psidev-ms-dev — Mass spectroscopy standard development

Re: [Psidev-ms-dev] [Psidev-pi-dev] [CompMS] Re: [Psi-announce] PSI2020 - Save the Date

[Eric D. <eri...@is...>]

Thanks, Joe, it looks like there is great interest. We have a workshop
planning call next week and will create a slot for a session on this. The
dates for the workshop are:



Mon Mar 23:

Tue Mar 24:

Wed Mar 25:

Thu Mar 26:



If anyone very interested in a glycoproteomics session has any major
constraints in participation on these days, please let me know and we can
try to work around it to maximize participation.



Thanks,

Eric









*From:* Zaia, Joseph <jz...@bu...>
*Sent:* Wednesday, November 27, 2019 7:16 AM
*To:* Eric Deutsch <eri...@is...>; Robert Chalkley <
cha...@cg...>; Jones, Andy <And...@li...>;
psi...@eb...; ps...@eb...; Mass spectrometry standard
development <psi...@li...>;
psi...@li...; Co...@go...
*Cc:* nj...@ge...
*Subject:* RE: [Psidev-pi-dev] [CompMS] Re: [Psi-announce] PSI2020 - Save
the Date



I have been in touch with Nathan Edwards (Georgetown University, copied).
He expressed interest in attending the session to discuss supporting
glycoproteomics data.



Best regards,



Joe



*From:* Eric Deutsch <eri...@is...>
*Sent:* Tuesday, November 26, 2019 7:40 PM
*To:* Robert Chalkley <cha...@cg...>; Zaia, Joseph <jz...@bu...>;
Jones, Andy <And...@li...>; psi...@eb...;
ps...@eb...; Mass spectrometry standard development <
psi...@li...>; psi...@li...;
Co...@go...
*Subject:* Re: [Psidev-pi-dev] [CompMS] Re: [Psi-announce] PSI2020 - Save
the Date



Hi Robert, great, thanks for contributing! We will try to schedule a
specific session for this and announce it so that everyone knows when it is
in advance.



Thanks,

Eric





*From:* co...@go... <co...@go...> *On Behalf Of *Robert
Chalkley
*Sent:* Monday, November 25, 2019 9:01 AM
*To:* Zaia, Joseph <jz...@bu...>; Jones, Andy <And...@li...>;
psi...@eb...; ps...@eb...; Mass spectrometry standard
development <psi...@li...>;
psi...@li...; Co...@go...
*Subject:* [CompMS] Re: [Psi-announce] [Psidev-pi-dev] PSI2020 - Save the
Date



I would also be keen to be involved in discussions about supporting
glycopeptide data.

Robert

On 11/22/2019 11:21 AM, Zaia, Joseph wrote:

Dear All,



I would like to initiate discussion for expanding the use cases for
proteomics to include complex protein glycosylation.  Glycosylation is as a
rule heterogeneous, with 30 or so glycoforms per glycosite.  In addition,
the glycan dissociates during tandem MS experiments.  The software and data
standards need to be expanded to include the glycosylation size,
heterogeneity, and tandem MS dissociation.  At present, quantitative
software (Skyline and others) do not recognize glycosylation.  Without this
recognition the quantitative tools developed for peptides cannot be adapted
without tedious effort on the part of the user.  Therefore, there is need
to expand the manner by which peptides are represented informatically.  It
is important that glycopeptides be included in the use cases for mzIdentML
and mzQuant.  It is also important that spectral library generating
software be expanded to allow glycosylated peptides to facilitate use of
data independent experiments for glycoproteins.



Would it be possible for me to communicate these ideas at the PSI Workshop
in San Diego?



Thank you.



Joe Zaia

*From:* Jones, Andy <And...@li...>
<And...@li...>
*Sent:* Thursday, November 21, 2019 11:29 AM
*To:* psi...@eb...; ps...@eb...; Mass spectrometry standard
development <psi...@li...>
<psi...@li...>; psi...@li...;
Co...@go...
*Subject:* [Psidev-pi-dev] PSI2020 - Save the Date



Hi all,



We are pleased to announce that the 2020 Annual workshop for the Proteomics
Standards Initiative (PSI) will take place in San Diego USA, Mon 23rd to
Thurs 26th March 2020. The workshop will focus on developing data standards
related to mass spectrometry for spectral libraries, the universal spectrum
identifier, quality control and capturing study metadata, and in the
molecular interactions side on mapping standards to Cytoscape. We will also
be welcoming the new PSI work group – Intrinsically Disordered Proteins
(IDP).



Please save the date if you might be interested to attend, we are always
pleased to welcome new groups into the PSI. The registration page will be
made available in the coming weeks.



Best wishes

Andy Jones on behalf of the PSI steering committee





_______________________________________________

Psi-announce mailing list

Psi...@eb...

https://listserver.ebi.ac.uk/mailman/listinfo/psi-announce

-- 

Robert Chalkley PhD

Adjunct Professor

Genentech Hall, N474A

Tel: 415 476 5189

Fax: 415 502 1655



Mass Spectrometry Facility

University of California San Francisco

600 16th Street,

Genentech Hall, suite N472A

San Francisco, CA 94143-2240







-- 
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.

Re: [Psidev-ms-dev] [Psidev-pi-dev] [CompMS] Re: [Psi-announce] PSI2020 - Save the Date

[Zaia, J. <jz...@bu...>]

I have been in touch with Nathan Edwards (Georgetown University, copied).  He expressed interest in attending the session to discuss supporting glycoproteomics data.

Best regards,

Joe

From: Eric Deutsch <eri...@is...>
Sent: Tuesday, November 26, 2019 7:40 PM
To: Robert Chalkley <cha...@cg...>; Zaia, Joseph <jz...@bu...>; Jones, Andy <And...@li...>; psi...@eb...; ps...@eb...; Mass spectrometry standard development <psi...@li...>; psi...@li...; Co...@go...
Subject: Re: [Psidev-pi-dev] [CompMS] Re: [Psi-announce] PSI2020 - Save the Date

Hi Robert, great, thanks for contributing! We will try to schedule a specific session for this and announce it so that everyone knows when it is in advance.

Thanks,
Eric


From: co...@go...<mailto:co...@go...> <co...@go...<mailto:co...@go...>> On Behalf Of Robert Chalkley
Sent: Monday, November 25, 2019 9:01 AM
To: Zaia, Joseph <jz...@bu...<mailto:jz...@bu...>>; Jones, Andy <And...@li...<mailto:And...@li...>>; psi...@eb...<mailto:psi...@eb...>; ps...@eb...<mailto:ps...@eb...>; Mass spectrometry standard development <psi...@li...<mailto:psi...@li...>>; psi...@li...<mailto:psi...@li...>; Co...@go...<mailto:Co...@go...>
Subject: [CompMS] Re: [Psi-announce] [Psidev-pi-dev] PSI2020 - Save the Date


I would also be keen to be involved in discussions about supporting glycopeptide data.

Robert
On 11/22/2019 11:21 AM, Zaia, Joseph wrote:
Dear All,

I would like to initiate discussion for expanding the use cases for proteomics to include complex protein glycosylation.  Glycosylation is as a rule heterogeneous, with 30 or so glycoforms per glycosite.  In addition, the glycan dissociates during tandem MS experiments.  The software and data standards need to be expanded to include the glycosylation size, heterogeneity, and tandem MS dissociation.  At present, quantitative software (Skyline and others) do not recognize glycosylation.  Without this recognition the quantitative tools developed for peptides cannot be adapted without tedious effort on the part of the user.  Therefore, there is need to expand the manner by which peptides are represented informatically.  It is important that glycopeptides be included in the use cases for mzIdentML and mzQuant.  It is also important that spectral library generating software be expanded to allow glycosylated peptides to facilitate use of data independent experiments for glycoproteins.

Would it be possible for me to communicate these ideas at the PSI Workshop in San Diego?

Thank you.

Joe Zaia
From: Jones, Andy <And...@li...><mailto:And...@li...>
Sent: Thursday, November 21, 2019 11:29 AM
To: psi...@eb...<mailto:psi...@eb...>; ps...@eb...<mailto:ps...@eb...>; Mass spectrometry standard development <psi...@li...><mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>; Co...@go...<mailto:Co...@go...>
Subject: [Psidev-pi-dev] PSI2020 - Save the Date

Hi all,

We are pleased to announce that the 2020 Annual workshop for the Proteomics Standards Initiative (PSI) will take place in San Diego USA, Mon 23rd to Thurs 26th March 2020. The workshop will focus on developing data standards related to mass spectrometry for spectral libraries, the universal spectrum identifier, quality control and capturing study metadata, and in the molecular interactions side on mapping standards to Cytoscape. We will also be welcoming the new PSI work group – Intrinsically Disordered Proteins (IDP).

Please save the date if you might be interested to attend, we are always pleased to welcome new groups into the PSI. The registration page will be made available in the coming weeks.

Best wishes
Andy Jones on behalf of the PSI steering committee



_______________________________________________

Psi-announce mailing list

Psi...@eb...<mailto:Psi...@eb...>

https://listserver.ebi.ac.uk/mailman/listinfo/psi-announce

--

Robert Chalkley PhD

Adjunct Professor

Genentech Hall, N474A

Tel: 415 476 5189

Fax: 415 502 1655



Mass Spectrometry Facility

University of California San Francisco

600 16th Street,

Genentech Hall, suite N472A

San Francisco, CA 94143-2240






--
You received this message because you are subscribed to the Google Groups "CompMS" group.
To unsubscribe from this group and stop receiving emails from it, send an email to com...@go...<mailto:com...@go...>.
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Re: [Psidev-ms-dev] [CompMS] Re: [Psi-announce] [Psidev-pi-dev] PSI2020 - Save the Date

[Eric D. <eri...@is...>]

Hi Robert, great, thanks for contributing! We will try to schedule a
specific session for this and announce it so that everyone knows when it is
in advance.



Thanks,

Eric





*From:* co...@go... <co...@go...> *On Behalf Of *Robert
Chalkley
*Sent:* Monday, November 25, 2019 9:01 AM
*To:* Zaia, Joseph <jz...@bu...>; Jones, Andy <And...@li...>;
psi...@eb...; ps...@eb...; Mass spectrometry standard
development <psi...@li...>;
psi...@li...; Co...@go...
*Subject:* [CompMS] Re: [Psi-announce] [Psidev-pi-dev] PSI2020 - Save the
Date



I would also be keen to be involved in discussions about supporting
glycopeptide data.

Robert

On 11/22/2019 11:21 AM, Zaia, Joseph wrote:

Dear All,



I would like to initiate discussion for expanding the use cases for
proteomics to include complex protein glycosylation.  Glycosylation is as a
rule heterogeneous, with 30 or so glycoforms per glycosite.  In addition,
the glycan dissociates during tandem MS experiments.  The software and data
standards need to be expanded to include the glycosylation size,
heterogeneity, and tandem MS dissociation.  At present, quantitative
software (Skyline and others) do not recognize glycosylation.  Without this
recognition the quantitative tools developed for peptides cannot be adapted
without tedious effort on the part of the user.  Therefore, there is need
to expand the manner by which peptides are represented informatically.  It
is important that glycopeptides be included in the use cases for mzIdentML
and mzQuant.  It is also important that spectral library generating
software be expanded to allow glycosylated peptides to facilitate use of
data independent experiments for glycoproteins.



Would it be possible for me to communicate these ideas at the PSI Workshop
in San Diego?



Thank you.



Joe Zaia

*From:* Jones, Andy <And...@li...>
<And...@li...>
*Sent:* Thursday, November 21, 2019 11:29 AM
*To:* psi...@eb...; ps...@eb...; Mass spectrometry standard
development <psi...@li...>
<psi...@li...>; psi...@li...;
Co...@go...
*Subject:* [Psidev-pi-dev] PSI2020 - Save the Date



Hi all,



We are pleased to announce that the 2020 Annual workshop for the Proteomics
Standards Initiative (PSI) will take place in San Diego USA, Mon 23rd to
Thurs 26th March 2020. The workshop will focus on developing data standards
related to mass spectrometry for spectral libraries, the universal spectrum
identifier, quality control and capturing study metadata, and in the
molecular interactions side on mapping standards to Cytoscape. We will also
be welcoming the new PSI work group – Intrinsically Disordered Proteins
(IDP).



Please save the date if you might be interested to attend, we are always
pleased to welcome new groups into the PSI. The registration page will be
made available in the coming weeks.



Best wishes

Andy Jones on behalf of the PSI steering committee





_______________________________________________

Psi-announce mailing list

Psi...@eb...

https://listserver.ebi.ac.uk/mailman/listinfo/psi-announce

-- 

Robert Chalkley PhD

Adjunct Professor

Genentech Hall, N474A

Tel: 415 476 5189

Fax: 415 502 1655



Mass Spectrometry Facility

University of California San Francisco

600 16th Street,

Genentech Hall, suite N472A

San Francisco, CA 94143-2240







-- 
You received this message because you are subscribed to the Google Groups
"CompMS" group.
To unsubscribe from this group and stop receiving emails from it, send an
email to com...@go....
To view this discussion on the web visit
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<https://groups.google.com/d/msgid/compms/53fa5771-c50a-6f0d-5d17-de723112a016%40cgl.ucsf.edu?utm_medium=email&utm_source=footer>
.

Re: [Psidev-ms-dev] [Psi-announce] [Psidev-pi-dev] PSI2020 - Save the Date

[Robert C. <cha...@cg...>]

I would also be keen to be involved in discussions about supporting 
glycopeptide data.

Robert

On 11/22/2019 11:21 AM, Zaia, Joseph wrote:
>
> Dear All,
>
> I would like to initiate discussion for expanding the use cases for 
> proteomics to include complex protein glycosylation. Glycosylation is 
> as a rule heterogeneous, with 30 or so glycoforms per glycosite.  In 
> addition, the glycan dissociates during tandem MS experiments.  The 
> software and data standards need to be expanded to include the 
> glycosylation size, heterogeneity, and tandem MS dissociation.  At 
> present, quantitative software (Skyline and others) do not recognize 
> glycosylation.  Without this recognition the quantitative tools 
> developed for peptides cannot be adapted without tedious effort on the 
> part of the user.  Therefore, there is need to expand the manner by 
> which peptides are represented informatically.  It is important that 
> glycopeptides be included in the use cases for mzIdentML and mzQuant.  
> It is also important that spectral library generating software be 
> expanded to allow glycosylated peptides to facilitate use of data 
> independent experiments for glycoproteins.
>
> Would it be possible for me to communicate these ideas at the PSI 
> Workshop in San Diego?
>
> Thank you.
>
> Joe Zaia
>
> *From:* Jones, Andy <And...@li...>
> *Sent:* Thursday, November 21, 2019 11:29 AM
> *To:* psi...@eb...; ps...@eb...; Mass spectrometry 
> standard development <psi...@li...>; 
> psi...@li...; Co...@go...
> *Subject:* [Psidev-pi-dev] PSI2020 - Save the Date
>
> Hi all,
>
> We are pleased to announce that the 2020 Annual workshop for the 
> Proteomics Standards Initiative (PSI) will take place in San Diego 
> USA, Mon 23^rd to Thurs 26^th March 2020. The workshop will focus on 
> developing data standards related to mass spectrometry for spectral 
> libraries, the universal spectrum identifier, quality control and 
> capturing study metadata, and in the molecular interactions side on 
> mapping standards to Cytoscape. We will also be welcoming the new PSI 
> work group – Intrinsically Disordered Proteins (IDP).
>
> Please save the date if you might be interested to attend, we are 
> always pleased to welcome new groups into the PSI. The registration 
> page will be made available in the coming weeks.
>
> Best wishes
>
> Andy Jones on behalf of the PSI steering committee
>
>
> _______________________________________________
> Psi-announce mailing list
> Psi...@eb...
> https://listserver.ebi.ac.uk/mailman/listinfo/psi-announce

-- 
Robert Chalkley PhD
Adjunct Professor
Genentech Hall, N474A
Tel: 415 476 5189
Fax: 415 502 1655

Mass Spectrometry Facility
University of California San Francisco
600 16th Street,
Genentech Hall, suite N472A
San Francisco, CA 94143-2240

Re: [Psidev-ms-dev] [CompMS] [Psidev-pi-dev] PSI2020 - Save the Date

[Zaia, J. <jz...@bu...>]

Thanks, Juan. I look forward to attending the spring HUPO-PSI meeting.

Joe

From: Juan Antonio Vizcaino <ju...@eb...>
Sent: Monday, November 25, 2019 8:04 AM
To: Zaia, Joseph <jz...@bu...>
Cc: Andy Jones <And...@li...>; psi...@eb...; ps...@eb...; Mass spectrometry standard development <psi...@li...>; psi...@li...; Co...@go...
Subject: Re: [CompMS] [Psidev-pi-dev] PSI2020 - Save the Date

Dear Joe,

Thanks for your e-mail.

You are very welcome to present in San Diego. We are still discussing the agenda, but we will make sure you get a slot.

Best regards,

Juan




On 22 Nov 2019, at 19:21, Zaia, Joseph <jz...@bu...<mailto:jz...@bu...>> wrote:

Dear All,

I would like to initiate discussion for expanding the use cases for proteomics to include complex protein glycosylation.  Glycosylation is as a rule heterogeneous, with 30 or so glycoforms per glycosite.  In addition, the glycan dissociates during tandem MS experiments.  The software and data standards need to be expanded to include the glycosylation size, heterogeneity, and tandem MS dissociation.  At present, quantitative software (Skyline and others) do not recognize glycosylation.  Without this recognition the quantitative tools developed for peptides cannot be adapted without tedious effort on the part of the user.  Therefore, there is need to expand the manner by which peptides are represented informatically.  It is important that glycopeptides be included in the use cases for mzIdentML and mzQuant.  It is also important that spectral library generating software be expanded to allow glycosylated peptides to facilitate use of data independent experiments for glycoproteins.

Would it be possible for me to communicate these ideas at the PSI Workshop in San Diego?

Thank you.

Joe Zaia
From: Jones, Andy <And...@li...<mailto:And...@li...>>
Sent: Thursday, November 21, 2019 11:29 AM
To: psi...@eb...<mailto:psi...@eb...>; ps...@eb...<mailto:ps...@eb...>; Mass spectrometry standard development <psi...@li...<mailto:psi...@li...>>; psi...@li...<mailto:psi...@li...>; Co...@go...<mailto:Co...@go...>
Subject: [Psidev-pi-dev] PSI2020 - Save the Date

Hi all,

We are pleased to announce that the 2020 Annual workshop for the Proteomics Standards Initiative (PSI) will take place in San Diego USA, Mon 23rd to Thurs 26th March 2020. The workshop will focus on developing data standards related to mass spectrometry for spectral libraries, the universal spectrum identifier, quality control and capturing study metadata, and in the molecular interactions side on mapping standards to Cytoscape. We will also be welcoming the new PSI work group – Intrinsically Disordered Proteins (IDP).

Please save the date if you might be interested to attend, we are always pleased to welcome new groups into the PSI. The registration page will be made available in the coming weeks.

Best wishes
Andy Jones on behalf of the PSI steering committee


--
You received this message because you are subscribed to the Google Groups "CompMS" group.
To unsubscribe from this group and stop receiving emails from it, send an email to com...@go...<mailto:com...@go...>.
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Re: [Psidev-ms-dev] [CompMS] [Psidev-pi-dev] PSI2020 - Save the Date

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

Dear Joe,

Thanks for your e-mail.

You are very welcome to present in San Diego. We are still discussing the agenda, but we will make sure you get a slot.

Best regards,

Juan



> On 22 Nov 2019, at 19:21, Zaia, Joseph <jz...@bu...> wrote:
> 
> Dear All,
>  
> I would like to initiate discussion for expanding the use cases for proteomics to include complex protein glycosylation.  Glycosylation is as a rule heterogeneous, with 30 or so glycoforms per glycosite.  In addition, the glycan dissociates during tandem MS experiments.  The software and data standards need to be expanded to include the glycosylation size, heterogeneity, and tandem MS dissociation.  At present, quantitative software (Skyline and others) do not recognize glycosylation.  Without this recognition the quantitative tools developed for peptides cannot be adapted without tedious effort on the part of the user.  Therefore, there is need to expand the manner by which peptides are represented informatically.  It is important that glycopeptides be included in the use cases for mzIdentML and mzQuant.  It is also important that spectral library generating software be expanded to allow glycosylated peptides to facilitate use of data independent experiments for glycoproteins.
>  
> Would it be possible for me to communicate these ideas at the PSI Workshop in San Diego? 
>  
> Thank you.
>  
> Joe Zaia
> From: Jones, Andy <And...@li... <mailto:And...@li...>> 
> Sent: Thursday, November 21, 2019 11:29 AM
> To: psi...@eb... <mailto:psi...@eb...>; ps...@eb... <mailto:ps...@eb...>; Mass spectrometry standard development <psi...@li... <mailto:psi...@li...>>; psi...@li... <mailto:psi...@li...>; Co...@go... <mailto:Co...@go...>
> Subject: [Psidev-pi-dev] PSI2020 - Save the Date
>  
> Hi all,
>  
> We are pleased to announce that the 2020 Annual workshop for the Proteomics Standards Initiative (PSI) will take place in San Diego USA, Mon 23rd to Thurs 26th March 2020. The workshop will focus on developing data standards related to mass spectrometry for spectral libraries, the universal spectrum identifier, quality control and capturing study metadata, and in the molecular interactions side on mapping standards to Cytoscape. We will also be welcoming the new PSI work group – Intrinsically Disordered Proteins (IDP).
>  
> Please save the date if you might be interested to attend, we are always pleased to welcome new groups into the PSI. The registration page will be made available in the coming weeks.
>  
> Best wishes
> Andy Jones on behalf of the PSI steering committee
>  
> 
> -- 
> You received this message because you are subscribed to the Google Groups "CompMS" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to com...@go... <mailto:com...@go...>.
> To view this discussion on the web visit https://groups.google.com/d/msgid/compms/BN7PR03MB38755FF1B30AC07417844AB8CE490%40BN7PR03MB3875.namprd03.prod.outlook.com <https://groups.google.com/d/msgid/compms/BN7PR03MB38755FF1B30AC07417844AB8CE490%40BN7PR03MB3875.namprd03.prod.outlook.com?utm_medium=email&utm_source=footer>.

[Psidev-ms-dev] PSI2020 - Save the Date

[Jones, A. <And...@li...>]

Hi all,

We are pleased to announce that the 2020 Annual workshop for the Proteomics Standards Initiative (PSI) will take place in San Diego USA, Mon 23rd to Thurs 26th March 2020. The workshop will focus on developing data standards related to mass spectrometry for spectral libraries, the universal spectrum identifier, quality control and capturing study metadata, and in the molecular interactions side on mapping standards to Cytoscape. We will also be welcoming the new PSI work group - Intrinsically Disordered Proteins (IDP).

Please save the date if you might be interested to attend, we are always pleased to welcome new groups into the PSI. The registration page will be made available in the coming weeks.

Best wishes
Andy Jones on behalf of the PSI steering committee

[Psidev-ms-dev] New version 4.1.32 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics/metabolomics community,

following are the new terms for the version 4.1.32 of the psi-ms.obo file,

which can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo


New CV terms in version 4.1.32 of psi-ms.obo:
=============================================
[Term]
id: MS:1003032
name: compound identification confidence code in MS-DIAL
def: "The confidence code to describe the confidence of annotated 
compounds as defined by the MS-DIAL program." [PMID:25938372, 
http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002895 ! small molecule identification attribute

Best Regards,
Gerhard

-- 

*----------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*Research associate*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

*Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496

*E-Mail: *ger...@ru... <mailto:ger...@ru...>

*Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc>

[Psidev-ms-dev] Release candidate 4.1.32_rc1 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics/metabolomics community,

following are the new terms for the release candidate 4.1.32_rc1 of
the psi-ms.obo file.

New CV terms in version 4.1.32_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1003032
name: compound identification confidence code in MS-DIAL
def: "The confidence code to describe the confidence of annotated 
compounds as defined by the MS-DIAL program." [PMID:25938372, 
http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002895 ! small molecule identification attribute

Best Regards,
Gerhard

-- 

*----------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*Research associate*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

*Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496

*E-Mail: *ger...@ru... <mailto:ger...@ru...>

*Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc>

[Psidev-ms-dev] New version 4.1.31 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics/metabolomics community,

following are the new and modified  terms from the version 4.1.31 of the 
psi-ms.obo file.
It can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo

New CV terms version 4.1.31_rc1 of psi-ms.obo:
==============================================
[Term]
id: MS:1003031
name: CPTAC accession number
def: "Main identifier of a CPTAC dataset." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier

Modified CV terms version 4.1.31_rc1 of psi-ms.obo:
===================================================
[Term]
id: MS:1002810
name: adduct ion mass X m/z
def: "Theoretical m/z of the X component in the adduct M+X or M-X. This 
term was formerly called 'adduct ion mass', but it is not really a mass. 
It corresponds to the column mislabeled as 'Mass' at 
https://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator." 
[DOI:10.1016/S1044-0305(99)00089-6, 
http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002809 ! adduct ion attribute

Best regards
Gerhard
-- 

*----------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*Research associate*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

*Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496

*E-Mail: *ger...@ru... <mailto:ger...@ru...>

*Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc>

[Psidev-ms-dev] Release candidate 4.1.31_rc1 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics/metabolomics community,


following are the new and modified terms for the release version 
4.1.31_rc1 of
the psi-ms.obo file.


New CV terms in version 4.1.31_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1003031
name: CPTAC accession number
def: "Main identifier of a CPTAC dataset." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier


Modified CV terms in version 4.1.31_rc1 of psi-ms.obo:
======================================================
[Term]
id: MS:1002810
name: adduct ion mass X m/z
def: "Theoretical m/z of the X component in the adduct M+X or M-X. This 
term was formerly called 'adduct ion mass', but it is not really a mass. 
It corresponds to the column mislabeled as 'Mass' at 
https://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator." 
[DOI:10.1016/S1044-0305(99)00089-6, 
http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002809 ! adduct ion attribute

Best Regards,
Gerhard

-- 

*----------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*Research associate*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

*Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496

*E-Mail: *ger...@ru... <mailto:ger...@ru...>

*Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc>

[Psidev-ms-dev] New version 4.1.30 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics/metabolomics community,

following are the new terms for the release version 4.1.30 of
the psi-ms.obo file. It can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo

New CV terms in version 4.1.30 of psi-ms.obo:
=============================================
************ New term for a Mascot report parameter
[Term]
id: MS:1003030
name: Mascot:MinNumSigUniqueSeqs
def: "Minimum number of significant unique sequences required in a 
protein hit. The setting is only relevant if the protein grouping 
strategy is 'family clustering'." [PSI:PI]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for 
this CV term."
is_a: MS:1002095 ! Mascot input parameter

Best Regards,
Gerhard

-- 

*----------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*Research associate*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

*Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496

*E-Mail: *ger...@ru... <mailto:ger...@ru...>

*Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc>

[Psidev-ms-dev] New version 4.1.29 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics/metabolomics community,


following are the new terms for the release version 4.1.29 of
the psi-ms.obo file. It contains two CV terms for new Thermo Scientific
instruments and can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo


New CV terms in version 4.1.29 of psi-ms.obo:
=============================================
************ New terms for Thermo Scientific instruments
[Term]
id: MS:1003028
name: Orbitrap Exploris 480
def: "Thermo Scientific Orbitrap Exploris 480 Quadrupole Orbitrap MS." 
[PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1003029
name: Orbitrap Eclipse
def: "Thermo Scientific Orbitrap Eclipse mass spectrometer with Tribrid 
architecture consisting of quadrupole mass filter, linear ion trap and 
Orbitrap mass analyzers." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model


Best Regards,
Gerhard

-- 

*----------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*Scientific assistant*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

*Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496

*E-Mail: *ger...@ru... <mailto:ger...@ru...>

*Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc>

[Psidev-ms-dev] New version 4.1.28 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics/metabolomics community,

following are the new terms for the release version 4.1.28 of
the psi-ms.obo file. It can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo

New CV terms in version 4.1.28 of psi-ms.obo:
=============================================
************ New terms for OpenPepXL
[Term]
id: MS:1003023
name: OpenPepXL
def: "Cross-Linking MS search engine." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1003024
name: OpenPepXL:score
def: "The OpenPepXL score for a cross-link spectrum match." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1003025
name: named element
def: "A named element that is an attribute in a proteomics standards 
file." [PSI:PI]
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass 
Spectrometry Vocabularies

[Term]
id: MS:1003026
name: named element in mzIdentML
def: "A named element that is an attribute in a mzIdentML file." [PSI:PI]
is_a: MS:1003025 ! named element

[Term]
id: MS:1003027
name: named element in mzML
def: "A named element that is an attribute in a mzML file." [PSI:PI]
is_a: MS:1003025 ! named element

Changed CV terms in version 4.1.28 of psi-ms.obo:
=================================================
************ Added 'is_a: MS:1003026 ! named element in mzIdentML'
[Term]
id: MS:1003021
name: Fixed modification
def: "Post-translational modification which is assumed to be present at 
each instance of a residue type." [PSI:PI]
is_a: MS:1001055 ! modification parameters
is_a: MS:1003026 ! named element in mzIdentML

[Term]
id: MS:1003022
name: Variable modification
def: "Post-translational modification which may or may not be present at 
a residue type." [PSI:PI]
is_a: MS:1001055 ! modification parameters
is_a: MS:1003026 ! named element in mzIdentML

Best Regards,
Gerhard

[Psidev-ms-dev] Release candidate 4.1.28_rc1 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics/metabolomics community,

following the new terms for the release candidate 4.1.28_rc1
of the psi-ms.obo file.


New CV terms in version 4.1.28_rc1 of psi-ms.obo:
=================================================
************ New terms for OpenPepXL
[Term]
id: MS:1003023
name: OpenPepXL
def: "Cross-Linking MS search engine." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1003024
name: OpenPepXL:score
def: "The OpenPepXL score for a cross-link spectrum match." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1003025
name: named element
def: "A named element that is an attribute in a proteomics standards 
file." [PSI:PI]
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass 
Spectrometry Vocabularies

[Term]
id: MS:1003026
name: named element in mzIdentML
def: "A named element that is an attribute in a mzIdentML file." [PSI:PI]
is_a: MS:1003025 ! named element

[Term]
id: MS:1003027
name: named element in mzML
def: "A named element that is an attribute in a mzML file." [PSI:PI]
is_a: MS:1003025 ! named element


Changed CV terms in version 4.1.28_rc1 of psi-ms.obo:
=====================================================
************ Added 'is_a: MS:1003026 ! named element in mzIdentML'
[Term]
id: MS:1003021
name: Fixed modification
def: "Post-translational modification which is assumed to be present at 
each instance of a residue type." [PSI:PI]
is_a: MS:1001055 ! modification parameters
is_a: MS:1003026 ! named element in mzIdentML

[Term]
id: MS:1003022
name: Variable modification
def: "Post-translational modification which may or may not be present at 
a residue type." [PSI:PI]
is_a: MS:1001055 ! modification parameters
is_a: MS:1003026 ! named element in mzIdentML

Best Regards,
Gerhard

Re: [Psidev-ms-dev] MS3+ spectra

[Chambers, M. <mat...@gm...>]

Ten years later, I'm faced with a Thermo RAW from a targeted method that only has MS3 spectra. And each MS3 is actually from "SPS" mode so 
it has multiple isolation windows contributing product ions (SPS mode has been available since the Orbitrap Velos). I need to be able to 
store both the hierarchy (because there is no precursor scan to reference) and the multiple isolation windows.

Fredrik's suggestion of using a cvParam in the <precursor> to indicate its order seems reasonable, but would require either a mapping file 
change or making the cvParam *is_a *'ion selection attribute' or 'isolation window attribute'. We could either make a new CV term or re-use 
'ms level': give it another *is_a* relationship to 'ion selection' or 'isolation window'.

Thoughts?
-Matt


On 9/22/2009 3:14 PM, Matthew Chambers wrote:
> A product ion spectrum that was produced from multiple isolation windows
> would need multiple precursors. I don't know if there's an instrument
> that can or does do this, but it's easy to imagine an instrument which
> can isolate each peak of an isotope envelope instead of isolating a wide
> window around all the isotopes (and all the noise in between).
>
> -Matt
>
>
> Fredrik Levander wrote:
>> Hi Matt,
>>
>> Are there any other examples of spectra which have more than one
>> precursor than the MS3(or higher) spectra? I think the general MS2 case
>> would be one precursor but possibly several selected ions. The only
>> situation I can  think of where there might be several possible
>> precursors selected would be some kind of merged spectrum, but that
>> could probably also in most cases be written as having one precursor
>> with several selected ions (if not the activation conditions were
>> different from each other for the original MS2 precursors).
>> A CV term that clarifies the order of a certain precursor in the
>> fragmentation hierarchy seems like a reasonable solution to clarify this
>> if needed, anyway. I guess it is not really correct in xml to just use
>> the order of apperance.
>>
>> -Fredrik
>>
>> Matthew Chambers skrev:
>>    
>>> Hi all,
>>>
>>> As far as I can tell, we don't have documentation or an official example
>>> of how to handle this case. Fredrik made an example for this and sent
>>> this example to the list on 12/28/2008:
>>> http://dev.thep.lu.se/fp6-prodac/svn/trunk/mzML/scans/5.ms3_scan.txt
>>>
>>> I'm concerned about the use of multiple precursors to represent the
>>> precursor "history." This seems quite confusing. Most of the time I
>>> would expect to see one precursor for the MS3 and if I wanted to know
>>> what the original MS precursor was, I'd look at the MS2's precursor.
>>> However, I can see that a method with a targeted MS3 (i.e. precursor and
>>> 1st generation product masses already known) might not even record the
>>> intermediate MS2 spectrum. So specifying the precursor hierarchy is
>>> sensible, but IMO we need to do it in a distinct way from the way we
>>> list multiple precursors that actually were fragmented to create the
>>> current scan. A clear solution to me seems to be to allow precursor to
>>> have a precursorList child element to explicitly indicate that the
>>> nested precursorList represents a previous generation of fragmentation.
>>> This is quite messy implementation-wise though, so another option is to
>>> use a cvParam in the precursorList to explicitly indicate what it means
>>> to have multiple precursors. This would mean that you couldn't mix
>>> multiple isolation windows with MS3+ though.
>>>
>>> Thoughts?
>>> -Matt
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9&#45;12, 2009. Register now&#33;
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> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 4.1.27_rc1 of psi-ms.obo

[Jones, A. <And...@li...>]

Yes that seems okay to me. I’m sure ontology purists would hate this approach, but it seems pragmatically useful for what we need to achieve.
Best wishes
Andy

From: Nuno Bandeira [mailto:ban...@uc...]
Sent: 07 June 2019 16:14
To: Mass spectrometry standard development <psi...@li...>
Cc: Jones, Andy <jo...@li...>; psi...@li...; psi...@li...; Eric Deutsch <ede...@sy...>; Gerhard Mayer <may...@ru...>
Subject: Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 4.1.27_rc1 of psi-ms.obo

+1 makes sense to me too.

Best,

Nuno

On Fri, Jun 7, 2019, 6:57 AM Eric Deutsch <ede...@sy...<mailto:ede...@sy...>> wrote:
I think this will be needed for the spectral library format at least since we will be needed a substantial number of concepts that are elements in mzIdentML. Pierre-Alain’s proposal seems pretty good to me. Anyone else have comments about doing it that way or refine the idea?

Thanks,
Eric


From: Binz Pierre-Alain <Pie...@ch...<mailto:Pie...@ch...>>
Sent: Thursday, June 6, 2019 11:42 PM
To: Jones, Andy <And...@li...<mailto:And...@li...>>; 'psi...@li...<mailto:psi...@li...>' <psi...@li...<mailto:psi...@li...>>; psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>
Cc: Gerhard Mayer <may...@ru...<mailto:may...@ru...>>
Subject: Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 4.1.27_rc1 of psi-ms.obo

Good point Andy.
If one need them for another format (these or others), should one systematically create all elements also as CV terms, have them annotated with a “is_a: MS:NNNNNN ! named element in mzIdentML “ /  mzML / etc., in order to make sure we have consistency of definition across formats?

Pierre-Alain


De : Jones, Andy <And...@li...<mailto:And...@li...>>
Envoyé : mercredi 5 juin 2019 16:43
À : 'psi...@li...<mailto:psi...@li...>' <psi...@li...<mailto:psi...@li...>>; psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>
Cc : Gerhard Mayer <may...@ru...<mailto:may...@ru...>>
Objet : Re: [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate 4.1.27_rc1 of psi-ms.obo

Hi Gerhard,

Apologies for joining this conversation presumably late – these are encoded in mzIdentML via named elements. Are these CV terms needed for a different format?
Best wishes
Andy

From: Gerhard Mayer via Psidev-ms-vocab [mailto:psi...@li...]
Sent: 05 June 2019 15:40
To: psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>
Cc: Gerhard Mayer <may...@ru...<mailto:may...@ru...>>
Subject: [Psidev-ms-vocab] Release candidate 4.1.27_rc1 of psi-ms.obo


Dear proteomics/metabolomics community,

following the new terms for the release candidate 4.1.27_rc1
of the psi-ms.obo file.

New CV terms in version 4.1.27_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1003021
name: fixed modification
def: "Modification which is assumed to be present at each instance of a residue type." [PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

[Term]
id: MS:1003022
name: variable modification
def: "A modification which may or may not be present at a residue type." [PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

Best Regards,
Gerhard
--

----------------------------------------------------------------------

Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER

Scientific assistant

Ruhr-Universität Bochum, Medizinisches Proteom-Center

DEPARTMENT Medical Bioinformatics

Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum

Fon: +49 (0)234 32-29272 | Fax: +49 (0)234 32-14554

E-Mail: ger...@ru...<mailto:ger...@ru...>

Web: www.ruhr-uni-bochum.de/mpc<http://www.ruhr-uni-bochum.de/mpc>

_______________________________________________
Psidev-ms-dev mailing list
Psi...@li...<mailto:Psi...@li...>
https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 4.1.27_rc1 of psi-ms.obo

[Nuno B. <ban...@uc...>]

+1 makes sense to me too.

Best,

Nuno

On Fri, Jun 7, 2019, 6:57 AM Eric Deutsch <ede...@sy...>
wrote:

> I think this will be needed for the spectral library format at least since
> we will be needed a substantial number of concepts that are elements in
> mzIdentML. Pierre-Alain’s proposal seems pretty good to me. Anyone else
> have comments about doing it that way or refine the idea?
>
>
>
> Thanks,
>
> Eric
>
>
>
>
>
> *From:* Binz Pierre-Alain <Pie...@ch...>
> *Sent:* Thursday, June 6, 2019 11:42 PM
> *To:* Jones, Andy <And...@li...>; '
> psi...@li...' <
> psi...@li...>;
> psi...@li...; psi...@li...
> *Cc:* Gerhard Mayer <may...@ru...>
> *Subject:* Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate
> 4.1.27_rc1 of psi-ms.obo
>
>
>
> Good point Andy.
>
> If one need them for another format (these or others), should one
> systematically create all elements also as CV terms, have them annotated
> with a “is_a: MS:NNNNNN ! named element in mzIdentML “ /  mzML / etc., in
> order to make sure we have consistency of definition across formats?
>
>
>
> Pierre-Alain
>
>
>
>
>
> *De :* Jones, Andy <And...@li...>
> *Envoyé :* mercredi 5 juin 2019 16:43
> *À :* 'psi...@li...' <
> psi...@li...>;
> psi...@li...; psi...@li...
> *Cc :* Gerhard Mayer <may...@ru...>
> *Objet :* Re: [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate
> 4.1.27_rc1 of psi-ms.obo
>
>
>
> Hi Gerhard,
>
>
>
> Apologies for joining this conversation presumably late – these are
> encoded in mzIdentML via named elements. Are these CV terms needed for a
> different format?
>
> Best wishes
>
> Andy
>
>
>
> *From:* Gerhard Mayer via Psidev-ms-vocab [
> mailto:psi...@li...
> <psi...@li...>]
> *Sent:* 05 June 2019 15:40
> *To:* psi...@li...;
> psi...@li...; psi...@li...
> *Cc:* Gerhard Mayer <may...@ru...>
> *Subject:* [Psidev-ms-vocab] Release candidate 4.1.27_rc1 of psi-ms.obo
>
>
>
> Dear proteomics/metabolomics community,
>
> following the new terms for the release candidate 4.1.27_rc1
> of the psi-ms.obo file.
>
> New CV terms in version 4.1.27_rc1 of psi-ms.obo:
> =================================================
> [Term]
> id: MS:1003021
> name: fixed modification
> def: "Modification which is assumed to be present at each instance of a
> residue type." [PSI:PI]
> is_a: MS:1002094 ! common search engine input parameter
>
> [Term]
> id: MS:1003022
> name: variable modification
> def: "A modification which may or may not be present at a residue type."
> [PSI:PI]
> is_a: MS:1002094 ! common search engine input parameter
>
> Best Regards,
> Gerhard
>
> --
>
> *----------------------------------------------------------------------*
>
> *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*
>
> *Scientific assistant*
>
> *Ruhr-Universität Bochum, Medizinisches Proteom-Center*
>
> *DEPARTMENT Medical Bioinformatics*
>
> *Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*
>
> *Fon: *+49 (0)234 32-29272 | *Fax: *+49 (0)234 32-14554
>
> *E-Mail: *ger...@ru...
>
> *Web: *www.ruhr-uni-bochum.de/mpc
>
>
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 4.1.27_rc1 of psi-ms.obo

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

I think this will be needed for the spectral library format at least since
we will be needed a substantial number of concepts that are elements in
mzIdentML. Pierre-Alain’s proposal seems pretty good to me. Anyone else
have comments about doing it that way or refine the idea?



Thanks,

Eric





*From:* Binz Pierre-Alain <Pie...@ch...>
*Sent:* Thursday, June 6, 2019 11:42 PM
*To:* Jones, Andy <And...@li...>; '
psi...@li...' <
psi...@li...>; psi...@li...;
psi...@li...
*Cc:* Gerhard Mayer <may...@ru...>
*Subject:* Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate
4.1.27_rc1 of psi-ms.obo



Good point Andy.

If one need them for another format (these or others), should one
systematically create all elements also as CV terms, have them annotated
with a “is_a: MS:NNNNNN ! named element in mzIdentML “ /  mzML / etc., in
order to make sure we have consistency of definition across formats?



Pierre-Alain





*De :* Jones, Andy <And...@li...>
*Envoyé :* mercredi 5 juin 2019 16:43
*À :* 'psi...@li...' <
psi...@li...>; psi...@li...;
psi...@li...
*Cc :* Gerhard Mayer <may...@ru...>
*Objet :* Re: [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate
4.1.27_rc1 of psi-ms.obo



Hi Gerhard,



Apologies for joining this conversation presumably late – these are encoded
in mzIdentML via named elements. Are these CV terms needed for a different
format?

Best wishes

Andy



*From:* Gerhard Mayer via Psidev-ms-vocab [
mailto:psi...@li...
<psi...@li...>]
*Sent:* 05 June 2019 15:40
*To:* psi...@li...;
psi...@li...; psi...@li...
*Cc:* Gerhard Mayer <may...@ru...>
*Subject:* [Psidev-ms-vocab] Release candidate 4.1.27_rc1 of psi-ms.obo



Dear proteomics/metabolomics community,

following the new terms for the release candidate 4.1.27_rc1
of the psi-ms.obo file.

New CV terms in version 4.1.27_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1003021
name: fixed modification
def: "Modification which is assumed to be present at each instance of a
residue type." [PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

[Term]
id: MS:1003022
name: variable modification
def: "A modification which may or may not be present at a residue type."
[PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

Best Regards,
Gerhard

-- 

*----------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*Scientific assistant*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

*Fon: *+49 (0)234 32-29272 | *Fax: *+49 (0)234 32-14554

*E-Mail: *ger...@ru...

*Web: *www.ruhr-uni-bochum.de/mpc

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 4.1.27_rc1 of psi-ms.obo

[Binz Pierre-A. <Pie...@ch...>]

Good point Andy.
If one need them for another format (these or others), should one systematically create all elements also as CV terms, have them annotated with a “is_a: MS:NNNNNN ! named element in mzIdentML “ /  mzML / etc., in order to make sure we have consistency of definition across formats?

Pierre-Alain


De : Jones, Andy <And...@li...>
Envoyé : mercredi 5 juin 2019 16:43
À : 'psi...@li...' <psi...@li...>; psi...@li...; psi...@li...
Cc : Gerhard Mayer <may...@ru...>
Objet : Re: [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate 4.1.27_rc1 of psi-ms.obo

Hi Gerhard,

Apologies for joining this conversation presumably late – these are encoded in mzIdentML via named elements. Are these CV terms needed for a different format?
Best wishes
Andy

From: Gerhard Mayer via Psidev-ms-vocab [mailto:psi...@li...]
Sent: 05 June 2019 15:40
To: psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>
Cc: Gerhard Mayer <may...@ru...<mailto:may...@ru...>>
Subject: [Psidev-ms-vocab] Release candidate 4.1.27_rc1 of psi-ms.obo


Dear proteomics/metabolomics community,

following the new terms for the release candidate 4.1.27_rc1
of the psi-ms.obo file.

New CV terms in version 4.1.27_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1003021
name: fixed modification
def: "Modification which is assumed to be present at each instance of a residue type." [PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

[Term]
id: MS:1003022
name: variable modification
def: "A modification which may or may not be present at a residue type." [PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

Best Regards,
Gerhard
--

----------------------------------------------------------------------

Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER

Scientific assistant

Ruhr-Universität Bochum, Medizinisches Proteom-Center

DEPARTMENT Medical Bioinformatics

Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum

Fon: +49 (0)234 32-29272 | Fax: +49 (0)234 32-14554

E-Mail: ger...@ru...<mailto:ger...@ru...>

Web: www.ruhr-uni-bochum.de/mpc<http://www.ruhr-uni-bochum.de/mpc>

[Psidev-ms-dev] New version 4.1.27 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics/metabolomics community,


following are the new modification terms for the release version 4.1.27
of the psi-ms.obo file. They were requested by Yasset for PRIDE.

It can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo


New CV terms in version 4.1.27 of psi-ms.obo:
=============================================
[Term]
id: MS:1003021
name: Fixed modification
def: "Post-translational modification which is assumed to be present at 
each instance of a residue type." [PSI:PI]
is_a: MS:1001055 ! modification parameters

[Term]
id: MS:1003022
name: Variable modification
def: "Post-translational modification which may or may not be present at 
a residue type." [PSI:PI]
is_a: MS:1001055 ! modification parameters


Best Regards,
Gerhard

-- 

*----------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*Scientific assistant*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

*Fon: *+49 (0)234 32-29272 | *Fax: *+49 (0)234 32-14554

*E-Mail: *ger...@ru... <mailto:ger...@ru...>

*Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc>

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 4.1.27_rc1 of psi-ms.obo

[Jones, A. <And...@li...>]

Hi Gerhard,

Apologies for joining this conversation presumably late – these are encoded in mzIdentML via named elements. Are these CV terms needed for a different format?
Best wishes
Andy

From: Gerhard Mayer via Psidev-ms-vocab [mailto:psi...@li...]
Sent: 05 June 2019 15:40
To: psi...@li...; psi...@li...; psi...@li...
Cc: Gerhard Mayer <may...@ru...>
Subject: [Psidev-ms-vocab] Release candidate 4.1.27_rc1 of psi-ms.obo


Dear proteomics/metabolomics community,

following the new terms for the release candidate 4.1.27_rc1
of the psi-ms.obo file.

New CV terms in version 4.1.27_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1003021
name: fixed modification
def: "Modification which is assumed to be present at each instance of a residue type." [PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

[Term]
id: MS:1003022
name: variable modification
def: "A modification which may or may not be present at a residue type." [PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

Best Regards,
Gerhard
--


----------------------------------------------------------------------

Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER

Scientific assistant

Ruhr-Universität Bochum, Medizinisches Proteom-Center

DEPARTMENT Medical Bioinformatics

Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum

Fon: +49 (0)234 32-29272 | Fax: +49 (0)234 32-14554

E-Mail: ger...@ru...<mailto:ger...@ru...>

Web: www.ruhr-uni-bochum.de/mpc<http://www.ruhr-uni-bochum.de/mpc>

[Psidev-ms-dev] Release candidate 4.1.27_rc1 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics/metabolomics community,

following the new terms for the release candidate 4.1.27_rc1
of the psi-ms.obo file.

New CV terms in version 4.1.27_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1003021
name: fixed modification
def: "Modification which is assumed to be present at each instance of a 
residue type." [PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

[Term]
id: MS:1003022
name: variable modification
def: "A modification which may or may not be present at a residue type." 
[PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

Best Regards,
Gerhard

-- 

*----------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*Scientific assistant*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

*Fon: *+49 (0)234 32-29272 | *Fax: *+49 (0)234 32-14554

*E-Mail: *ger...@ru... <mailto:ger...@ru...>

*Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc>

[Psidev-ms-dev] New version 4.1.26 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics/metabolomics community,


following are the new/changed terms for the version 4.1.26 of the
psi-ms.obo file. It can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo


New CV terms in version 4.1.26 of psi-ms.obo:
=============================================
[Term]
id: MS:1003019
name: pressure chromatogram
def: "Representation of chromatographic pressure versus time." [PSI:MS]
is_a: MS:1000626 ! chromatogram type


[Term]
id: MS:1003020
name: flow rate chromatogram
def: "Representation of the chromatographic flow rate versus time." [PSI:MS]
is_a: MS:1000626 ! chromatogram type


Changed CV terms in version 4.1.26 of psi-ms.obo:
=================================================
************ Changed definition from
************ 'The representation of detector response versus time.' to
************ 'Representation of a chromatographic separation attribute 
measurement versus time.'
[Term]
id: MS:1000625
name: chromatogram
def: "Representation of a chromatographic separation attribute 
measurement versus time." [PSI:MS]
relationship: part_of MS:1001458 ! spectrum generation information


************ Changed definition from
************ 'Broad category or type of a chromatogram.' to
************ 'Type of chromatogram measurement being represented.'
[Term]
id: MS:1000626
name: chromatogram type
def: "Type of chromatogram measurement being represented." [PSI:MS]
relationship: part_of MS:1000625 ! chromatogram


************ Changed name from
************ 'mass chromatogram' to
************ 'ion current chromatogram'
************ and definition from
************ 'A plot of the relative abundance of a beam or other 
collection of ions as a function of the retention time.' to
************ 'Representation of the current of ions versus time.'
[Term]
id: MS:1000810
name: ion current chromatogram
def: "Representation of the current of ions versus time." [PSI:MS]
is_a: MS:1000524 ! data file content
is_a: MS:1000626 ! chromatogram type


************ Changed definition from
************ 'The measurement of electromagnetic properties as a 
function of the retention time.' to
************ 'Representation of electromagnetic properties versus time.'
[Term]
id: MS:1000811
name: electromagnetic radiation chromatogram
def: "Representation of electromagnetic properties versus time." [PSI:MS]
synonym: "EMR radiation chromatogram" EXACT []
is_a: MS:1000524 ! data file content
is_a: MS:1000626 ! chromatogram type


************ Changed definition from
************ 'The measurement of light absorbed by the sample as a 
function of the retention time.' to
************ 'Representation of light absorbed by the sample versus time.'
[Term]
id: MS:1000812
name: absorption chromatogram
def: "Representation of light absorbed by the sample versus time." [PSI:MS]
is_a: MS:1000811 ! electromagnetic radiation chromatogram


************ Changed definition from
************ 'The measurement of light emitted by the sample as a 
function of the retention time.' to
************ 'Representation of light emitted by the sample versus time.'
[Term]
id: MS:1000813
name: emission chromatogram
def: "Representation of light emitted by the sample versus time." [PSI:MS]
is_a: MS:1000811 ! electromagnetic radiation chromatogram


************ Changed definition from
************ 'Chromatogram obtained by plotting the total ion current 
detected in each of a series of mass spectra recorded as a function of 
retention time.' to
************ 'Representation of the total ion current detected in each 
of a series of mass spectra versus time.'
************ and is_a relationship from
************ 'is_a: MS:1000810 ! mass chromatogram' to
************ 'is_a: MS:1000810 ! ion current chromatogram'
[Term]
id: MS:1000235
name: total ion current chromatogram
def: "Representation of the total ion current detected in each of a 
series of mass spectra versus time." [PSI:MS]
synonym: "TIC chromatogram" EXACT []
is_a: MS:1000810 ! ion current chromatogram


************ Changed definition from
************ 'Chromatogram created by creating an array of the 
measurements of a specific single ion current at each time point.' to
************ 'Representation of an array of the measurements of a 
specific single ion current versus time.'
************ and is_a relationship from
************ 'is_a: MS:1000810 ! mass chromatogram' to
************ 'is_a: MS:1000810 ! ion current chromatogram'
[Term]
id: MS:1000627
name: selected ion current chromatogram
def: "Representation of an array of the measurements of a specific 
single ion current versus time." [PSI:MS]
synonym: "SIC chromatogram" EXACT []
is_a: MS:1000810 ! ion current chromatogram


************ Changed definition from
************ 'Chromatogram created by creating an array of the most 
intense peaks at each time point.' to
************ 'Representation of an array of the most intense peaks 
versus time.'
************ and is_a relationship from
************ 'is_a: MS:1000810 ! mass chromatogram' to
************ 'is_a: MS:1000810 ! ion current chromatogram'
[Term]
id: MS:1000628
name: basepeak chromatogram
def: "Representation of an array of the most intense peaks versus time." 
[PSI:MS]
is_a: MS:1000810 ! ion current chromatogram


************ Changed definition from
************ 'Chromatogram created by creating an array of the 
measurements of a selectively monitored ion at each time point.' to
************ 'Representation of an array of the measurements of a 
selectively monitored ion versus time.'
************ and is_a relationship from
************ 'is_a: MS:1000810 ! mass chromatogram' to
************ 'is_a: MS:1000810 ! ion current chromatogram'
[Term]
id: MS:1001472
name: selected ion monitoring chromatogram
def: "Representation of an array of the measurements of a selectively 
monitored ion versus time." [PSI:MS]
synonym: "SIM chromatogram" EXACT []
is_a: MS:1000810 ! ion current chromatogram


************ Changed definition from
************ 'Chromatogram created by creating an array of the 
measurements of a selectively monitored reaction at each time point.' to
************ 'Representation of an array of the measurements of a 
selectively monitored reaction versus time.'
************ and is_a relationship from
************ 'is_a: MS:1000810 ! mass chromatogram' to
************ 'is_a: MS:1000810 ! ion current chromatogram'
[Term]
id: MS:1001473
name: selected reaction monitoring chromatogram
def: "Representation of an array of the measurements of a selectively 
monitored reaction versus time." [PSI:MS]
synonym: "SRM chromatogram" EXACT []
is_a: MS:1000810 ! ion current chromatogram


************ Changed definition from
************ 'OBSOLETE Chromatogram created by creating an array of the 
measurements of a series of monitored reactions at each time point.' to
************ 'OBSOLETE Representation of an array of the measurements of 
a series of monitored reactions versus time.'
************ and is_a relationship from
************ 'is_a: MS:1000810 ! mass chromatogram' to
************ 'is_a: MS:1000810 ! ion current chromatogram'
[Term]
id: MS:1001474
name: consecutive reaction monitoring chromatogram
def: "OBSOLETE Representation of an array of the measurements of a 
series of monitored reactions versus time." [PSI:MS]
comment: This term was made obsolete because, by design, it can't be 
properly represented in mzML 1.1. CRM experiments must be represented in 
a spectrum-centric way.
synonym: "CRM chromatogram" EXACT []
is_a: MS:1000810 ! ion current chromatogram
is_obsolete: true


Best Regards,
Gerhard

-- 

*----------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*Scientific assistant*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

*Fon: *+49 (0)234 32-29272 | *Fax: *+49 (0)234 32-14554

*E-Mail: *ger...@ru... <mailto:ger...@ru...>

*Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc>

[Psidev-ms-dev] Release candidate 4.1.26_rc1 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics/metabolomics community,

following are the new/changed terms for the release candidate 4.1.26_rc1
of the psi-ms.obo file.


New CV terms in version 4.1.26_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1003019
name: pressure chromatogram
def: "Representation of chromatographic pressure versus time." [PSI:MS]
is_a: MS:1000626 ! chromatogram type


[Term]
id: MS:1003020
name: flow rate chromatogram
def: "Representation of the chromatographic flow rate versus time." [PSI:MS]
is_a: MS:1000626 ! chromatogram type


Changed CV terms in version 4.1.26_rc1 of psi-ms.obo:
=====================================================
************ Changed definition from
************ 'The representation of detector response versus time.' to
************ 'Representation of a chromatographic separation attribute 
measurement versus time.'
[Term]
id: MS:1000625
name: chromatogram
def: "Representation of a chromatographic separation attribute 
measurement versus time." [PSI:MS]
relationship: part_of MS:1001458 ! spectrum generation information


************ Changed definition from
************ 'Broad category or type of a chromatogram.' to
************ 'Type of chromatogram measurement being represented.'
[Term]
id: MS:1000626
name: chromatogram type
def: "Type of chromatogram measurement being represented." [PSI:MS]
relationship: part_of MS:1000625 ! chromatogram


************ Changed name from
************ 'mass chromatogram' to
************ 'ion current chromatogram'
************ and definition from
************ 'A plot of the relative abundance of a beam or other 
collection of ions as a function of the retention time.' to
************ 'Representation of the current of ions versus time.'
[Term]
id: MS:1000810
name: ion current chromatogram
def: "Representation of the current of ions versus time." [PSI:MS]
is_a: MS:1000524 ! data file content
is_a: MS:1000626 ! chromatogram type


************ Changed definition from
************ 'The measurement of electromagnetic properties as a 
function of the retention time.' to
************ 'Representation of electromagnetic properties versus time.'
[Term]
id: MS:1000811
name: electromagnetic radiation chromatogram
def: "Representation of electromagnetic properties versus time." [PSI:MS]
synonym: "EMR radiation chromatogram" EXACT []
is_a: MS:1000524 ! data file content
is_a: MS:1000626 ! chromatogram type


************ Changed definition from
************ 'The measurement of light absorbed by the sample as a 
function of the retention time.' to
************ 'Representation of light absorbed by the sample versus time.'
[Term]
id: MS:1000812
name: absorption chromatogram
def: "Representation of light absorbed by the sample versus time." [PSI:MS]
is_a: MS:1000811 ! electromagnetic radiation chromatogram


************ Changed definition from
************ 'The measurement of light emitted by the sample as a 
function of the retention time.' to
************ 'Representation of light emitted by the sample versus time.'
[Term]
id: MS:1000813
name: emission chromatogram
def: "Representation of light emitted by the sample versus time." [PSI:MS]
is_a: MS:1000811 ! electromagnetic radiation chromatogram


************ Changed definition from
************ 'Chromatogram obtained by plotting the total ion current 
detected in each of a series of mass spectra recorded as a function of 
retention time.' to
************ 'Representation of the total ion current detected in each 
of a series of mass spectra versus time.'
************ and is_a relationship from
************ 'is_a: MS:1000810 ! mass chromatogram' to
************ 'is_a: MS:1000810 ! ion current chromatogram'
[Term]
id: MS:1000235
name: total ion current chromatogram
def: "Representation of the total ion current detected in each of a 
series of mass spectra versus time." [PSI:MS]
synonym: "TIC chromatogram" EXACT []
is_a: MS:1000810 ! ion current chromatogram


************ Changed definition from
************ 'Chromatogram created by creating an array of the 
measurements of a specific single ion current at each time point.' to
************ 'Representation of an array of the measurements of a 
specific single ion current versus time.'
************ and is_a relationship from
************ 'is_a: MS:1000810 ! mass chromatogram' to
************ 'is_a: MS:1000810 ! ion current chromatogram'
[Term]
id: MS:1000627
name: selected ion current chromatogram
def: "Representation of an array of the measurements of a specific 
single ion current versus time." [PSI:MS]
synonym: "SIC chromatogram" EXACT []
is_a: MS:1000810 ! ion current chromatogram


************ Changed definition from
************ 'Chromatogram created by creating an array of the most 
intense peaks at each time point.' to
************ 'Representation of an array of the most intense peaks 
versus time.'
************ and is_a relationship from
************ 'is_a: MS:1000810 ! mass chromatogram' to
************ 'is_a: MS:1000810 ! ion current chromatogram'
[Term]
id: MS:1000628
name: basepeak chromatogram
def: "Representation of an array of the most intense peaks versus time." 
[PSI:MS]
is_a: MS:1000810 ! ion current chromatogram


************ Changed definition from
************ 'Chromatogram created by creating an array of the 
measurements of a selectively monitored ion at each time point.' to
************ 'Representation of an array of the measurements of a 
selectively monitored ion versus time.'
************ and is_a relationship from
************ 'is_a: MS:1000810 ! mass chromatogram' to
************ 'is_a: MS:1000810 ! ion current chromatogram'
[Term]
id: MS:1001472
name: selected ion monitoring chromatogram
def: "Representation of an array of the measurements of a selectively 
monitored ion versus time." [PSI:MS]
synonym: "SIM chromatogram" EXACT []
is_a: MS:1000810 ! ion current chromatogram


************ Changed definition from
************ 'Chromatogram created by creating an array of the 
measurements of a selectively monitored reaction at each time point.' to
************ 'Representation of an array of the measurements of a 
selectively monitored reaction versus time.'
************ and is_a relationship from
************ 'is_a: MS:1000810 ! mass chromatogram' to
************ 'is_a: MS:1000810 ! ion current chromatogram'
[Term]
id: MS:1001473
name: selected reaction monitoring chromatogram
def: "Representation of an array of the measurements of a selectively 
monitored reaction versus time." [PSI:MS]
synonym: "SRM chromatogram" EXACT []
is_a: MS:1000810 ! ion current chromatogram


************ Changed definition from
************ 'OBSOLETE Chromatogram created by creating an array of the 
measurements of a series of monitored reactions at each time point.' to
************ 'OBSOLETE Representation of an array of the measurements of 
a series of monitored reactions versus time.'
************ and is_a relationship from
************ 'is_a: MS:1000810 ! mass chromatogram' to
************ 'is_a: MS:1000810 ! ion current chromatogram'
[Term]
id: MS:1001474
name: consecutive reaction monitoring chromatogram
def: "OBSOLETE Representation of an array of the measurements of a 
series of monitored reactions versus time." [PSI:MS]
comment: This term was made obsolete because, by design, it can't be 
properly represented in mzML 1.1. CRM experiments must be represented in 
a spectrum-centric way.
synonym: "CRM chromatogram" EXACT []
is_a: MS:1000810 ! ion current chromatogram
is_obsolete: true

Best Regards,
Gerhard

-- 

*----------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*Scientific assistant*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

*Fon: *+49 (0)234 32-29272 | *Fax: *+49 (0)234 32-14554

*E-Mail: *ger...@ru... <mailto:ger...@ru...>

*Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc>