psidev-ms-dev — Mass spectroscopy standard development

[Psidev-ms-dev] Save the Date: PSI Spring Meeting 2017

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

Hi everyone, please mark your calendars and plan on participating in the
next PSI Spring Meeting to be held in Beijing April 24-26, with some
related events one day before and after. More information will be
forthcoming soon at:



http://www.psidev.info/content/hupo-psi-meeting-2017



Registration will be opened in January, but consider starting to make some
plans to attend.



If you have any questions, let me know.



Regards,

Eric

Re: [Psidev-ms-dev] Release candidate 4.0.5_rc1 of psi-ms.obo

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

I would suggest just removing the PATO reference completely. I don’t
believe that saying a “negative scan” IS A “electric charge” is
semantically correct



*From:* mayerg97 [mailto:ger...@ru...]
*Sent:* Thursday, November 24, 2016 12:53 AM
*To:* psi...@li...;
psi...@li...; psi...@li...
*Subject:* [Psidev-ms-dev] Release candidate 4.0.5_rc1 of psi-ms.obo



Dear proteomics community,

attached there's the release candidate 4.0.5_rc1 of the psi-ms.obo file.

It contains a changed is_a relation for two terms, since
PATO:0002186 defines the polarity (polar/nonpolar) and not
the electric charge (negative/positive/neutral) defined by PATO:0002193


Changed CV terms in version 4.0.5_rc1 of psi-ms.obo:
====================================================
************ Changed is_a: PATO:0002186 ! polarity
************ to         is_a: PATO:0002193 ! electric charge
[Term]
id: MS:1000129
name: negative scan
def: "Polarity of the scan is negative." [PSI:MS]
is_a: PATO:0002193 ! electric charge
is_a: MS:1000465 ! scan polarity
is_a: MS:1000808 ! chromatogram attribute

[Term]
id: MS:1000130
name: positive scan
def: "Polarity of the scan is positive." [PSI:MS]
is_a: PATO:0002193 ! electric charge
is_a: MS:1000465 ! scan polarity
is_a: MS:1000808 ! chromatogram attribute

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554

*E-mail *ger...@ru...

www.medizinisches-proteom-center.de

[Psidev-ms-dev] Release candidate 4.0.5_rc1 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics community,

attached there's the release candidate 4.0.5_rc1 of the psi-ms.obo file.

It contains a changed is_a relation for two terms, since
PATO:0002186 defines the polarity (polar/nonpolar) and not
the electric charge (negative/positive/neutral) defined by PATO:0002193


Changed CV terms in version 4.0.5_rc1 of psi-ms.obo:
====================================================
************ Changed is_a: PATO:0002186 ! polarity
************ to         is_a: PATO:0002193 ! electric charge
[Term]
id: MS:1000129
name: negative scan
def: "Polarity of the scan is negative." [PSI:MS]
is_a: PATO:0002193 ! electric charge
is_a: MS:1000465 ! scan polarity
is_a: MS:1000808 ! chromatogram attribute

[Term]
id: MS:1000130
name: positive scan
def: "Polarity of the scan is positive." [PSI:MS]
is_a: PATO:0002193 ! electric charge
is_a: MS:1000465 ! scan polarity
is_a: MS:1000808 ! chromatogram attribute

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554

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

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>

[Psidev-ms-dev] PSI recommendation document (file format proBed), 60-days public review

[Martin E. <mar...@ru...>]

Dear colleague,

dear member of the Proteomics community,

 

this is a short reminder about the ongoing public 

review of the newly suggested PSI format ‘proBed’.

 

PLEASE ADD COMMENTS to the submission page

( <http://www.psidev.info/proBed-in-docproc>
http://www.psidev.info/proBed-in-docproc) 

(or send them directly to martin.eisenacher: at : rub.de).

 

For further details see below.

 

   Many thanks for your valuable time and participation

      Martin Eisenacher (PSI Editor)

 

--

PD DR. MARTIN EISENACHER

Department Leader

DEPARTMENT Medical Bioinformatics

Medizinisches Proteom-Center

Ruhr-University Bochum

Building ZKF E.141 | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-29288 | Fax +49 (0)234 32-14554

E-mail  <mailto:mar...@ru...> mar...@ru...

 <http://www.medizinisches-proteom-center.de/>
www.medizinisches-proteom-center.de

 



 

 

 

Von: psi...@eb... [mailto:psi...@eb...]
Im Auftrag von Martin Eisenacher
Gesendet: Donnerstag, 20. Oktober 2016 11:11
An: psi...@li...;
psi...@li...; psi...@li...;
ps...@eb...; psi...@eb...
Betreff: [Psi-announce] PSI recommendation document (file format proBed),
60-days public review

 

Dear colleague,

dear member of the Proteomics community,

 

please forward this message to potentially interested colleagues!

 

The HUPO Proteomics Standards Initiative (PSI) develops standards 

for documentation and storage of Proteomics data (see 

 <http://www.psidev.info> http://www.psidev.info for an overview of
activities).

 

A recommendation document specifying the proBed file format

has been submitted to the PSI document process.

The submission can be found here:

http://www.psidev.info/proBed-in-docproc

 

After having passed a 30-day review of the PSI steering group 

with minor changes, the proposed document version 1.0.0 DRAFT 

now goes through 60-days public comments and external 

review phase (end: 19th December 2016).

 

"The format represents systematically the output of proteogenomics

analyses, by mapping peptide identification data retrieved from 

mass spectrometry (MS)-based experiments to the genome."

(see also Cover Letter attached to the submission page)

 

The format is based on the BED format (Browser Extensive Data,

 <https://genome.ucsc.edu/FAQ/FAQformat.html#format1>
https://genome.ucsc.edu/FAQ/FAQformat.html#format1),

developed by the UCSC (University of California, Santa Cruz) team.

 

The public comment period enables the wider community to provide 

feedback on a proposed standard before it is formally accepted, and 

thus is an important step in the standardisation process.

 

PLEASE ADD COMMENTS to the submission page

(http://www.psidev.info/proBed-in-docproc) 

(or send them directly to martin.eisenacher: at : rub.de) for 

 example regarding the following criteria:

 

- That it is well formed – that is, it is presented in accordance with the
templates and is clearly written.

- That it is sufficiently detailed and clearly contains and comprehensively
describes the necessary and sufficient explanation of the format.

- That the examples are in accordance with the specification.> >

 

This message is to encourage you to contribute to the standards

development activity by commenting on the material that is 

available online. We invite both positive and negative comments.

If negative comments are being made, these could be on the relevance, 

clarity, correctness, appropriateness, etc, of the proposal as 

a whole or of specific parts of the proposal.

 

If you do not feel well placed to comment on this document, but 

know someone who may be, please consider forwarding this request. 

There is no requirement that people commenting should have had any 

prior contact with the PSI.

 

    Many thanks for your valuable time and participation

      Martin Eisenacher (PSI Editor)

 

--

PD DR. MARTIN EISENACHER

Department Leader

DEPARTMENT Medical Bioinformatics

Medizinisches Proteom-Center

Ruhr-University Bochum

Building ZKF E.141 | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-29288 | Fax +49 (0)234 32-14554

E-mail  <mailto:mar...@ru...> mar...@ru...

 <http://www.medizinisches-proteom-center.de/>
www.medizinisches-proteom-center.de

 



 

[Psidev-ms-dev] New version 4.0.4 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics community,

attached there's the new version 4.0.4 of the psi-ms.obo file.

It contains a new term for the Orbitrap Fusion Lumos instrument.

New CV terms in version 4.0.4 of psi-ms.obo:
============================================
[Term]
id: MS:1002732
name: Orbitrap Fusion Lumos
def: "Thermo Scientific Orbitrap Fusion Lumos 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*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554

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

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>

[Psidev-ms-dev] Google Summer of Code 2017

[Adam T. <ada...@ve...>]

Is anyone on this list interested in being part of GSoC next year? I was a
mentor with OpenChemistry this year, which was a great experience for two
of our projects (cclib and Avogadro). While I still like contributing there
where I can, I'm more involved with MS-based software these days and would
consider mentoring for such projects as well.

I'm mostly familiar with the Java projects MSDK and MZmine, and somewhat
familiar with the C++ project OpenMS, but am interested in seeing what
other projects under active development would be interested in GSoC.

You can see the timeline at
https://developers.google.com/open-source/gsoc/timeline, which the
application period being 1/19-2/9.

Best regards,

Adam

-- 

Adam Tenderholt, Ph.D.

Program Manager, Veritomyx, Inc.

[Psidev-ms-dev] [Psi‐announce] Submission of an update of the specifications for mzIdentML 1.2 : open for public review until December, 6th

[Sylvie Ricard-B. <syl...@un...>]

Dear colleague,

Dear member of the Proteomics community,


The update of the specifications for mzIdentML 1.2 is open for public 
review until *December, 6th* and not until November, 6th as mistakenly 
indicated in my previous e-mail copied below.


The public review enables the community to provide feedback on a 
proposed standard before it is formally accepted. It is thus an 
important step in the standardisation process. Both positive and 
negative comments on the relevance, clarity, correctness, and 
appropriateness of the entire document or of specific parts of it are 
welcome.

I invite you to forward this message to interested colleagues and I 
thank you in advance for your valuable contribution to the standards 
development effort.


Best wishes.


Sylvie RICARD-BLUM (PSI editor).

Professor Sylvie RICARD-BLUM
Pericellular and Extracellular Supramolecular Assemblies
UMR 5246 CNRS - University Lyon 1
Institute of Molecular and Supramolecular Chemistry and Biochemistry
Raulin Building - 2nd Floor North
University Claude Bernard Lyon 1
43 Boulevard du 11 novembre 1918
69622 Villeurbanne Cedex, France
Tel : +33(0)4 72 44 82 32
E-mail: syl...@un...


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

Le 06/10/2016 12:11, Sylvie Ricard-Blum a écrit :


Dear colleague,

Dear member of the Proteomics community,

The HUPO Proteomics Standards Initiative (PSI) develops standards for 
documentation and storage of proteomics data (see http://www.psidev.info 
for an overview of activities).

The PSI Proteomics Informatics Working Group has submitted an update of 
the specifications for mzIdentML 1.2 to the PSI document process.

The specification document can be found here: 
<https://github.com/HUPO-PSI/mzIdentML/blob/master/specification_document/specdoc1_2/mzIdentML1%202-draft.docx>https://github.com/HUPO-PSI/mzIdentML/blob/master/specification_document/specdoc1_2/mzIdentML1%202-draft.docx


Example files to demonstrate the standard are here: 
https://github.com/HUPO-PSI/mzIdentML/tree/master/examples/1_2examples


The validator is here: 
https://github.com/HUPO-PSI/mzIdentML/blob/master/validator/mzIdentMLValidator_GUI_v1.4.24-SNAPSHOT.zip

After a 30-day review of the PSI steering committee, the proposed 
document now goes through external review phase until *December, 6**^th 
**, 2016*.

The public review enables the community to provide feedback on a 
proposed standard before it is formally accepted. It is thus an 
important step in the standardisation process. Both positive and 
negative comments on the relevance, clarity, correctness, and 
appropriateness of the entire document or of specific parts of it are 
welcome.

Please add comments to the submission page 
(http://www.psidev.info/mzidentml-12-docproc) or send them directly to 
syl...@un... 
<mailto:syl...@un...> with a particular focus on the 
following criteria:

- The document is presented in accordance with the templates and is 
clearly written.

- The document is sufficiently detailed and clearly describes the format.

- The examples are in accordance with the specification.

I invite you to forward this message to interested colleagues and I 
thank you in advance for your valuable contribution to the standards 
development effort.

Best wishes.

Sylvie RICARD-BLUM (PSI editor)

Professor Sylvie RICARD-BLUM

Pericellular and Extracellular Supramolecular Assemblies

UMR 5246 CNRS - University Lyon 1

Institute of Molecular and Supramolecular Chemistry and Biochemistry

Raulin Building - 2^nd Floor North

University Claude Bernard Lyon 1

43 Boulevard du 11 novembre 1918

69622 Villeurbanne Cedex, France

Tel : +33(0)4 72 44 82 32

E-mail: syl...@un... 
<mailto:syl...@un...>

http://www.icbms.fr <http://www.icbms.fr/>

The French Society for Matrix Biology http://www.sfbmec.fr

The International Society for Matrix Biology http://ismb.org

[Psidev-ms-dev] New version 4.0.3 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics community,

attached there's the new version 4.0.3 of the psi-ms.obo file.

It contains new terms and some changes for Waters instruments.


New CV terms in version 4.0.3 of psi-ms.obo:
============================================
************ New instruments terms for Waters instruments
[Term]
id: MS:1002726
name: SYNAPT G2-Si
def: "Waters Corporation SYNAPT G2-Si orthogonal acceleration 
time-of-flight mass spectrometer." [PSI:PI]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1002727
name: MALDI SYNAPT G2-Si
def: "Waters Corporation MALDI SYNAPT G2-Si orthogonal acceleration 
time-of-flight mass spectrometer." [PSI:PI]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1002728
name: Vion IMS QTof
def: "Waters Corporation Vion IMS QTof orthogonal acceleration 
time-of-flight mass spectrometer." [PSI:PI]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1002729
name: Xevo G2 XS Tof
def: "Waters Corporation Xevo G2 XS Tof orthogonal acceleration 
time-of-flight mass spectrometer." [PSI:PI]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1002730
name: Xevo TQ-XS
def: "Waters Corporation Xevo TQ-XS triple quadrupole mass 
spectrometer." [PSI:PI]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1002731
name: Xevo TQ-S micro
def: "Waters Corporation Xevo TQ-S micro triple quadrupole mass 
spectrometer." [PSI:PI]
is_a: MS:1000126 ! Waters instrument model



Changed CV terms in version 4.0.3 of psi-ms.obo:
================================================
************ changed name: Unify --> UNIFI
[Term]
id: MS:1001796
name: UNIFY
def: "Waters UNIFY software for liquid chromatography and mass 
spectrometry acquisition." [PSI:MS]
is_a: MS:1000694 ! Waters software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

************ added '1D' to the name and definition
[Term]
id: MS:1001767
name: nanoACQUITY UPLC System with 1D Technology
def: "Waters LC-system nanoACQUITY UPLC System with 1D Technology." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

************ changed name capitalization:
************ Q-Tof ultima --> Q-Tof Ultima
[Term]
id: MS:1000189
name: Q-Tof Ultima
def: "Waters oa-ToF based Q-Tof Ultima." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

************ changed the definition:
************ Waters quadrupole ... --> Waters (triple) quadrupole ...
[Term]
id: MS:1001789
name: Quattro micro GC
def: "Waters (triple) quadrupole based Quattro micro GC." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

************ changed the definition:
************ added 'magnetic sector based'
[Term]
id: MS:1000150
name: Auto Spec Ultima NT
def: "Waters magnetic sector based AutoSpec Ultima NT MS." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

************ changed the definition:
************ oa-ToF based --> (triple) quadrupole based
[Term]
id: MS:1000191
name: quattro micro
def: "Waters (triple) quadrupole based micro." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

************ changed the definition:
************ oa-ToF based --> (triple) quadrupole based
[Term]
id: MS:1000192
name: Quattro Ultima
def: "Waters (triple) quadrupole based Ultima." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

************ added: ... magnetic sector instrument to the definition
[Term]
id: MS:1002277
name: AutoSpec Premier
def: "Waters AutoSpec Premier magnetic sector instrument." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554

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

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>

[Psidev-ms-dev] PSI recommendation document (file format proBed), 60-days public review

[Martin E. <mar...@ru...>]

Dear colleague,

dear member of the Proteomics community,

 

please forward this message to potentially interested colleagues!

 

The HUPO Proteomics Standards Initiative (PSI) develops standards 

for documentation and storage of Proteomics data (see 

 <http://www.psidev.info> http://www.psidev.info for an overview of
activities).

 

A recommendation document specifying the proBed file format

has been submitted to the PSI document process.

The submission can be found here:

http://www.psidev.info/proBed-in-docproc

 

After having passed a 30-day review of the PSI steering group 

with minor changes, the proposed document version 1.0.0 DRAFT 

now goes through 60-days public comments and external 

review phase (end: 19th December 2016).

 

"The format represents systematically the output of proteogenomics

analyses, by mapping peptide identification data retrieved from 

mass spectrometry (MS)-based experiments to the genome."

(see also Cover Letter attached to the submission page)

 

The format is based on the BED format (Browser Extensive Data,

 <https://genome.ucsc.edu/FAQ/FAQformat.html#format1>
https://genome.ucsc.edu/FAQ/FAQformat.html#format1),

developed by the UCSC (University of California, Santa Cruz) team.

 

The public comment period enables the wider community to provide 

feedback on a proposed standard before it is formally accepted, and 

thus is an important step in the standardisation process.

 

PLEASE ADD COMMENTS to the submission page

(http://www.psidev.info/proBed-in-docproc) 

(or send them directly to martin.eisenacher: at : rub.de) for 

 example regarding the following criteria:

 

- That it is well formed – that is, it is presented in accordance with the
templates and is clearly written.

- That it is sufficiently detailed and clearly contains and comprehensively
describes the necessary and sufficient explanation of the format.

- That the examples are in accordance with the specification.> >

 

This message is to encourage you to contribute to the standards

development activity by commenting on the material that is 

available online. We invite both positive and negative comments.

If negative comments are being made, these could be on the relevance, 

clarity, correctness, appropriateness, etc, of the proposal as 

a whole or of specific parts of the proposal.

 

If you do not feel well placed to comment on this document, but 

know someone who may be, please consider forwarding this request. 

There is no requirement that people commenting should have had any 

prior contact with the PSI.

 

    Many thanks for your valuable time and participation

      Martin Eisenacher (PSI Editor)

 

--

PD DR. MARTIN EISENACHER

Department Leader

DEPARTMENT Medical Bioinformatics

Medizinisches Proteom-Center

Ruhr-University Bochum

Building ZKF E.141 | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-29288 | Fax +49 (0)234 32-14554

E-mail  <mailto:mar...@ru...> mar...@ru...

 <http://www.medizinisches-proteom-center.de/>
www.medizinisches-proteom-center.de

 



 

[Psidev-ms-dev] Release candidate 4.0.3_rc1 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics community,

attached there's the release candidate 4.0.3_rc1 of the psi-ms.obo file.
It contains new terms and some changes for Waters instruments.


New CV terms in version 4.0.3_rc1 of psi-ms.obo:
================================================
************ New instruments terms for Waters instruments
[Term]
id: MS:1002726
name: SYNAPT G2-Si
def: "Waters Corporation SYNAPT G2-Si orthogonal acceleration 
time-of-flight mass spectrometer." [PSI:PI]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1002727
name: MALDI SYNAPT G2-Si
def: "Waters Corporation MALDI SYNAPT G2-Si orthogonal acceleration 
time-of-flight mass spectrometer." [PSI:PI]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1002728
name: Vion IMS QTof
def: "Waters Corporation Vion IMS QTof orthogonal acceleration 
time-of-flight mass spectrometer." [PSI:PI]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1002729
name: Xevo G2 XS Tof
def: "Waters Corporation Xevo G2 XS Tof orthogonal acceleration 
time-of-flight mass spectrometer." [PSI:PI]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1002730
name: Xevo TQ-XS
def: "Waters Corporation Xevo TQ-XS triple quadrupole mass 
spectrometer." [PSI:PI]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1002731
name: Xevo TQ-S micro
def: "Waters Corporation Xevo TQ-S micro triple quadrupole mass 
spectrometer." [PSI:PI]
is_a: MS:1000126 ! Waters instrument model


Changed CV terms in version 4.0.3_rc1 of psi-ms.obo:
====================================================
************ changed name: Unify --> UNIFI
[Term]
id: MS:1001796
name: UNIFY
def: "Waters UNIFY software for liquid chromatography and mass 
spectrometry acquisition." [PSI:MS]
is_a: MS:1000694 ! Waters software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

************ added '1D' to the name and definition
[Term]
id: MS:1001767
name: nanoACQUITY UPLC System with 1D Technology
def: "Waters LC-system nanoACQUITY UPLC System with 1D Technology." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

************ changed name capitalization:
************ Q-Tof ultima --> Q-Tof Ultima
[Term]
id: MS:1000189
name: Q-Tof Ultima
def: "Waters oa-ToF based Q-Tof Ultima." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

************ changed the definition:
************ Waters quadrupole ... --> Waters (triple) quadrupole ...
[Term]
id: MS:1001789
name: Quattro micro GC
def: "Waters (triple) quadrupole based Quattro micro GC." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

************ changed the definition:
************ added 'magnetic sector based'
[Term]
id: MS:1000150
name: Auto Spec Ultima NT
def: "Waters magnetic sector based AutoSpec Ultima NT MS." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

************ changed the definition:
************ oa-ToF based --> (triple) quadrupole based
[Term]
id: MS:1000191
name: quattro micro
def: "Waters (triple) quadrupole based micro." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

************ changed the definition:
************ oa-ToF based --> (triple) quadrupole based
[Term]
id: MS:1000192
name: Quattro Ultima
def: "Waters (triple) quadrupole based Ultima." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

************ added: ... magnetic sector instrument to the definition
[Term]
id: MS:1002277
name: AutoSpec Premier
def: "Waters AutoSpec Premier magnetic sector instrument." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554

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

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>

[Psidev-ms-dev] New version 4.0.2 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics community,

attached there's the new version 4.0.2 of the psi-ms.obo file.

It contains new terms for the Pegasus BT instrument and for MSPathFinder 
scores


New CV terms in version 4.0.2 of psi-ms.obo:
============================================
************ New instrument term
[Term]
id: MS:1002719
name: Pegasus BT
def: "LECO bench-top GC time-of-flight mass spectrometer." [PSI:PI]
is_a: MS:1001800 ! LECO instrument model

************ New terms for MSPathFinder scores
[Term]
id: MS:1002720
name: MSPathFinder
def: "PNNL top-down/bottom-up analysis software for identifying peptides 
and proteoforms in fragmentation mass spectra." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002721
name: MSPathFinder:SpecEValue
def: "MSPathFinder spectral E-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002353 ! PSM-level e-value
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002109 ! lower score better

[Term]
id: MS:1002722
name: MSPathFinder:EValue
def: "MSPathFinder E-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002353 ! PSM-level e-value
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002109 ! lower score better

[Term]
id: MS:1002723
name: MSPathFinder:QValue
def: "MSPathFinder Q-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002354 ! PSM-level q-value
is_a: MS:1001143 ! PSM-level search engine specific statistic

[Term]
id: MS:1002724
name: MSPathFinder:PepQValue
def: "MSPathFinder peptide-level Q-value." [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

[Term]
id: MS:1002725
name: MSPathFinder:RawScore
def: "MSPathFinder raw score." [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


Changed CV terms in version 4.0.2 of psi-ms.obo:
================================================
************ Changed the name and definition
[Term]
id: MS:1002678
name: supplemental beam-type collision-induced dissociation
def: "A supplemental collision-induced dissociation process that occurs 
in a beam-type collision cell in addition to another primary type of 
dissociation." [PSI:MS]
is_a: MS:1000422 ! beam-type collision-induced dissociation

************ Changed is_a: MS:1000044 ! dissociation method
************ into    is_a: MS:1000133 ! collision-induced dissociation
[Term]
id: MS:1002679
name: supplemental collision-induced dissociation
def: "The dissociation of an ion after supplemental collisional 
excitation." [PSI:MS]
is_a: MS:1000133 ! collision-induced dissociation

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554

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

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>

[Psidev-ms-dev] [Psi‐announce] Submission of an update to the specifications for mzIdentML 1.2 document: open for public review

[Sylvie Ricard-B. <syl...@un...>]

Dear colleague,

Dear member of the Proteomics community,

The HUPO Proteomics Standards Initiative (PSI) develops standards for 
documentation and storage of proteomics data (see http://www.psidev.info 
for an overview of activities).

The PSI Proteomics Informatics Working Group has submitted an update of 
the specifications for mzIdentML 1.2 to the PSI document process.

The specification document can be found here: 
https://github.com/HUPO-PSI/mzIdentML/blob/master/specification_document/specdoc1_2/mzIdentML1%202-draft.docx


Example files to demonstrate the standard are here: 
https://github.com/HUPO-PSI/mzIdentML/tree/master/examples/1_2examples


The validator is here: 
https://github.com/HUPO-PSI/mzIdentML/blob/master/validator/mzIdentMLValidator_GUI_v1.4.24-SNAPSHOT.zip

After a 30-day review of the PSI steering committee, the proposed 
document now goes through external review phase until November, 6^th , 
2016.

The public review enables the community to provide feedback on a 
proposed standard before it is formally accepted. It is thus an 
important step in the standardisation process. Both positive and 
negative comments on the relevance, clarity, correctness, and 
appropriateness of the entire document or of specific parts of it are 
welcome.

Please add comments to the submission page 
(http://www.psidev.info/mzidentml-12-docproc) or send them directly to 
syl...@un... 
<mailto:syl...@un...> with a particular focus on the 
following criteria:

- The document is presented in accordance with the templates and is 
clearly written.

- The document is sufficiently detailed and clearly describes the format.

- The examples are in accordance with the specification.

I invite you to forward this message to interested colleagues and I 
thank you in advance for your valuable contribution to the standards 
development effort.

Best wishes.

Sylvie RICARD-BLUM (PSI editor)

Professor Sylvie RICARD-BLUM

Pericellular and Extracellular Supramolecular Assemblies

UMR 5246 CNRS - University Lyon 1

Institute of Molecular and Supramolecular Chemistry and Biochemistry

Raulin Building - 2^nd Floor North

University Claude Bernard Lyon 1

43 Boulevard du 11 novembre 1918

69622 Villeurbanne Cedex, France

Tel : +33(0)4 72 44 82 32

E-mail: syl...@un... 
<mailto:syl...@un...>

http://www.icbms.fr <http://www.icbms.fr/>

The French Society for Matrix Biology http://www.sfbmec.fr 
<http://www.sfbmec.fr/>

The International Society for Matrix Biology http://ismb.org 
<http://ismb.org/>

Re: [Psidev-ms-dev] Demultiplexing overlapped/MSX spectra

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

Hi Matt, thanks for bringing this up. I don't see an immediate best
solution, so I'll think out loud for a bit...

The schema at <spectrum>
http://www.peptideatlas.org/tmp/mzML1.1.0.html#spectrum

The CV  for identifier formats:
http://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibr
ary.org%2Fobo%2FMS_1000767

One could imagine just using the plain nativeID term to just use an
arbitrary index for each spectrum.

Perhaps it might be useful to extend the vendor specific terms by adding a
demux= field, but I wonder if that would break most existing code:

controllerType=xsd:nonNegativeInteger controllerNumber=xsd:positiveInteger
scan=xsd:positiveInteger demux=xsd:positiveInteger

and it would need to be done for each vendor.

Maybe there should be a child term under spectrum representation called
"demultiplexed spectrum"
http://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibr
ary.org%2Fobo%2FMS_1000525

I think I agree that the demultiplexed spectrum should refer to the
original scan in the <scan> element.

Maybe it would best to come up with a single hand-crafted example for us
to debate over.

Can you come up with a good example of what you think would work best for
ProteoWizard?

Thanks,
Eric



-----Original Message-----
From: Chambers, Matthew [mailto:mat...@gm...]
Sent: Tuesday, September 27, 2016 1:35 PM
To: Mass spectrometry standard development
<psi...@li...>
Subject: [Psidev-ms-dev] Demultiplexing overlapped/MSX spectra

I am integrating some demultiplexing algorithms into ProteoWizard that
take overlapping DIA spectra or multi-isolation-window (MSX) spectra and
expand them to multiple single-isolation-window spectra. What nativeID
should the new spectra get? This is basically the opposite of the
scan-summing problem, which we theoretically came up with a solution for,
but don't see it used much. Should each demux'd spectrum refer back to the
original spectrum in the <scan> element?

-Matt

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

[Psidev-ms-dev] Demultiplexing overlapped/MSX spectra

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

I am integrating some demultiplexing algorithms into ProteoWizard that take overlapping DIA spectra or multi-isolation-window (MSX) spectra 
and expand them to multiple single-isolation-window spectra. What nativeID should the new spectra get? This is basically the opposite of the 
scan-summing problem, which we theoretically came up with a solution for, but don't see it used much. Should each demux'd spectrum refer 
back to the original spectrum in the <scan> element?

-Matt

[Psidev-ms-dev] New version 4.0.1 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics community,

attached there's the new version 4.0.1 of the psi-ms.obo file.


Changed CV terms in version 4.0.1 of psi-ms.obo:
============================================
************ Removed is_a: MS:1002489 ! special processing
************ from the following two terms, since they are used now under
************ <SearchType> and not <AdditionalSearchParams> (see GitHub 
issue #72)
[Term]
id: MS:1001010
name: de novo search
def: "A de novo sequencing search (without database)." [PSI:PI]
is_a: MS:1001080 ! search type

[Term]
id: MS:1001031
name: spectral library search
def: "A search using a library of spectra." [PSI:PI]
is_a: MS:1001080 ! search type

************ Removed the value slot from the following term
[Term]
id: MS:1001460
name: unknown modification
def: "This term should be given if the modification was unknown." [PSI:PI]
is_a: MS:1001471 ! peptide modification details

Best Regards,
Gerhard
-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554

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

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>

[Psidev-ms-dev] FW: mzTab mailing list

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

Hi all,

We are now actively developing mzTab for metabolomics, which we are going to coordinate via a dedicated google group, rather than the PSI-PI/MS mailing lists. If you would like to contribute, please sign up below, and forward this on to anyone else who may be interested.

Best wishes
Andy

From: Reza Salek [mailto:rez...@eb...]
Sent: 14 July 2016 15:54
To: Jones, Andy <jo...@li...>
Cc: Juan Antonio Vizcaino (ju...@eb...) <ju...@eb...>
Subject: Re: mzTab mailing list

Hi Andy,

Sounds good and will do my part.

You can send:

https://groups.google.com/forum/#!forum/mztab4metabolomics

You are manger so need to approve the memberships and should get an email. I can add more people if they wish to help managing it.

Best Wishes
Reza

Re: [Psidev-ms-dev] [Psidev-ms-vocab] new Cross-Linker ontology XLMOD.obo

[Mathias W. <wa...@in...>]

So if you create a new XLMOD.obo it's fine with me regarding restructuring hierarchy and numeration etc; provided the linkers themselves present now do not disappear. 

best,
 mths  

----- Original Message -----
From: "Andy Jones" <And...@li...>
To: psi...@li..., psi...@li..., psi...@li...
Sent: Friday, 1 July, 2016 12:13:47 PM
Subject: Re: [Psidev-ms-dev] [Psidev-ms-vocab] new Cross-Linker ontology	XLMOD.obo





For me it is fine to start with a clean slate, since it hasn’t been widely distributed or used yet. 

Best wishes 

Andy 





From: mayerg97 [mailto:ger...@ru...] 
Sent: 01 July 2016 11:03 
To: psi...@li...; psi...@li...; psi...@li... 
Subject: [Psidev-ms-vocab] new Cross-Linker ontology XLMOD.obo 



Hi all, 

together with Lutz I developed a new proposal of our cross-linker ontology. 
We have now more structuring and possibilities to model the properties of the cross-linkers. 

Since we put a lot of new intermediate terms for structuring, some ID's changed, but I think it's still ok 
at the moment to restart with a clean state, since until now nowhere beside of our .mzid 1.2 examples 
the ontology is used so far. 

So we just must update our cross-linker example files. Is that ok? 

Best regards, 
Gerhard 


-- 

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

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

PhD student 

Medizinisches Proteom-Center 

DEPARTMENT Medical Bioinformatics 

Building ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum 

Fon +49 (0)234 32-21006 | Fax +49 (0)234 32-14554 

E-mail ger...@ru... 

www.medizinisches-proteom-center.de 


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Re: [Psidev-ms-dev] [Psidev-ms-vocab] new Cross-Linker ontology XLMOD.obo

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

For me it is fine to start with a clean slate, since it hasn’t been widely distributed or used yet.
Best wishes
Andy

From: mayerg97 [mailto:ger...@ru...]
Sent: 01 July 2016 11:03
To: psi...@li...; psi...@li...; psi...@li...
Subject: [Psidev-ms-vocab] new Cross-Linker ontology XLMOD.obo

Hi all,

together with Lutz I developed a new proposal of our cross-linker ontology.
We have now more structuring and possibilities to model the properties of the cross-linkers.

Since we put a lot of new intermediate terms for structuring, some ID's changed, but I think it's still ok
at the moment to restart with a clean state, since until now nowhere beside of our .mzid 1.2 examples
the ontology is used so far.

So we just must update our cross-linker example files. Is that ok?

Best regards,
Gerhard
--

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

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

PhD student

Medizinisches Proteom-Center

DEPARTMENT Medical Bioinformatics

Building ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-21006 | Fax +49 (0)234 32-14554

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

www.medizinisches-proteom-center.de<http://www.medizinisches-proteom-center.de>
[cid:image001.jpg@01D1D389.A27A7650]

[Psidev-ms-dev] new Cross-Linker ontology XLMOD.obo

[mayerg97 <ger...@ru...>]

format-version: 1.2
data-version: releases/2016-07-01
ontology: xl
date: 01:07:2016 11:46
saved-by: Gerhard Mayer
auto-generated-by: OBO-Edit 2.3.1
default-namespace: XL
remark: namespace: XL
remark: version: 1.0.0_rc1
remark: release date: 2016-07-01
remark: coverage: cross-linking reagents
remark: creator: Lutz Fischer <lfischer <-at-> staffmail.ed.ac.uk>
remark: creator: Gerhard Mayer <mayerg97 <-at-> rub.de>
remark: This work is licensed under the Creative Commons Attribution 3.0 Unported License.
remark: To view a copy of this license, visit http://creativecommons.org/licenses/by/3.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA.

[Typedef]
id: part_of
name: part_of
is_transitive: true

[Typedef]
id: is_labelled
name: is_labelled

[Typedef]
id: is_partially_reacted
name: is_partially_reacted

[Typedef]
id: has_property
name: has_property

[Term]
id: XL:00000
name: Proteomics Standards Initiative cross-linking controlled vocabulary
def: "Proteomics Standards Initiative cross-linking controlled vocabulary." [PSI:XL]

[Term]
id: XL:00001
name: cross-linking entity
def: "Entity relevant to the domain of cross-linking in proteomics." [PSI:XL]
relationship: part_of XL:00000 ! Proteomics Standards Initiative cross-linking controlled vocabulary

[Term]
id: XL:00002
name: cross-linker related PTM
def: "A cross-linker reagent with one reactive group." [PSI:XL]
relationship: part_of XL:00000 ! Proteomics Standards Initiative cross-linking controlled vocabulary

[Term]
id: XL:00003
name: label transfer reagent
def: "A cross-linker acting as label (e.g. biotin) transfer reagent." [PSI:XL]
relationship: part_of XL:00000 ! Proteomics Standards Initiative cross-linking controlled vocabulary

[Term]
id: XL:00004
name: cross-linker
def: "Compound that can link two or more polymer chains." [PSI:XL]
is_a: XL:00001 ! cross-linking entity

[Term]
id: XL:00005
name: homofunctional cross-linker
def: "A cross-linker reagent with identical reactive groups at each end of the spacer arm." [PSI:XL]
is_a: XL:00004 ! cross-linker

[Term]
id: XL:00006
name: heterofunctional cross-linker
def: "A cross-linker reagent with at least two different reactive groups." [PSI:XL]
is_a: XL:00004 ! cross-linker

[Term]
id: XL:00007
name: photoreactive cross-linker
def: "A cross-linker reagent that becomes reactive when exposed to ultraviolet or visible light." [PSI:XL]
synonym: "non-selective cross-linker" EXACT [PSI:XL]
is_a: XL:00004 ! cross-linker

[Term]
id: XL:00008
name: zero-length cross-linker
def: "A cross-linker reagent causing direct conjugation without becoming part of the final cross-link between the target molecules." [PSI:XL]
is_a: XL:00004 ! cross-linker

[Term]
id: XL:00010
name: deuterium-labelled
def: "Indicates that a cross-linker is deuterium-labelled." [PSI:XL]
relationship: part_of XL:00001 ! cross-linking entity

[Term]
id: XL:00011
name: hydrolyzed
def: "Indicates that a cross-linker is hydrolyzed." [PSI:XL]
relationship: part_of XL:00001 ! cross-linking entity

[Term]
id: XL:00012
name: amidated
def: "Indicates that a cross-linker is amidated." [PSI:XL]
relationship: part_of XL:00001 ! cross-linking entity

[Term]
id: XL:00013
name: membrane permeable
def: "Indicates that a cross-linker is membrane permeable." [PSI:XL]
relationship: part_of XL:00001 ! cross-linking entity

[Term]
id: XL:00014
name: water soluble
def: "Indicates that a cross-linker is water soluble." [PSI:XL]
relationship: part_of XL:00001 ! cross-linking entity

[Term]
id: XL:00101
name: BS3
def: "Bis(sulfosuccinimidyl)suberate." [PSI:XL, CAS:82436-77-9, PubChem_Compound:6097991]
property_value: reactionSites: "2" xsd:nonNegativeInteger
property_value: monoisotopicMass: "138.06807961" xsd:double
property_value: specificities: "(K,S,T,Y,Protein N-term)&(K,S,T,Y,Protein N-term)" xsd:string
property_value: spacerLength: "11.4" xsd:double
is_a: XL:00005 ! homofunctional cross-linker
relationship: has_property XL:00014 ! water soluble

[Term]
id: XL:00102
name: DSS
def: "Disuccinimidyl suberate." [PSI:XL, CAS:68528-80-3, PubChem_Compound:100658]
property_value: reactionSites: "2" xsd:nonNegativeInteger
property_value: monoisotopicMass: "138.06807961" xsd:double
property_value: specificities: "(K,S,T,Y,Protein N-term)&(K,S,T,Y,Protein N-term)" xsd:string
property_value: spacerLength: "11.4" xsd:double
is_a: XL:00005 ! homofunctional cross-linker
relationship: has_property XL:00013 ! membrane_permeable

[Term]
id: XL:00103
name: DSS-d4
def: "Deuterium-labelled disuccinimidyl 2,2,7,7-suberate." [PSI:XL, PubChem_Compound:91757798]
property_value: reactionSites: "2" xsd:nonNegativeInteger
property_value: monoisotopicMass: "142.093186586" xsd:double
property_value: specificities: "(K,S,T,Y,Protein N-term)&(K,S,T,Y,Protein N-term)" xsd:string
property_value: spacerLength: "11.4" xsd:double
is_a: XL:00005 ! homofunctional cross-linker
relationship: is_labelled XL:00010 ! deuterium-labelled

[Term]
id: XL:00104
name: DSS-d12
def: "Deuterium-labelled disuccinimidyl 2,2,3,3,4,4,5,5,6,6,7,7-suberate." [PSI:XL]
property_value: reactionSites: "2" xsd:nonNegativeInteger
property_value: monoisotopicMass: "150.143400538" xsd:double
property_value: specificities: "(K,S,T,Y,Protein N-term)&(K,S,T,Y,Protein N-term)" xsd:string
property_value: spacerLength: "11.4" xsd:double
is_a: XL:00005 ! homofunctional cross-linker
relationship: is_labelled XL:00010 ! deuterium-labelled

[Term]
id: XL:00105
name: BS3-d4
def: "Deuterium-labelled (bis(sulfosuccinimidyl) 2,2,7,7-suberate-d4)." [PSI:XL, PubChem_Compound:91757801]
property_value: reactionSites: "2" xsd:nonNegativeInteger
property_value: monoisotopicMass: "142.093186586" xsd:double
property_value: specificities: "(K,S,T,Y,Protein N-term)&(K,S,T,Y,Protein N-term)" xsd:string
property_value: spacerLength: "11.4" xsd:double
is_a: XL:00005 ! homofunctional cross-linker
relationship: is_labelled XL:00010 ! deuterium-labelled

[Term]
id: XL:00106
name: BS2G
def: "Bis(sulfosuccinimidyl) glutarat." [PSI:XL, PubChem_Compound:91757794]
property_value: reactionSites: "2" xsd:nonNegativeInteger
property_value: monoisotopicMass: "96.0211294" xsd:double
property_value: specificities: "(K,S,T,Y,Protein N-term)&(K,S,T,Y,Protein N-term)" xsd:string
property_value: spacerLength: "7.7" xsd:double
is_a: XL:00005 ! homofunctional cross-linker

[Term]
id: XL:00107
name: DSG
def: "Disuccinimidyl glutarate." [PSI:XL, CAS:79642-50-5, PubChem_Compound:4432628]
property_value: reactionSites: "2" xsd:nonNegativeInteger
property_value: monoisotopicMass: "96.0211294" xsd:double
property_value: specificities: "(K,S,T,Y,Protein N-term)&(K,S,T,Y,Protein N-term)" xsd:string
property_value: spacerLength: "7.7" xsd:double
is_a: XL:00005 ! homofunctional cross-linker
relationship: has_property XL:00013 ! membrane_permeable

[Term]
id: XL:00108
name: DSG-d4
def: "Deuterium-labelled disuccinimidyl 2,2,4,4-glutarate." [PSI:XL, PubChem_Compound:91757797]
property_value: reactionSites: "2" xsd:nonNegativeInteger
property_value: monoisotopicMass: "146.118293562" xsd:double
property_value: specificities: "(K,S,T,Y,Protein N-term)&(K,S,T,Y,Protein N-term)" xsd:string
property_value: spacerLength: "7.7" xsd:double
is_a: XL:00005 ! homofunctional cross-linker
relationship: is_labelled XL:00010 ! deuterium-labelled

[Term]
id: XL:00109
name: BS2G-d4
def: "Deuterium-labelled bis(sulfosuccinimidyl) 2,2,4,4-glutarate." [PSI:XL, PubChem_Compound:91757799]
property_value: reactionSites: "2" xsd:nonNegativeInteger
property_value: monoisotopicMass: "100.046236376" xsd:double
property_value: specificities: "(K,S,T,Y,Protein N-term)&(K,S,T,Y,Protein N-term)" xsd:string
property_value: spacerLength: "7.7" xsd:double
is_a: XL:00005 ! homofunctional cross-linker
relationship: is_labelled XL:00010 ! deuterium-labelled

[Term]
id: XL:00110
name: Disulfide
def: "Disulfide." [PSI:XL]
property_value: reactionSites: "2" xsd:nonNegativeInteger
property_value: monoisotopicMass: "-2.01565007" xsd:double
property_value: specificities: "(C)&(C)" xsd:string
is_a: XL:00005 ! homofunctional cross-linker

[Term]
id: XL:00111
name: EDC
def: "1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride." [PSI:XL, CAS:25952-53-8, PubChem_Compound:2723939]
property_value: reactionSites: "2" xsd:nonNegativeInteger
property_value: monoisotopicMass: "-18.01056027" xsd:double
property_value: specificities: "(K,S,T,Y,Protein N-term)&(E,D,Protein C-term)" xsd:string
is_a: XL:00008 ! zero-length cross-linker

[Term]
id: XL:00112
name: BDP-NHP
def: "Biotin Aspartate Proline n-hydroxyphthalamide." [PSI:XL]
property_value: reactionSites: "2" xsd:nonNegativeInteger
property_value: monoisotopicMass: "1241.469925525" xsd:double
property_value: specificities: "(K,Protein N-term)&(K,Protein N-term)" xsd:string
is_a: XL:00003 ! label transfer agent

[Term]
id: XL:01000
name: hydrolyzed BS3
def: "Hydrolyzed bis(sulfosuccinimidyl)suberate." [PSI:XL]
property_value: reactionSites: "1" xsd:nonNegativeInteger
property_value: monoisotopicMass: "156.07864431" xsd:double
property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string
property_value: spacerLength: "11.4" xsd:double
is_a: XL:00005 ! homofunctional cross-linker
relationship: is_partially_reacted XL:00011 ! hydrolyzed

[Term]
id: XL:01001
name: amidated BS3
def: "Amidated bis(sulfosuccinimidyl)suberate." [PSI:XL]
property_value: reactionSites: "1" xsd:nonNegativeInteger
property_value: monoisotopicMass: "155.094628715" xsd:double
property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string
property_value: spacerLength: "11.4" xsd:double
is_a: XL:00005 ! homofunctional cross-linker
relationship: is_partially_reacted XL:00012 ! amidated

[Term]
id: XL:01002
name: hydrolyzed DSS
def: "Hydrolyzed disuccinimidyl suberate." [PSI:XL]
property_value: reactionSites: "1" xsd:nonNegativeInteger
property_value: monoisotopicMass: "156.07864431" xsd:double
property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string
property_value: spacerLength: "11.4" xsd:double
is_a: XL:00005 ! homofunctional cross-linker
relationship: is_partially_reacted XL:00011 ! hydrolyzed

[Term]
id: XL:01003
name: amidated DSS
def: "Amidated disuccinimidyl suberate." [PSI:XL]
property_value: reactionSites: "1" xsd:nonNegativeInteger
property_value: monoisotopicMass: "155.094628715" xsd:double
property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string
property_value: spacerLength: "11.4" xsd:double
is_a: XL:00005 ! homofunctional cross-linker
relationship: is_partially_reacted XL:00012 ! amidated

[Term]
id: XL:01004
name: hydrolyzed DSS-d4
def: "Deuterium-labelled hydrolyzed disuccinimidyl 2,2,7,7-suberate." [PSI:XL]
property_value: reactionSites: "1" xsd:nonNegativeInteger
property_value: monoisotopicMass: "160.1037416836" xsd:double
property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string
property_value: spacerLength: "11.4" xsd:double
is_a: XL:00005 ! homofunctional cross-linker
relationship: is_partially_reacted XL:00011 ! hydrolyzed

[Term]
id: XL:01005
name: amidated DSS-d4
def: "Deuterium-labelled amidated disuccinimidyl 2,2,7,7-suberate." [PSI:XL]
property_value: reactionSites: "1" xsd:nonNegativeInteger
property_value: monoisotopicMass: "159.1197260886" xsd:double
property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string
property_value: spacerLength: "11.4" xsd:double
is_a: XL:00005 ! homofunctional cross-linker
relationship: is_partially_reacted XL:00012 ! amidated
relationship: is_labelled XL:00010 ! deuterium-labelled

[Term]
id: XL:01006
name: hydrolyzed DSS-d12
def: "Deuterium-labelled hydrolyzed disuccinimidyl 2,2,3,3,4,4,5,5,6,6,7,7-suberate." [PSI:XL]
property_value: reactionSites: "1" xsd:nonNegativeInteger
property_value: monoisotopicMass: "168.153965238" xsd:double
property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string
property_value: spacerLength: "11.4" xsd:double
is_a: XL:00005 ! homofunctional cross-linker
relationship: is_partially_reacted XL:00011 ! hydrolyzed
relationship: is_labelled XL:00010 ! deuterium-labelled

[Term]
id: XL:01007
name: amidated DSS-d12
def: "Deuterium-labelled amidated disuccinimidyl 2,2,3,3,4,4,5,5,6,6,7,7-suberate." [PSI:XL]
property_value: reactionSites: "1" xsd:nonNegativeInteger
property_value: monoisotopicMass: "167.169949643" xsd:double
property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string
property_value: spacerLength: "11.4" xsd:double
is_a: XL:00005 ! homofunctional cross-linker
relationship: is_partially_reacted XL:00012 ! amidated
relationship: is_labelled XL:00010 ! deuterium-labelled

[Term]
id: XL:01008
name: hydrolyzed BS3-d4
def: "Deuterium-labelled hydrolyzed bis(sulfosuccinimidyl) 2,2,7,7-suberate." [PSI:XL]
property_value: reactionSites: "1" xsd:nonNegativeInteger
property_value: monoisotopicMass: "160.103751286" xsd:double
property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string
property_value: spacerLength: "11.4" xsd:double
property_value: spacerLength: "11.4" xsd:double
is_a: XL:00005 ! homofunctional cross-linker
relationship: is_partially_reacted XL:00011 ! hydrolyzed
relationship: is_labelled XL:00010 ! deuterium-labelled

[Term]
id: XL:01009
name: amidated BS3-d4
def: "Deuterium-labelled amidated bis(sulfosuccinimidyl) 2,2,7,7-suberate." [PSI:XL]
property_value: reactionSites: "1" xsd:nonNegativeInteger
property_value: monoisotopicMass: "159.119735691" xsd:double
property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string
property_value: spacerLength: "11.4" xsd:double
is_a: XL:00005 ! homofunctional cross-linker
relationship: is_partially_reacted XL:00012 ! amidated
relationship: is_labelled XL:00010 ! deuterium-labelled

[Term]
id: XL:01010
name: hydrolyzed BS2G
def: "Hydrolyzed bis(sulfosuccinimidyl) glutarate." [PSI:XL]
property_value: reactionSites: "1" xsd:nonNegativeInteger
property_value: monoisotopicMass: "114.0316941" xsd:double
property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string
property_value: spacerLength: "7.7" xsd:double
is_a: XL:00005 ! homofunctional cross-linker
relationship: is_partially_reacted XL:00011 ! hydrolyzed

[Term]
id: XL:01011
name: amidated BS2G
def: "Amidated bis(sulfosuccinimidyl) glutarate." [PSI:XL]
property_value: reactionSites: "1" xsd:nonNegativeInteger
property_value: monoisotopicMass: "113.047678505" xsd:double
property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string
property_value: spacerLength: "7.7" xsd:double
is_a: XL:00005 ! homofunctional cross-linker
relationship: is_partially_reacted XL:00012 ! amidated

[Term]
id: XL:01012
name: hydrolyzed DSG
def: "Hydrolyzed disuccinimidyl glutarate." [PSI:XL]
property_value: reactionSites: "1" xsd:nonNegativeInteger
property_value: monoisotopicMass: "114.0316941" xsd:double
property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string
property_value: spacerLength: "7.7" xsd:double
is_a: XL:00004 ! cross-linker
relationship: is_partially_reacted XL:00011 ! hydrolyzed

[Term]
id: XL:01013
name: amidated DSG
def: "Amidated disuccinimidyl glutarate." [PSI:XL]
property_value: reactionSites: "1" xsd:nonNegativeInteger
property_value: monoisotopicMass: "113.047678505" xsd:double
property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string
property_value: spacerLength: "7.7" xsd:double
is_a: XL:00005 ! homofunctional cross-linker
relationship: is_partially_reacted XL:00012 ! amidated

[Term]
id: XL:01014
name: hydrolyzed DSG-d4
def: "Deuterium-labelled amidated disuccinimidyl 2,2,4,4-glutarate." [PSI:XL]
property_value: reactionSites: "1" xsd:nonNegativeInteger
property_value: monoisotopicMass: "164.128858262" xsd:double
property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string
property_value: spacerLength: "7.7" xsd:double
is_a: XL:00005 ! homofunctional cross-linker
relationship: is_partially_reacted XL:00011 ! hydrolyzed
relationship: is_labelled XL:00010 ! deuterium-labelled

[Term]
id: XL:01015
name: amidated DSG-d4
def: "Deuterium-labelled hydrolyzed disuccinimidyl 2,2,4,4-glutarate." [PSI:XL]
property_value: reactionSites: "1" xsd:nonNegativeInteger
property_value: monoisotopicMass: "163.144842667" xsd:double
property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string
property_value: spacerLength: "7.7" xsd:double
is_a: XL:00005 ! homofunctional cross-linker
relationship: is_partially_reacted XL:00012 ! amidated
relationship: is_labelled XL:00010 ! deuterium-labelled

[Term]
id: XL:01016
name: hydrolyzed BS2G-d4
def: "Deuterium-labelled hydrolyzed bis(sulfosuccinimidyl) 2,2,4,4-glutarate." [PSI:XL]
property_value: reactionSites: "1" xsd:nonNegativeInteger
property_value: monoisotopicMass: "118.056801076" xsd:double
property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string
property_value: spacerLength: "7.7" xsd:double
is_a: XL:00005 ! homofunctional cross-linker
relationship: is_partially_reacted XL:00011 ! hydrolyzed
relationship: is_labelled XL:00010 ! deuterium-labelled

[Term]
id: XL:01017
name: amidated BS2G-d4
def: "Deuterium-labelled amidated bis(sulfosuccinimidyl) 2,2,4,4-glutarate." [PSI:XL]
property_value: reactionSites: "1" xsd:nonNegativeInteger
property_value: monoisotopicMass: "117.072785481" xsd:double
property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string
property_value: spacerLength: "7.7" xsd:double
is_a: XL:00005 ! homofunctional cross-linker
relationship: is_partially_reacted XL:00012 ! amidated
relationship: is_labelled XL:00010 ! deuterium-labelled

[Term]
id: XL:01017
name: BDP-NHP-stump
def: "Biotin Aspartate Proline n-hydroxyphthalimide-stump." [PSI:XL]
property_value: reactionSites: "1" xsd:nonNegativeInteger
property_value: monoisotopicMass: "197.032422395" xsd:double
property_value: specificities: "(K,Protein N-term)" xsd:string
is_a: XL:00003 ! label transfer agent

[Psidev-ms-dev] New version 4.0.0 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics community,

attached there's the new version 4.0.0 of the psi-ms.obo file.

It contains a clean up and restructuring of many scoring terms,
see GitHub issue #25: https://github.com/HUPO-PSI/mzIdentML/issues/25

Therefore the version number was set to 4.0.0

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554

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

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>

[Psidev-ms-dev] New version 3.90.0 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics community,

attached there's the new version 3.90.0 of the psi-ms.obo file
containing new terms for the annotation of cross-linking files, for 
supplemental activation
and for the OpenXQuest search engine.


New CV terms in version 3.90.0 of psi-ms.obo:
=============================================
************ terms for cross-linking annotation
[Term]
id: MS:1002675
name: cross-linking result details
def: "This subsection describes terms which can describe details of 
cross-linking results." [PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation

[Term]
id: MS:1002676
name: protein-pair-level global FDR
def: "Estimation of the global false discovery rate of proteins-pairs in 
cross-linking experiments." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002675 ! cross-linking result details
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1002677
name: residue-pair-level global FDR
def: "Estimation of the global false discovery rate of residue-pairs in 
cross-linking experiments." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002675 ! cross-linking result details
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

************ Terms for supplemental activation
[Term]
id: MS:1002678
name: supplemental higher energy beam-type collision-induced dissociation
def: "A supplemental collision-induced dissociation process wherein the 
projectile ion has the translational energy higher than approximately 
1000 eV." [PSI:MS]
is_a: MS:1000422 ! beam-type collision-induced dissociation

[Term]
id: MS:1002679
name: supplemental collision-induced dissociation
def: "The dissociation of an ion after supplemental collisional 
excitation." [PSI:MS]
is_a: MS:1000044 ! dissociation method

[Term]
id: MS:1002680
name: supplemental collision energy
def: "Energy for an ion experiencing supplemental collision with a 
stationary gas particle resulting in dissociation of the ion." [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:0000266 ! electronvolt

************ OpenXQuest search engine scores
[Term]
id: MS:1002681
name: OpenXQuest:combined score
def: "OpenXQuest's combined 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 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002682
name: OpenXQuest:xcorr xlink
def: "OpenXQuest's cross-correlation of cross-linked ions subscore." 
[PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002683
name: OpenXQuest:xcorr common
def: "OpenXQuest's cross-correlation of unlinked ions subscore." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002684
name: OpenXQuest:match-odds
def: "OpenXQuest's match-odds subscore." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002306 ! value greater than zero

[Term]
id: MS:1002685
name: OpenXQuest:intsum
def: "OpenXQuest's sum of matched peak intensity subscore." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002306 ! value greater than zero

[Term]
id: MS:1002686
name: OpenXQuest:wTIC
def: "OpenXQuest's weighted percent of total ion current subscore." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive


Changed CV terms in version 3.90.0 of psi-ms.obo:
=================================================
************ Removed the units UO:0000166 and UO:0000187 from the 
following FDR- and q-value terms
[Term]
id: MS:1001250
name: local FDR
def: "Result of quality estimation: the local FDR at the current 
position of a sorted list." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001092 ! peptide identification confidence metric
is_a: MS:1001198 ! protein identification confidence metric

[Term]
id: MS:1001868
name: distinct peptide-level q-value
def: "Estimation of the q-value for distinct peptides once redundant 
identifications of the same peptide have been removed (id est multiple 
PSMs, possibly with different mass modifications, mapping to the same 
sequence have been collapsed to one entry)." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002484 ! peptide-level statistical threshold
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1001869
name: protein-level q-value
def: "Estimation of the q-value for proteins." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001198 ! protein identification confidence metric
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1002354
name: PSM-level q-value
def: "Estimation of the q-value for peptide spectrum matches." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002347 ! PSM-level identification confidence metric
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1002373
name: protein group-level q-value
def: "Estimation of the q-value for protein groups." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002348 ! protein group-level identification confidence metric
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

Best Regards,
Gerhard

-- 

*--*

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554

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

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>

RUB Logo

ANNOUNCEMENT de.NBI summer school September 2016:

*Analysis of Mass-Spectrometric Data - *

*Big Data Bioinformatics in Proteomics and Metabolomics*

http://www.denbi.de/index.php/11-training-cat/95-lss2016

[Psidev-ms-dev] Release candidate 3.90.0_rc2

[mayerg97 <ger...@ru...>]

Dear proteomics community,

attached there's the release candidate 3.90.0_rc2 of the psi-ms.obo file
containing new terms for the annotation of cross-linking files and for 
supplemental, activation.


New CV terms in version 3.90.0_rc2 of psi-ms.obo:
=================================================
************ terms for cross-linking annotation
[Term]
id: MS:1002675
name: cross-linking result details
def: "This subsection describes terms which can describe details of 
cross-linking results." [PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation

[Term]
id: MS:1002676
name: protein-pair-level global FDR
def: "Estimation of the global false discovery rate of proteins-pairs in 
cross-linking experiments." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002675 ! cross-linking result details
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1002677
name: residue-pair-level global FDR
def: "Estimation of the global false discovery rate of residue-pairs in 
cross-linking experiments." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002675 ! cross-linking result details
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

************ Terms for supplemental activation
************ @Matt: When I uderstood you correctly, the supplemental 
terms are needed only for HCD and CID, is that correct ?
[Term]
id: MS:1002678
name: supplemental higher energy beam-type collision-induced dissociation
def: "A supplemental collision-induced dissociation process wherein the 
projectile ion has the translational energy higher than approximately 
1000 eV." [PSI:MS]
is_a: MS:1000422 ! beam-type collision-induced dissociation

[Term]
id: MS:1002679
name: supplemental collision-induced dissociation
def: "The dissociation of an ion after supplemental collisional 
excitation." [PSI:MS]
is_a: MS:1000044 ! dissociation method

[Term]
id: MS:1002680
name: supplemental collision energy
def: "Energy for an ion experiencing supplemental collision with a 
stationary gas particle resulting in dissociation of the ion." [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:0000266 ! electronvolt

Best Regards,
Gerhard
-- 

*--*

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554

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

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>

RUB Logo

ANNOUNCEMENT de.NBI summer school September 2016:

*Analysis of Mass-Spectrometric Data - *

*Big Data Bioinformatics in Proteomics and Metabolomics*

http://www.denbi.de/index.php/11-training-cat/95-lss2016

[Psidev-ms-dev] Release candidate 3.90.0_rc1 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics community,
>
>
> attached there's the release candidate 3.90.0_rc1 of the psi-ms.obo file
> containing new terms for the annotation of cross-linking files.
>
> New CV terms in version 3.90.0_rc1 of psi-ms.obo:
> =================================================
> [Term]
> id: MS:1002675
> name: cross-linking result details
> def: "This subsection describes terms which can describe details of 
> cross-linking results." [PSI:PI]
> relationship: part_of MS:1001000 ! spectrum interpretation
>
> [Term]
> id: MS:1002676
> name: protein-pair-level global FDR
> def: "Estimation of the global false discovery rate of proteins-pairs 
> in cross-linking experiments." [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1002675 ! cross-linking result details
> relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
>
> [Term]
> id: MS:1002677
> name: residue-pair-level global FDR
> def: "Estimation of the global false discovery rate of residue-pairs 
> in cross-linking experiments." [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1002675 ! cross-linking result details
> relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
>
> Best Regards,
> Gerhard
>
> -- 
>
> *--*
>
> *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*
>
> *PhD student*
>
> *Medizinisches Proteom-Center*
>
> *DEPARTMENT Medical Bioinformatics*
>
> *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum
>
> *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554
>
> *E-mail***ger...@ru...
>
> www.medizinisches-proteom-center.de
>
> RUB Logo
>
> ANNOUNCEMENT de.NBI summer school September 2016:
>
> *Analysis of Mass-Spectrometric Data - *
>
> *Big Data Bioinformatics in Proteomics and Metabolomics*
>
> <http://www.denbi.de/index.php/11-training-cat/95-lss2016>http://www.denbi.de/index.php/11-training-cat/95-lss2016
>
<http://www.denbi.de/index.php/11-training-cat/95-lss2016>

[Psidev-ms-dev] New version 3.89.0 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics community,

attached there's the new version 3.89.0 of the psi-ms.obo file.
It contains a generic neutral loss term and terms for reporter ions.


New CV terms in version 3.89.0 of psi-ms.obo:
=============================================
************ Added a string value slot holding the molecular formula in 
Hill notation
[Term]
id: MS:1000336
name: neutral loss
def: "The loss of an uncharged species during a rearrangement process. 
The value slot holds the molecular formula in Hill notation of the 
neutral loss molecule, see PMID: 21182243. This term must be used in 
conjunction with a child of the term MS:1002307 (fragmentation ion 
type)." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001055 ! modification parameters

************ New terms for reporter ions
************ The mass can be specified in the value slot.
[Term]
id: MS:1002668
name: frag: iTRAQ 4plex reporter ion
def: "Standard reporter ion for iTRAQ 4Plex. The value slot holds the 
integer mass of the iTRAQ 4Plex reporter ion, e.g. 114." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002669
name: frag: iTRAQ 8plex reporter ion
def: "Standard reporter ion for iTRAQ 8Plex. The value slot holds the 
integer mass of the iTRAQ 8Plex reporter ion, e.g. 113." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002670
name: frag: TMT reporter ion
def: "Standard reporter ion for TMT. The value slot holds the integer 
mass of the TMT reporter ion and can be suffixed with either N or C, 
indicating whether the mass difference is encoded at a Nitrogen or 
Carbon atom, e.g. 127N." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002671
name: frag: TMT ETD reporter ion
def: "Standard reporter ion for TMT with ETD fragmentation. The value 
slot holds the integer mass of the TMT ETD reporter ion and can be 
suffixed with either N or C, indicating whether the mass difference is 
encoded at a Nitrogen or Carbon atom, e.g. 127C." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002672
name: no modification threshold
def: "No statistical threshold for accepting or rejecting that a 
modification position." [PSI:PI]
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:1002673
name: OpenXQuest
def: "Cross-Linking MS search engine." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002674
name: X500R QTOF
def: "SCIEX X500R QTOF, a quadrupole - quadrupole - time-of-flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000121 ! SCIEX instrument model


Changed CV terms in version 3.89.0 of psi-ms.obo:
=================================================
************ Changed the regular expression to allow null for the 
interaction position
[Term]
id: MS:1002665
name: regular expression for protein interaction scores derived from 
cross-linking
def: 
"([:digit:]+[.][a|b]:([:digit:]+|null):[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\})" 
[PSI:PI]
is_a: MS:1002479 ! regular expression

************ Obsoleted the following terms.
[Term]
id: MS:1002455
name: H2O neutral loss
def: "OBSOLETE Neutral loss of water." [PSI:PI]
comment: This term was obsoleted because it should be replaced by 
MS:1000336 with value H2O.
is_a: MS:1000336 ! neutral loss
is_a: MS:1002473 ! ion series considered in search
is_obsolete: true

[Term]
id: MS:1002456
name: NH3 neutral loss
def: "OBSOLETE Neutral loss of ammonia." [PSI:PI]
comment: This term was obsoleted because it should be replaced by 
MS:1000336 with value NH3.
is_a: MS:1000336 ! neutral loss
is_a: MS:1002473 ! ion series considered in search
is_obsolete: true

[Term]
id: MS:1002457
name: H3PO4 neutral loss
def: "OBSOLETE Neutral loss of phosphoric acid." [PSI:PI]
comment: This term was obsoleted because it should be replaced by 
MS:1000336 with value H3PO4.
is_a: MS:1000336 ! neutral loss
is_a: MS:1002473 ! ion series considered in search
is_obsolete: true

************ REARRANGEMENT OF PSM-level result details BRANCH ************
************ The following two terms moved from
************ is_a: MS:1001872 ! distinct peptide-level e-value
************ to is_a: MS:1002353 ! PSM-level e-value
[Term]
id: MS:1001328
name: OMSSA:evalue
def: "OMSSA E-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002353 ! PSM-level e-value

[Term]
id: MS:1001330
name: X\!Tandem:expect
def: "The X!Tandem expectation value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002353 ! PSM-level e-value

************ The following two terms moved from
************ is_a: MS:1001870 ! distinct peptide-level p-value
************ to is_a: MS:1002352 ! PSM-level p-value
[Term]
id: MS:1001329
name: OMSSA:pvalue
def: "OMSSA p-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002352 ! PSM-level p-value

[Term]
id: MS:1001396
name: Phenyx:PepPvalue
def: "The p-value of a peptide sequence match in Phenyx." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002352 ! PSM-level p-value

************ The following two terms moved from
************ is_a: MS:1002347 ! PSM-level identification confidence metric
************ to is_a: MS:1001092 ! peptide identification confidence metric
[Term]
id: MS:1001872
name: distinct peptide-level e-value
def: "Estimation of the e-value for distinct peptides once redundant 
identifications of the same peptide have been removed (id est multiple 
PSMs have been collapsed to one entry)." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
MS:1001092 ! peptide identification confidence metric
relationship: has_domain MS:1002306 ! value greater than zero

[Term]
id: MS:1001870
name: distinct peptide-level p-value
def: "Estimation of the p-value for distinct peptides once redundant 
identifications of the same peptide have been removed (id est multiple 
PSMs have been collapsed to one entry)." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
MS:1001092 ! peptide identification confidence metric
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

Best Regards,
Gerhard

-- 

*--*

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554

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

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>

RUB Logo

ANNOUNCEMENT de.NBI summer school September 2016:

*Analysis of Mass-Spectrometric Data - *

*Big Data Bioinformatics in Proteomics and Metabolomics*

http://www.denbi.de/index.php/11-training-cat/95-lss2016

[Psidev-ms-dev] Release candidate 3.89.0_rc3 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics community,

attached there's the release candidate 3.89.0_rc3 of the psi-ms.obo file.


New CV terms in version 3.89.0_rc3 of psi-ms.obo:
=================================================
************ Added a string value slot holding the molecular formula in 
Hill notation
[Term]
id: MS:1000336
name: neutral loss
def: "The loss of an uncharged species during a rearrangement process. 
The value slot holds the molecular formula in Hill notation of the 
neutral loss molecule, see PMID: 21182243. This term must be used in 
conjunction with a child of the term MS:1002307 (fragmentation ion 
type)." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001055 ! modification parameters

************ New terms for reporter ions
************ The mass can be specified in the value slot.
[Term]
id: MS:1002668
name: frag: iTRAQ 4plex reporter ion
def: "Standard reporter ion for iTRAQ 4Plex. The value slot holds the 
mass of the iTRAQ 4Plex reporter ion." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002669
name: frag: iTRAQ 8plex reporter ion
def: "Standard reporter ion for iTRAQ 8Plex. The value slot holds the 
mass of the iTRAQ 8Plex reporter ion." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002670
name: frag: TMT reporter ion
def: "Standard reporter ion for TMT. The value slot holds the mass of 
the iTRAQ 8Plex reporter ion and can be suffixed with either N or C, 
indicating whether the mass difference is encoded at a Nitrogen or 
Carbon atom." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002671
name: frag: TMT ETD reporter ion
def: "Standard reporter ion for TMT with ETD fragmentation. The value 
slot holds the mass of the iTRAQ 8Plex reporter ion and can be suffixed 
with either N or C, indicating whether the mass difference is encoded at 
a Nitrogen or Carbon atom." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002672
name: no modification threshold
def: "No statistical threshold for accepting or rejecting that a 
modification position." [PSI:PI]
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:1002673
name: OpenXQuest
def: "Cross-Linking MS search engine." [PSI:PI]
is_a: MS:1000752 ! TOPP software


Changed CV terms in version 3.89.0_rc3 of psi-ms.obo:
=====================================================
************ Changed the regular expression to allow null for the 
interaction position
[Term]
id: MS:1002665
name: regular expression for protein interaction scores derived from 
cross-linking
def: 
"([:digit:]+[.][a|b]:([:digit:]+|null):[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\})" 
[PSI:PI]
is_a: MS:1002479 ! regular expression

************ Obsoleted the following terms.
[Term]
id: MS:1002455
name: H2O neutral loss
def: "OBSOLETE Neutral loss of water." [PSI:PI]
comment: This term was obsoleted because it should be replaced by 
MS:1000336 with value H2O.
is_a: MS:1000336 ! neutral loss
is_a: MS:1002473 ! ion series considered in search
is_obsolete: true

[Term]
id: MS:1002456
name: NH3 neutral loss
def: "OBSOLETE Neutral loss of ammonia." [PSI:PI]
comment: This term was obsoleted because it should be replaced by 
MS:1000336 with value NH3.
is_a: MS:1000336 ! neutral loss
is_a: MS:1002473 ! ion series considered in search
is_obsolete: true

[Term]
id: MS:1002457
name: H3PO4 neutral loss
def: "OBSOLETE Neutral loss of phosphoric acid." [PSI:PI]
comment: This term was obsoleted because it should be replaced by 
MS:1000336 with value H3PO4.
is_a: MS:1000336 ! neutral loss
is_a: MS:1002473 ! ion series considered in search
is_obsolete: true

************ REARRANGEMENT OF PSM-level result details BRANCH 
************ (see attached figure)
************ The following two terms moved from
************ is_a: MS:1001872 ! distinct peptide-level e-value
************ to is_a: MS:1002353 ! PSM-level e-value
[Term]
id: MS:1001328
name: OMSSA:evalue
def: "OMSSA E-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002353 ! PSM-level e-value

[Term]
id: MS:1001330
name: X\!Tandem:expect
def: "The X!Tandem expectation value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002353 ! PSM-level e-value

************ The following two terms moved from
************ is_a: MS:1001870 ! distinct peptide-level p-value
************ to is_a: MS:1002352 ! PSM-level p-value
[Term]
id: MS:1001329
name: OMSSA:pvalue
def: "OMSSA p-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002352 ! PSM-level p-value

[Term]
id: MS:1001396
name: Phenyx:PepPvalue
def: "The p-value of a peptide sequence match in Phenyx." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002352 ! PSM-level p-value

************ The following two terms moved from
************ is_a: MS:1002347 ! PSM-level identification confidence metric
************ to is_a: MS:1001092 ! peptide identification confidence metric
[Term]
id: MS:1001872
name: distinct peptide-level e-value
def: "Estimation of the e-value for distinct peptides once redundant 
identifications of the same peptide have been removed (id est multiple 
PSMs have been collapsed to one entry)." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
MS:1001092 ! peptide identification confidence metric
relationship: has_domain MS:1002306 ! value greater than zero

[Term]
id: MS:1001870
name: distinct peptide-level p-value
def: "Estimation of the p-value for distinct peptides once redundant 
identifications of the same peptide have been removed (id est multiple 
PSMs have been collapsed to one entry)." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
MS:1001092 ! peptide identification confidence metric
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive


Best Regards,
Gerhard

-- 

*--*

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554

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

www.medizinisches-proteom-center.de 
<http://www.medizinisches-proteom-center.de/>

RUB Logo

ANNOUNCEMENT de.NBI summer school September 2016:

*Analysis of Mass-Spectrometric Data - *

*Big Data Bioinformatics in Proteomics and Metabolomics*

http://www.denbi.de/index.php/11-training-cat/95-lss2016