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

From: mayerg97 <ger...@ru...> - 2016-11-16 12:46:14

Attachments: psi-ms_4.0.4.7z

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

From: Sylvie Ricard-B. <syl...@un...> - 2016-11-01 14:14:32

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*.

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-pi-dev] New version 4.0.3 of psi-ms.obo

From: mayerg97 <ger...@ru...> - 2016-10-24 12:48:56

Attachments: psi-ms_4.0.3.7z

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

From: mayerg97 <ger...@ru...> - 2016-10-18 15:01:15

Attachments: psi-ms_4.0.3_rc1.obo.7z

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/>

Re: [Psidev-pi-dev] MS ontology

From: Eric D. <ede...@sy...> - 2016-10-17 16:58:56

Attachments: image001.png image002.gif image003.png

That seems great to me.



Gerhard, anything else needed on these?



Thanks,

Eric





*From:* Hans Vissers [mailto:Han...@wa...]
*Sent:* Monday, October 17, 2016 9:49 AM
*To:* Eric Deutsch
*Cc:* mayerg97; Juan Antonio Vizcaino; psi...@li...;
Robert Tonge
*Subject:* RE: [Psidev-pi-dev] MS ontology



Hi Eric,

Of course. Would this suffice?

Name: SYNAPT G2-Si
Desc: Waters Corporation SYNAPT G2-Si orthogonal acceleration
time-of-flight mass spectrometer

Name: MALDI SYNAPT G2-Si
Desc: Waters Corporation MALDI SYNAPT G2-Si orthogonal acceleration
time-of-flight mass spectrometer

Name: Vion IMS QTof
Desc: Waters Corporation Vion IMS QTof orthogonal acceleration
time-of-flight mass spectrometer

Name: Xevo G2 XS Tof
Desc: Waters Corporation Xevo G2 XS Tof orthogonal acceleration
time-of-flight mass spectrometer

Name: Xevo TQ-XS
Desc: Waters Corporation Xevo TQ-XS triple quadrupole mass spectrometer

Name: Xevo TQ-S micro
Desc: Waters Corporation Xevo TQ-XS triple quadrupole mass spectrometer

Best regards,

Hans

*Hans Vissers*

*Scientific Operations*

Waters Corporation
Stamford Avenue | Altrincham Road
Wilmslow | SK9 4AX | UK

[T] +44 (0) 161 435 4100
[F] +44 (0) 161 435 4444
[W] www.waters.com
[E] han...@wa...

Micromass UK Limited is registered in England under No 3162904
Registered Office: Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX


[image: Inactive hide details for Eric Deutsch ---10/17/2016 06:19:13
PM---Hi Hans, thanks for sending this information. Would you prov]Eric
Deutsch ---10/17/2016 06:19:13 PM---Hi Hans, thanks for sending this
information. Would you provide some definitions for these new terms

From: Eric Deutsch <ede...@sy...>
To: Hans Vissers <Han...@wa...>, mayerg97 <ger...@ru...>,
Juan Antonio Vizcaino <ju...@eb...>, psi...@li...
Cc: Robert Tonge <Rob...@wa...>, Eric Deutsch <
ede...@sy...>
Date: 10/17/2016 06:19 PM
Subject: RE: [Psidev-pi-dev] MS ontology
------------------------------




Hi Hans, thanks for sending this information. Would you provide some
definitions for these new terms? I assume that the items in parentheses
should not be part of the name, but rather is part of the description?

So maybe the first entry would look like:
Name: SYNAPT G2-Si
Desc: Waters Corporation SYNAPT G2-Si orthogonal acceleration
time-of-flight mass spectrometer

Etc.?

Would you provide complete definitions for each, ideally ones that clearly
distinguish one model from another?

Thanks!
Eric


*From:* Hans Vissers [mailto:Han...@wa...]
*Sent:* Monday, October 17, 2016 7:27 AM
*To:* mayerg97; Juan Antonio Vizcaino; psi...@li...
*Cc:* Robert Tonge
*Subject:* [Psidev-pi-dev] MS ontology


Dear Gerhard, Juan, PSI

Can the following MS instrument be added to the MS ontology please?

SYNAPT G2-Si (oaTof based)
MALDI SYNAPT G2-Si (oaTof based)
Vion IMS QTof (oaTof based)
Xevo G2 XS Tof (oaTof based) (oaTof based)

Xevo TQ-XS (quadrupole based)
Xevo TQ-S micro (quadrupole based)

Please find attached as well some corrections for you to consider. The ICP
instruments are redundant.


Best regards,

Hans

*Hans Vissers*

*Scientific Operations*

Waters Corporation
Stamford Avenue | Altrincham Road
Wilmslow | SK9 4AX | UK

[T] +44 (0) 161 435 4100
[F] +44 (0) 161 435 4444
[W] www.waters.com
[E] han...@wa...

Micromass UK Limited is registered in England under No 3162904
Registered Office: Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX

*(See attached file: MS ontology.xls)*


=========================================================== The information
in this email is confidential, and is intended solely for the addressee(s).
Access to this email by anyone else is unauthorized and therefore
prohibited. If you are not the intended recipient you are notified that
disclosing, copying, distributing or taking any action in reliance on the
contents of this information is strictly prohibited and may be unlawful.
===========================================================

=========================================================== The information
in this email is confidential, and is intended solely for the addressee(s).
Access to this email by anyone else is unauthorized and therefore
prohibited. If you are not the intended recipient you are notified that
disclosing, copying, distributing or taking any action in reliance on the
contents of this information is strictly prohibited and may be unlawful.
===========================================================

Re: [Psidev-pi-dev] MS ontology

From: Hans V. <Han...@wa...> - 2016-10-17 16:48:56

Attachments: ecblank.gif graycol.gif 41548547.gif

Hi Eric,

Of course. Would this suffice?

Name: SYNAPT G2-Si
Desc: Waters Corporation SYNAPT G2-Si orthogonal acceleration time-of-flight mass spectrometer

Name: MALDI SYNAPT G2-Si
Desc: Waters Corporation MALDI SYNAPT G2-Si orthogonal acceleration time-of-flight mass spectrometer

Name: Vion IMS QTof
Desc: Waters Corporation Vion IMS QTof orthogonal acceleration time-of-flight mass spectrometer

Name: Xevo G2 XS Tof
Desc: Waters Corporation Xevo G2 XS Tof orthogonal acceleration time-of-flight mass spectrometer

Name: Xevo TQ-XS
Desc: Waters Corporation Xevo TQ-XS triple quadrupole mass spectrometer

Name: Xevo TQ-S micro
Desc: Waters Corporation Xevo TQ-XS triple quadrupole mass spectrometer

Best regards,

Hans
                                               
   Hans Vissers                                
                                               
   Scientific Operations                       
                                               
   Waters Corporation                          
   Stamford Avenue |                           
   Altrincham Road                             
   Wilmslow | SK9 4AX | UK                     
                                               
   [T] +44 (0) 161 435                         
   4100                                        
   [F] +44 (0) 161 435                         
   4444                                        
   [W] www.waters.com                          
   [E]                                         
   han...@wa...                     
                                               
                                               
                                               



Micromass UK Limited is registered in England under No 3162904
Registered Office: Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX





From:	Eric Deutsch <ede...@sy...>
To:	Hans Vissers <Han...@wa...>, mayerg97 <ger...@ru...>, Juan Antonio Vizcaino <ju...@eb...>,
            psi...@li...
Cc:	Robert Tonge <Rob...@wa...>, Eric Deutsch <ede...@sy...>
Date:	10/17/2016 06:19 PM
Subject:	RE: [Psidev-pi-dev] MS ontology



Hi Hans, thanks for sending this information. Would you provide some definitions for these new terms? I assume that the items in parentheses should
not be part of the name, but rather is part of the description?

So maybe the first entry would look like:
Name: SYNAPT G2-Si
Desc: Waters Corporation SYNAPT G2-Si orthogonal acceleration time-of-flight mass spectrometer

Etc.?

Would you provide complete definitions for each, ideally ones that clearly distinguish one model from another?

Thanks!
Eric


From: Hans Vissers [mailto:Han...@wa...]
Sent: Monday, October 17, 2016 7:27 AM
To: mayerg97; Juan Antonio Vizcaino; psi...@li...
Cc: Robert Tonge
Subject: [Psidev-pi-dev] MS ontology



Dear Gerhard, Juan, PSI

Can the following MS instrument be added to the MS ontology please?

SYNAPT G2-Si (oaTof based)
MALDI SYNAPT G2-Si (oaTof based)
Vion IMS QTof (oaTof based)
Xevo G2 XS Tof (oaTof based) (oaTof based)

Xevo TQ-XS (quadrupole based)
Xevo TQ-S micro (quadrupole based)

Please find attached as well some corrections for you to consider. The ICP instruments are redundant.

      Best regards,

      Hans


                                            
             Hans Vissers                   
                                            
             Scientific Operations          
                                            
             Waters Corporation             
             Stamford Avenue |              
             Altrincham Road                
             Wilmslow | SK9 4AX | UK        
                                            
             [T] +44 (0) 161 435            
             4100                           
             [F] +44 (0) 161 435            
             4444                           
             [W] www.waters.com             
             [E]                            
             han...@wa...        
                                            
                                            
                                            


      Micromass UK Limited is registered in England under No 3162904
      Registered Office: Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX

      (See attached file: MS ontology.xls)


=========================================================== The information in this email is confidential, and is intended solely for the addressee
(s). Access to this email by anyone else is unauthorized and therefore prohibited. If you are not the intended recipient you are notified that
disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and may be unlawful.
===========================================================





===========================================================
The information in this email is confidential, and is intended solely for the addressee(s). 
Access to this email by anyone else is unauthorized and therefore prohibited.  If you are 
not the intended recipient you are notified that disclosing, copying, distributing or taking 
any action in reliance on the contents of this information is strictly prohibited and may be unlawful.
===========================================================

Re: [Psidev-pi-dev] MS ontology

From: Eric D. <ede...@sy...> - 2016-10-17 16:19:19

Attachments: image002.png

Hi Hans, thanks for sending this information. Would you provide some
definitions for these new terms? I assume that the items in parentheses
should not be part of the name, but rather is part of the description?



So maybe the first entry would look like:

Name: SYNAPT G2-Si

Desc: Waters Corporation SYNAPT G2-Si orthogonal acceleration
time-of-flight mass spectrometer



Etc.?



Would you provide complete definitions for each, ideally ones that clearly
distinguish one model from another?



Thanks!

Eric





*From:* Hans Vissers [mailto:Han...@wa...]
*Sent:* Monday, October 17, 2016 7:27 AM
*To:* mayerg97; Juan Antonio Vizcaino; psi...@li...
*Cc:* Robert Tonge
*Subject:* [Psidev-pi-dev] MS ontology



Dear Gerhard, Juan, PSI

Can the following MS instrument be added to the MS ontology please?

SYNAPT G2-Si (oaTof based)
MALDI SYNAPT G2-Si (oaTof based)
Vion IMS QTof (oaTof based)
Xevo G2 XS Tof (oaTof based) (oaTof based)

Xevo TQ-XS (quadrupole based)
Xevo TQ-S micro (quadrupole based)

Please find attached as well some corrections for you to consider. The ICP
instruments are redundant.


Best regards,

Hans

*Hans Vissers*

*Scientific Operations*

Waters Corporation
Stamford Avenue | Altrincham Road
Wilmslow | SK9 4AX | UK

[T] +44 (0) 161 435 4100
[F] +44 (0) 161 435 4444
[W] www.waters.com
[E] han...@wa...

Micromass UK Limited is registered in England under No 3162904
Registered Office: Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX

*(See attached file: MS ontology.xls)*

=========================================================== The information
in this email is confidential, and is intended solely for the addressee(s).
Access to this email by anyone else is unauthorized and therefore
prohibited. If you are not the intended recipient you are notified that
disclosing, copying, distributing or taking any action in reliance on the
contents of this information is strictly prohibited and may be unlawful.
===========================================================

[Psidev-pi-dev] MS ontology

From: Hans V. <Han...@wa...> - 2016-10-17 14:27:38

Attachments: MS ontology.xls ecblank.gif


Dear Gerhard, Juan, PSI

Can the following MS instrument be added to the MS ontology please?

SYNAPT G2-Si (oaTof based)
MALDI SYNAPT G2-Si (oaTof based)
Vion IMS QTof (oaTof based)
Xevo G2 XS Tof (oaTof based) (oaTof based)

Xevo TQ-XS (quadrupole based)
Xevo TQ-S micro (quadrupole based)

Please find attached as well some corrections for you to consider. The ICP instruments are redundant.

Best regards,

Hans
                                               
   Hans Vissers                                
                                               
   Scientific Operations                       
                                               
   Waters Corporation                          
   Stamford Avenue |                           
   Altrincham Road                             
   Wilmslow | SK9 4AX | UK                     
                                               
   [T] +44 (0) 161 435                         
   4100                                        
   [F] +44 (0) 161 435                         
   4444                                        
   [W] www.waters.com                          
   [E]                                         
   han...@wa...                     
                                               
                                               
                                               



Micromass UK Limited is registered in England under No 3162904
Registered Office: Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX

(See attached file: MS ontology.xls)
===========================================================
The information in this email is confidential, and is intended solely for the addressee(s). 
Access to this email by anyone else is unauthorized and therefore prohibited.  If you are 
not the intended recipient you are notified that disclosing, copying, distributing or taking 
any action in reliance on the contents of this information is strictly prohibited and may be unlawful.
===========================================================

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

From: mayerg97 <ger...@ru...> - 2016-10-11 12:39:30

Attachments: psi-ms.7z

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-pi-dev] Release candidate 4.0.2_rc1 of psi-ms.obo

From: mayerg97 <ger...@ru...> - 2016-10-07 14:18:04

Attachments: psi-ms_4.0.2_rc1.obo.7z

Dear proteomics community,

attached there's the new version 4.0.2_rc1 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_rc1 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: MSMSPathFinderGF: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_rc1 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-pi-dev] [Psi‐announce] Submission of an update to the specifications for mzIdentML 1.2 document: open for public review

From: Sylvie Ricard-B. <syl...@un...> - 2016-10-06 10:42:11

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.

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/>

[Psidev-pi-dev] proBed file format

From: Juan A. V. <ju...@eb...> - 2016-10-04 20:40:37

Hi all,

Following the e-mail sent by Gerben about the proBAM format, I wanted to report the development of the proBed file format, also aiming to report proteogenomics results. This development was already reported in the last two PSI meetings, but it is only now that we have managed to get version 1.0.0 ready.

The current version of the proBed specification document and links to relevant example (and related files) can be found at http://www.psidev.info/probed <http://www.psidev.info/probed>.

We have tried to make both proBAM and proBed as internally consistent as possible. The proBed format specification has been submitted already to the PSI process (version 1.0.0) and will soon go to external review, so it is the right moment to provide feedback, if you are interested in implementing the format in the future.

Many thanks,

Juan Antonio 

(on behalf of all the authors)

[Psidev-pi-dev] proBAM proteogenomics file format

From: Gerben M. <ger...@gm...> - 2016-10-03 08:22:41

Hi all,

As some of you might already know, some members of the PSI-dev have recently been working on file formats for proteogenomics.
The proBAM format is meant to be a common format for mapping peptides identified by mass spectrometry to a genome. 

Information on this novel file format and a link to the specification document (docx|pdf) can be found at www.psidev.info/proBAM <http://www.psidev.info/proBAM>. 
Whit this mail we would like to inform you all about this work-in-progress, asking for input/remarks on this draft version. 

The idea is to have a first version finalised by the end of October so if you could provide us with feedback before then, that would be very much appreciated.

Many thanks in advance,

Xiaojing Wang,
Eric Deutch,
Andrew Jones,
Juan Antonio Vizcaino,
Gerben Menschaert

[Psidev-pi-dev] mzid 1.2

From: Jones, A. <And...@li...> - 2016-07-25 12:45:27

Hi all,

I submitted the mzid 1.2 manuscript on Friday last week, and now we should be in a position to submit the specification docs to the PSI process in parallel. I have removed tracked changes and comments from the spec doc, and on a quick look through it seems clean to me. Can anyone else who wants to check, please review it and send comments back by the end of tomorrow if at all possible, so I can submit on Wednesday before I head off holiday.

The issues list now only has some very minor items on it. Please let me know if there is anything else outstanding, otherwise I will submit the specs to the process on Wednesday.
Best wishes
Andy

Re: [Psidev-pi-dev] mzIdentML specifications

From: Eric D. <ede...@sy...> - 2016-07-19 22:22:08

Hi everyone, I have looked through this lightly and everything looks good
to me. I have not looked at it in careful detail, I’m a bit swamped at the
moment.

The answer to JAV3 is: copy-and-paste is your friend. These funny
characters happen during hand editing, I think.

I have also just generated fresh HTML documentation based on the latest
files and examples files. Here are the fancier HTML ones:

http://www.peptideatlas.org/PSI/schemas/mzIdentML/1.2/mzIdentML1.2.0.html

http://www.peptideatlas.org/PSI/schemas/mzIdentML/1.2/mzIdentML1.2.0_all.html

http://www.peptideatlas.org/PSI/schemas/mzIdentML/1.2/mzIdentML1.2.0_PeptideShaker.html

http://www.peptideatlas.org/PSI/schemas/mzIdentML/1.2/mzIdentML1.2.0_combined.html

http://www.peptideatlas.org/PSI/schemas/mzIdentML/1.2/mzIdentML1.2.0_OpenxQuest.html

And here is the one that is formatted for copy-and-paste into Word:

http://www.peptideatlas.org/PSI/schemas/mzIdentML/1.2/mzIdentML1.2.0_paste.html

Let me know if you have any questions about those.

Ready to go!

Thanks,

Eric

*From:* Jones, Andy [mailto:And...@li...]
*Sent:* Monday, July 18, 2016 5:53 AM
*To:* psi...@li...
*Cc:* ju...@ed...; Robert Chalkley; le...@im...
*Subject:* [Psidev-pi-dev] mzIdentML specifications

Hi all,

We are almost ready to submit to the mzIdentML specifications and example
files to the PSI document process. This week I will also finalise the
manuscript for submission.

At this stage, it would be useful if some of you (Gerhard / Juan / Eric?),
can review the specs here:
https://github.com/HUPO-PSI/mzIdentML/blob/master/specification_document/specdoc1_2/mzIdentML1%202-draft.docx.

There are a few minor things to solve, but otherwise I think it is ready.
The validator and example files seem okay, barring one or two minor issues.

If you let me know when you’ve proofed the spec doc, I will do a final
clean up and submit.

Best wishes

Andy

*From:* Jones, Andy
*Sent:* 27 April 2016 10:22
*To:* psi...@li...
*Cc:* eug...@tu...; le...@im...;
sul...@ug...; ju...@ed...; eli...@ug...; Lutz
Fischer <lfi...@st...>; Robert Chalkley <
cha...@cg...>; 'Andrea Sinz' <and...@ph...>
*Subject:* RE: Cross-linking discussions at PSI meeting

Hi all,

This is to confirm that we will have a call at 4pm UK, 5pm EU, 8am
California:
http://www.timeanddate.com/worldclock/fixedtime.html?msg=PSI-PI+call+on+crosslinking&iso=20160428T16&p1=301&ah=1

The main topic for discussion will be encoding cross-linking in mzIdentML
1.2. Current issues with mzIdentML 1.2 are being discussed on GitHub here:
https://github.com/HUPO-PSI/mzIdentML/issues, I will update it with open
issues around cross-linking by tomorrow.

The current version of the specifications are here (rather long I’m afraid)
along with a powerpoint explaining the encodings for new features:
https://github.com/HUPO-PSI/mzIdentML/tree/master/specification_document/specdoc1_2

If Lutz is able to create a CV file for reagents before the call, we will
also post that online for discussions.

Best wishes

Andy

Numbers:

+ UK: 0808 109 5644

+ US: 877-420-0272

+ Belgium: 0800 509 80

+ Germany: 0800 101 2079

+ Switzerland: 0800 000 860

+ Generic international: +44 (0) 20 8322 2500 (UK number)

Access code: 297427 #

*From:* Jones, Andy
*Sent:* 19 April 2016 15:56
*To:* tobias <to...@eb...>
*Cc:* eug...@tu...; le...@im...;
sul...@ug...; ju...@ed...; eli...@ug...; Lutz
Fischer <lfi...@st...>; Robert Chalkley <
cha...@cg...>; Juan Antonio Vizcaino <ju...@eb...>; Yasset
Perez-Riverol <yp...@eb...>; psi...@li...
*Subject:* Cross-linking discussions at PSI meeting

Hi all,

This email is addressed to those who participated in the XL session at PSI
today, plus Lutz and Robert (and plus Yasset for GitHub issues). Please
forward this on to others who should be consulted. I have also copied to
the PSI-PI list.

The major outcomes from today are as follows:

1. General agreement that we are nearly there with the mzid 1.2 encoding of
XL info.
2. Plan for Lutz to maintain (via mzIdentML GitHub for example), a separate
CV of crosslinker reagents, based off the attached sheet (converted to CSV
format, with unique IDs per row e.g. XL:0001, XL:0002, more discussion
needed to finalise format)
3. Some additions to mzid 1.2 to cover:
- cases of combined evidence from multiple input spectra (L v H isotopes;
ETD+HCD; MS3 etc) to make an identification (not post-processing but
intrinsic to the ID mechanism)
- Adding protein-level interaction evidence
- Re-using additions already proposed in mzid 1.2 for mod or XL
localization ambiguity
4. No major interest at this stage to encode XL info in mztab, we may do
this at our side following same model as mzid 1.2
5. Plan for wider project over medium to long term to write a cross-linking
standards paper, including mzid 1.2 plus a minimum reporting guidelines doc
(Juri / Alexander to progress this), with wider authorship
6. We will role these changes into mzid 1.2 specifications, and publish
that paper separately (submitted in the short term). For those that
contribute example files or major input of the specs, I will invite to join
the author list of that paper.

I have started to write this up in the mzid 1.2 specification document
(attached here and committed to our GitHub) - see pages 20-23), and an XML
snippet for how the protein interaction part will look.

ACTION items:

- We discussed Lutz updating the xi export examples to include protein
interaction scores, following our proposed spec
- Alexander and Eugen to update the examples exported from OpenMS and add
to the mzid GitHub (please email Yasset - cc'd to get write access to the
GitHub)
- Ideally, would be great if the Edinburgh visualisation software could
read the mzid 1.2 files to see if all info is really covered
- Andy to continue cleaning and updating specification document

I would like to propose a conference call to progress this for *4pm UK/5pm
Europe on Thurs 28th April* - please reply to let me know if you can make
it.

best wishes
Andy

[Psidev-pi-dev] mzIdentML specifications

From: Jones, A. <And...@li...> - 2016-07-18 12:53:06

Hi all,

We are almost ready to submit to the mzIdentML specifications and example files to the PSI document process. This week I will also finalise the manuscript for submission.

At this stage, it would be useful if some of you (Gerhard / Juan / Eric?), can review the specs here: https://github.com/HUPO-PSI/mzIdentML/blob/master/specification_document/specdoc1_2/mzIdentML1%202-draft.docx.

There are a few minor things to solve, but otherwise I think it is ready. The validator and example files seem okay, barring one or two minor issues.

If you let me know when you’ve proofed the spec doc, I will do a final clean up and submit.

Best wishes
Andy


From: Jones, Andy
Sent: 27 April 2016 10:22
To: psi...@li...
Cc: eug...@tu...; le...@im...; sul...@ug...; ju...@ed...; eli...@ug...; Lutz Fischer <lfi...@st...>; Robert Chalkley <cha...@cg...>; 'Andrea Sinz' <and...@ph...>
Subject: RE: Cross-linking discussions at PSI meeting

Hi all,

This is to confirm that we will have a call at 4pm UK, 5pm EU, 8am California: http://www.timeanddate.com/worldclock/fixedtime.html?msg=PSI-PI+call+on+crosslinking&iso=20160428T16&p1=301&ah=1

The main topic for discussion will be encoding cross-linking in mzIdentML 1.2. Current issues with mzIdentML 1.2 are being discussed on GitHub here: https://github.com/HUPO-PSI/mzIdentML/issues, I will update it with open issues around cross-linking by tomorrow.

The current version of the specifications are here (rather long I’m afraid) along with a powerpoint explaining the encodings for new features:  https://github.com/HUPO-PSI/mzIdentML/tree/master/specification_document/specdoc1_2

If Lutz is able to create a CV file for reagents before the call, we will also post that online for discussions.
Best wishes
Andy

Numbers:
+ UK: 0808 109 5644
+ US: 877-420-0272
+ Belgium: 0800 509 80
+ Germany: 0800 101 2079
+ Switzerland: 0800 000 860
+ Generic international: +44 (0) 20 8322 2500 (UK number)

Access code: 297427 #



From: Jones, Andy
Sent: 19 April 2016 15:56
To: tobias <to...@eb...<mailto:to...@eb...>>
Cc: eug...@tu...<mailto:eug...@tu...>; le...@im...<mailto:le...@im...>; sul...@ug...<mailto:sul...@ug...>; ju...@ed...<mailto:ju...@ed...>; eli...@ug...<mailto:eli...@ug...>; Lutz Fischer <lfi...@st...<mailto:lfi...@st...>>; Robert Chalkley <cha...@cg...<mailto:cha...@cg...>>; Juan Antonio Vizcaino <ju...@eb...<mailto:ju...@eb...>>; Yasset Perez-Riverol <yp...@eb...<mailto:yp...@eb...>>; psi...@li...<mailto:psi...@li...>
Subject: Cross-linking discussions at PSI meeting

Hi all,

This email is addressed to those who participated in the XL session at PSI today, plus Lutz and Robert (and plus Yasset for GitHub issues). Please forward this on to others who should be consulted. I have also copied to the PSI-PI list.

The major outcomes from today are as follows:

1. General agreement that we are nearly there with the mzid 1.2 encoding of XL info.
2. Plan for Lutz to maintain (via mzIdentML GitHub for example), a separate CV of crosslinker reagents, based off the attached sheet (converted to CSV format, with unique IDs per row e.g. XL:0001, XL:0002, more discussion needed to finalise format)
3. Some additions to mzid 1.2 to cover:
- cases of combined evidence from multiple input spectra (L v H isotopes; ETD+HCD; MS3 etc) to make an identification (not post-processing but intrinsic to the ID mechanism)
- Adding protein-level interaction evidence
- Re-using additions already proposed in mzid 1.2 for mod or XL localization ambiguity
4. No major interest at this stage to encode XL info in mztab, we may do this at our side following same model as mzid 1.2
5. Plan for wider project over medium to long term to write a cross-linking standards paper, including mzid 1.2 plus a minimum reporting guidelines doc (Juri / Alexander to progress this), with wider authorship
6. We will role these changes into mzid 1.2 specifications, and publish that paper separately (submitted in the short term). For those that contribute example files or major input of the specs, I will invite to join the author list of that paper.

I have started to write this up in the mzid 1.2 specification document (attached here and committed to our GitHub) - see pages 20-23), and an XML snippet for how the protein interaction part will look.

ACTION items:

- We discussed Lutz updating the xi export examples to include protein interaction scores, following our proposed spec
- Alexander and Eugen to update the examples exported from OpenMS and add to the mzid GitHub (please email Yasset - cc'd to get write access to the GitHub)
- Ideally, would be great if the Edinburgh visualisation software could read the mzid 1.2 files to see if all info is really covered
- Andy to continue cleaning and updating specification document

I would like to propose a conference call to progress this for 4pm UK/5pm Europe on Thurs 28th April - please reply to let me know if you can make it.

best wishes
Andy

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

From: mayerg97 <ger...@ru...> - 2016-07-15 12:33:06

Attachments: psi-ms_4.0.1.7z

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-pi-dev] FW: mzTab mailing list

From: Jones, A. <And...@li...> - 2016-07-15 08:58:03

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-pi-dev] mzid call

From: Yasset Perez-R. <yp...@eb...> - 2016-07-08 15:00:11

We can wait in our side until next week. Let me know if I need to start 
the conference call.
Regards
Yasset
On 08/07/2016 15:48, Jones, Andy wrote:
>
> Hi all,
>
> Unfortunately I’m unwell today so I won’t be able to join the mzid 
> call. Feel free to go ahead without me if anyone else can coordinate 
> or otherwise we can re-arrange for next week.
>
> Best wishes
>
> Andy
>
>
>
> ------------------------------------------------------------------------------
> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
> present their vision of the future. This family event has something for
> everyone, including kids. Get more information and register today.
> http://sdm.link/attshape
>
>
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev

-- 
Yasset Perez-Riverol PhD.
Bioinformatician
Proteomics Services Team, PRIDE Group European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Twitter: @ypriverol

[Psidev-pi-dev] mzid call

From: Jones, A. <And...@li...> - 2016-07-08 14:48:23

Hi all,

Unfortunately I'm unwell today so I won't be able to join the mzid call. Feel free to go ahead without me if anyone else can coordinate or otherwise we can re-arrange for next week.

Best wishes
Andy

Re: [Psidev-pi-dev] mzid 1.2 specs

From: mayerg97 <ger...@ru...> - 2016-07-04 16:17:22

Hello Andy,

I updated now the mzid 1.2 spec doc (table 2 and the following examples 
for the different use cases
(proteogenomics, cross-linking, protein grouping, modification scoring, 
peptide-level scoring):
- SpectrumIdentificationProtocol (AdditionalSearchParams)
                                     peptide-level statistics
                                     sample pre-fractionation
                                     proteogenomics
                                     cross-linking
                                     modification position scoring
                                     de novo sequencing
                                     consensus scoring
- PeptideEvidence                    proteogenomics
- DBSequence                        proteogenomics
- SpectrumIdentificationItem        peptide-level statistics
                                     cross-linking
- Peptide                            cross-linking
- ProteinDetectionHypothesis        protein grouping
- ProteinAmbiguityGroup                protein grouping
- Peptide                            cross-linking
- Modification                        cross-linking

Cheers,
Gerhard


Am 09.06.2016 um 13:13 schrieb Jones, Andy:
>
> Hi Gerhard,
>
> I have just pushed a few minor changes to the mzid 1.2 spec document 
> to GitHub. Would you mind taking over with the document and having a 
> general check through the text, and updating section 6. This will need 
> for you to coordinate for Eric to re-run the auto-generator, insert 
> the result, and then we may wish to manually add snippets of XML to 
> the following sections with an example snippet illustrating the 
> different use cases (proteogenomics, cross-linking, protein grouping, 
> modification scoring, peptide-level scoring):
>
> -SpectrumIdentificationProtocol
>
> -PeptideEvidence
>
> -DBSequence
>
> -SpectrumIdentificationItem
>
> -Peptide
>
> -ProteinDetectionHypothesis
>
> -ProteinAmbiguityGroup
>
> Many thanks
>
> Andy
>

-- 

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

*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/>

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

From: Jones, A. <And...@li...> - 2016-07-01 10:13:56

Attachments: image001.jpg

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-pi-dev] new Cross-Linker ontology XLMOD.obo

From: mayerg97 <ger...@ru...> - 2016-07-01 10:03:34

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-pi-dev] Call minutes

From: Jones, A. <And...@li...> - 2016-06-30 08:26:46

Hi all,

Brief notes from the call yesterday:


1.       Various issues progressed and discussed - as tracked online: https://github.com/HUPO-PSI/mzIdentML/issues/

2.       A few files are not yet validating - please all get these fixed, then close issues and report back to me when done

3.       CV largely updated with the new structure suggested by Eric. Eric is going to run another round of checks on it, then we should be good to run with it

4.       Gerhard is going to do a bit of manual work on the spec doc and then pass to me to edit and check. We are then in a position to submit to the doc proc, and get the manuscript submitted.

Next call will be Fri 8th July at 4pm UK time.

Best wishes
Andy

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

From: mayerg97 <ger...@ru...> - 2016-06-30 07:52:59

Attachments: psi-ms_4.0.0.7z

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/>

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