psidev-ms-dev — Mass spectroscopy standard development

Re: [Psidev-ms-dev] PSI-MS: reporter ion cv terms

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

Hi,

I'd be a bit hesitant to have one term 
per neutral loss. The Table 2 in 
http://pubs.acs.org/doi/full/10.1021/ac101825k#tbl2-fn1
contains already >30 neutral losses, and it is not complete ...

What about a generic neutral loss that has 
a value which is a formula ? 

Yours,
Steffen


On Di, 2016-05-24 at 15:55 +0200, mayerg97 wrote:
> ************ New terms for neutral losses
> [Term]
> id: MS:1002668
> name: HPO3 neutral loss
> def: "Neutral loss of phosphite." [PSI:PI]
> is_a: MS:1000336 ! neutral loss
> is_a: MS:1002473 ! ion series considered in search
> ...
> name: CH4OS neutral loss
> name: C3H9N neutral loss



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Re: [Psidev-ms-dev] PSI-MS: reporter ion cv terms

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

Hi Gerhard, many thanks for adjusting this. Regarding the reporter ions,
what does “mass resp. type” mean? If there is a value that must be
supplied, the term name and definition really should be about that value.

Thanks,

Eric



*From:* mayerg97 [mailto:ger...@ru...]
*Sent:* Tuesday, May 24, 2016 6:56 AM
*To:* Harald Barsnes; psi...@li...;
psi...@li...; psi...@li...
*Subject:* Re: [Psidev-ms-dev] PSI-MS: reporter ion cv terms



Hi all,

how about the following terms?

************ New terms for neutral losses
[Term]
id: MS:1002668
name: HPO3 neutral loss
def: "Neutral loss of phosphite." [PSI:PI]
is_a: MS:1000336 ! neutral loss
is_a: MS:1002473 ! ion series considered in search

[Term]
id: MS:1002669
name: CH4OS neutral loss
def: "Neutral loss of methanesulfenic acid." [PSI:PI]
is_a: MS:1000336 ! neutral loss
is_a: MS:1002473 ! ion series considered in search

[Term]
id: MS:1002670
name: C3H9N neutral loss
def: "Neutral loss of C3H9N." [PSI:PI]
is_a: MS:1000336 ! neutral loss
is_a: MS:1002473 ! ion series considered in search

************ New terms for reporter ions. The mass resp. type can be
specified in the value slot.
[Term]
id: MS:1002671
name: frag: iTRAQ 4plex reporter ion
def: "Standard reporter ion for iTRAQ 4Plex." [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:1002672
name: frag: iTRAQ 8plex reporter ion
def: "Standard reporter ion for iTRAQ 8Plex." [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:1002673
name: frag: TMT reporter ion
def: "Standard reporter ion for TMT." [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:1002674
name: frag: TMT ETD reporter ion
def: "Standard reporter ion for TMT ETD." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002307 ! fragmentation ion type

Best regards,
Gerhard

Am 24.05.2016 um 12:55 schrieb Harald Barsnes:


Hi Gerhard,

Thanks for adding the neutral losses CV terms. Would be great if you could
also add CV terms for the following reporter ions.


iTRAQ 4plex:

Name: frag: iTRAQ 4plex 114 reporter ion
Description: Standard reporter ion for iTRAQ 4Plex 114.

Name: frag: iTRAQ 4plex 115 reporter ion
Description: Standard reporter ion for iTRAQ 4Plex 115.

Name: frag: iTRAQ 4plex 116 reporter ion
Description: Standard reporter ion for iTRAQ 4Plex 116.

Name: frag: iTRAQ 4plex 117 reporter ion
Description: Standard reporter ion for iTRAQ 4Plex 117.


iTRAQ 8plex:

Name: frag: iTRAQ 8plex 113 reporter ion
Description: Standard reporter ion for iTRAQ 8Plex 113.

Name: frag: iTRAQ 8plex 114 reporter ion
Description: Standard reporter ion for iTRAQ 8Plex 114.

Name: frag: iTRAQ 8plex 115 reporter ion
Description: Standard reporter ion for iTRAQ 8Plex 115.

Name: frag: iTRAQ 8plex 116 reporter ion
Description: Standard reporter ion for iTRAQ 8Plex 116.

Name: frag: iTRAQ 8plex 117 reporter ion
Description: Standard reporter ion for iTRAQ 8Plex 117.

Name: frag: iTRAQ 8plex 118 reporter ion
Description: Standard reporter ion for iTRAQ 8Plex 118.

Name: frag: iTRAQ 8plex 119 reporter ion
Description: Standard reporter ion for iTRAQ 8Plex 119.

Name: frag: iTRAQ 8plex 121 reporter ion
Description: Standard reporter ion for iTRAQ 8Plex 121.


TMT:

Name: frag: TMT 126 reporter ion
Description: Standard reporter ion for TMT 126.

Name: frag: TMT 127N reporter ion
Description: Standard reporter ion for TMT 127N.

Name: frag: TMT 127C reporter ion
Description: Standard reporter ion for TMT 127C.

Name: frag: TMT 128N reporter ion
Description: Standard reporter ion for TMT 128N.

Name: frag: TMT 128C reporter ion
Description: Standard reporter ion for TMT 128C.

Name: frag: TMT 128N reporter ion
Description: Standard reporter ion for TMT 128N.

Name: frag: TMT 128C reporter ion
Description: Standard reporter ion for TMT 128C.

Name: frag: TMT 130N reporter ion
Description: Standard reporter ion for TMT 130N.

Name: frag: TMT 130C reporter ion
Description: Standard reporter ion for TMT 130C.

Name: frag: TMT 131 reporter ion
Description: Standard reporter ion for TMT 131.

Name: frag: TMT 126 ETD reporter ion
Description: Standard reporter ion for TMT 126 ETD.

Name: frag: TMT 127N ETD reporter ion
Description: Standard reporter ion for TMT 127N ETD.

Name: frag: TMT 127C ETD reporter ion
Description: Standard reporter ion for TMT 127C ETD.

Name: frag: TMT 128N ETD reporter ion
Description: Standard reporter ion for TMT 128N ETD.

Name: frag: TMT 128C ETD reporter ion
Description: Standard reporter ion for TMT 128C ETD.

Name: frag: TMT 129N ETD reporter ion
Description: Standard reporter ion for TMT 129N ETD.

Name: frag: TMT 129C ETD reporter ion
Description: Standard reporter ion for TMT 129C ETD.

Name: frag: TMT 130N ETD reporter ion
Description: Standard reporter ion for TMT 130N ETD.

Name: frag: TMT 130C ETD reporter ion
Description: Standard reporter ion for TMT 130C ETD.

Name: frag: TMT 131 ETD reporter ion
Description: Standard reporter ion for TMT 131 ETD.


All should be children of MS:1002307 (fragmentation ion type).


Thanks in advance.

Best regards,
Harald



-- 

*--*

*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

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Re: [Psidev-ms-dev] PSI-MS: reporter ion cv terms

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

Hi all,

how about the following terms?

************ New terms for neutral losses
[Term]
id: MS:1002668
name: HPO3 neutral loss
def: "Neutral loss of phosphite." [PSI:PI]
is_a: MS:1000336 ! neutral loss
is_a: MS:1002473 ! ion series considered in search

[Term]
id: MS:1002669
name: CH4OS neutral loss
def: "Neutral loss of methanesulfenic acid." [PSI:PI]
is_a: MS:1000336 ! neutral loss
is_a: MS:1002473 ! ion series considered in search

[Term]
id: MS:1002670
name: C3H9N neutral loss
def: "Neutral loss of C3H9N." [PSI:PI]
is_a: MS:1000336 ! neutral loss
is_a: MS:1002473 ! ion series considered in search

************ New terms for reporter ions. The mass resp. type can be 
specified in the value slot.
[Term]
id: MS:1002671
name: frag: iTRAQ 4plex reporter ion
def: "Standard reporter ion for iTRAQ 4Plex." [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:1002672
name: frag: iTRAQ 8plex reporter ion
def: "Standard reporter ion for iTRAQ 8Plex." [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:1002673
name: frag: TMT reporter ion
def: "Standard reporter ion for TMT." [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:1002674
name: frag: TMT ETD reporter ion
def: "Standard reporter ion for TMT ETD." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002307 ! fragmentation ion type

Best regards,
Gerhard

Am 24.05.2016 um 12:55 schrieb Harald Barsnes:
>
> Hi Gerhard,
>
> Thanks for adding the neutral losses CV terms. Would be great if you 
> could also add CV terms for the following reporter ions.
>
>
> iTRAQ 4plex:
>
> Name: frag: iTRAQ 4plex 114 reporter ion
> Description: Standard reporter ion for iTRAQ 4Plex 114.
>
> Name: frag: iTRAQ 4plex 115 reporter ion
> Description: Standard reporter ion for iTRAQ 4Plex 115.
>
> Name: frag: iTRAQ 4plex 116 reporter ion
> Description: Standard reporter ion for iTRAQ 4Plex 116.
>
> Name: frag: iTRAQ 4plex 117 reporter ion
> Description: Standard reporter ion for iTRAQ 4Plex 117.
>
>
> iTRAQ 8plex:
>
> Name: frag: iTRAQ 8plex 113 reporter ion
> Description: Standard reporter ion for iTRAQ 8Plex 113.
>
> Name: frag: iTRAQ 8plex 114 reporter ion
> Description: Standard reporter ion for iTRAQ 8Plex 114.
>
> Name: frag: iTRAQ 8plex 115 reporter ion
> Description: Standard reporter ion for iTRAQ 8Plex 115.
>
> Name: frag: iTRAQ 8plex 116 reporter ion
> Description: Standard reporter ion for iTRAQ 8Plex 116.
>
> Name: frag: iTRAQ 8plex 117 reporter ion
> Description: Standard reporter ion for iTRAQ 8Plex 117.
>
> Name: frag: iTRAQ 8plex 118 reporter ion
> Description: Standard reporter ion for iTRAQ 8Plex 118.
>
> Name: frag: iTRAQ 8plex 119 reporter ion
> Description: Standard reporter ion for iTRAQ 8Plex 119.
>
> Name: frag: iTRAQ 8plex 121 reporter ion
> Description: Standard reporter ion for iTRAQ 8Plex 121.
>
>
> TMT:
>
> Name: frag: TMT 126 reporter ion
> Description: Standard reporter ion for TMT 126.
>
> Name: frag: TMT 127N reporter ion
> Description: Standard reporter ion for TMT 127N.
>
> Name: frag: TMT 127C reporter ion
> Description: Standard reporter ion for TMT 127C.
>
> Name: frag: TMT 128N reporter ion
> Description: Standard reporter ion for TMT 128N.
>
> Name: frag: TMT 128C reporter ion
> Description: Standard reporter ion for TMT 128C.
>
> Name: frag: TMT 128N reporter ion
> Description: Standard reporter ion for TMT 128N.
>
> Name: frag: TMT 128C reporter ion
> Description: Standard reporter ion for TMT 128C.
>
> Name: frag: TMT 130N reporter ion
> Description: Standard reporter ion for TMT 130N.
>
> Name: frag: TMT 130C reporter ion
> Description: Standard reporter ion for TMT 130C.
>
> Name: frag: TMT 131 reporter ion
> Description: Standard reporter ion for TMT 131.
>
> Name: frag: TMT 126 ETD reporter ion
> Description: Standard reporter ion for TMT 126 ETD.
>
> Name: frag: TMT 127N ETD reporter ion
> Description: Standard reporter ion for TMT 127N ETD.
>
> Name: frag: TMT 127C ETD reporter ion
> Description: Standard reporter ion for TMT 127C ETD.
>
> Name: frag: TMT 128N ETD reporter ion
> Description: Standard reporter ion for TMT 128N ETD.
>
> Name: frag: TMT 128C ETD reporter ion
> Description: Standard reporter ion for TMT 128C ETD.
>
> Name: frag: TMT 129N ETD reporter ion
> Description: Standard reporter ion for TMT 129N ETD.
>
> Name: frag: TMT 129C ETD reporter ion
> Description: Standard reporter ion for TMT 129C ETD.
>
> Name: frag: TMT 130N ETD reporter ion
> Description: Standard reporter ion for TMT 130N ETD.
>
> Name: frag: TMT 130C ETD reporter ion
> Description: Standard reporter ion for TMT 130C ETD.
>
> Name: frag: TMT 131 ETD reporter ion
> Description: Standard reporter ion for TMT 131 ETD.
>
>
> All should be children of MS:1002307 (fragmentation ion type).
>
>
> Thanks in advance.
>
> Best regards,
> Harald
>

-- 

*--*

*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] Fwd: [Psi-announce] Bioinformatics hub at ASMS 2016

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

> Begin forwarded message:
> 
> From: Oliver Kohlbacher <oli...@un...>
> Subject: [Psi-announce] Bioinformatics hub at ASMS 2016
> Date: 23 May 2016 at 05:07:13 BST
> To: Co...@go..., psi...@eb...
> 
> Dear colleagues,
> 
> We are preparing another Bioinformatics Hub at ASMS 2016 in San Antonio, TX.
> 
> Similar to the HUPO 2015 Bioinformatics Hub [http://www.psidev.info/hupo2015-bioinformatics-hub] last year, we intend to create a place where ASMS participants and bioinformatics experts can meet. The objective of this hands-on meeting is to develop and execute original bioinformatics analyses on the publicly available human proteomics data during the conference, facilitated by several leading proteomics informatics groups, and completely open for participation by any and all interested conference attendees. In Ask-The-Experts sessions, proteomics bioinformatics experts and the audience will discuss and answer any hot topic questions in proteomics bioinformatics.
> 
> Goals of the Bioinformatics Hub:
> - To provide advice on computational methods and their correct usage to experimentalists
> - To come up with novel approaches and ideas to perform integrative proteomics data analysis and interpretation.
> - To discuss limitations of existing tools and data processing algorithms.
> - To foster collaborative interactions between wet-lab researchers and bioinformaticians.
> - To identify gaps in the existing computational mass spectrometry tools, inspiring future work to fill these gaps.
> - Networking.
> 
> As a bioinformatics expert, we would be delighted if you could contribute to this effort.
> 
> We would thus be grateful, if you could indicate your availability in the Google form
> at http://goo.gl/forms/tt488yl4v7JKWEiE3.
> 
> We would also greatly appreciate if you would forward this email to 
> other bioinformaticians attending ASMS.
> 
> Thanks a lot
> The organizers
> (Oliver Kohlbacher, Yassene Mohammed, Juan Antonio Vizcaino, Sue Weintraub)
> 
> ---
> Oliver Kohlbacher
> Professor, Center for Bioinformatics, Dept. of Computer Science, & Faculty of Medicine
> Director, Quantitative Biology Center, University of Tuebingen, Germany
> Fellow, Max Planck Institute for Developmental Biology
> 
> email  oli...@un...  /  oli...@tu...
> WWW    kohlbacherLab.org   twitter  @OKohlbacher    
> phone  +49 7071 29 70457   fax      +49 7071 29 5152
> 
> 
> _______________________________________________
> Psi-announce mailing list
> Psi...@eb...
> https://listserver.ebi.ac.uk/mailman/listinfo/psi-announce

[Psidev-ms-dev] Release candidate 3.89.0_rc1 of psi-ms.obo

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

Dear proteomics community,

attached there's the release candidate 3.89.0_rc1 of the psi-ms.obo file.


New CV terms in version 3.89.0_rc1 of psi-ms.obo:
=================================================
************ New terms for fragment ions with neutral losses
[Term]
id: MS:1002668
name: frag: a ion - H3PO4
def: "Fragmentation information, type of product: a ion with a loss of 
H3PO4." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002669
name: frag: a ion - HPO3
def: "Fragmentation information, type of product: a ion with a loss of 
HPO3." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002670
name: frag: a ion - CH4OS
def: "Fragmentation information, type of product: a ion with a loss of 
CH4OS." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002671
name: frag: a ion - C3H9N
def: "Fragmentation information, type of product: a ion with a loss of 
C3H9N." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002672
name: frag: b ion - H3PO4
def: "Fragmentation information, type of product: b ion with a loss of 
H3PO4." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002673
name: frag: b ion - HPO3
def: "Fragmentation information, type of product: b ion with a loss of 
HPO3." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002674
name: frag: b ion - CH4OS
def: "Fragmentation information, type of product: b ion with a loss of 
CH4OS." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002675
name: frag: b ion - C3H9N
def: "Fragmentation information, type of product: b ion with a loss of 
C3H9N." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002676
name: frag: c ion - H3PO4
def: "Fragmentation information, type of product: c ion with a loss of 
H3PO4." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002677
name: frag: c ion - HPO3
def: "Fragmentation information, type of product: c ion with a loss of 
HPO3." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002678
name: frag: c ion - CH4OS
def: "Fragmentation information, type of product: c ion with a loss of 
CH4OS." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002679
name: frag: c ion - C3H9N
def: "Fragmentation information, type of product: c ion with a loss of 
C3H9N." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002680
name: frag: x ion - H3PO4
def: "Fragmentation information, type of product: x ion with a loss of 
H3PO4." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002681
name: frag: x ion - HPO3
def: "Fragmentation information, type of product: x ion with a loss of 
HPO3." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002682
name: frag: x ion - CH4OS
def: "Fragmentation information, type of product: x ion with a loss of 
CH4OS." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002683
name: frag: x ion - C3H9N
def: "Fragmentation information, type of product: x ion with a loss of 
C3H9N." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002684
name: frag: y ion - H3PO4
def: "Fragmentation information, type of product: y ion with a loss of 
H3PO4." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002685
name: frag: y ion - HPO3
def: "Fragmentation information, type of product: y ion with a loss of 
HPO3." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002686
name: frag: y ion - CH4OS
def: "Fragmentation information, type of product: y ion with a loss of 
CH4OS." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002687
name: frag: y ion - C3H9N
def: "Fragmentation information, type of product: y ion with a loss of 
C3H9N." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002688
name: frag: z ion - H3PO4
def: "Fragmentation information, type of product: z ion with a loss of 
H3PO4." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002689
name: frag: z ion - HPO3
def: "Fragmentation information, type of product: z ion with a loss of 
HPO3." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002690
name: frag: z ion - CH4OS
def: "Fragmentation information, type of product: z ion with a loss of 
CH4OS." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002691
name: frag: z ion - C3H9N
def: "Fragmentation information, type of product: z ion with a loss of 
C3H9N." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type

************ New terms for precursor ions with neutral losses
[Term]
id: MS:1002692
name: frag: precursor ion - H3PO4
def: "Fragmentation information, type of product: precursor ion with a 
loss of H3PO4." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002693
name: frag: precursor ion - HPO3
def: "Fragmentation information, type of product: precursor ion with a 
loss of HPO3." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002694
name: frag: precursor ion - CH4OS
def: "Fragmentation information, type of product: precursor ion with a 
loss of CH4OS." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1002695
name: frag: precursor ion - C3H9N
def: "Fragmentation information, type of product: precursor ion with a 
loss of C3H9N." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type



Changed CV terms in version 3.89.0_rc1 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

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] New version 3.88.0 of psi-ms.obo

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

Dear proteomics community,

attached there's the new version 3.88.0 of the psi-ms.obo file.


New CV terms in version 3.88.0 of psi-ms.obo:
=============================================
************ Two new instrument terms
[Term]
id: MS:1002666
name: impact II
def: "Bruker Daltonics' impact II." [PSI:MS]
is_a: MS:1001536 ! Bruker Daltonics micrOTOF series

[Term]
id: MS:1002667
name: impact HD
def: "Bruker Daltonics' impact HD." [PSI:MS]
is_a: MS:1001536 ! Bruker Daltonics micrOTOF series


Changed CV terms in version 3.88.0 of psi-ms.obo:
=================================================
************ replaced the imports to pato and uo by PURL's
import: http://purl.obolibrary.org/obo/pato.owl
import: http://purl.obolibrary.org/obo/uo.owl

************ added is_a: MS:1001302 ! search engine specific input parameter
[Term]
id: MS:1002389
name: PIA workflow parameter
def: "A parameter set for a single PIA analysis." [PSI:PI]
is_a: MS:1002105 ! software specific input parameter
is_a: MS:1001302 ! search engine specific input parameter

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 3.88.0_rc1

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

Dear proteomics community,

attached there's the release candidate 3.88.0_rc1 of the psi-ms.obo file.


New CV terms in version 3.88.0_rc1 of psi-ms.obo:
=================================================
************ Two new instrument terms
[Term]
id: MS:1002666
name: impact II
def: "Bruker Daltonics' impact II." [PSI:MS]
is_a: MS:1001536 ! Bruker Daltonics micrOTOF series

[Term]
id: MS:1002667
name: impact HD
def: "Bruker Daltonics' impact HD." [PSI:MS]
is_a: MS:1001536 ! Bruker Daltonics micrOTOF series


Changed CV terms in version 3.87.0_rc1 of psi-ms.obo:
=====================================================
************ added is_a: MS:1001302 ! search engine specific input parameter
[Term]
id: MS:1002389
name: PIA workflow parameter
def: "A parameter set for a single PIA analysis." [PSI:PI]
is_a: MS:1002105 ! software specific input parameter
is_a: MS:1001302 ! search engine specific input parameter


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

Re: [Psidev-ms-dev] New version 3.87.0 of psi-ms.obo

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

This looks good. Thank you for your continued efforts, Gerhard!



*From:* mayerg97 [mailto:ger...@ru...]
*Sent:* Tuesday, May 10, 2016 5:46 AM
*To:* psi...@li...;
psi...@li...; psi...@li...
*Subject:* [Psidev-ms-dev] New version 3.87.0 of psi-ms.obo



Dear proteomics community,

attached there's the new version 3.87.0 of the psi-ms.obo file.


New CV terms in version 3.87.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002659
name: UniProtKB text sequence format
def: "Text-based format used by UniProtKB for sequence entries." [PSI:PI]
xref: SWO:http://edamontology.org/format_2187
is_a: MS:1001347 ! database file formats

[Term]
id: MS:1002660
name: UniProtKB XML sequence format
def: "XML-based format used by UniProtKB for sequence entries." [PSI:PI]
is_a: MS:1001347 ! database file formats

[Term]
id: MS:1002661
name: Morpheus
def: "Morpheus search engine." [PMID:23323968]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002662
name: Morpheus:Morpheus score
def: "Morpheus score for PSMs." [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:1001405 ! spectrum identification result details
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002663
name: Morpheus:summed Morpheus score
def: "Summed Morpheus score for protein groups." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002368 ! search engine specific score for protein groups
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001147 ! protein ambiguity group result details
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002664
name: protein interaction scores derived from cross-linking
def: "Parent term for protein interaction scores derived from
cross-linking." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002508 ! cross-linking attribute
relationship: has_regexp MS:1002665 !
([:digit:]+[.][a|b]:[:digit:]+:[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\})

[Term]
id: MS:1002665
name: regular expression for protein interaction scores derived from
cross-linking
def:
"([:digit:]+[.][a|b]:[:digit:]+:[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\})"
[PSI:PI]
is_a: MS:1002479 ! regular expression


Changed CV terms in version 3.87.0 of psi-ms.obo:
=================================================
************ added is_a: MS:1001405 ! spectrum identification result details
[Term]
id: MS:1002600
name: PRIDE XML
def: "Internal data and submission format of the PRIDE database." [
http://ftp.pride.ebi.ac.uk/pride/resources/schema/pride/pride.xsd]
is_a: MS:1002130 ! identification file format
is_a: MS:1001405 ! spectrum identification result details

************ obsoleted the following term
[Term]
id: MS:1002639
name: peptide start on chromosome
def: "OBSOLETE The overall start position on the chromosome to which a
peptide has been mapped i.e. the position of the first base of the first
codon, using a zero-based counting system." [PSI:PI]
comment: This term was obsoleted because it contains redundant info
contained in term MS:1002643 - peptide start positions on chromosome.
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute
is_obsolete: true


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

[image: 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] New version 3.87.0 of psi-ms.obo

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

Dear proteomics community,

attached there's the new version 3.87.0 of the psi-ms.obo file.


New CV terms in version 3.87.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002659
name: UniProtKB text sequence format
def: "Text-based format used by UniProtKB for sequence entries." [PSI:PI]
xref: SWO:http://edamontology.org/format_2187
is_a: MS:1001347 ! database file formats

[Term]
id: MS:1002660
name: UniProtKB XML sequence format
def: "XML-based format used by UniProtKB for sequence entries." [PSI:PI]
is_a: MS:1001347 ! database file formats

[Term]
id: MS:1002661
name: Morpheus
def: "Morpheus search engine." [PMID:23323968]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002662
name: Morpheus:Morpheus score
def: "Morpheus score for PSMs." [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:1001405 ! spectrum identification result details
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002663
name: Morpheus:summed Morpheus score
def: "Summed Morpheus score for protein groups." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002368 ! search engine specific score for protein groups
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001147 ! protein ambiguity group result details
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002664
name: protein interaction scores derived from cross-linking
def: "Parent term for protein interaction scores derived from 
cross-linking." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002508 ! cross-linking attribute
relationship: has_regexp MS:1002665 ! 
([:digit:]+[.][a|b]:[:digit:]+:[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\})

[Term]
id: MS:1002665
name: regular expression for protein interaction scores derived from 
cross-linking
def: 
"([:digit:]+[.][a|b]:[:digit:]+:[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\})" 
[PSI:PI]
is_a: MS:1002479 ! regular expression


Changed CV terms in version 3.87.0 of psi-ms.obo:
=================================================
************ added is_a: MS:1001405 ! spectrum identification result details
[Term]
id: MS:1002600
name: PRIDE XML
def: "Internal data and submission format of the PRIDE database." 
[http://ftp.pride.ebi.ac.uk/pride/resources/schema/pride/pride.xsd]
is_a: MS:1002130 ! identification file format
is_a: MS:1001405 ! spectrum identification result details

************ obsoleted the following term
[Term]
id: MS:1002639
name: peptide start on chromosome
def: "OBSOLETE The overall start position on the chromosome to which a 
peptide has been mapped i.e. the position of the first base of the first 
codon, using a zero-based counting system." [PSI:PI]
comment: This term was obsoleted because it contains redundant info 
contained in term MS:1002643 - peptide start positions on chromosome.
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute
is_obsolete: true


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] FW: mzTab for metabolomics

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

Hi all,

We will have a workshop attempting to finalise mzTab format for metabolomics, in Liverpool, UK on 4th and 5th July (two full days). Please can you forward on to your respective groups/collaborators and see if there are people who might be able to attend. The meeting will be free to attend, I will cover lunches and dinner, although participants will need to cover their own travel costs. If anyone is very keen to attend and work on mzTab longer term, but has no travel money, please contact me to see if we can work something out.

Ideally I would like to have around 5-10 people attending (but can have more given sufficient interest), with knowledge of a range of MS metabolomics informatics approaches/pipelines, so we can make sure that mzTab is a viable format for input to statistical analysis and public data deposition, covering most common approaches.

If anyone is interested in attending, please email me to confirm attendance. I would also appreciate if you can forward this message to any suitable mailing lists or collaborators.

Best wishes
Andy

[Psidev-ms-dev] Release candidate 3.87.0_rc1 of psi-ms.obo

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

Dear proteomics community,

attached there's the release candidate 3.87.0_rc1 of the psi-ms.obo file.


New CV terms in version 3.87.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002659
name: UniProtKB text sequence format
def: "Text-based format used by UniProtKB for sequence entries." [PSI:PI]
xref: SWO:http://edamontology.org/format_2187
is_a: MS:1001347 ! database file formats

[Term]
id: MS:1002660
name: UniProtKB XML sequence format
def: "XML-based format used by UniProtKB for sequence entries." [PSI:PI]
is_a: MS:1001347 ! database file formats

[Term]
id: MS:1002661
name: Morpheus
def: "Morpheus search engine." [PMID:23323968]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002662
name: Morpheus:Morpheus score
def: "Morpheus score for PSMs." [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:1001405 ! spectrum identification result details
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002663
name: Morpheus:summed Morpheus score
def: "Summed Morpheus score for protein groups." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002368 ! search engine specific score for protein groups
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001147 ! protein ambiguity group result details
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002664
name: protein interaction scores derived from cross-linking
def: "Parent term for protein interaction scores derived from 
cross-linking." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002508 ! cross-linking attribute
relationship: has_regexp MS:1002665 ! 
([:digit:]+[.][a|b]:[:digit:]+:[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\})

[Term]
id: MS:1002665
name: regular expression for protein interaction scores derived from 
cross-linking
def: 
"([:digit:]+[.][a|b]:[:digit:]+:[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\})" 
[PSI:PI]
is_a: MS:1002479 ! regular expression


Changed CV terms in version 3.87.0_rc1 of psi-ms.obo:
=====================================================
************ added is_a: MS:1001405 ! spectrum identification result details
[Term]
id: MS:1002600
name: PRIDE XML
def: "Internal data and submission format of the PRIDE database." 
[http://ftp.pride.ebi.ac.uk/pride/resources/schema/pride/pride.xsd]
is_a: MS:1002130 ! identification file format
is_a: MS:1001405 ! spectrum identification result details

************ obsoleted the following term
[Term]
id: MS:1002639
name: peptide start on chromosome
def: "OBSOLETE The overall start position on the chromosome to which a 
peptide has been mapped i.e. the position of the first base of the first 
codon, using a zero-based counting system." [PSI:PI]
comment: This term was obsoleted because it contains redundant info 
contained in term MS:1002643 - peptide start positions on chromosome.
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute
is_obsolete: true


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] Version 3.86.2 of psi-ms.obo

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

Dear proteomics community,

attached there's the new version 3.86.2 of the psi-ms.obo file.


Changed CV terms in version 3.86.2 of psi-ms.obo:
=================================================
************ Updated the import links to pato.obo and unit.obo (pointing 
now to GitHub)
import: https://raw.githubusercontent.com/pato-ontology/pato/master/pato.obo
import: 
https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo
remark: URL: 
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo


************ Renamed cross-link receiver --> cross-link acceptor
[Term]
id: MS:1002510
name: cross-link acceptor
def: "Cross-linking acceptor, assigned according to the following rules: 
the export software SHOULD use the following rules to choose the 
cross-link donor as the: longer peptide, then higher peptide neutral 
mass, then alphabetical order." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002508 ! cross-linking attribute

*********** Changed the regular expression
[Term]
id: MS:1002505
name: regular expression for modification localization scoring
def: 
"([:digit:]+:[0|1]\{1\}.[:digit:]+[Ee]{0,1}[+-]{0,1}[:digit:]*:[:digit:]+[|]\{1\}[:digit:]+:(true|false)\{1\})" 
[PSI:PI]
is_a: MS:1002479 ! regular expression

************ Re-added units to the following two terms
[Term]
id: MS:1002225
name: average product ion intensity
def: "Average value of product ion intensity in a collection of 
identified spectra." [PSI:PI]
is_a: MS:1001226 ! product ion intensity
relationship: has_units MS:1000131 ! number of detector counts
relationship: has_units MS:1000132 ! percent of base peak
relationship: has_units MS:1000814 ! counts per second
relationship: has_units MS:1000905 ! percent of base peak times 100

[Term]
id: MS:1002226
name: product ion intensity standard deviation
def: "Standard deviation of product ion intensity in a collection of 
identified spectra." [PSI:PI]
is_a: MS:1001226 ! product ion intensity
relationship: has_units MS:1000131 ! number of detector counts
relationship: has_units MS:1000132 ! percent of base peak
relationship: has_units MS:1000814 ! counts per second
relationship: has_units MS:1000905 ! percent of base peak times 100

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-ms-dev] Version 3.86.1 of psi-ms.obo

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

Thanks, Gerhard!

Although I didn’t make it explicit in my earlier message, I think these two
terms need the same units as 1226:

[Term]
id: MS:1002225
name: average product ion intensity
def: "Average value of product ion intensity in a collection of identified
spectra." [PSI:PI]
is_a: MS:1001226 ! product ion intensity

[Term]
id: MS:1002226
name: product ion intensity standard deviation
def: "Standard deviation of product ion intensity in a collection of
identified spectra." [PSI:PI]
is_a: MS:1001226 ! product ion intensity



*From:* mayerg97 [mailto:ger...@ru...]
*Sent:* Wednesday, April 27, 2016 4:50 AM
*To:* psi...@li...;
psi...@li...; psi...@li...
*Subject:* [Psidev-ms-dev] Version 3.86.1 of psi-ms.obo



Dear proteomics community,

attached there's the new version 3.86.1 of the psi-ms.obo file.


Changed CV terms in version 3.86.1 of psi-ms.obo:
=================================================
************ Added units again to the terms MS:10000904 and MS:1001226
[Term]
id: MS:1000904
name: product ion m/z delta
def: "The difference in m/z of the predicted m/z based on the assigned
product ion minus the actual observed peak m/z." [PSI:PI]
is_a: MS:1001221 ! fragmentation information
relationship: has_units MS:1000040 ! m/z

[Term]
id: MS:1001226
name: product ion intensity
def: "The intensity of a single product ion." [PSI:PI]
synonym: "fragment ion intensity" EXACT []
is_a: MS:1001221 ! fragmentation information
relationship: has_units MS:1000131 ! number of detector counts
relationship: has_units MS:1000132 ! percent of base peak
relationship: has_units MS:1000814 ! counts per second
relationship: has_units MS:1000905 ! percent of base peak times 100

************ Added value type to all child terms of MS:1002646 ! native
spectrum identifier format, combined spectra
to allow specification of the comma separated list of spectra

************ Changed regular expression of term MS:1002505
************ to allow scientific notation of the modification localization
score
[Term]
id: MS:1002505
name: regular expression for modification localization scoring
def:
"([:digit:]+:[0|1]\{1\}.[:digit:]+[Ee]{0,1}[+-]{0,1}[:digit:]+:[:digit:]+[|]\{1\}[:digit:]+:(true|false)\{1\})"
[PSI:PI]
is_a: MS:1002479 ! regular expression

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] Version 3.86.1 of psi-ms.obo

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

Dear proteomics community,

attached there's the new version 3.86.1 of the psi-ms.obo file.


Changed CV terms in version 3.86.1 of psi-ms.obo:
=================================================
************ Added units again to the terms MS:10000904 and MS:1001226
[Term]
id: MS:1000904
name: product ion m/z delta
def: "The difference in m/z of the predicted m/z based on the assigned 
product ion minus the actual observed peak m/z." [PSI:PI]
is_a: MS:1001221 ! fragmentation information
relationship: has_units MS:1000040 ! m/z

[Term]
id: MS:1001226
name: product ion intensity
def: "The intensity of a single product ion." [PSI:PI]
synonym: "fragment ion intensity" EXACT []
is_a: MS:1001221 ! fragmentation information
relationship: has_units MS:1000131 ! number of detector counts
relationship: has_units MS:1000132 ! percent of base peak
relationship: has_units MS:1000814 ! counts per second
relationship: has_units MS:1000905 ! percent of base peak times 100

************ Added value type to all child terms of MS:1002646 ! native 
spectrum identifier format, combined spectra
to allow specification of the comma separated list of spectra

************ Changed regular expression of term MS:1002505
************ to allow scientific notation of the modification 
localization score
[Term]
id: MS:1002505
name: regular expression for modification localization scoring
def: 
"([:digit:]+:[0|1]\{1\}.[:digit:]+[Ee]{0,1}[+-]{0,1}[:digit:]+:[:digit:]+[|]\{1\}[:digit:]+:(true|false)\{1\})" 
[PSI:PI]
is_a: MS:1002479 ! regular expression

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-ms-dev] [Psidev-ms-vocab] New version 3.86.0 of psi-ms.obo

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

Yes in fact we did. Gerhard would you mind adding the units back in

From: Eric Deutsch [mailto:ede...@sy...]
Sent: 26 April 2016 16:21
To: Mass spectrometry standard development <psi...@li...>; psi...@li...; psi...@li...
Subject: Re: [Psidev-ms-vocab] [Psidev-ms-dev] New version 3.86.0 of psi-ms.obo

One little detail: didn’t we want to keep the units on all the terms in this section, and just remove the datatype?

************ Removed the value and unit from the following terms:
[Term]
id: MS:1000904
name: product ion m/z delta
def: "The difference in m/z of the predicted m/z based on the assigned product ion minus the actual observed peak m/z." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001226
name: product ion intensity
..
..


From: Jones, Andy [mailto:And...@li...<mailto:And...@li...>]
Sent: Tuesday, April 26, 2016 6:35 AM
To: Mass spectrometry standard development; psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>
Subject: Re: [Psidev-ms-dev] New version 3.86.0 of psi-ms.obo

Hi Gerhard,
Many thanks for this, looks good.
Best wishes
Andy

From: mayerg97 [mailto:ger...@ru...]
Sent: 26 April 2016 14:23
To: psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>
Subject: [Psidev-ms-dev] New version 3.86.0 of psi-ms.obo


Dear proteomics community,

attached there's the new version 3.86.0 of the psi-ms.obo file.
It contains all changes agreed on at the HUPO-PSI meeting in Ghent.


New CV terms in version 3.86.0 of psi-ms.obo:
=================================================
************ added 11 terms for identifier formats for combined spectra
[Term]
id: MS:1002646
name: native spectrum identifier format, combined spectra
def: "Describes how the native spectrum identifiers that have been combined prior to searching or interpretation are formated." [PSI:PI]
synonym: "nativeID format, combined spectra" EXACT []
relationship: part_of MS:1000577 ! raw data file

[Term]
id: MS:1002647
name: Thermo nativeID format, combined spectra
def: "Thermo comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002648
name: Waters nativeID format, combined spectra
def: "Waters comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002649
name: WIFF nativeID format, combined spectra
def: "WIFF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002650
name: Bruker/Agilent YEP nativeID format, combined spectra
def: "Bruker/Agilent comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002651
name: Bruker BAF nativeID format, combined spectra
def: "Bruker BAF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002652
name: Bruker FID nativeID format, combined spectra
def: "Bruker FID comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: The nativeID must be the same as the source file ID.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002653
name: multiple peak list nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: Used for conversion of peak list files with multiple spectra, i.e. MGF, PKL, merged DTA files. Index is the spectrum number in the file, starting from 0.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002654
name: single peak list nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: The nativeID must be the same as the source file ID. Used for conversion of peak list files with one spectrum per file, typically folder of PKL or DTAs, each sourceFileRef is different.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002655
name: scan number only nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: Used for conversion from mzXML, or DTA folder where native scan numbers can be derived.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002656
name: spectrum identifier nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: Used for conversion from mzData. The spectrum id attribute is referenced.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002657
name: mzML unique identifier, combined spectra
def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: A unique identifier of a spectrum stored in an mzML file.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002658
name: identification parameter
def: "Identification parameter for the search engine run." [PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation



Changed CV terms in version 3.86.0 of psi-ms.obo:
=================================================
************ Added is_a: MS:1002489 ! special processing
[Term]
id: MS:1001010
name: de novo search
def: "A de novo sequencing search (without database)." [PSI:PI]
is_a: MS:1001080 ! search type
is_a: MS:1002489 ! special processing

************ New parent MS:1002657 ! identification parameter
[Term]
id: MS:1002496
name: group PSMs by sequence
def: "Group PSMs by distinct peptide sequence ignoring modifications." [PSI:PI]
is_a: MS:1002658 ! identification parameter

[Term]
id: MS:1002497
name: group PSMs by sequence with modifications
def: "Group PSMs by distinct peptide sequence with taking modifications into account." [PSI:PI]
is_a: MS:1002658 ! identification parameter

[Term]
id: MS:1002498
name: group PSMs by sequence with modifications and charge
def: "Group PSMs by distinct peptide sequence with taking modifications and charge into account." [PSI:PI]
is_a: MS:1002658 ! identification parameter

************ Obsoleted the term 'peptide level score'
[Term]
id: MS:1002499
name: peptide level score
def: "OBSOLETE Peptide level score." [PSI:PI]
comment: This term was obsoleted because it was never intended to go in the CV.
is_a: MS:1002358 ! search engine specific score for distinct peptides
is_obsolete: true

************ Changed the definition
[Term]
id: MS:1002643
name: peptide start positions on chromosome
def: "A comma separated list of start positions within exons to which the peptide has been mapped, relative to peptide-chromosome start, assuming a zero-based counting system. The first value MUST match the value in peptide start on chromosome." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

************ Added is_a: MS:1001184 ! search statistics
[Term]
id: MS:1002404
name: count of identified proteins
def: "The number of proteins that have been identified, which must match the number of groups that pass the threshold in the file." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1001085 ! protein result details
is_a: MS:1001184 ! search statistics

************ Removed the value and unit from the following terms:
[Term]
id: MS:1000904
name: product ion m/z delta
def: "The difference in m/z of the predicted m/z based on the assigned product ion minus the actual observed peak m/z." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001226
name: product ion intensity
def: "The intensity of a single product ion." [PSI:PI]
synonym: "fragment ion intensity" EXACT []
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1002225
name: average product ion intensity
def: "Average value of product ion intensity in a collection of identified spectra." [PSI:PI]
is_a: MS:1001226 ! product ion intensity

[Term]
id: MS:1002226
name: product ion intensity standard deviation
def: "Standard deviation of product ion intensity in a collection of identified spectra." [PSI:PI]
is_a: MS:1001226 ! product ion intensity


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@01D1A066.7C96A1D0]

Re: [Psidev-ms-dev] New version 3.86.0 of psi-ms.obo

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

One little detail: didn’t we want to keep the units on all the terms in
this section, and just remove the datatype?



************ Removed the value and unit from the following terms:
[Term]
id: MS:1000904
name: product ion m/z delta
def: "The difference in m/z of the predicted m/z based on the assigned
product ion minus the actual observed peak m/z." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001226
name: product ion intensity
..

..





*From:* Jones, Andy [mailto:And...@li...]
*Sent:* Tuesday, April 26, 2016 6:35 AM
*To:* Mass spectrometry standard development;
psi...@li...; psi...@li...
*Subject:* Re: [Psidev-ms-dev] New version 3.86.0 of psi-ms.obo



Hi Gerhard,

Many thanks for this, looks good.

Best wishes

Andy



*From:* mayerg97 [mailto:ger...@ru... <ger...@ru...>]
*Sent:* 26 April 2016 14:23
*To:* psi...@li...;
psi...@li...; psi...@li...
*Subject:* [Psidev-ms-dev] New version 3.86.0 of psi-ms.obo



Dear proteomics community,

attached there's the new version 3.86.0 of the psi-ms.obo file.
It contains all changes agreed on at the HUPO-PSI meeting in Ghent.


New CV terms in version 3.86.0 of psi-ms.obo:
=================================================
************ added 11 terms for identifier formats for combined spectra
[Term]
id: MS:1002646
name: native spectrum identifier format, combined spectra
def: "Describes how the native spectrum identifiers that have been combined
prior to searching or interpretation are formated." [PSI:PI]
synonym: "nativeID format, combined spectra" EXACT []
relationship: part_of MS:1000577 ! raw data file

[Term]
id: MS:1002647
name: Thermo nativeID format, combined spectra
def: "Thermo comma separated list of spectra that have been combined prior
to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002648
name: Waters nativeID format, combined spectra
def: "Waters comma separated list of spectra that have been combined prior
to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002649
name: WIFF nativeID format, combined spectra
def: "WIFF comma separated list of spectra that have been combined prior to
searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002650
name: Bruker/Agilent YEP nativeID format, combined spectra
def: "Bruker/Agilent comma separated list of spectra that have been
combined prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002651
name: Bruker BAF nativeID format, combined spectra
def: "Bruker BAF comma separated list of spectra that have been combined
prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002652
name: Bruker FID nativeID format, combined spectra
def: "Bruker FID comma separated list of spectra that have been combined
prior to searching or interpretation." [PSI:PI]
comment: The nativeID must be the same as the source file ID.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002653
name: multiple peak list nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to
searching or interpretation." [PSI:PI]
comment: Used for conversion of peak list files with multiple spectra, i.e.
MGF, PKL, merged DTA files. Index is the spectrum number in the file,
starting from 0.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002654
name: single peak list nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to
searching or interpretation." [PSI:PI]
comment: The nativeID must be the same as the source file ID. Used for
conversion of peak list files with one spectrum per file, typically folder
of PKL or DTAs, each sourceFileRef is different.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002655
name: scan number only nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to
searching or interpretation." [PSI:PI]
comment: Used for conversion from mzXML, or DTA folder where native scan
numbers can be derived.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002656
name: spectrum identifier nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to
searching or interpretation." [PSI:PI]
comment: Used for conversion from mzData. The spectrum id attribute is
referenced.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002657
name: mzML unique identifier, combined spectra
def: "Comma separated list of spectra that have been combined prior to
searching or interpretation." [PSI:PI]
comment: A unique identifier of a spectrum stored in an mzML file.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002658
name: identification parameter
def: "Identification parameter for the search engine run." [PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation



Changed CV terms in version 3.86.0 of psi-ms.obo:
=================================================
************ Added is_a: MS:1002489 ! special processing
[Term]
id: MS:1001010
name: de novo search
def: "A de novo sequencing search (without database)." [PSI:PI]
is_a: MS:1001080 ! search type
is_a: MS:1002489 ! special processing

************ New parent MS:1002657 ! identification parameter
[Term]
id: MS:1002496
name: group PSMs by sequence
def: "Group PSMs by distinct peptide sequence ignoring modifications."
[PSI:PI]
is_a: MS:1002658 ! identification parameter

[Term]
id: MS:1002497
name: group PSMs by sequence with modifications
def: "Group PSMs by distinct peptide sequence with taking modifications
into account." [PSI:PI]
is_a: MS:1002658 ! identification parameter

[Term]
id: MS:1002498
name: group PSMs by sequence with modifications and charge
def: "Group PSMs by distinct peptide sequence with taking modifications and
charge into account." [PSI:PI]
is_a: MS:1002658 ! identification parameter

************ Obsoleted the term 'peptide level score'
[Term]
id: MS:1002499
name: peptide level score
def: "OBSOLETE Peptide level score." [PSI:PI]
comment: This term was obsoleted because it was never intended to go in the
CV.
is_a: MS:1002358 ! search engine specific score for distinct peptides
is_obsolete: true

************ Changed the definition
[Term]
id: MS:1002643
name: peptide start positions on chromosome
def: "A comma separated list of start positions within exons to which the
peptide has been mapped, relative to peptide-chromosome start, assuming a
zero-based counting system. The first value MUST match the value in peptide
start on chromosome." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

************ Added is_a: MS:1001184 ! search statistics
[Term]
id: MS:1002404
name: count of identified proteins
def: "The number of proteins that have been identified, which must match
the number of groups that pass the threshold in the file." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1001085 ! protein result details
is_a: MS:1001184 ! search statistics

************ Removed the value and unit from the following terms:
[Term]
id: MS:1000904
name: product ion m/z delta
def: "The difference in m/z of the predicted m/z based on the assigned
product ion minus the actual observed peak m/z." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001226
name: product ion intensity
def: "The intensity of a single product ion." [PSI:PI]
synonym: "fragment ion intensity" EXACT []
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1002225
name: average product ion intensity
def: "Average value of product ion intensity in a collection of identified
spectra." [PSI:PI]
is_a: MS:1001226 ! product ion intensity

[Term]
id: MS:1002226
name: product ion intensity standard deviation
def: "Standard deviation of product ion intensity in a collection of
identified spectra." [PSI:PI]
is_a: MS:1001226 ! product ion intensity


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

Re: [Psidev-ms-dev] New version 3.86.0 of psi-ms.obo

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

Hi Gerhard,
Many thanks for this, looks good.
Best wishes
Andy

From: mayerg97 [mailto:ger...@ru...]
Sent: 26 April 2016 14:23
To: psi...@li...; psi...@li...; psi...@li...
Subject: [Psidev-ms-dev] New version 3.86.0 of psi-ms.obo


Dear proteomics community,

attached there's the new version 3.86.0 of the psi-ms.obo file.
It contains all changes agreed on at the HUPO-PSI meeting in Ghent.


New CV terms in version 3.86.0 of psi-ms.obo:
=================================================
************ added 11 terms for identifier formats for combined spectra
[Term]
id: MS:1002646
name: native spectrum identifier format, combined spectra
def: "Describes how the native spectrum identifiers that have been combined prior to searching or interpretation are formated." [PSI:PI]
synonym: "nativeID format, combined spectra" EXACT []
relationship: part_of MS:1000577 ! raw data file

[Term]
id: MS:1002647
name: Thermo nativeID format, combined spectra
def: "Thermo comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002648
name: Waters nativeID format, combined spectra
def: "Waters comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002649
name: WIFF nativeID format, combined spectra
def: "WIFF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002650
name: Bruker/Agilent YEP nativeID format, combined spectra
def: "Bruker/Agilent comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002651
name: Bruker BAF nativeID format, combined spectra
def: "Bruker BAF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002652
name: Bruker FID nativeID format, combined spectra
def: "Bruker FID comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: The nativeID must be the same as the source file ID.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002653
name: multiple peak list nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: Used for conversion of peak list files with multiple spectra, i.e. MGF, PKL, merged DTA files. Index is the spectrum number in the file, starting from 0.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002654
name: single peak list nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: The nativeID must be the same as the source file ID. Used for conversion of peak list files with one spectrum per file, typically folder of PKL or DTAs, each sourceFileRef is different.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002655
name: scan number only nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: Used for conversion from mzXML, or DTA folder where native scan numbers can be derived.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002656
name: spectrum identifier nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: Used for conversion from mzData. The spectrum id attribute is referenced.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002657
name: mzML unique identifier, combined spectra
def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: A unique identifier of a spectrum stored in an mzML file.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002658
name: identification parameter
def: "Identification parameter for the search engine run." [PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation



Changed CV terms in version 3.86.0 of psi-ms.obo:
=================================================
************ Added is_a: MS:1002489 ! special processing
[Term]
id: MS:1001010
name: de novo search
def: "A de novo sequencing search (without database)." [PSI:PI]
is_a: MS:1001080 ! search type
is_a: MS:1002489 ! special processing

************ New parent MS:1002657 ! identification parameter
[Term]
id: MS:1002496
name: group PSMs by sequence
def: "Group PSMs by distinct peptide sequence ignoring modifications." [PSI:PI]
is_a: MS:1002658 ! identification parameter

[Term]
id: MS:1002497
name: group PSMs by sequence with modifications
def: "Group PSMs by distinct peptide sequence with taking modifications into account." [PSI:PI]
is_a: MS:1002658 ! identification parameter

[Term]
id: MS:1002498
name: group PSMs by sequence with modifications and charge
def: "Group PSMs by distinct peptide sequence with taking modifications and charge into account." [PSI:PI]
is_a: MS:1002658 ! identification parameter

************ Obsoleted the term 'peptide level score'
[Term]
id: MS:1002499
name: peptide level score
def: "OBSOLETE Peptide level score." [PSI:PI]
comment: This term was obsoleted because it was never intended to go in the CV.
is_a: MS:1002358 ! search engine specific score for distinct peptides
is_obsolete: true

************ Changed the definition
[Term]
id: MS:1002643
name: peptide start positions on chromosome
def: "A comma separated list of start positions within exons to which the peptide has been mapped, relative to peptide-chromosome start, assuming a zero-based counting system. The first value MUST match the value in peptide start on chromosome." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

************ Added is_a: MS:1001184 ! search statistics
[Term]
id: MS:1002404
name: count of identified proteins
def: "The number of proteins that have been identified, which must match the number of groups that pass the threshold in the file." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1001085 ! protein result details
is_a: MS:1001184 ! search statistics

************ Removed the value and unit from the following terms:
[Term]
id: MS:1000904
name: product ion m/z delta
def: "The difference in m/z of the predicted m/z based on the assigned product ion minus the actual observed peak m/z." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001226
name: product ion intensity
def: "The intensity of a single product ion." [PSI:PI]
synonym: "fragment ion intensity" EXACT []
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1002225
name: average product ion intensity
def: "Average value of product ion intensity in a collection of identified spectra." [PSI:PI]
is_a: MS:1001226 ! product ion intensity

[Term]
id: MS:1002226
name: product ion intensity standard deviation
def: "Standard deviation of product ion intensity in a collection of identified spectra." [PSI:PI]
is_a: MS:1001226 ! product ion intensity


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:ima...@01...5838F0]

[Psidev-ms-dev] New version 3.86.0 of psi-ms.obo

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

Dear proteomics community,

attached there's the new version 3.86.0 of the psi-ms.obo file.
It contains all changes agreed on at the HUPO-PSI meeting in Ghent.


New CV terms in version 3.86.0 of psi-ms.obo:
=================================================
************ added 11 terms for identifier formats for combined spectra
[Term]
id: MS:1002646
name: native spectrum identifier format, combined spectra
def: "Describes how the native spectrum identifiers that have been 
combined prior to searching or interpretation are formated." [PSI:PI]
synonym: "nativeID format, combined spectra" EXACT []
relationship: part_of MS:1000577 ! raw data file

[Term]
id: MS:1002647
name: Thermo nativeID format, combined spectra
def: "Thermo comma separated list of spectra that have been combined 
prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002648
name: Waters nativeID format, combined spectra
def: "Waters comma separated list of spectra that have been combined 
prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002649
name: WIFF nativeID format, combined spectra
def: "WIFF comma separated list of spectra that have been combined prior 
to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002650
name: Bruker/Agilent YEP nativeID format, combined spectra
def: "Bruker/Agilent comma separated list of spectra that have been 
combined prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002651
name: Bruker BAF nativeID format, combined spectra
def: "Bruker BAF comma separated list of spectra that have been combined 
prior to searching or interpretation." [PSI:PI]
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002652
name: Bruker FID nativeID format, combined spectra
def: "Bruker FID comma separated list of spectra that have been combined 
prior to searching or interpretation." [PSI:PI]
comment: The nativeID must be the same as the source file ID.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002653
name: multiple peak list nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to 
searching or interpretation." [PSI:PI]
comment: Used for conversion of peak list files with multiple spectra, 
i.e. MGF, PKL, merged DTA files. Index is the spectrum number in the 
file, starting from 0.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002654
name: single peak list nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to 
searching or interpretation." [PSI:PI]
comment: The nativeID must be the same as the source file ID. Used for 
conversion of peak list files with one spectrum per file, typically 
folder of PKL or DTAs, each sourceFileRef is different.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002655
name: scan number only nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to 
searching or interpretation." [PSI:PI]
comment: Used for conversion from mzXML, or DTA folder where native scan 
numbers can be derived.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002656
name: spectrum identifier nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to 
searching or interpretation." [PSI:PI]
comment: Used for conversion from mzData. The spectrum id attribute is 
referenced.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002657
name: mzML unique identifier, combined spectra
def: "Comma separated list of spectra that have been combined prior to 
searching or interpretation." [PSI:PI]
comment: A unique identifier of a spectrum stored in an mzML file.
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

[Term]
id: MS:1002658
name: identification parameter
def: "Identification parameter for the search engine run." [PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation



Changed CV terms in version 3.86.0 of psi-ms.obo:
=================================================
************ Added is_a: MS:1002489 ! special processing
[Term]
id: MS:1001010
name: de novo search
def: "A de novo sequencing search (without database)." [PSI:PI]
is_a: MS:1001080 ! search type
is_a: MS:1002489 ! special processing

************ New parent MS:1002657 ! identification parameter
[Term]
id: MS:1002496
name: group PSMs by sequence
def: "Group PSMs by distinct peptide sequence ignoring modifications." 
[PSI:PI]
is_a: MS:1002658 ! identification parameter

[Term]
id: MS:1002497
name: group PSMs by sequence with modifications
def: "Group PSMs by distinct peptide sequence with taking modifications 
into account." [PSI:PI]
is_a: MS:1002658 ! identification parameter

[Term]
id: MS:1002498
name: group PSMs by sequence with modifications and charge
def: "Group PSMs by distinct peptide sequence with taking modifications 
and charge into account." [PSI:PI]
is_a: MS:1002658 ! identification parameter

************ Obsoleted the term 'peptide level score'
[Term]
id: MS:1002499
name: peptide level score
def: "OBSOLETE Peptide level score." [PSI:PI]
comment: This term was obsoleted because it was never intended to go in 
the CV.
is_a: MS:1002358 ! search engine specific score for distinct peptides
is_obsolete: true

************ Changed the definition
[Term]
id: MS:1002643
name: peptide start positions on chromosome
def: "A comma separated list of start positions within exons to which 
the peptide has been mapped, relative to peptide-chromosome start, 
assuming a zero-based counting system. The first value MUST match the 
value in peptide start on chromosome." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

************ Added is_a: MS:1001184 ! search statistics
[Term]
id: MS:1002404
name: count of identified proteins
def: "The number of proteins that have been identified, which must match 
the number of groups that pass the threshold in the file." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1001085 ! protein result details
is_a: MS:1001184 ! search statistics

************ Removed the value and unit from the following terms:
[Term]
id: MS:1000904
name: product ion m/z delta
def: "The difference in m/z of the predicted m/z based on the assigned 
product ion minus the actual observed peak m/z." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001226
name: product ion intensity
def: "The intensity of a single product ion." [PSI:PI]
synonym: "fragment ion intensity" EXACT []
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1002225
name: average product ion intensity
def: "Average value of product ion intensity in a collection of 
identified spectra." [PSI:PI]
is_a: MS:1001226 ! product ion intensity

[Term]
id: MS:1002226
name: product ion intensity standard deviation
def: "Standard deviation of product ion intensity in a collection of 
identified spectra." [PSI:PI]
is_a: MS:1001226 ! product ion intensity


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 DocProc document revision 1.1.1 - 14-days public review

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

Dear persons active in the PSI,

in 2014 a minor update of the PSI DocProc document has been agreed to 
by the steering committee.
It includes minor clarifications and DocProc document updates as well as a 
specification of version numbering.

It has not gone through a 14-day public review yet, after which its status
could
change to FINAL.
I attached version 1.1.1 PREFINAL with changes marked, so please add 
or comment until May 2nd!

  Thank you
    Bye
    Martin


--
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 mar...@ru...
www.medizinisches-proteom-center.de

[Psidev-ms-dev] Computational Biology Facility posts

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

Hi all,

A couple of informatics posts going at Liverpool - please forward on to any colleagues who might be interested.
Best wishes
Andy


Data Analyst
https://www.liverpool.ac.uk/working/jobvacancies/currentvacancies/research/r-590620/

Software Engineer
https://www.liverpool.ac.uk/working/jobvacancies/currentvacancies/research/r-590617/

[Psidev-ms-dev] PSI workshop April 18-20 in Ghent

[Omenn, G. <go...@me...>]

Dear PSI and PX colleagues—
    My best wishes for another productive HUPO-PSI leadership meeting in the beautiful city of Ghent.
    I remain keenly interested personally in your agenda and your important work.  We have major ties through the HUPO Human Proteome Project.
    I’m sure Eric will share the Guidelines for MS/MS data interpretation and the Checklist adopted by the HPP and the Journal of Proteome Research for the current Call for Papers for the 2016 C-HPP special issue.  See http://www.thehpp.org/guidelines/.  We welcome comments and queries from you, as we aim to stimulate consideration of adoption of these guidelines much more widely in the proteomics community and with additional journals.   There is an explicit process for amendment and updating of these Guidelines.
    Best wishes
       Gil


From: <psi...@eb...<mailto:psi...@eb...>> on behalf of "ede...@sy...<mailto:ede...@sy...>" <ede...@sy...<mailto:ede...@sy...>>
Date: Friday, March 25, 2016 at 2:11 PM
To: "psi...@eb...<mailto:psi...@eb...>" <psi...@eb...<mailto:psi...@eb...>>, Mass spectrometry standard development <psi...@li...<mailto:psi...@li...>>, "psi...@li...<mailto:psi...@li...>" <psi...@li...<mailto:psi...@li...>>
Subject: Re: [Psi-announce] Registration is open for PSI workshop April 18-20

Hi everyone, I just wanted to remind everyone that the PSI Spring Workshop is less than a month away! We have good registration numbers already, but if you’re planning on participating and have not yet registered, please do so right away so that we can have an accurate count for planning.

I look forward to seeing you in Ghent!

Regards,
Eric


From: Eric Deutsch [mailto:ede...@sy...<mailto:ede...@sy...>]
Sent: Friday, February 05, 2016 8:21 AM
To: psi...@eb...<mailto:psi...@eb...>; Mass spectrometry standard development; psi...@li...<mailto:psi...@li...>
Cc: Eric Deutsch
Subject: Registration is open for PSI workshop April 18-20

Hi everyone, I am pleased to announce that registration is now open for the PSI annual spring workshop in Ghent April 18-20.

The success of the PSI standards is only achieved through wide participation from the broader community, so please consider participating and contributing to this important effort. Registration is free as the workshop is supported by several grants.

You will find a link to the registration page, a draft workshop agenda, accommodation information, and additional details at:

http://www.psidev.info/content/hupo-psi-meeting-2016

Please let me know if you have any questions.

I look forward to seeing you in Ghent!

Regards,
Eric

**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues 

[Psidev-ms-dev] New version 3.84.0 of psi-ms.obo

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

Dear proteomics community,


here's the new version 3.84.0 of the psi-ms.obo file.
It contains mainly new terms for proteogenomics searches.


New CV terms in version 3.84.0 of psi-ms.obo:
=============================================
************
[Term]
id: MS:1002631
name: Electron-Transfer/Higher-Energy Collision Dissociation (EThcD)
def: "A dissociation process combining electron-transfer and 
higher-energy collision dissociation (EThcD). It combines ETD (reaction 
time) followed by HCD (activation energy)." [PSI:PI]
synonym: "EThcD" EXACT []
is_a: MS:1000044 ! dissociation method

[Term]
id: MS:1002632
name: jPOST dataset identifier
def: "Dataset identifier issued by the jPOST repository. A dataset can 
refer to either a single sample as part of a study, or all samples that 
are part of the study corresponding to a publication." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier

[Term]
id: MS:1002633
name: jPOST dataset URI
def: "URI that allows the access to one dataset in the jPOST repository. 
A dataset can refer to either a single sample as part of a study, or all 
samples that are part of the study corresponding to a publication." [PSI:PI]
xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier

[Term]
id: MS:1002634
name: Q Exactive Plus
def: "Thermo Scientific Q Exactive Plus." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1002635
name: proteogenomics search
def: "Proteogenomics search performed." [PSI:PI]
is_a: MS:1002489 ! special processing

[Term]
id: MS:1002636
name: proteogenomics attribute
def: "Proteogenomics attribute." [PSI:PI]
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1002637
name: chromosome name
def: "The name or number of the chromosome to which a given peptide has 
been mapped." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002638
name: chromosome strand
def: "The strand (+ or -) to which the peptide has been mapped." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002639
name: peptide start on chromosome
def: "The overall start position on the chromosome to which a peptide 
has been mapped i.e. the position of the first base of the first codon, 
using a zero-based counting system." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002640
name: peptide end on chromosome
def: "The overall end position on the chromosome to which a peptide has 
been mapped i.e. the position of the third base of the last codon, using 
a zero-based counting system." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002641
name: peptide exon count
def: "The number of exons to which the peptide has been mapped." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002642
name: peptide exon nucleotide sizes
def: "A comma separated list of the number of DNA bases within each exon 
to which a peptide has been mapped. Assuming standard operation of a 
search engine, the peptide exon sizes should sum to exactly three times 
the peptide length." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002643
name: peptide start positions on chromosome
def: "A comma separated list of start positions within exons to which 
the peptide has been mapped, relative to peptide-chromosome start." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002644
name: genome reference version
def: "The reference genome and versioning string as used for mapping. 
All coordinates are within this frame of reference." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute

[Term]
id: MS:1002645
name: MSDK
def: "Mass Spectrometry Development Kit (MSDK) is a Java library of 
algorithms for processing of mass spectrometry data." [PSI:PI, 
http://msdk.github.io/]
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software


Changed CV terms in version 3.84.0 of psi-ms.obo:
=================================================
************ added is_a: MS:1002489 ! special processing
[Term]
id: MS:1001031
name: spectral library search
def: "A search using a library of spectra." [PSI:PI]
is_a: MS:1001080 ! search type
is_a: MS:1002489 ! special processing

************ added relationship: has_units UO:0000169 ! parts per million
[Term]
id: MS:1001412
name: search tolerance plus value
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001411 ! search tolerance specification
relationship: has_units UO:0000166 ! parts per notation unit
relationship: has_units UO:0000169 ! parts per million
relationship: has_units UO:0000187 ! percent
relationship: has_units UO:0000221 ! dalton

************ added relationship: has_units UO:0000169 ! parts per million
[Term]
id: MS:1001413
name: search tolerance minus value
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001411 ! search tolerance specification
relationship: has_units UO:0000166 ! parts per notation unit
relationship: has_units UO:0000169 ! parts per million
relationship: has_units UO:0000187 ! percent
relationship: has_units UO:0000221 ! dalton

************ added value-type:xsd\:float to the following six 
PeptideShaker terms
[Term]
id: MS:1002466
name: PeptideShaker PSM score
def: "The probability based PeptideShaker PSM score." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for PSMs
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002467
name: PeptideShaker PSM confidence
def: "The probability based PeptideShaker PSM confidence." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for PSMs
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002468
name: PeptideShaker peptide score
def: "The probability based PeptideShaker peptide score." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002358 ! search engine specific score for distinct peptides
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002469
name: PeptideShaker peptide confidence
def: "The probability based PeptideShaker peptide confidence." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002470
name: PeptideShaker protein group score
def: "The probability based PeptideShaker protein group score." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
is_a: MS:1002368 ! search engine specific score for protein groups
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002471
name: PeptideShaker protein group confidence
def: "The probability based PeptideShaker protein group confidence." 
[PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better


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-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] Proteogenomics update in mzid 1.2

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

Hi Matthias,

Thanks for your comments, answers in line:

-----Original Message-----
From: Mathias Walzer [mailto:wa...@in...] 
Sent: 31 March 2016 16:57
To: Mass spectrometry standard development
Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] Proteogenomics update in mzid 1.2

Hi all,

I feel a little silly, seems I was not able to dial in (enter access code does not work) - the institute's telephone system was switched, I guess it does not support this kind of function anymore. 
Anyways, maybe just some points in brief.

mzid schema general issues: why is experimental m/z in not in SpectrumIdentificationResult but (repeatedly) in SpectrumIdentificationItem? Why is peptide_ref in SpectrumIdentificationItem optional? As are the PeptideEvidence elements. Because of the potential small molecule usecase?

>> You are correct that "experimental m/z" should be an attribute of SpectrumIdentificationResult - this was an error in mzid 1.1. I hadn't considered changing it, since we are trying to make mzid 1.2 as near as backwards compatible as possible. Any opinions as to whether this is worth changing?

Why is peptide_ref in SpectrumIdentificationItem optional?

>>I don't know why we ever did this in mzid 1.1, possibly a mistake or a use case we never fully explored. I would vote for making it mandatory now in mzid 1.2, as we are revisiting cardinality and optionality of elements/attributes. Opinions all?

>> As are the PeptideEvidence elements.

This is to account for de novo sequencing and spectral library approaches, where peptides may not be linked to a parent protein. In a regular sequence database search, the validator checks that they are always present.



mzid ppxl issues: we will need many more CV entries. E.g. the types of cross-link. Be it a mono-link, loop-link or cross-link.

>> Please suggest terms needed and we will add them. 

And there are only mono-link definitions in unimod (and only for DSS), so I guess we need more reagents used for crosslinking in one of the ontologies that define the pairs, 

>> Lutz is working on a list of reagent CV terms to be added to PSI-MS CV, please coordinate with him.

Also, to my understanding, isotope labeling is often used as a measure of reassurance of the identified cross-links. I suppose that kind of detected pairing information would go in the SpectrumIdentificationResult?

>> Good point, although we haven't got a formal way of doing this. Scores can obviously be added but we don't have a way of formally linking differentially labelled pairs (nor for regular SILAC either though). This might be considered out of scope in mzIdentML, but please send a suggestion for how the data looks from a search engine.

And there seems to be ambiguous definition available on the pairing of the different SpectrumIdentificationItem elements in one SpectrumIdentificationResult as linked peptides. It is the value of cv term 'cross-link spectrum identification item', isn't it - so we can use rank for sorting?

>> The value of 'cross-link spectrum identification item' is a local unique identifier tying together the crosslinked peptides. Do you think this is still ambiguous?

Best wishes
Andy 

best,
 Mathias

----- Original Message -----
From: "Andy Jones" <And...@li...>
To: psi...@li...
Cc: psi...@li...
Sent: Thursday, 31 March, 2016 4:45:07 PM
Subject: Re: [Psidev-ms-dev]	[Psidev-pi-dev]	[Psidev-ms-vocab]		Proteogenomics update in mzid 1.2





Dial-in details, call in 15 mins: 



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 [mailto:And...@li...] 
Sent: 29 March 2016 16:10 
To: psi...@li... 
Cc: psi...@li... 
Subject: Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev] Proteogenomics update in mzid 1.2 



Hi all, 

Just confirming we will have a call to discuss mzid 1.2 this coming Thurs at 4pm UK time: http://www.timeanddate.com/worldclock/fixedtime.html?msg=mzid+1.2+call&iso=20160331T16&p1=301 

Agenda: 

1. Discussion of encoding proteogenomics results in mzid 1.2 (review of docs sent previously) 

2. General review of mzid 1.2 specifications (attached here) – please take a look in advance if you can. We will probably not have time for a full review on the call, but we will see how far we get 

3. Any other business 



Juan – are you okay to start the call, and if so, can you circulate dial-in details? 

Thanks 

Andy 









From: Binz Pierre-Alain [ mailto:Pie...@ch... ] 
Sent: 22 March 2016 15:45 
To: psi...@li... 
Subject: Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev] Proteogenomics update in mzid 1.2 



Fine for me too 

Pierre-Alain 





De : Eric Deutsch [ mailto:ede...@sy... ] 
Envoyé : mardi 22 mars 2016 14:53 
À : psi...@li... ; Mass spectrometry standard development; psi...@li... 
Objet : Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev] Proteogenomics update in mzid 1.2 



That works fine for me! 





From: Jones, Andy [mailto: And...@li... ] 
Sent: Tuesday, March 22, 2016 2:49 AM 
To: Mass spectrometry standard development; psi...@li... ; psi...@li... 
Subject: Re: [Psidev-ms-vocab] [Psidev-ms-dev] Proteogenomics update in mzid 1.2 



Hi all, 

I think the 24 th is out for various people as an Easter-related holiday in some countries. Eric is correct, that time zones will be changing. 

On the 31 st , my preferred slot is actually 4pm British summer time: 

http://www.timeanddate.com/worldclock/fixedtime.html?msg=mzid+1.2+call&iso=20160331T16&p1=301 

This would be 8am in Seattle; 5pm Germany; 5pm Norway; (and 4pm in the independent nation state of the EBI) 

Does this work for everyone? 

Best wishes 

Andy 









From: Eric Deutsch [ mailto:ede...@sy... ] 
Sent: 22 March 2016 03:32 
To: Mass spectrometry standard development < psi...@li... >; psi...@li... ; psi...@li... 
Cc: Eric Deutsch < ede...@sy... > 
Subject: Re: [Psidev-ms-dev] Proteogenomics update in mzid 1.2 



Thanks, Andy, I like this idea. The times are not good for me, however. Normally 4pm London time is 8am Seattle time, but for these few weeks, 4pm London time is 9am Seattle time and I have a standing meeting I cannot change. 

http://www.timeanddate.com/worldclock/fixedtime.html?iso=20160324T16&p1=1440 

An hour earlier would be fine for the 24 th . 

I hope I’m not getting confused between 4pm GMT and London local time? I think on the 24 th 16:00 GMT = 4pm local London, but on the 31 st , 16:00 GMT is 5pm London time? 

Thanks, 

Eric 





From: Jones, Andy [mailto: And...@li... ] 
Sent: Monday, March 21, 2016 4:21 AM 
To: psi...@li... ; psi...@li... ; psi...@li... 
Subject: [Psidev-ms-dev] Proteogenomics update in mzid 1.2 



Hi all, 

Over the coming weeks, I will be trying to get mzid 1.2 largely tied up for a final review in Ghent, before we submit the spec doc and associated manuscript. I have cross-posted this message (since PSI-PI has not been active lately), but probably will drop PSI-MS from the list in future. If you’re interested in mzid 1.2, please make sure to follow the PSI-PI list. 

One feature I would like to add into mzid 1.2 is better support for proteogenomics approaches. There are some parallel efforts to adapt genome formats BED and BAM for proteomics (and updates will be presented in Ghent I think). It would be nice if the info needed for proBed and proBAM was consistently expressed in mzid 1.2 files (mainly genome coordinates for peptides). 

Along with Juan et al., we have come up with a proposal for how this might be done in mzid 1.2. Please see attached. Feel free to annotate any comments on the document, or email back to the list any parts you feel need adapting or comments for discussion. 

It might be useful to have one or two conference calls on mzid 1.2 before Ghent. How would following dates suit: 

- This Thurs (24 th March) at 4pm GMT 

- Next Thurs (31 st March) at 4pm GMT 

Best wishes 

Andy 






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Re: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] Proteogenomics update in mzid 1.2

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

Hi Harald, excellent, thanks. I hope someone can give you push access to
mzIdentML, I don't think I can.

I think the new home for the Unit Ontology is here:
https://github.com/bio-ontology-research-group/unit-ontology

thanks!
Eric


-----Original Message-----
From: Harald Barsnes [mailto:Har...@ui...]
Sent: Friday, April 01, 2016 8:55 AM
To: Eric Deutsch
Cc: Jones, Andy; psi...@li...;
psi...@li...
Subject: Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev]
Proteogenomics update in mzid 1.2


Hi Eric,

I've updated the PRIDE and PSI-MS obo URLs for the PeptideShaker example. Do
you have the new URL for the UO obo file?

As for the other PeptideShaker issues:

> ERROR: cvParam software vendor has a value, but it should not!

Fixed.

> WARNING: MS:1000588 should be 'contact URL' instead of 'contact url'

Fixed.

> ERROR: cvParam Phospho has a value, but it should not!
> ERROR: cvParam Oxidation has a value, but it should not!
> ERROR: cvParam Glu->pyro-Glu has a value, but it should not!
> ERROR: cvParam Carbamidomethyl has a value, but it should not!

Fixed.

Seems like I don't have push access to the new GitHub HUPO-PSI/mzIdentML
repository, so I've put the updated PeptideShaker example file on Dropbox in
the meantime:
https://www.dropbox.com/s/pucr2arc2tknp15/PeptideShaker_mzid_1_2_example.mzid.gz?dl=0

Let me now if you come across other issues with the PeptideShaker export.

Best regards,
Harald





Den 2016-04-01 00:40, skrev Eric Deutsch:
> Hi Andy, I fired up the schema generation script and refreshed
> everything based on what’s in github now. You can see the current
> result here:
>
> http://www.peptideatlas.org/PSI/schemas/mzIdentML/1.2/mzIdentML1.2.0.h
> tml
> [3]
>
> The schema seems pretty fine, but the example files have some issues.
> Here are a few observations of things to fix:
>
> - Examples files still have older CV URLS like:
>
> <cv id="PSI-MS"
> uri="http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/ps
> i-ms/mzML/controlledVocabulary/psi-ms.obo
> [4]" version="3.73.0" fullName="PSI-MS"/>
>
> <cv id="UO"
> uri="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenot
> ype/unit.obo
> [1]" fullName="UNIT-ONTOLOGY"/>
>
>     <cv id="PRIDE"
> uri="http://code.google.com/p/ebi-pride/source/browse/trunk/pride-core
> /schema/pride_cv.obo
> [2]" fullName="PRIDE"/>
>
> I ran a few of the files through my validator and have the following
> things:
>
> PeptideShaker_mzid_1_2_example.mzid
>
> ERROR: cvParam software vendor has a value, but it should not!
>
> WARNING: MS:1000588 should be 'contact URL' instead of 'contact url'
>
> ERROR: cvParam Phospho has a value, but it should not!
>
> ERROR: cvParam Oxidation has a value, but it should not!
>
> ERROR: cvParam Glu->pyro-Glu has a value, but it should not!
>
> ERROR: cvParam Carbamidomethyl has a value, but it should not!
>
> combined_fdr_1.2.mzid
>
> WARNING: MS:1001400 should be 'OMSSA xml format' instead of 'OMSSA xml
> file'
>
> WARNING: MS:1001062 should be 'Mascot MGF format' instead of 'Mascot
> MGF file'
>
> ERROR: cvParam distinct peptide-level q-value should have units, but
> it does not!
>
> xiFDR-CrossLinkExample.mzid
>
> WARNING: MS:1002543 should be 'xiFDR' instead of 'XiFDR'
>
> ERROR: cvParam contact address should have a value, but it does not!
>
> ERROR: cvParam contact name should have a value, but it does not!
>
> ERROR: cvParam unknown modification should have a value, but it does
> not!
>
> This is not exhaustive, but just some results from a first foray into
> this.
>
> If someone is interested in fixing these things and checking them it,
> I can push further and report other problems.
>
> Regards,
>
> Eric
>
> FROM: Jones, Andy [mailto:And...@li...]
> SENT: Tuesday, March 29, 2016 8:10 AM
> TO: psi...@li...
> CC: psi...@li...
> SUBJECT: Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev]
> Proteogenomics update in mzid 1.2
>
> Hi all,
>
> Just confirming we will have a call to discuss mzid 1.2 this coming
> Thurs at 4pm UK time:
> http://www.timeanddate.com/worldclock/fixedtime.html?msg=mzid+1.2+call
> &iso=20160331T16&p1=301
> [5]
>
> Agenda:
>
> 1.       Discussion of encoding proteogenomics results in mzid 1.2
> (review of docs sent previously)
>
> 2.       General review of mzid 1.2 specifications (attached here) –
> please take a look in advance if you can. We will probably not have
> time for a full review on the call, but we will see how far we get
>
> 3.       Any other business
>
> Juan – are you okay to start the call, and if so, can you circulate
> dial-in details?
>
> Thanks
>
> Andy
>
> FROM: Binz Pierre-Alain [mailto:Pie...@ch...]
> SENT: 22 March 2016 15:45
> TO: psi...@li...
> SUBJECT: Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev]
> Proteogenomics update in mzid 1.2
>
> Fine for me too
>
> Pierre-Alain
>
> DE : Eric Deutsch [mailto:ede...@sy...]
> ENVOYÉ : mardi 22 mars 2016 14:53
> À : psi...@li...; Mass spectrometry standard
> development; psi...@li...
> OBJET : Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev]
> Proteogenomics update in mzid 1.2
>
> That works fine for me!
>
> FROM: Jones, Andy [mailto:And...@li...]
> SENT: Tuesday, March 22, 2016 2:49 AM
> TO: Mass spectrometry standard development;
> psi...@li...;
> psi...@li...
> SUBJECT: Re: [Psidev-ms-vocab] [Psidev-ms-dev] Proteogenomics update
> in mzid 1.2
>
> Hi all,
>
> I think the 24th is out for various people as an Easter-related
> holiday in some countries. Eric is correct, that time zones will be
> changing.
>
> On the 31st, my preferred slot is actually 4pm British summer time:
>
> http://www.timeanddate.com/worldclock/fixedtime.html?msg=mzid+1.2+call
> &iso=20160331T16&p1=301
> [5]
>
> This would be 8am in Seattle; 5pm Germany;  5pm Norway; (and 4pm in
> the independent nation state of the EBI)
>
> Does this work for everyone?
>
> Best wishes
>
> Andy
>
> FROM: Eric Deutsch [mailto:ede...@sy...]
> SENT: 22 March 2016 03:32
> TO: Mass spectrometry standard development
> <psi...@li...>;
> psi...@li...;
> psi...@li...
> CC: Eric Deutsch <ede...@sy...>
> SUBJECT: Re: [Psidev-ms-dev] Proteogenomics update in mzid 1.2
>
> Thanks, Andy, I like this idea. The times are not good for me,
> however. Normally 4pm London time is 8am Seattle time, but for these
> few weeks, 4pm London time is 9am Seattle time and I have a standing
> meeting I cannot change.
>
> http://www.timeanddate.com/worldclock/fixedtime.html?iso=20160324T16&p
> 1=1440
> [6]
>
> An hour earlier would be fine for the 24th.
>
> I hope I’m not getting confused between 4pm GMT and London local time?
> I think on the 24th 16:00 GMT = 4pm local London, but on the 31st,
> 16:00 GMT is 5pm London time?
>
> Thanks,
>
> Eric
>
> FROM: Jones, Andy [mailto:And...@li...]
> SENT: Monday, March 21, 2016 4:21 AM
> TO: psi...@li...;
> psi...@li...;
> psi...@li...
> SUBJECT: [Psidev-ms-dev] Proteogenomics update in mzid 1.2
>
> Hi all,
>
> Over the coming weeks, I will be trying to get mzid 1.2 largely tied
> up for a final review in Ghent, before we submit the spec doc and
> associated manuscript. I have cross-posted this message (since PSI-PI
> has not been active lately), but probably will drop PSI-MS from the
> list in future. If you’re interested in mzid 1.2, please make sure to
> follow the PSI-PI list.
>
> One feature I would like to add into mzid 1.2 is better support for
> proteogenomics approaches.  There are some parallel efforts to adapt
> genome formats BED and BAM for proteomics (and updates will be
> presented in Ghent I think). It would be nice if the info needed for
> proBed and proBAM was consistently expressed in mzid 1.2 files (mainly
> genome coordinates for peptides).
>
> Along with Juan et al., we have come up with a proposal for how this
> might be done in mzid 1.2. Please see attached. Feel free to annotate
> any comments on the document, or email back to the list any parts you
> feel need adapting or comments for discussion.
>
> It might be useful to have one or two conference calls on mzid 1.2
> before Ghent. How would following dates suit:
>
> -          This Thurs (24th March) at 4pm GMT
>
> -          Next Thurs (31st March) at 4pm GMT
>
> Best wishes
>
> Andy
>
>
>
> Links:
> ------
> [1]
> http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/u
> nit.obo
> [2]
> http://code.google.com/p/ebi-pride/source/browse/trunk/pride-core/sche
> ma/pride_cv.obo
> [3]
> http://www.peptideatlas.org/PSI/schemas/mzIdentML/1.2/mzIdentML1.2.0.h
> tml
> [4]
> http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/
> mzML/controlledVocabulary/psi-ms.obo
> [5]
> http://www.timeanddate.com/worldclock/fixedtime.html?msg=mzid+1.2+call
> &amp;iso=20160331T16&amp;p1=301
> [6]
> http://www.timeanddate.com/worldclock/fixedtime.html?iso=20160324T16&a
> mp;p1=1440
>
> ----------------------------------------------------------------------
> --------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with Intel Data
> Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140
>
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev

Re: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] Proteogenomics update in mzid 1.2

[Harald B. <Har...@ui...>]

Hi Eric,

I've updated the PRIDE and PSI-MS obo URLs for the PeptideShaker 
example. Do you have the new URL for the UO obo file?

As for the other PeptideShaker issues:

> ERROR: cvParam software vendor has a value, but it should not!

Fixed.

> WARNING: MS:1000588 should be 'contact URL' instead of 'contact url'

Fixed.

> ERROR: cvParam Phospho has a value, but it should not!
> ERROR: cvParam Oxidation has a value, but it should not!
> ERROR: cvParam Glu->pyro-Glu has a value, but it should not!
> ERROR: cvParam Carbamidomethyl has a value, but it should not!

Fixed.

Seems like I don't have push access to the new GitHub HUPO-PSI/mzIdentML 
repository, so I've put the updated PeptideShaker example file on 
Dropbox in the meantime: 
https://www.dropbox.com/s/pucr2arc2tknp15/PeptideShaker_mzid_1_2_example.mzid.gz?dl=0

Let me now if you come across other issues with the PeptideShaker 
export.

Best regards,
Harald





Den 2016-04-01 00:40, skrev Eric Deutsch:
> Hi Andy, I fired up the schema generation script and refreshed
> everything based on what’s in github now. You can see the current
> result here:
> 
> http://www.peptideatlas.org/PSI/schemas/mzIdentML/1.2/mzIdentML1.2.0.html
> [3]
> 
> The schema seems pretty fine, but the example files have some issues.
> Here are a few observations of things to fix:
> 
> - Examples files still have older CV URLS like:
> 
> <cv id="PSI-MS"
> uri="http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo
> [4]" version="3.73.0" fullName="PSI-MS"/>
> 
> <cv id="UO"
> uri="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo
> [1]" fullName="UNIT-ONTOLOGY"/>
> 
>     <cv id="PRIDE"
> uri="http://code.google.com/p/ebi-pride/source/browse/trunk/pride-core/schema/pride_cv.obo
> [2]" fullName="PRIDE"/>
> 
> I ran a few of the files through my validator and have the following
> things:
> 
> PeptideShaker_mzid_1_2_example.mzid
> 
> ERROR: cvParam software vendor has a value, but it should not!
> 
> WARNING: MS:1000588 should be 'contact URL' instead of 'contact url'
> 
> ERROR: cvParam Phospho has a value, but it should not!
> 
> ERROR: cvParam Oxidation has a value, but it should not!
> 
> ERROR: cvParam Glu->pyro-Glu has a value, but it should not!
> 
> ERROR: cvParam Carbamidomethyl has a value, but it should not!
> 
> combined_fdr_1.2.mzid
> 
> WARNING: MS:1001400 should be 'OMSSA xml format' instead of 'OMSSA xml
> file'
> 
> WARNING: MS:1001062 should be 'Mascot MGF format' instead of 'Mascot
> MGF file'
> 
> ERROR: cvParam distinct peptide-level q-value should have units, but
> it does not!
> 
> xiFDR-CrossLinkExample.mzid
> 
> WARNING: MS:1002543 should be 'xiFDR' instead of 'XiFDR'
> 
> ERROR: cvParam contact address should have a value, but it does not!
> 
> ERROR: cvParam contact name should have a value, but it does not!
> 
> ERROR: cvParam unknown modification should have a value, but it does
> not!
> 
> This is not exhaustive, but just some results from a first foray into
> this.
> 
> If someone is interested in fixing these things and checking them it,
> I can push further and report other problems.
> 
> Regards,
> 
> Eric
> 
> FROM: Jones, Andy [mailto:And...@li...]
> SENT: Tuesday, March 29, 2016 8:10 AM
> TO: psi...@li...
> CC: psi...@li...
> SUBJECT: Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev]
> Proteogenomics update in mzid 1.2
> 
> Hi all,
> 
> Just confirming we will have a call to discuss mzid 1.2 this coming
> Thurs at 4pm UK time:
> http://www.timeanddate.com/worldclock/fixedtime.html?msg=mzid+1.2+call&iso=20160331T16&p1=301
> [5]
> 
> Agenda:
> 
> 1.       Discussion of encoding proteogenomics results in mzid 1.2
> (review of docs sent previously)
> 
> 2.       General review of mzid 1.2 specifications (attached here) –
> please take a look in advance if you can. We will probably not have
> time for a full review on the call, but we will see how far we get
> 
> 3.       Any other business
> 
> Juan – are you okay to start the call, and if so, can you circulate
> dial-in details?
> 
> Thanks
> 
> Andy
> 
> FROM: Binz Pierre-Alain [mailto:Pie...@ch...]
> SENT: 22 March 2016 15:45
> TO: psi...@li...
> SUBJECT: Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev]
> Proteogenomics update in mzid 1.2
> 
> Fine for me too
> 
> Pierre-Alain
> 
> DE : Eric Deutsch [mailto:ede...@sy...]
> ENVOYÉ : mardi 22 mars 2016 14:53
> À : psi...@li...; Mass spectrometry standard
> development; psi...@li...
> OBJET : Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev]
> Proteogenomics update in mzid 1.2
> 
> That works fine for me!
> 
> FROM: Jones, Andy [mailto:And...@li...]
> SENT: Tuesday, March 22, 2016 2:49 AM
> TO: Mass spectrometry standard development;
> psi...@li...;
> psi...@li...
> SUBJECT: Re: [Psidev-ms-vocab] [Psidev-ms-dev] Proteogenomics update
> in mzid 1.2
> 
> Hi all,
> 
> I think the 24th is out for various people as an Easter-related
> holiday in some countries. Eric is correct, that time zones will be
> changing.
> 
> On the 31st, my preferred slot is actually 4pm British summer time:
> 
> http://www.timeanddate.com/worldclock/fixedtime.html?msg=mzid+1.2+call&iso=20160331T16&p1=301
> [5]
> 
> This would be 8am in Seattle; 5pm Germany;  5pm Norway; (and 4pm in
> the independent nation state of the EBI)
> 
> Does this work for everyone?
> 
> Best wishes
> 
> Andy
> 
> FROM: Eric Deutsch [mailto:ede...@sy...]
> SENT: 22 March 2016 03:32
> TO: Mass spectrometry standard development
> <psi...@li...>;
> psi...@li...;
> psi...@li...
> CC: Eric Deutsch <ede...@sy...>
> SUBJECT: Re: [Psidev-ms-dev] Proteogenomics update in mzid 1.2
> 
> Thanks, Andy, I like this idea. The times are not good for me,
> however. Normally 4pm London time is 8am Seattle time, but for these
> few weeks, 4pm London time is 9am Seattle time and I have a standing
> meeting I cannot change.
> 
> http://www.timeanddate.com/worldclock/fixedtime.html?iso=20160324T16&p1=1440
> [6]
> 
> An hour earlier would be fine for the 24th.
> 
> I hope I’m not getting confused between 4pm GMT and London local
> time? I think on the 24th 16:00 GMT = 4pm local London, but on the
> 31st, 16:00 GMT is 5pm London time?
> 
> Thanks,
> 
> Eric
> 
> FROM: Jones, Andy [mailto:And...@li...]
> SENT: Monday, March 21, 2016 4:21 AM
> TO: psi...@li...;
> psi...@li...;
> psi...@li...
> SUBJECT: [Psidev-ms-dev] Proteogenomics update in mzid 1.2
> 
> Hi all,
> 
> Over the coming weeks, I will be trying to get mzid 1.2 largely tied
> up for a final review in Ghent, before we submit the spec doc and
> associated manuscript. I have cross-posted this message (since PSI-PI
> has not been active lately), but probably will drop PSI-MS from the
> list in future. If you’re interested in mzid 1.2, please make sure
> to follow the PSI-PI list.
> 
> One feature I would like to add into mzid 1.2 is better support for
> proteogenomics approaches.  There are some parallel efforts to adapt
> genome formats BED and BAM for proteomics (and updates will be
> presented in Ghent I think). It would be nice if the info needed for
> proBed and proBAM was consistently expressed in mzid 1.2 files (mainly
> genome coordinates for peptides).
> 
> Along with Juan et al., we have come up with a proposal for how this
> might be done in mzid 1.2. Please see attached. Feel free to annotate
> any comments on the document, or email back to the list any parts you
> feel need adapting or comments for discussion.
> 
> It might be useful to have one or two conference calls on mzid 1.2
> before Ghent. How would following dates suit:
> 
> -          This Thurs (24th March) at 4pm GMT
> 
> -          Next Thurs (31st March) at 4pm GMT
> 
> Best wishes
> 
> Andy
> 
> 
> 
> Links:
> ------
> [1]
> http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo
> [2]
> http://code.google.com/p/ebi-pride/source/browse/trunk/pride-core/schema/pride_cv.obo
> [3] 
> http://www.peptideatlas.org/PSI/schemas/mzIdentML/1.2/mzIdentML1.2.0.html
> [4]
> http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo
> [5]
> http://www.timeanddate.com/worldclock/fixedtime.html?msg=mzid+1.2+call&amp;iso=20160331T16&amp;p1=301
> [6]
> http://www.timeanddate.com/worldclock/fixedtime.html?iso=20160324T16&amp;p1=1440
> 
> ------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140
> 
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev