in the current CV:
  In the PSI-MS CV, the term "ion trap" is not correctly positioned. It is a generic term with a correct definition for a generic term. The term as defined now should includes Orbi and FTICR as childs, though. And the synonym "IT" should become a synonym of quadrupole ion trap (as it is mostly used and marketed in that context). If we keep the term we should make the following (concentrate on the ion trap part):

  Here is therefore the proposal:

  mass analyzer
  +-Time of Flight
  +-quadrupole mass filter
  +-magnetic sector
  +-ion trap
     +-image current detection based ion trap    <!-- new term -->
        +-Orbitrap         <!-- note that this refers to the analyzer, not the instrument name, which is correctly defined in the CV -->
        +-FTICR (Penning cell) 
     +-mass selective scanning detection based ion trap   <!-- "renamed" quadrupole ion trap -->
        +-Paul ion trap (classical quadrupolar ion trap with circular electrode)   
        +-Linear ion trap                                                    
           +-radial ejection linear ion trap
           +-axial ejection lineal ion trap

  The term Pal ion trap should therefore not be obsolete.

  Suggestions for the CV:
  [Term] id: MS:XXXXXXX 
  name: image current detection based ion trap
  def: "Ion trap analyzer where ions are moving in an orbit which trajectory frequency can be measured as an image current " [PSI:MS] is_a: MS:1000264 ! ion trap 

  [Term] id: MS:XXXXXXX 
  name: mass selective scanning detection based ion trap 
  def: "Ion trap analyzer where ions are m/z selectively ejected from the trapping device and detected outside of it " [PSI:MS] 
  is_a: MS:1000264 ! ion trap

  [Term]
  id: MS:1000484
  name: orbitrap
  def: "An ion trapping device that consists of an outer barrel-like electrode and a coaxial inner spindle-like electrode that form an electrostatic field with quadro-logarithmic potential distribution. The frequency of harmonic oscillations of the orbitally trapped ions along the axis of the electrostatic field is independent of the ion velocity and is inversely proportional to the square root of m/z so that the trap can be used as a mass analyzer." [PSI:MS]
  is_a: MS:XXXXXXX ! image current detection based ion trap

  [Term]
  id: MS:1000079
  name: fourier transform ion cyclotron resonance mass spectrometer
  def: "A mass spectrometer based on the principle of ion cyclotron resonance in which an ion in a magnetic field moves in a circular orbit at a frequency characteristic of its m/z value. Ions are coherently excited to a larger radius orbit using a pulse of radio frequency energy and their image charge is detected on receiver plates as a time domain signal. Fourier transformation of the time domain signal results in a frequency domain signal which is converted to a mass spectrum based in the inverse relationship between frequency and m/z." [PSI:MS]
  synonym: "FT_ICR" EXACT []
  is_a: MS:XXXXXXX ! image current detection based ion trap

  [Term]
  id: MS:1000297
  name: Paul ion trap
  def: "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]
  synonym: "quadrupole ion trap" RELATED []
  is_a: MS:XXXXXXX ! mass selective scanning detection based ion trap 

  [Term]
  id: MS:1000291
  name: linear ion trap
  def: "A two dimensional ion trap in which ions are confined in the axial dimension by means of an electric field at the ends of the trap." [PSI:MS]
  is_a: MS:XXXXXXX ! mass selective scanning detection based ion trap 


  Note: I do have a doubt whether we need to separate a FT cell (Penning cell) where ions are detected as image current from the older FT-ICR where ions in teh Penning cell are detected while hitting the walls of the cell, but I suspect it is ok to leave like this.

  Pierre-Alain



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[Psidev-ms-dev] item Paul ion trap

[pierre-alain b. <pie...@is...>]

Hi all,

one action item was to clarify the existence, relevance and position of 
the Paul ion trap term.

Marcus Macht from Bruker did help in this, and here is the explanation 
and proposal:


We have the following terms discussed here:
-    Quadrupole ion trap
-    Paul ion trap
-    Linear trap
-    Ion trap


-    The term "quadrupole ion trap" refers to the nature of the fields 
inside an ion trap and NOT to the geometry of the analyzer.
-    A quadrupole ion trap, in its _classical_ design, and as described 
by Paul is made of a circular electrode and 2 end-caps electrodes. It is 
NOT constituted by a quadrupole (i.e. 4  linear or curved rods) with 2 
end caps electrodes.
-    The Paul ion trap is synonym to the classical quadrupole ion trap.
-    The linear trap (as in LTQ or Qtrap for instance) has the geometry 
of a quadrupole + end caps electrodes and generates quadrupolar ion trap 
fields. It is a quadrupole ion trap.
-    Both Paul ion trap an linear trap are quadrupole ion traps.

We should therefore have in the PSI-MS CV:
   +-quadrupole ion trap
      +-Paul ion trap (classical quadrupole ion trap with circular 
electrode such as in : Bruker Esquire, HCT, amaZon; Thermo LCQ; Shimadzu 
LC-IT-TOF and Axima Resonance (MALDI), Agilent/Varian 500-MS)
      +-Linear quadrupole ion trap (such as in ABSCIEX QTRAPs, Thermo LTQs)


Now about the term ion trap in the current CV:
In the PSI-MS CV, the term "ion trap" is not correctly positioned. It is 
a generic term with a correct definition for a generic term. The term as 
defined now should includes Orbi and FTICR as childs, though. And the 
synonym "IT" should become a synonym of quadrupole ion trap (as it is 
mostly used and marketed in that context). If we keep the term we should 
make the following (concentrate on the ion trap part):

Here is therefore the proposal:

mass analyzer
+-Time of Flight
+-quadrupole mass filter
+-magnetic sector
+-ion trap
    +-image current detection based ion trap <!-- new term -->
       +-Orbitrap <!-- note that this refers to the analyzer, not the 
instrument name, which is correctly defined in the CV -->
       +-FTICR (Penning cell)
    +-mass selective scanning detection based ion trap <!-- "renamed" 
quadrupole ion trap -->
       +-Paul ion trap (classical quadrupolar ion trap with circular 
electrode)
       +-Linear ion trap
          +-radial ejection linear ion trap
          +-axial ejection lineal ion trap

The term Pal ion trap should therefore not be obsolete.

Suggestions for the CV:
[Term] id: MS:XXXXXXX
name: image current detection based ion trap
def: "Ion trap analyzer where ions are moving in an orbit which 
trajectory frequency can be measured as an image current " [PSI:MS] 
is_a: MS:1000264 ! ion trap

[Term] id: MS:XXXXXXX
name: mass selective scanning detection based ion trap
def: "Ion trap analyzer where ions are m/z selectively ejected from the 
trapping device and detected outside of it " [PSI:MS]
is_a: MS:1000264 ! ion trap

[Term]
id: MS:1000484
name: orbitrap
def: "An ion trapping device that consists of an outer barrel-like 
electrode and a coaxial inner spindle-like electrode that form an 
electrostatic field with quadro-logarithmic potential distribution. The 
frequency of harmonic oscillations of the orbitally trapped ions along 
the axis of the electrostatic field is independent of the ion velocity 
and is inversely proportional to the square root of m/z so that the trap 
can be used as a mass analyzer." [PSI:MS]
is_a: MS:XXXXXXX ! image current detection based ion trap

[Term]
id: MS:1000079
name: fourier transform ion cyclotron resonance mass spectrometer
def: "A mass spectrometer based on the principle of ion cyclotron 
resonance in which an ion in a magnetic field moves in a circular orbit 
at a frequency characteristic of its m/z value. Ions are coherently 
excited to a larger radius orbit using a pulse of radio frequency energy 
and their image charge is detected on receiver plates as a time domain 
signal. Fourier transformation of the time domain signal results in a 
frequency domain signal which is converted to a mass spectrum based in 
the inverse relationship between frequency and m/z." [PSI:MS]
synonym: "FT_ICR" EXACT []
is_a: MS:XXXXXXX ! image current detection based ion trap

[Term]
id: MS:1000297
name: Paul ion trap
def: "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]
synonym: "quadrupole ion trap" RELATED []
is_a: MS:XXXXXXX ! mass selective scanning detection based ion trap

[Term]
id: MS:1000291
name: linear ion trap
def: "A two dimensional ion trap in which ions are confined in the axial 
dimension by means of an electric field at the ends of the trap." [PSI:MS]
is_a: MS:XXXXXXX ! mass selective scanning detection based ion trap


Note: I do have a doubt whether we need to separate a FT cell (Penning 
cell) where ions are detected as image current from the older FT-ICR 
where ions in teh Penning cell are detected while hitting the walls of 
the cell, but I suspect it is ok to leave like this.

Pierre-Alain

[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

[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

[Psidev-ms-dev] PSI MSS WG call notes

[Eric D. <ede...@sy...>]

PSI MSS WG teleconference notes



Present: David, Steffen, Matt, Pierre-Alain, Eric



TraML:

- Manuscript revisions and reviewer response has been circulated.
Additional comments?

- It has been noted that unlike other PSI formats, we are missing
userParams in the schema.

- Do we want to add userParam capability everywhere there’s cvParam?

- After discussion, yes, let’s do this

- Eric will update the schema and send to Matt for inspection

- Will declare 1.0 and release and resubmit manuscript



CV:

- What do we do with “Paul ion trap”? It appears in MIAPE-MS. Resurrect
from purgatory? Or obsolete and make a synonym of “quadrupole ion trap”

+ Decide that we will remove “Paul trap” from MIAPE-MS 3.1.1, obsolete
MS:1000297, and make “Paul ion trap” an exact synonym of “quadrupole ion
trap”

+ Put axial and redial ejection linear ion traps under linear ion traps

+ Not fully sure

+ Pierre-Alain will find an MS guru at Bruker to clarify



name: electrospray supply type

name: static supply electrospray

name: fed supply electrospray

( need to update mapping files to accommodate this)



- What’s the difference between a “source interface” and “inlet type”?



- “xxxx manufacturer” and “xxxx model” terms need string datatypes?



- Ran out of time. Let’s continue discussion via email



Next meeting:

- Dec 13  8am Seattle Time?

+ yes





*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Monday, November 28, 2011 4:05 PM
*To:* Mass spectrometry standard development
*Cc:* Eric Deutsch
*Subject:* PSI MSS WG call reminder



Hi everyone, this is a reminder about the PSI MSS WG teleconference call
tomorrow, Tuesday, postponed from last week.



08:00 San Francisco

11:00 New York

16:00 London

17:00 Geneva



+ Germany: 08001012079

+ Switzerland: 0800000860

+ Finland: 080011569

+ UK: 08081095644

+ USA: 1-866-832-8490

Generic international: +44 2083222500 (UK number)



access code: 297427 #





Agenda:

1) Discuss response to TraML review and final release plans

2) Discuss David’s new terms



Next meeting:

- Dec 13 8am Seattle Time?

[Psidev-ms-dev] (no subject)

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

Hi community,

In order to validate some concepts covered by MIAPE-MS, some new terms
should be added to the controlled vocabulary, and a couple of point could
be discussed as well:
- Fourteen new c.v. terms
- Rellocation of two terms (Paul ion trap - it appears in the last
MIAPE-MS version... that's the only reason to take this obscure term into
consideration - and associating "sample plate type" to "precoated plate")
- Discussing the convenience of adding "Hexapole"
- What to do to convinently validate "post-source decay (MS:1000135)" (two
children having the meaning of "on"/"off" where proposed)
- How to validate matrix solution (MS:1000834)

(These terms have been initially checked by Eric and I have already
introduced all his suggested changes in the following terms.)


Fourteen new terms proposed under source (MS:1000458) to cover concepts
like "supply type", "source interface", "sprayer" and "sample plate"
=======================================================================
==================
[Term]
id: MS:XXXXXX1
name: 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:XXXXXXX
name: static supply
def: "The sprayer is loaded with sample once." [PSI:MS]
is_a: MS:XXXXXX1 ! supply type

[Term]
id: MS:XXXXXXX
name: fed supply
def: "The sprayer is continuously fed with sample." [PSI:MS]
is_a: MS:XXXXXX1 ! supply type

[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


Two existent terms changed
================
The term "paul ion trap" moved from "purgatory" to "mass analyzer term"
and a new relation in "precolated plate", now also a "sample plate
type"

[Term]
id: MS:1000297
name: paul ion trap
def: "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] synonym: "quadrupole ion trap" RELATED []
is_a: MS:1000443 ! mass analyzer 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

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. I would propose instead, ways in which the users could
define these hybrid analyzers (Q-TOF and 3Q would be an example). This
is a really important part of the information we expect to validate and
I'd like to read here your opinions.

post-source decay (MS:1000135)
====================
We can assume that the presence of this term means "yes", and the
absence, "no".

matrix solution (MS:1000834)
===================
A description of the matrix solution employed, as free text, could be
enough here. The alternative should be listing a complete inventory of
the several matrix solutions used.



Best,
David

[Psidev-ms-dev] PSI MSS WG call reminder

[Eric D. <ede...@sy...>]

Hi everyone, this is a reminder about the PSI MSS WG teleconference call
tomorrow, Tuesday, postponed from last week.



08:00 San Francisco

11:00 New York

16:00 London

17:00 Geneva



+ Germany: 08001012079

+ Switzerland: 0800000860

+ Finland: 080011569

+ UK: 08081095644

+ USA: 1-866-832-8490

Generic international: +44 2083222500 (UK number)



access code: 297427 #





Agenda:

1) Discuss response to TraML review and final release plans

2) Discuss David’s new terms



Next meeting:

- Dec 13 8am Seattle Time?

[Psidev-ms-dev] psi-ms controlled vocabulary v. 3.16.0 released

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

Dear community,

Just released the new version of the controlled vocabulary.

Changes:
The changes in the new version 3.16.0 are:
- Import unit ontology changed from
"http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"
to "http://unit-ontology.googlecode.com/svn/trunk/unit.obo"
- Six new terms (MS:1001908 to MS:1001913): 4 new instruments, 1 new
software and 1 source attribute term

Best,
David

[Psidev-ms-dev] PSI MSS WG call postponed

[Eric D. <ede...@sy...>]

Hi everyone, it doesn’t seem that we have any pressing agenda items at the
moment. One set of CV terms is pending but I don’t think we need discussion
on them. The TraML manuscript is still under review. And since this is a
holiday week in the US, let’s postpone the call until next week. Please
send me any agenda items you’d like to hit next week.



Thanks,

Eric

[Psidev-ms-dev] psi-ms controlled voc. version 3.15.0 released

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

Hello again, community,

3.15.0 version of the controlled vocabulary version has just been released.
Please, CHECK the changes!!!!! As an exceptional event, I didn't send 
this before validation to the community.

The changes are:
Two names (and definitions) changed: id: MS:1001843 (MS1 feature maximum 
intensity) and MS:1001844(MS1 feature area)
One term obsoleted (MS:1001845).
Added 18 new terms (MS:1001890 to MS:1001907)



Detailed list of changes:
Two names (and definitions) changed
===============================
[Term]
id: MS:1001843
name: MS1 feature maximum intensity
def: "Maximum intensity of MS1 feature." [PSI:PI]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1001844
name: MS1 feature area
def: "Area of MS1 feature." [PSI:PI]
is_a: MS:1001805 ! quantification datatype

One term obsoleted
=================
[Term]
id: MS:1001845
name: peak area
def: "OBSOLETE Area of MS1 peak (e.g. SILAC, 15N)." [PSI:PI]
comment: This term was made obsolete because it was a duplication of 
MS:1001844
is_a: MS:1001805 ! quantification datatype
is_obsolete: true


New terms
===========
[Term]
id: MS:1001890
name: Progenesis:protein normalised abundance
def: "The data type normalised abundance for proteins produced by 
Progenesis LC-MS." [PSI:MS]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1001891
name: Progenesis:peptide normalised abundance
def: "The data type normalised abundance for peptides produced by 
Progenesis LC-MS." [PSI:MS]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1001892
name: Progenesis:protein raw abundance
def: "The data type raw abundance for proteins produced by Progenesis 
LC-MS."  [PSI:MS]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1001893
name: Progenesis:peptide raw abundance
def: "The data type raw abundance for peptide produced by Progenesis 
LC-MS." [PSI:MS]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1001894
name: Progenesis:confidence score
def: "The data type confidence score  produced by Progenesis LC-MS." 
[PSI:MS]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1001895
name: Progenesis:peptide count
def: "The data type peptide count produced by Progenesis LC-MS." [PSI:MS]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1001896
name: Progenesis:feature intensity
def: "The data type feature intensity produced by Progenesis LC-MS." 
[PSI:MS]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1001897
name: MaxQuant:peptide counts (unique)
def: "The data type peptide counts (unique) produced by MaxQuant." [PSI:MS]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1001898
name: MaxQuant:peptide counts (all)
def: "The data type peptide counts (all) produced by MaxQuant." [PSI:MS]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1001899
name: MaxQuant:peptide counts (razor+unique)
def: "The data type peptide counts (razor+unique)  produced by 
MaxQuant." [PSI:MS]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1001900
name: MaxQuant:sequence length
def: "The data type sequence length produced by MaxQuant." [PSI:MS]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1001901
name: MaxQuant:PEP
def: "The data type PEP (posterior error probability) produced by 
MaxQuant." [PSI:MS]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1001902
name: MaxQuant:LFQ intensity
def: "The data type LFQ intensity produced by MaxQuant." [PSI:MS]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1001903
name: MaxQuant:feature intensity
def: "The data type feature intensity produced by MaxQuant." [PSI:MS]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1001904
name: MaxQuant:MS/MS count
def: "The data type MS/MS count produced by MaxQuant." [PSI:MS]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1001905
name: emPAI value
def: "The emPAI value of protein abundance, produced from the emPAI 
algorithm." [PSI:MS]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1001906
name: APEX value
def: "The APEX value of protein abundance, produced from the APEX 
software." [PSI:MS]
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1001907
name: retention time window width
def: "The full width of a retention time window for a chromatographic 
peak." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000915 ! retention time window attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute


Best,
David

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