psidev-ms-dev — Mass spectroscopy standard development

Re: [Psidev-ms-dev] REVISED VERSION: PSI recommendation document (file format mzTab), 30-days public review

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

Dear colleague,
dear member of the Proteomics community,

the success of the PSI standards depend on active input from the community.

It would be great, if you could give some feedback on the mzTab revision 
until Thursday, which I will then assess afterwards together with invited 
reviewer feedback!

See mail with links to the necessary information below.

  Best regards from Bochum
     Martin (PSI Editor)


--
Dr. Martin Eisenacher
Group Leader Bioinformatics / Biostatistics
Medizinisches Proteom-Center (MPC)
Ruhr-Universität Bochum

phone: +49 / 234 / 32 - 29288
fax: +49 / 234 / 32 - 14554
http://www.medizinisches-proteom-center.de/Bioinfo


-----Ursprüngliche Nachricht-----
Von: Martin Eisenacher [mailto:mar...@ru...] 
Gesendet: Montag, 23. Dezember 2013 15:10
An: 'psi...@li...';
'psi...@li...'; 'psi...@eb...'
Cc: 'Andy Jones'
Betreff: REVISED VERSION: PSI recommendation document (file format mzTab),
30-days public review

Dear colleague,
dear member of the Proteomics community,

please forward this message to potentially interested colleagues!

A revised version of the recommendation document specifying the mzTab
file format has been submitted to the PSI document process.
It can be found at http://www.psidev.info/mzTab-in-docproc  

After previous review steps and an unforeseen major restructuring 
("identification / quantification" type, "summary / complete" detail level) 
the proposed document version 1.0, release candidate 5 (file name prefix R3)
now 
goes through 30-days public comments phase (starting after christmas break, 
end: 14th February 2014). 
Also previous commenters will be asked to review the changes.
(Due to the unforeseen restructuring the previous judgement "Final after 
Editor approval" had to be modified.)

The public comment period enables the wider community to provide feedback
on a proposed standard before it is formally accepted, and thus is an
important step in the standardisation process.


PLEASE ADD COMMENTS to the submission page
(http://www.psidev.info/mzTab-in-docproc)
(or send them directly to martin.eisenacher: at : rub.de), especially those
related to the incorporated changes / restructuring.


   Many thanks for your valuable time and participation
     Martin Eisenacher (PSI Editor)

--
Dr. Martin Eisenacher
Group Leader Bioinformatics / Biostatistics
Medizinisches Proteom-Center (MPC)
Ruhr-Universität Bochum

phone: +49 / 234 / 32 - 29288
fax: +49 / 234 / 32 - 14554
http://www.medizinisches-proteom-center.de/

-----Ursprüngliche Nachricht-----
Von: Martin Eisenacher [mailto:mar...@ru...] 
Gesendet: Sonntag, 10. März 2013 23:32
An: psi...@li...;
psi...@li...; psi...@eb...
Cc: 'Andy Jones'
Betreff: [Psidev-pi-dev] REVISED VERSION: PSI recommendation document (file
format mzTab): open for 14-days Public Comment phase

Dear colleague,
dear member of the Proteomics community,

please forward this message to potentially interested colleagues!

A revised version of the recommendation document specifying the mzTab
file format has been submitted to the PSI document process.
It can be found at http://www.psidev.info/mzTab-in-docproc 

After steering committee review and major changes following the public
and external review phase the proposed document version 1.0, release 
candidate 2 (file name prefix R2) now goes through shortened 14-days 
public comments phase (end: 24th March 2013). Also the previous commenters 
will be asked to review the changes.

The public comment period enables the wider community to provide feedback
on a proposed standard before it is formally accepted, and thus is an
important step in the standardisation process.


PLEASE ADD COMMENTS to the submission page
(http://www.psidev.info/mzTab-in-docproc )
(or send them directly to mar...@ru...), especially those
related to the incorporated changes.


   Many thanks for your valuable time and participation
     Martin Eisenacher (PSI Editor)

--
Dr. Martin Eisenacher
Group Leader Bioinformatics / Biostatistics
Medizinisches Proteom-Center (MPC)
Ruhr-Universität Bochum

phone: +49 / 234 / 32 - 29288
fax: +49 / 234 / 32 - 14554
http://www.medizinisches-proteom-center.de/



> -----Ursprüngliche Nachricht-----
> Von: Martin Eisenacher [mailto:mar...@ru...]
> Gesendet: Mittwoch, 17. Oktober 2012 17:17
> An: psi...@li...; psidev-pi-
> de...@li...; 'psi...@eb...'
> Cc: 'Andy Jones'
> Betreff: PROLONGED: submission of PSI recommendation document (mzTab):
> now open for Public Comment
> 
> Dear colleague,
> dear member of the Proteomics community,
> 
> as it was and IS not easy to receive comments from invited reviewers,
> the deadline
> for the mzTab Public and External Comment phase is prolonged (until
> 26th October 2012).
> 
> Please make use of this participation mechanism to improve the standard
> format!
> 
> Even small / short comments are helpful, please motivate colleagues and
> co-workers
> to have a look at specification and / or examples!
> 
>   Best regards
>     Martin Eisenacher (PSI Editor)
> 
> 
> > -----Ursprüngliche Nachricht-----
> > Von: Martin Eisenacher [mailto:mar...@ru...]
> > Gesendet: Montag, 13. August 2012 20:45
> > An: psi...@li...; psidev-pi-
> > de...@li...; 'psi...@eb...'
> > Cc: 'Andy Jones'
> > Betreff: submission of PSI recommendation document (mzTab): now open
> > for Public Comment
> >
> > Dear colleague,
> > dear member of the Proteomics community,
> >
> > please forward this message to potentially interested colleagues!
> >
> > The HUPO Proteomics Standards Initiative (PSI) develops standards
> > for documentation and storage of Proteomics data
> > (see http://www.psidev.info for an overview of activities).
> >
> >
> > A recommendation document specifying the mzTab file format has been
> > submitted to the PSI document process.
> > The submission can be found here: http://www.psidev.info/node/83
> >
> > After having passed a 30-day review of the PSI steering commitee with
> > minor formal changes, the proposed document version 1.0 release
> > candidate
> > now goes through 60-days public comments and external review phase
> > (end: 12th October 2012).
> >
> > "mzTab is intended as a lightweight supplement to the already
> existing
> > standard file formats mzIdentML and mzQuantML, providing a summary
> > of the final results of a MS-based proteomics experiment. mzTab
> > files can contain protein, peptide, and small molecule
> identifications
> > together with basic quantitative information and supports different
> > levels
> > of metadata reporting." (see also Cover Letter submitted)
> >
> > It is important to highlight again that mzTab is not intended to
> store
> > an experiment’s complete data / evidence but only its final reported
> > results.
> >
> > The public comment period enables the wider community to provide
> > feedback
> > on a proposed standard before it is formally accepted, and thus is an
> > important
> > step in the standardisation process.
> >
> >
> > PLEASE ADD COMMENTS to the submission page
> > (http://www.psidev.info/node/83)
> > (or send them directly to martin.eisenacher: at : rub.de) for example
> > regarding the following criteria:
> >
> > - That it is well formed – that is, it is presented in accordance
> with
> > the
> >   templates and is clearly written.
> > - That it is sufficiently detailed and clearly contains and
> > comprehensively
> >   describes the necessary and sufficient explanation of the format.
> > - That the examples are in accordance with the specification.
> >
> > This message is to encourage you to contribute to the standards
> > development
> > activity by commenting on the material that is available online. We
> > invite
> > both positive and negative comments. If negative comments are being
> > made, these
> > could be on the relevance, clarity, correctness, appropriateness,
> etc,
> > of
> > the proposal as a whole or of specific parts of the proposal.
> >
> >    Many thanks for your valuable time and participation
> >      Martin Eisenacher (PSI Editor)
> >
> >
> > --
> > Dr. Martin Eisenacher
> > Group Leader Bioinformatics / Biostatistics
> > Medizinisches Proteom-Center (MPC)
> > Ruhr-Universität Bochum
> >
> > phone: +49 / 234 / 32 - 29288
> > fax: +49 / 234 / 32 - 14554
> > http://www.medizinisches-proteom-center.de/

[Psidev-ms-dev] New version 3.60.0 of psi-ms.obo

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

Dear proteomics community,

attached you find the new version 3.60.0 of the psi-ms.obo file.

It contains new CV terms for the ProteinPilot / Paragon algorithm.


Changed CV terms in version 3.60.0 of psi-ms.obo:
=================================================
************ For the following five terms we removed the relationship
************ is_a: MS:1001405 ! spectrum identification result details,
************ so that they now appear under search engine specific score
MS:1001974 DeBunker:score
MS:1001978 MSQuant:PTM-score
MS:1001979 MaxQuant:PTM Score
MS:1001983 MaxQuant:PTM Delta Score
MS:1001985 Ascore:Ascore


New CV terms in version 3.60.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002421
name: Paragon input parameter
def: "Search engine input parameters specific to Paragon." [PSI:PI]
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002422
name: Paragon: sample type
def: "The Paragon method setting indicating the type of sample at the
high level, generally meaning the type of quantitation labeling or lack
thereof. 'Identification' is indicated for samples without any labels
for quantitation." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter

[Term]
id: MS:1002423
name: Paragon: cysteine alkylation
def: "The Paragon method setting indicating the actual cysteine
alkylation agent; 'None' is indicated if there was no cysteine
alkylation." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter

[Term]
id: MS:1002424
name: Paragon: instrument setting
def: "The Paragon method setting (translating to a large number of lower
level settings) indicating the instrument used or a category of
instrument." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter

[Term]
id: MS:1002425
name: Paragon: search effort
def: "The Paragon method setting that controls the two major modes of
search effort of the Paragon algorithm: the Rapid mode uses a
conventional database search, while the Thorough mode uses a hybrid
search, starting with the same approach as the Rapid mode but then
follows it with a separate tag-based approach enabling a more extensive
search." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter

[Term]
id: MS:1002426
name: Paragon: ID focus
def: "A Paragon method setting that allows the inclusion of large sets
of features such as biological modification or substitutions." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter

[Term]
id: MS:1002427
name: Paragon: FDR analysis
def: "The Paragon method setting that controls whether FDR analysis is
conducted." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter

[Term]
id: MS:1002428
name: Paragon: quantitation
def: "The Paragon method setting that controls whether quantitation
analysis is conducted." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter

[Term]
id: MS:1002429
name: Paragon: background correction
def: "The Paragon method setting that controls whether the 'Background
Correction' analysis is conducted; this processing estimates a
correction to the attenuation in extremity ratios that can occur in
isobaric quantatitation workflows on complex samples." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter

[Term]
id: MS:1002430
name: Paragon: bias correction
def: "The Paragon method setting that controls whether 'Bias Correction'
is invoked in quantitation analysis; this correction is a normalization
to set the central tendency of protein ratios to unity." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter

[Term]
id: MS:1002431
name: Paragon: channel to use as denominator in ratios
def: "The Paragon method setting that controls which label channel is
used as the denominator in calculating relative expression ratios." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter

[Term]
id: MS:1002432
name: search engine specific input metadata
def: "Search engine specific metadata that are not user-controlled
settings." [PSI:PI]
is_a: MS:1001249 ! search input details

[Term]
id: MS:1002433
name: Paragon: modified data dictionary or parameter translation
def: "This metric detects if any changes have been made to the
originally installed key control files for the software; if no changes
have been made, then the software version and settings are sufficient to
enable exact reproduction; if changes have been made, then the modified
ParameterTranslation- and ProteinPilot DataDictionary-XML files much
also be provided in order to exactly reproduce a result." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002432 ! search engine specific input metadata

[Term]
id: MS:1002434
name: number of spectra searched
def: "Number of spectra in a search." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1001249 ! search input details

[Term]
id: MS:1002435
name: data processing start time
def: "The time that a data processing action was started." [PSI:MS]
xref: value-type:xsd\:date "The allowed value-type for this CV term."
is_a: MS:1000630 ! data processing parameter

[Term]
id: MS:1002436
name: Paragon: digestion
def: "The Paragon method setting indicating the actual digestion agent -
unlike other search tools, this setting does not include options that
control partial specificity like 'semitrypsin'; if trypsin is used,
trypsin is set, and partially conforming peptides are found in the
Thorough mode of search; 'None' should be indicated only if there was
really no digestion done." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001249 ! search input details

[Term]
id: MS:1002437
name: number of decoy sequences
def: "The number of decoy sequences, if the concatenated target-decoy
approach is used." [PSI:PI]
xref: value-type:xsd\:positiveInteger "The allowed value-type for this
CV term."
is_a: MS:1001011 ! search database details

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum

Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Release candidate 3.60.0_rc2 of psi-ms.obo

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

Dear proteomics community,

attached you find the release candidate 3.60.0_rc2 of the psi-ms.obo file.

It contains new CV terms for the ProteinPilot / Paragon algorithm.


Changed CV terms in version 3.60.0_rc2 of psi-ms.obo:
=====================================================
************ For the following five terms we removed the relationship
************ is_a: MS:1001405 ! spectrum identification result details,
************ so that they now appear under search engine specific score
MS:1001974 DeBunker:score
MS:1001978 MSQuant:PTM-score
MS:1001979 MaxQuant:PTM Score
MS:1001983 MaxQuant:PTM Delta Score
MS:1001985 Ascore:Ascore

************ Changed the definition: Added
************ " ... but not including decoy sequences, if the
concatenated target-decoy approach is used."
[Term]
id: MS:1001029
name: number of sequences searched
def: "The number of sequences (proteins / nucleotides) from the database
search after filtering but not including decoy sequences, if the
concatenated target-decoy approach is used." [PSI:PI]
xref: value-type:xsd\:positiveInteger "The allowed value-type for this
CV term."
is_a: MS:1001011 ! search database details


New CV terms in version 3.60.0_rc2 of psi-ms.obo:
=================================================
[Term]
id: MS:1002421
name: Paragon input parameter
def: "Search engine input parameters specific to Paragon." [PSI:PI]
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002422
name: Paragon: sample type
def: "The Paragon method setting indicating the type of sample at the
high level, generally meaning the type of quantitation labeling or lack
thereof. 'Identification' is indicated for samples without any labels
for quantitation." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter

[Term]
id: MS:1002423
name: Paragon: cysteine alkylation
def: "The Paragon method setting indicating the actual cysteine
alkylation agent; 'None' is indicated if there was no cysteine
alkylation." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter

[Term]
id: MS:1002424
name: Paragon: instrument setting
def: "The Paragon method setting (translating to a large number of lower
level settings) indicating the instrument used or a category of
instrument." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter

[Term]
id: MS:1002425
name: Paragon: search effort
def: "The Paragon method setting that controls the two major modes of
search effort of the Paragon algorithm: the Rapid mode uses a
conventional database search, while the Thorough mode uses a hybrid
search, starting with the same approach as the Rapid mode but then
follows it with a separate tag-based approach enabling a more extensive
search." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter

[Term]
id: MS:1002426
name: Paragon: ID focus
def: "A Paragon method setting that allows the inclusion of large sets
of features such as biological modification or substitutions." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter

[Term]
id: MS:1002427
name: Paragon: FDR analysis
def: "The Paragon method setting that controls whether FDR analysis is
conducted." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter

[Term]
id: MS:1002428
name: Paragon: quantitation
def: "The Paragon method setting that controls whether quantitation
analysis is conducted." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter

[Term]
id: MS:1002429
name: Paragon: background correction
def: "The Paragon method setting that controls whether the 'Background
Correction' analysis is conducted; this processing estimates a
correction to the attenuation in extremity ratios that can occur in
isobaric quantatitation workflows on complex samples." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter

[Term]
id: MS:1002430
name: Paragon: bias correction
def: "The Paragon method setting that controls whether 'Bias Correction'
is invoked in quantitation analysis; this correction is a normalization
to set the central tendency of protein ratios to unity." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter

[Term]
id: MS:1002431
name: Paragon: channel to use as denominator in ratios
def: "The Paragon method setting that controls which label channel is
used as the denominator in calculating relative expression ratios." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter

[Term]
id: MS:1002432
name: search engine specific input metadata
def: "Search engine specific metadata that are not user-controlled
settings." [PSI:PI]
is_a: MS:1001249 ! search input details

[Term]
id: MS:1002433
name: Paragon: modified data dictionary or parameter translation
def: "This metric detects if any changes have been made to the
originally installed key control files for the software; if no changes
have been made, then the software version and settings are sufficient to
enable exact reproduction; if changes have been made, then the modified
ParameterTranslation- and ProteinPilot DataDictionary-XML files much
also be provided in order to exactly reproduce a result." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002432 ! search engine specific input metadata

[Term]
id: MS:1002434
name: number of spectra searched
def: "Number of spectra in a search." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1001249 ! search input details

[Term]
id: MS:1002435
name: data processing start time
def: "The time that a data processing action was started." [PSI:MS]
xref: value-type:xsd\:date "The allowed value-type for this CV term."
is_a: MS:1000630 ! data processing parameter

[Term]
id: MS:1002436
name: Paragon: digestion
def: "The Paragon method setting indicating the actual digestion agent -
unlike other search tools, this setting does not include options that
control partial specificity like 'semitrypsin'; if trypsin is used,
trypsin is set, and partially conforming peptides are found in the
Thorough mode of search; 'None' should be indicated only if there was
really no digestion done." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001249 ! search input details

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum

Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] New version 3.59.0 of psi-ms.obo

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

Dear proteomics community,

attached you find the new version 3.59.0 of the psi-ms.obo file.

It contains only one updated term and we the put the .obo file
under the Creative Commons Attribution 3.0 licence.

In addition all "has_order" and "has_domain" are now relationships
(this alleviates to read them out in Java), i.e.

has_order: MS:1002108 ! higher score better
is now
relationship: has_order MS:1002108 ! higher score better
and so on.


Changed CV terms in version 3.59.0 of psi-ms.obo:
=================================================
************ Added two is_a relationships to the PIA term
[Term]
id: MS:1002387
name: PIA
def: "PIA - Protein Inference Algorithms, a toolbox for protein
inference and identification analysis." [PSI:PI,
http://www.medizinisches-proteom-center.de/pia]
is_a: MS:1002414 ! postprocessing software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

Best Regards,
Gerhard
-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum

Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Licence for psi-ms.obo / Release candidate 3.59.0_rc1 of psi-ms.obo

[Henning H. <hh...@eb...>]

The Obo Foundry recommends http://creativecommons.org/licenses/by/3.0/
and the terms seem reasonable to me.

On 16/01/2014 16:05, Eric Deutsch wrote:
> Thanks for bringing this up, Gerhard. Since the CV is not really software,
> maybe something like the Create Commons license:
>
> http://en.wikipedia.org/wiki/Creative_Commons_license
>
> would be more appropriate than a software license? I don't know.
>
> Eric
>
>
> -----Original Message-----
> From: Gerhard Mayer [mailto:Ger...@ru...]
> Sent: Thursday, January 16, 2014 6:15 AM
> To: psi...@li...;
> psi...@li...; Mass spectrometry standard
> development
> Subject: [Psidev-ms-vocab] Licence for psi-ms.obo / Release candidate
> 3.59.0_rc1 of psi-ms.obo
>
> Dear proteomics community,
>
> until now we never defined a licence for our psi-ms.obo file.
>
> It would be a good idea to catch up that now.
> I propose to put it under a free copyleft licence.
> Unfortunately I'm not an expert in these juristic things.
>
> Following some links about the different possible licences:
>
> http://en.wikipedia.org/wiki/List_of_software_licenses
> http://en.wikipedia.org/wiki/Software_license#Free_and_open-source_softwar
> e_licenses
> http://opensource.org/licenses
>
> Has someone an idea, which licence would fit best to our needs / aims?
> Any opinions?
>
> I also attached the new release candidate 3.59.0_rc1 of the psi-ms.obo
> file. It contains only one updated term.
>
>
> Changed CV terms in version 3.59.0_rc1 of psi-ms.obo:
> =====================================================
> ************ Added two is_a relationships (MS:1001456 and MS:1001457)
> [Term]
> id: MS:1002387
> name: PIA
> def: "PIA - Protein Inference Algorithms, a toolbox for protein
> inference and identification analysis." [PSI:PI,
> http://www.medizinisches-proteom-center.de/pia]
> is_a: MS:1002414 ! postprocessing software
> is_a: MS:1001456 ! analysis software
> is_a: MS:1001457 ! data processing software
>
>
> Best Regards,
> Gerhard
>
> --
> ---
> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> Bioinformatics / Biostatistics
> Medizinisches-Proteom-Center (MPC)
> Ruhr-Universität Bochum
> Zentrum für klinische Forschung I (ZKF I), E.049a
> Universitätsstraße 150
> D-44801 Bochum
>
> Phone:	+49(0)234/32-21006
> Fax:	+49(0)234/32-14554
> Email:	ger...@ru...
> Web:	http://www.medizinisches-proteom-center.de
>
> --------------------------------------------------------------------------
> ----
> CenturyLink Cloud: The Leader in Enterprise Cloud Services.
> Learn Why More Businesses Are Choosing CenturyLink Cloud For
> Critical Workloads, Development Environments & Everything In Between.
> Get a Quote or Start a Free Trial Today.
> http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clkt
> rk
> _______________________________________________
> Psidev-ms-vocab mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab
>
> ------------------------------------------------------------------------------
> CenturyLink Cloud: The Leader in Enterprise Cloud Services.
> Learn Why More Businesses Are Choosing CenturyLink Cloud For
> Critical Workloads, Development Environments & Everything In Between.
> Get a Quote or Start a Free Trial Today.
> http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>

-- 

Best regards,

Henning

-----------------------------------------------------------------------
Henning Hermjakob
Team Leader Proteomics Services
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494671
Fax: +44 (0)1223 494468
http://www.ebi.ac.uk/proteomics

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Licence for psi-ms.obo / Release candidate 3.59.0_rc1 of psi-ms.obo

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

Thanks for bringing this up, Gerhard. Since the CV is not really software,
maybe something like the Create Commons license:

http://en.wikipedia.org/wiki/Creative_Commons_license

would be more appropriate than a software license? I don't know.

Eric


-----Original Message-----
From: Gerhard Mayer [mailto:Ger...@ru...]
Sent: Thursday, January 16, 2014 6:15 AM
To: psi...@li...;
psi...@li...; Mass spectrometry standard
development
Subject: [Psidev-ms-vocab] Licence for psi-ms.obo / Release candidate
3.59.0_rc1 of psi-ms.obo

Dear proteomics community,

until now we never defined a licence for our psi-ms.obo file.

It would be a good idea to catch up that now.
I propose to put it under a free copyleft licence.
Unfortunately I'm not an expert in these juristic things.

Following some links about the different possible licences:

http://en.wikipedia.org/wiki/List_of_software_licenses
http://en.wikipedia.org/wiki/Software_license#Free_and_open-source_softwar
e_licenses
http://opensource.org/licenses

Has someone an idea, which licence would fit best to our needs / aims?
Any opinions?

I also attached the new release candidate 3.59.0_rc1 of the psi-ms.obo
file. It contains only one updated term.


Changed CV terms in version 3.59.0_rc1 of psi-ms.obo:
=====================================================
************ Added two is_a relationships (MS:1001456 and MS:1001457)
[Term]
id: MS:1002387
name: PIA
def: "PIA - Protein Inference Algorithms, a toolbox for protein
inference and identification analysis." [PSI:PI,
http://www.medizinisches-proteom-center.de/pia]
is_a: MS:1002414 ! postprocessing software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software


Best Regards,
Gerhard

--
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum

Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

--------------------------------------------------------------------------
----
CenturyLink Cloud: The Leader in Enterprise Cloud Services.
Learn Why More Businesses Are Choosing CenturyLink Cloud For
Critical Workloads, Development Environments & Everything In Between.
Get a Quote or Start a Free Trial Today.
http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clkt
rk
_______________________________________________
Psidev-ms-vocab mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab

[Psidev-ms-dev] Licence for psi-ms.obo / Release candidate 3.59.0_rc1 of psi-ms.obo

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

Dear proteomics community,

until now we never defined a licence for our psi-ms.obo file.

It would be a good idea to catch up that now.
I propose to put it under a free copyleft licence.
Unfortunately I'm not an expert in these juristic things.

Following some links about the different possible licences:

http://en.wikipedia.org/wiki/List_of_software_licenses
http://en.wikipedia.org/wiki/Software_license#Free_and_open-source_software_licenses
http://opensource.org/licenses

Has someone an idea, which licence would fit best to our needs / aims?
Any opinions?

I also attached the new release candidate 3.59.0_rc1 of the psi-ms.obo
file. It contains only one updated term.


Changed CV terms in version 3.59.0_rc1 of psi-ms.obo:
=====================================================
************ Added two is_a relationships (MS:1001456 and MS:1001457)
[Term]
id: MS:1002387
name: PIA
def: "PIA - Protein Inference Algorithms, a toolbox for protein
inference and identification analysis." [PSI:PI,
http://www.medizinisches-proteom-center.de/pia]
is_a: MS:1002414 ! postprocessing software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software


Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum

Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Isotopic peaks

[Babylakshmi M. <bab...@gm...>]

Hi,

In order to calculate iBAQ values using mzML  files, I would like isotopic
peak intensitity at MS level. I am afraid, I am not finding this
information through out the mzML documentation. I would appreciate if
someone helps me  locating the  tags where isotopic intensity values for
every scan are provided in the mzML file.

Thanks,
Babylakshmi

-- 
Babylakshmi Muthusamy
Ph.D. student
Institute of Bioinformatics
7th Floor, Discoverer Building
International Technology Park
Bangalore - 560 066
India
Ph: +91-80-28416140

[Psidev-ms-dev] REVISED VERSION: PSI recommendation document (file format mzTab), 30-days public review

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

Dear colleague,
dear member of the Proteomics community,

please forward this message to potentially interested colleagues!

A revised version of the recommendation document specifying the mzTab
file format has been submitted to the PSI document process.
It can be found at http://www.psidev.info/mzTab-in-docproc 

After previous review steps and an unforeseen major restructuring 
("identification / quantification" type, "summary / complete" detail level) 
the proposed document version 1.0, release candidate 5 (file name prefix R3)
now 
goes through 30-days public comments phase (starting after christmas break, 
end: 14th February 2014). 
Also previous commenters will be asked to review the changes.
(Due to the unforeseen restructuring the previous judgement "Final after 
Editor approval" had to be modified.)

The public comment period enables the wider community to provide feedback
on a proposed standard before it is formally accepted, and thus is an
important step in the standardisation process.


PLEASE ADD COMMENTS to the submission page
(http://www.psidev.info/mzTab-in-docproc)
(or send them directly to martin.eisenacher: at : rub.de), especially those
related to the incorporated changes / restructuring.


   Many thanks for your valuable time and participation
     Martin Eisenacher (PSI Editor)

--
Dr. Martin Eisenacher
Group Leader Bioinformatics / Biostatistics
Medizinisches Proteom-Center (MPC)
Ruhr-Universität Bochum

phone: +49 / 234 / 32 - 29288
fax: +49 / 234 / 32 - 14554
http://www.medizinisches-proteom-center.de/

-----Ursprüngliche Nachricht-----
Von: Martin Eisenacher [mailto:mar...@ru...] 
Gesendet: Sonntag, 10. März 2013 23:32
An: psi...@li...;
psi...@li...; psi...@eb...
Cc: 'Andy Jones'
Betreff: [Psidev-pi-dev] REVISED VERSION: PSI recommendation document (file
format mzTab): open for 14-days Public Comment phase

Dear colleague,
dear member of the Proteomics community,

please forward this message to potentially interested colleagues!

A revised version of the recommendation document specifying the mzTab
file format has been submitted to the PSI document process.
It can be found at http://www.psidev.info/mzTab-in-docproc 

After steering committee review and major changes following the public
and external review phase the proposed document version 1.0, release 
candidate 2 (file name prefix R2) now goes through shortened 14-days 
public comments phase (end: 24th March 2013). Also the previous commenters 
will be asked to review the changes.

The public comment period enables the wider community to provide feedback
on a proposed standard before it is formally accepted, and thus is an
important step in the standardisation process.


PLEASE ADD COMMENTS to the submission page
(http://www.psidev.info/mzTab-in-docproc )
(or send them directly to mar...@ru...), especially those
related to the incorporated changes.


   Many thanks for your valuable time and participation
     Martin Eisenacher (PSI Editor)

--
Dr. Martin Eisenacher
Group Leader Bioinformatics / Biostatistics
Medizinisches Proteom-Center (MPC)
Ruhr-Universität Bochum

phone: +49 / 234 / 32 - 29288
fax: +49 / 234 / 32 - 14554
http://www.medizinisches-proteom-center.de/



> -----Ursprüngliche Nachricht-----
> Von: Martin Eisenacher [mailto:mar...@ru...]
> Gesendet: Mittwoch, 17. Oktober 2012 17:17
> An: psi...@li...; psidev-pi-
> de...@li...; 'psi...@eb...'
> Cc: 'Andy Jones'
> Betreff: PROLONGED: submission of PSI recommendation document (mzTab):
> now open for Public Comment
> 
> Dear colleague,
> dear member of the Proteomics community,
> 
> as it was and IS not easy to receive comments from invited reviewers,
> the deadline
> for the mzTab Public and External Comment phase is prolonged (until
> 26th October 2012).
> 
> Please make use of this participation mechanism to improve the standard
> format!
> 
> Even small / short comments are helpful, please motivate colleagues and
> co-workers
> to have a look at specification and / or examples!
> 
>   Best regards
>     Martin Eisenacher (PSI Editor)
> 
> 
> > -----Ursprüngliche Nachricht-----
> > Von: Martin Eisenacher [mailto:mar...@ru...]
> > Gesendet: Montag, 13. August 2012 20:45
> > An: psi...@li...; psidev-pi-
> > de...@li...; 'psi...@eb...'
> > Cc: 'Andy Jones'
> > Betreff: submission of PSI recommendation document (mzTab): now open
> > for Public Comment
> >
> > Dear colleague,
> > dear member of the Proteomics community,
> >
> > please forward this message to potentially interested colleagues!
> >
> > The HUPO Proteomics Standards Initiative (PSI) develops standards
> > for documentation and storage of Proteomics data
> > (see http://www.psidev.info for an overview of activities).
> >
> >
> > A recommendation document specifying the mzTab file format has been
> > submitted to the PSI document process.
> > The submission can be found here: http://www.psidev.info/node/83
> >
> > After having passed a 30-day review of the PSI steering commitee with
> > minor formal changes, the proposed document version 1.0 release
> > candidate
> > now goes through 60-days public comments and external review phase
> > (end: 12th October 2012).
> >
> > "mzTab is intended as a lightweight supplement to the already
> existing
> > standard file formats mzIdentML and mzQuantML, providing a summary
> > of the final results of a MS-based proteomics experiment. mzTab
> > files can contain protein, peptide, and small molecule
> identifications
> > together with basic quantitative information and supports different
> > levels
> > of metadata reporting." (see also Cover Letter submitted)
> >
> > It is important to highlight again that mzTab is not intended to
> store
> > an experiment’s complete data / evidence but only its final reported
> > results.
> >
> > The public comment period enables the wider community to provide
> > feedback
> > on a proposed standard before it is formally accepted, and thus is an
> > important
> > step in the standardisation process.
> >
> >
> > PLEASE ADD COMMENTS to the submission page
> > (http://www.psidev.info/node/83)
> > (or send them directly to martin.eisenacher: at : rub.de) for example
> > regarding the following criteria:
> >
> > - That it is well formed – that is, it is presented in accordance
> with
> > the
> >   templates and is clearly written.
> > - That it is sufficiently detailed and clearly contains and
> > comprehensively
> >   describes the necessary and sufficient explanation of the format.
> > - That the examples are in accordance with the specification.
> >
> > This message is to encourage you to contribute to the standards
> > development
> > activity by commenting on the material that is available online. We
> > invite
> > both positive and negative comments. If negative comments are being
> > made, these
> > could be on the relevance, clarity, correctness, appropriateness,
> etc,
> > of
> > the proposal as a whole or of specific parts of the proposal.
> >
> >    Many thanks for your valuable time and participation
> >      Martin Eisenacher (PSI Editor)
> >
> >
> > --
> > Dr. Martin Eisenacher
> > Group Leader Bioinformatics / Biostatistics
> > Medizinisches Proteom-Center (MPC)
> > Ruhr-Universität Bochum
> >
> > phone: +49 / 234 / 32 - 29288
> > fax: +49 / 234 / 32 - 14554
> > http://www.medizinisches-proteom-center.de/

[Psidev-ms-dev] New version 3.58.0 of psi-ms.obo

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

Dear proteomics community,

attached there's the new version 3.58.0 of
the psi-ms.obo file.

It contains new terms for protein grouping, for the encoding
of SRM in mzQuantML files and for some new Thermo Scientific
instrument models.

Terms under 'intermediate analysis format' and
'mass spectrometer file format' are now renamed
from '... file' into '... format'


Changed CV terms in version 3.58.0 of psi-ms.obo:
=================================================
************ Added is_a relationship:
************ is_a: MS:1001139 ! quantitation software name
[Term]
id: MS:1000922
name: Skyline
def: "Software used to predict, select, and optimize transitions as well
as analyze the results of selected reaction monitoring runs developed
and distributed by the MacCoss lab at the University of Washington."
[https://brendanx-uw1.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=default
""]
is_a: MS:1000871 ! SRM software
is_a: MS:1001139 ! quantitation software name

************ Added value type for the next 2 terms:
************ value xsd\:anyURI
[Term]
id: MS:1002031
name: PASSEL transition group browser URI
def: "URI to retrieve transition group data for a PASSEL (PeptideAtlas
SRM Experiment Library) experiment." [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:1002032
name: PeptideAtlas dataset URI
def: "URI that allows access to a PeptideAtlas dataset." [PSI:PI]
xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier

************ PIA is now a postprocessing software
[Term]
id: MS:1002387
name: PIA
def: "PIA - Protein Inference Algorithms, a toolbox for protein
inference and identification analysis." [PSI:PI,
http://www.medizinisches-proteom-center.de/pia]
is_a: MS:1002414 ! postprocessing software

************ Renamed:
************ identification file format attribute --> identification
file format
************ and changed is_a from quantification object attribute -->
file format
[Term]
id: MS:1002130
name: identification file format
def: "Attribute describing an identification file format." [PSI:PI]
is_a: MS:1001459 ! file format

************ Renamed:
************ method file format attribute --> method file format
************ and changed is_a: quantification object attribute --> file
format
[Term]
id: MS:1002128
name: method file format attribute
def: "Attribute describing a method file format." [PSI:PI]
is_a: MS:1001459 ! file format

************ Renamed:
************ tab delimited text file --> tab delimited text format
[Term]
id: MS:1000914
name: tab delimited text format
def: "A file format that has two or more columns of tabular data where
each column is separated by a TAB character." [PSI:MS]
is_a: MS:1001459 ! file format
is_a: MS:1001040 ! intermediate analysis format

********** Renamed:
********** mzIdentML --> mzIdentML format
********** added URl to the Dbxref list
[Term]
id: MS:1002073
name: mzIdentML format
def: "The mzIdentML format for peptide and protein identification data
from the PSI. File extension '.mzid'." [PSI:PI,
http://www.psidev.info/mzidentml]
is_a: MS:1001040 ! intermediate analysis format

********** Renamed:
********** mzQuantML --> mzQuantML format
********** added URl to the Dbxref list
[Term]
id: MS:1002075
name: mzQuantML format
def: "The mzQuantML format for quantification data from the PSI. File
extension '.mzq'." [PSI:PI, http://www.psidev.info/mzquantml]
is_a: MS:1002074 ! quantification file format

************ Renamed the following 'intermediate analysis format' terms:
************ '... file' --> '... format'
Bioworks SRF file	--> Bioworks SRF format
DTASelect file		--> DTASelect format
Mascot DAT file		--> Mascot DAT format
OMSSA csv file		--> OMSSA csv format
OMSSA xml file		--> OMSSA xml format
MS2 file			--> MS2 file format
pepXML file			--> pepXML format
PIA XML file		--> PIA XML format
protXML file		--> protXML format
X!Tandem xml file	--> X!Tandem xml format
Discoverer MSF		--> Discoverer MSF format
IdentityE XML		--> IdentityE XML format
ProteinLynx XML		--> ProteinLynx XML format
SEQUEST SQT			--> SEQUEST SQT format
SEQUEST out file	--> SEQUEST out file format

************ Renamed the following 'mass spectrometer file format' terms:
************ '... file' --> '... format'
AB SCIEX TOF/TOF T2D file	--> AB SCIEX TOF/TOF T2D format
ABI WIFF file			--> ABI WIFF format
Agilent MassHunter file	--> Agilent MassHunter format
Bruker BAF file			--> Bruker BAF format
Bruker Container file	--> Bruker Container format
Bruker FID file			--> Bruker FID format
Bruker U2 file			--> Bruker U2 format
Bruker XML file			--> Bruker XML format
Bruker/Agilent YEP file	--> Bruker/Agilent YEP format
DTA file				--> DTA format
ISB mzXML file			--> ISB mzXML format
Mascot MGF file			--> Mascot MGF format
Micromass PKL file		--> Micromass PKL format
mz5 file				--> mz5 format
mzML file				--> mzML format
PerSeptive PKS file		--> PerSeptive PKS format
ProteinLynx Global Server mass spectrum XML file -- ProteinLynx Global
Server mass spectrum XML format
PSI mzData file			--> PSI mzData format
Sciex API III file		--> Sciex API III format
SCiLS Lab file			--> SCiLS Lab format
text file				--> text format
Thermo RAW file			--> Thermo RAW format
Waters raw file			--> Waters raw format



New CV terms in version 3.58.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002401
name: leading protein
def: "At least one protein within each group should be annotated as a
leading protein to indicate it has the strongest evidence, or
approximately equal evidence as other group members." [PSI:PI]
is_a: MS:1001101 ! protein group or subset relationship

[Term]
id: MS:1002402
name: non-leading protein
def: "Zero to many proteins within each group should be annotated as
non-leading to indicate that other proteins have stronger evidence."
[PSI:PI]
is_a: MS:1001101 ! protein group or subset relationship

[Term]
id: MS:1002403
name: group representative
def: "An arbitrary and optional flag applied to exactly one protein per
group to indicate it can serve as the representative of the group,
amongst leading proteins, in effect serving as a tiebreaker for
approaches that require exactly one group representative." [PSI:PI]
is_a: MS:1001101 ! protein group or subset relationship

[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

[Term]
id: MS:1002405
name: protein cluster details
def: "Details describing a protein cluster." [PSI:PI]
is_a: MS:1001085 ! protein result details

[Term]
id: MS:1002406
name: count of identified clusters
def: "The number of protein clusters that have been identified, which
must match the number of clusters 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:1002405 ! protein cluster details

[Term]
id: MS:1002407
name: cluster identifier
def: "An identifier applied to protein groups to indicate that they are
linked by shared peptides." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1001147 ! protein ambiguity group result details

[Term]
id: MS:1002408
name: number of distinct protein sequences
def: "The number of protein clusters that have been identified, which
must match the number of clusters 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:1002405 ! protein cluster details

[Term]
id: MS:1002409
name: marginally distinguished protein
def: "Assigned to a non-leading protein that has some independent
evidence to support its presence relative to the leading protein(s),
e.g. the protein may have a unique peptide but not sufficient to be
promoted as a leading protein of another group." [PSI:PI]
is_a: MS:1001101 ! protein group or subset relationship

[Term]
id: MS:1002410
name: Anubis
def: "Anubis software for selected reaction monitoring data." [PSI:PI,
http://quantitativeproteomics.org/anubis]
is_a: MS:1000871 ! SRM software
is_a: MS:1001139 ! quantitation software name

[Term]
id: MS:1002411
name: TraML format
def: "The TraML format for transitions in SRM from the PSI. File
extension '.TraML'." [PSI:PI,  http://www.psidev.info/traml]
is_a: MS:1002128 ! method file format

[Term]
id: MS:1002412
name: total XIC area
def: "Summed area of all the extracted ion chromatogram for the peptide
(e.g. of all the transitions in SRM)." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002413
name: product background
def: "The background area for the quantified transition." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002414
name: postprocessing software
def: "Postprocessing software." [PSI:PI]
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002415
name: protein group passes threshold
def: "A Boolean attribute to determine whether the protein group has
passed the threshold indicated in the file." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001147 ! protein ambiguity group result details

[Term]
id: MS:1002416
name: Orbitrap Fusion
def: "Thermo Scientific Orbitrap Fusion." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1002417
name: Orbitrap Fusion ETD
def: "Thermo Scientific Orbitrap Fusion with ETD." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1002418
name: TSQ Quantiva
def: "Thermo Scientific TSQ Quantiva MS." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1002419
name: TSQ Endura
def: "Thermo Scientific TSQ Endura MS." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1002420
name: PASSEL experiment URI
def: "URI that allows access to a PASSEL experiment." [PSI:PI]
xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.049a
Universitätsstraße 150
D-44801 Bochum

Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] Release candidate 3.58.0_rc2 of psi-ms.obo

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

Many thanks for your diligent efforts, Gerhard! This all looks good to me.

Thanks,
Eric


-----Original Message-----
From: Gerhard Mayer [mailto:Ger...@ru...]
Sent: Monday, December 16, 2013 8:18 AM
To: psi...@li...;
psi...@li...; Mass spectrometry standard
development
Subject: [Psidev-ms-dev] Release candidate 3.58.0_rc2 of psi-ms.obo

Dear proteomics community,

attached there's the release candidate 3.58.0_rc2 of
the psi-ms.obo file.

It contains new terms for protein grouping, for the encoding
of SRM in mzQuantML files and for some new Thermo Scientific
instrument models.

Terms under 'intermediate analysis format' and
'mass spectrometer file format' are now renamed
from '... file' into '... format'


Changed CV terms in version 3.58.0_rc2 of psi-ms.obo:
=====================================================
************ Added is_a relationship:
************ is_a: MS:1001139 ! quantitation software name
[Term]
id: MS:1000922
name: Skyline
def: "Software used to predict, select, and optimize transitions as well
as analyze the results of selected reaction monitoring runs developed
and distributed by the MacCoss lab at the University of Washington."
[https://brendanx-uw1.gs.washington.edu/labkey/wiki/home/software/Skyline/
page.view?name=default
""]
is_a: MS:1000871 ! SRM software
is_a: MS:1001139 ! quantitation software name

************ Added value type for the next 2 terms:
************ value xsd\:anyURI
[Term]
id: MS:1002031
name: PASSEL transition group browser URI
def: "URI to retrieve transition group data for a PASSEL (PeptideAtlas
SRM Experiment Library) experiment." [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:1002032
name: PeptideAtlas dataset URI
def: "URI that allows access to a PeptideAtlas dataset." [PSI:PI]
xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier

************ PIA is now a postprocessing software
[Term]
id: MS:1002387
name: PIA
def: "PIA - Protein Inference Algorithms, a toolbox for protein
inference and identification analysis." [PSI:PI,
http://www.medizinisches-proteom-center.de/pia]
is_a: MS:1002414 ! postprocessing software

************ Renamed:
************ identification file format attribute --> identification
file format
************ and changed is_a from quantification object attribute -->
file format
[Term]
id: MS:1002130
name: identification file format
def: "Attribute describing an identification file format." [PSI:PI]
is_a: MS:1001459 ! file format

************ Renamed:
************ method file format attribute --> method file format
************ and changed is_a: quantification object attribute --> file
format
[Term]
id: MS:1002128
name: method file format attribute
def: "Attribute describing a method file format." [PSI:PI]
is_a: MS:1001459 ! file format

************ Renamed:
************ tab delimited text file --> tab delimited text format
[Term]
id: MS:1000914
name: tab delimited text format
def: "A file format that has two or more columns of tabular data where
each column is separated by a TAB character." [PSI:MS]
is_a: MS:1001459 ! file format
is_a: MS:1001040 ! intermediate analysis format

********** Renamed:
********** mzIdentML --> mzIdentML format
********** added URl to the Dbxref list
[Term]
id: MS:1002073
name: mzIdentML format
def: "The mzIdentML format for peptide and protein identification data
from the PSI. File extension '.mzid'." [PSI:PI,
http://www.psidev.info/mzidentml]
is_a: MS:1001040 ! intermediate analysis format

********** Renamed:
********** mzQuantML --> mzQuantML format
********** added URl to the Dbxref list
[Term]
id: MS:1002075
name: mzQuantML format
def: "The mzQuantML format for quantification data from the PSI. File
extension '.mzq'." [PSI:PI, http://www.psidev.info/mzquantml]
is_a: MS:1002074 ! quantification file format

************ Renamed the following 'intermediate analysis format' terms:
************ '... file' --> '... format'
Bioworks SRF file	--> Bioworks SRF format
DTASelect file		--> DTASelect format
Mascot DAT file		--> Mascot DAT format
OMSSA csv file		--> OMSSA csv format
OMSSA xml file		--> OMSSA xml format
MS2 file			--> MS2 file format
pepXML file			--> pepXML format
PIA XML file		--> PIA XML format
protXML file		--> protXML format
X!Tandem xml file	--> X!Tandem xml format
Discoverer MSF		--> Discoverer MSF format
IdentityE XML		--> IdentityE XML format
ProteinLynx XML		--> ProteinLynx XML format
SEQUEST SQT			--> SEQUEST SQT format
SEQUEST out file	--> SEQUEST out file format

************ Renamed the following 'mass spectrometer file format' terms:
************ '... file' --> '... format'
AB SCIEX TOF/TOF T2D file	--> AB SCIEX TOF/TOF T2D format
ABI WIFF file			--> ABI WIFF format
Agilent MassHunter file	--> Agilent MassHunter format
Bruker BAF file			--> Bruker BAF format
Bruker Container file	--> Bruker Container format
Bruker FID file			--> Bruker FID format
Bruker U2 file			--> Bruker U2 format
Bruker XML file			--> Bruker XML format
Bruker/Agilent YEP file	--> Bruker/Agilent YEP format
DTA file				--> DTA format
ISB mzXML file			--> ISB mzXML format
Mascot MGF file			--> Mascot MGF format
Micromass PKL file		--> Micromass PKL format
mz5 file				--> mz5 format
mzML file				--> mzML format
PerSeptive PKS file		--> PerSeptive PKS format
ProteinLynx Global Server mass spectrum XML file -- ProteinLynx Global
Server mass spectrum XML format
PSI mzData file			--> PSI mzData format
Sciex API III file		--> Sciex API III format
SCiLS Lab file			--> SCiLS Lab format
text file				--> text format
Thermo RAW file			--> Thermo RAW format
Waters raw file			--> Waters raw format



New CV terms in version 3.58.0_rc2 of psi-ms.obo:
=================================================
[Term]
id: MS:1002401
name: leading protein
def: "At least one protein within each group should be annotated as a
leading protein to indicate it has the strongest evidence, or
approximately equal evidence as other group members." [PSI:PI]
is_a: MS:1001101 ! protein group or subset relationship

[Term]
id: MS:1002402
name: non-leading protein
def: "Zero to many proteins within each group should be annotated as
non-leading to indicate that other proteins have stronger evidence."
[PSI:PI]
is_a: MS:1001101 ! protein group or subset relationship

[Term]
id: MS:1002403
name: group representative
def: "An arbitrary and optional flag applied to exactly one protein per
group to indicate it can serve as the representative of the group,
amongst leading proteins, in effect serving as a tiebreaker for
approaches that require exactly one group representative." [PSI:PI]
is_a: MS:1001101 ! protein group or subset relationship

[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

[Term]
id: MS:1002405
name: protein cluster details
def: "Details describing a protein cluster." [PSI:PI]
is_a: MS:1001085 ! protein result details

[Term]
id: MS:1002406
name: count of identified clusters
def: "The number of protein clusters that have been identified, which
must match the number of clusters 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:1002405 ! protein cluster details

[Term]
id: MS:1002407
name: cluster identifier
def: "An identifier applied to protein groups to indicate that they are
linked by shared peptides." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1001147 ! protein ambiguity group result details

[Term]
id: MS:1002408
name: number of distinct protein sequences
def: "The number of protein clusters that have been identified, which
must match the number of clusters 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:1002405 ! protein cluster details

[Term]
id: MS:1002409
name: Marginally distinguished protein
def: "Assigned to a non-leading protein that has some independent
evidence to support its presence relative to the leading protein(s),
e.g. the protein may have a unique peptide but not sufficient to be
promoted as a leading protein of another group." [PSI:PI]
is_a: MS:1001101 ! protein group or subset relationship

[Term]
id: MS:1002410
name: Anubis
def: "Anubis software for selected reaction monitoring data." [PSI:PI,
http://quantitativeproteomics.org/anubis]
is_a: MS:1000871 ! SRM software
is_a: MS:1001139 ! quantitation software name

[Term]
id: MS:1002411
name: TraML format
def: "The TraML format for transitions in SRM from the PSI. File
extension '.TraML'." [PSI:PI,  http://www.psidev.info/traml]
is_a: MS:1002128 ! method file format

[Term]
id: MS:1002412
name: total XIC area
def: "Summed area of all the extracted ion chromatogram for the peptide
(e.g. of all the transitions in SRM)." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002413
name: product background
def: "The background area for the quantified transition." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002414
name: postprocessing software
def: "Postprocessing software." [PSI:PI]
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002415
name: protein group passes threshold
def: "A Boolean attribute to determine whether the protein group has
passed the threshold indicated in the file." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001147 ! protein ambiguity group result details

[Term]
id: MS:1002416
name: Orbitrap Fusion
def: "Thermo Scientific Orbitrap Fusion." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1002417
name: Orbitrap Fusion ETD
def: "Thermo Scientific Orbitrap Fusion with ETD." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1002418
name: TSQ Quantiva
def: "Thermo Scientific TSQ Quantiva MS." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1002419
name: TSQ Endura
def: "Thermo Scientific TSQ Endura MS." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1002420
name: PASSEL experiment URI
def: "URI that allows access to a PASSEL experiment." [PSI:PI]
xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier

Best Regards,
Gerhard

--
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.049a
Universitätsstraße 150
D-44801 Bochum

Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Release candidate 3.58.0_rc2 of psi-ms.obo

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

Dear proteomics community,

attached there's the release candidate 3.58.0_rc2 of
the psi-ms.obo file.

It contains new terms for protein grouping, for the encoding
of SRM in mzQuantML files and for some new Thermo Scientific
instrument models.

Terms under 'intermediate analysis format' and
'mass spectrometer file format' are now renamed
from '... file' into '... format'


Changed CV terms in version 3.58.0_rc2 of psi-ms.obo:
=====================================================
************ Added is_a relationship:
************ is_a: MS:1001139 ! quantitation software name
[Term]
id: MS:1000922
name: Skyline
def: "Software used to predict, select, and optimize transitions as well
as analyze the results of selected reaction monitoring runs developed
and distributed by the MacCoss lab at the University of Washington."
[https://brendanx-uw1.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=default
""]
is_a: MS:1000871 ! SRM software
is_a: MS:1001139 ! quantitation software name

************ Added value type for the next 2 terms:
************ value xsd\:anyURI
[Term]
id: MS:1002031
name: PASSEL transition group browser URI
def: "URI to retrieve transition group data for a PASSEL (PeptideAtlas
SRM Experiment Library) experiment." [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:1002032
name: PeptideAtlas dataset URI
def: "URI that allows access to a PeptideAtlas dataset." [PSI:PI]
xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier

************ PIA is now a postprocessing software
[Term]
id: MS:1002387
name: PIA
def: "PIA - Protein Inference Algorithms, a toolbox for protein
inference and identification analysis." [PSI:PI,
http://www.medizinisches-proteom-center.de/pia]
is_a: MS:1002414 ! postprocessing software

************ Renamed:
************ identification file format attribute --> identification
file format
************ and changed is_a from quantification object attribute -->
file format
[Term]
id: MS:1002130
name: identification file format
def: "Attribute describing an identification file format." [PSI:PI]
is_a: MS:1001459 ! file format

************ Renamed:
************ method file format attribute --> method file format
************ and changed is_a: quantification object attribute --> file
format
[Term]
id: MS:1002128
name: method file format attribute
def: "Attribute describing a method file format." [PSI:PI]
is_a: MS:1001459 ! file format

************ Renamed:
************ tab delimited text file --> tab delimited text format
[Term]
id: MS:1000914
name: tab delimited text format
def: "A file format that has two or more columns of tabular data where
each column is separated by a TAB character." [PSI:MS]
is_a: MS:1001459 ! file format
is_a: MS:1001040 ! intermediate analysis format

********** Renamed:
********** mzIdentML --> mzIdentML format
********** added URl to the Dbxref list
[Term]
id: MS:1002073
name: mzIdentML format
def: "The mzIdentML format for peptide and protein identification data
from the PSI. File extension '.mzid'." [PSI:PI,
http://www.psidev.info/mzidentml]
is_a: MS:1001040 ! intermediate analysis format

********** Renamed:
********** mzQuantML --> mzQuantML format
********** added URl to the Dbxref list
[Term]
id: MS:1002075
name: mzQuantML format
def: "The mzQuantML format for quantification data from the PSI. File
extension '.mzq'." [PSI:PI, http://www.psidev.info/mzquantml]
is_a: MS:1002074 ! quantification file format

************ Renamed the following 'intermediate analysis format' terms:
************ '... file' --> '... format'
Bioworks SRF file	--> Bioworks SRF format
DTASelect file		--> DTASelect format
Mascot DAT file		--> Mascot DAT format
OMSSA csv file		--> OMSSA csv format
OMSSA xml file		--> OMSSA xml format
MS2 file			--> MS2 file format
pepXML file			--> pepXML format
PIA XML file		--> PIA XML format
protXML file		--> protXML format
X!Tandem xml file	--> X!Tandem xml format
Discoverer MSF		--> Discoverer MSF format
IdentityE XML		--> IdentityE XML format
ProteinLynx XML		--> ProteinLynx XML format
SEQUEST SQT			--> SEQUEST SQT format
SEQUEST out file	--> SEQUEST out file format

************ Renamed the following 'mass spectrometer file format' terms:
************ '... file' --> '... format'
AB SCIEX TOF/TOF T2D file	--> AB SCIEX TOF/TOF T2D format
ABI WIFF file			--> ABI WIFF format
Agilent MassHunter file	--> Agilent MassHunter format
Bruker BAF file			--> Bruker BAF format
Bruker Container file	--> Bruker Container format
Bruker FID file			--> Bruker FID format
Bruker U2 file			--> Bruker U2 format
Bruker XML file			--> Bruker XML format
Bruker/Agilent YEP file	--> Bruker/Agilent YEP format
DTA file				--> DTA format
ISB mzXML file			--> ISB mzXML format
Mascot MGF file			--> Mascot MGF format
Micromass PKL file		--> Micromass PKL format
mz5 file				--> mz5 format
mzML file				--> mzML format
PerSeptive PKS file		--> PerSeptive PKS format
ProteinLynx Global Server mass spectrum XML file -- ProteinLynx Global
Server mass spectrum XML format
PSI mzData file			--> PSI mzData format
Sciex API III file		--> Sciex API III format
SCiLS Lab file			--> SCiLS Lab format
text file				--> text format
Thermo RAW file			--> Thermo RAW format
Waters raw file			--> Waters raw format



New CV terms in version 3.58.0_rc2 of psi-ms.obo:
=================================================
[Term]
id: MS:1002401
name: leading protein
def: "At least one protein within each group should be annotated as a
leading protein to indicate it has the strongest evidence, or
approximately equal evidence as other group members." [PSI:PI]
is_a: MS:1001101 ! protein group or subset relationship

[Term]
id: MS:1002402
name: non-leading protein
def: "Zero to many proteins within each group should be annotated as
non-leading to indicate that other proteins have stronger evidence."
[PSI:PI]
is_a: MS:1001101 ! protein group or subset relationship

[Term]
id: MS:1002403
name: group representative
def: "An arbitrary and optional flag applied to exactly one protein per
group to indicate it can serve as the representative of the group,
amongst leading proteins, in effect serving as a tiebreaker for
approaches that require exactly one group representative." [PSI:PI]
is_a: MS:1001101 ! protein group or subset relationship

[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

[Term]
id: MS:1002405
name: protein cluster details
def: "Details describing a protein cluster." [PSI:PI]
is_a: MS:1001085 ! protein result details

[Term]
id: MS:1002406
name: count of identified clusters
def: "The number of protein clusters that have been identified, which
must match the number of clusters 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:1002405 ! protein cluster details

[Term]
id: MS:1002407
name: cluster identifier
def: "An identifier applied to protein groups to indicate that they are
linked by shared peptides." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1001147 ! protein ambiguity group result details

[Term]
id: MS:1002408
name: number of distinct protein sequences
def: "The number of protein clusters that have been identified, which
must match the number of clusters 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:1002405 ! protein cluster details

[Term]
id: MS:1002409
name: Marginally distinguished protein
def: "Assigned to a non-leading protein that has some independent
evidence to support its presence relative to the leading protein(s),
e.g. the protein may have a unique peptide but not sufficient to be
promoted as a leading protein of another group." [PSI:PI]
is_a: MS:1001101 ! protein group or subset relationship

[Term]
id: MS:1002410
name: Anubis
def: "Anubis software for selected reaction monitoring data." [PSI:PI,
http://quantitativeproteomics.org/anubis]
is_a: MS:1000871 ! SRM software
is_a: MS:1001139 ! quantitation software name

[Term]
id: MS:1002411
name: TraML format
def: "The TraML format for transitions in SRM from the PSI. File
extension '.TraML'." [PSI:PI,  http://www.psidev.info/traml]
is_a: MS:1002128 ! method file format

[Term]
id: MS:1002412
name: total XIC area
def: "Summed area of all the extracted ion chromatogram for the peptide
(e.g. of all the transitions in SRM)." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002413
name: product background
def: "The background area for the quantified transition." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002414
name: postprocessing software
def: "Postprocessing software." [PSI:PI]
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002415
name: protein group passes threshold
def: "A Boolean attribute to determine whether the protein group has
passed the threshold indicated in the file." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001147 ! protein ambiguity group result details

[Term]
id: MS:1002416
name: Orbitrap Fusion
def: "Thermo Scientific Orbitrap Fusion." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1002417
name: Orbitrap Fusion ETD
def: "Thermo Scientific Orbitrap Fusion with ETD." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1002418
name: TSQ Quantiva
def: "Thermo Scientific TSQ Quantiva MS." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1002419
name: TSQ Endura
def: "Thermo Scientific TSQ Endura MS." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1002420
name: PASSEL experiment URI
def: "URI that allows access to a PASSEL experiment." [PSI:PI]
xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.049a
Universitätsstraße 150
D-44801 Bochum

Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.58.0_rc1 of psi-ms.obo

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

Hi Gerhard,
Many thanks for this. Minor corrections due to my mistakes below,
Best wishes
Andy

 [Term]
id: MS:1002401
name: leading protein
def: "At least one protein within each group should be annotated as a leading protein to indicate it has the strongest evidence (or approximately equal) evidence other group members." [PSI:PI]
is_a: MS:1001101 ! protein group or subset relationship

TO

def: "At least one protein within each group should be annotated as a leading protein to indicate it has the strongest evidence, or approximately equal evidence as other group members." [PSI:PI]

I presume the following term is a placeholder only for leaf nodes describing clusters - if so, okay with me:
[Term]
id: MS:1002405
name: protein cluster details
def: "Details describing a protein cluster." [PSI:PI]
is_a: MS:1001085 ! protein result details

Another minor typo:

[Term]
id: MS:1002409
name: Marginally distinguished protein
def: "Assigned to a non-leading protein that has some independent evidence to support its presence relative to the leading protein(s), e.g. the protein may have a unique peptide but not sufficient to be promoted as a leading protein of another a group." [PSI:PI]
is_a: MS:1001101 ! protein group or subset relationship

To

def: "Assigned to a non-leading protein that has some independent evidence to support its presence relative to the leading protein(s), e.g. the protein may have a unique peptide but not sufficient to be promoted as a leading protein of another group." [PSI:PI]


-----Original Message-----
From: Gerhard Mayer [mailto:Ger...@ru...] 
Sent: 12 December 2013 10:00
To: psi...@li...; psi...@li...; Mass spectrometry standard development
Subject: [Psidev-ms-vocab] Release candidate 3.58.0_rc1 of psi-ms.obo

Dear proteomics community,

attached there's the release candidate 3.58.0_rc1 of the psi-ms.obo file.

It contains new terms for protein grouping and for the encoding of SRM in mzQuantML files.


Changed CV terms in version 3.58.0_rc1 of psi-ms.obo:
=====================================================
************ Added is_a: MS:1001139 ! quantitation software name [Term]
id: MS:1000922
name: Skyline
def: "Software used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the MacCoss lab at the University of Washington."
[https://brendanx-uw1.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=default
""]
is_a: MS:1000871 ! SRM software
is_a: MS:1001139 ! quantitation software name

************ Added value xsd\:anyURI for the next 2 terms [Term]
id: MS:1002031
name: PASSEL transition group browser URI
def: "URI to retrieve transition group data for a PASSEL (PeptideAtlas SRM Experiment Library) experiment." [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:1002032
name: PeptideAtlas dataset URI
def: "URI that allows access to a PeptideAtlas dataset." [PSI:PI]
xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier

************ PIA is now a postprocessing software [Term]
id: MS:1002387
name: PIA
def: "PIA - Protein Inference Algorithms, a toolbox for protein inference and identification analysis." [PSI:PI, http://www.medizinisches-proteom-center.de/pia]
is_a: MS:1002415 ! postprocessing software


New CV terms in version 3.58.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002401
name: leading protein
def: "At least one protein within each group should be annotated as a leading protein to indicate it has the strongest evidence (or approximately equal) evidence other group members." [PSI:PI]
is_a: MS:1001101 ! protein group or subset relationship

[Term]
id: MS:1002402
name: non-leading protein
def: "Zero to many proteins within each group should be annotated as non-leading to indicate that other proteins have stronger evidence."
[PSI:PI]
is_a: MS:1001101 ! protein group or subset relationship

[Term]
id: MS:1002403
name: group representative
def: "An arbitrary and optional flag applied to exactly one protein per group to indicate it can serve as the representative of the group, amongst leading proteins, in effect serving as a tiebreaker for approaches that require exactly one group representative." [PSI:PI]
is_a: MS:1001101 ! protein group or subset relationship

[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

[Term]
id: MS:1002405
name: protein cluster details
def: "Details describing a protein cluster." [PSI:PI]
is_a: MS:1001085 ! protein result details

[Term]
id: MS:1002406
name: count of identified clusters
def: "The number of protein clusters that have been identified, which must match the number of clusters 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:1002405 ! protein cluster details

[Term]
id: MS:1002407
name: cluster identifier
def: "An identifier applied to protein groups to indicate that they are linked by shared peptides." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1001147 ! protein ambiguity group result details

[Term]
id: MS:1002408
name: number of distinct protein sequences
def: "The number of protein clusters that have been identified, which must match the number of clusters 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:1002405 ! protein cluster details

[Term]
id: MS:1002409
name: Marginally distinguished protein
def: "Assigned to a non-leading protein that has some independent evidence to support its presence relative to the leading protein(s), e.g. the protein may have a unique peptide but not sufficient to be promoted as a leading protein of another a group." [PSI:PI]
is_a: MS:1001101 ! protein group or subset relationship

[Term]
id: MS:1002410
name: Anubis
def: "Anubis software for selected reaction monitoring data." [PSI:PI, http://quantitativeproteomics.org/anubis]
is_a: MS:1000871 ! SRM software
is_a: MS:1001139 ! quantitation software name

[Term]
id: MS:1002411
name: method file format
def: "Method specific file format." [PSI:PI]
is_a: MS:1001459 ! file format

[Term]
id: MS:1002412
name: TraML file
def: "The PSI TraML format." [PSI:PI,  http://www.psidev.info/traml]
is_a: MS:1002411 ! method file format

[Term]
id: MS:1002413
name: total XIC area
def: "Summed area of all the extracted ion chromatogram for the peptide (e.g. of all the transitions in SRM)." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002414
name: product background
def: "The background area for the quantified transition." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002415
name: postprocessing software
def: "Postprocessing software." [PSI:MS]
is_a: MS:1001457 ! data processing software

Best Regards,
Gerhard

--
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer Bioinformatics / Biostatistics Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum Zentrum für klinische Forschung I (ZKF I) E.049a Universitätsstraße 150
D-44801 Bochum

Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Release candidate 3.58.0_rc1 of psi-ms.obo

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

Dear proteomics community,

attached there's the release candidate 3.58.0_rc1 of
the psi-ms.obo file.

It contains new terms for protein grouping and for the encoding
of SRM in mzQuantML files.


Changed CV terms in version 3.58.0_rc1 of psi-ms.obo:
=====================================================
************ Added is_a: MS:1001139 ! quantitation software name
[Term]
id: MS:1000922
name: Skyline
def: "Software used to predict, select, and optimize transitions as well
as analyze the results of selected reaction monitoring runs developed
and distributed by the MacCoss lab at the University of Washington."
[https://brendanx-uw1.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=default
""]
is_a: MS:1000871 ! SRM software
is_a: MS:1001139 ! quantitation software name

************ Added value xsd\:anyURI for the next 2 terms
[Term]
id: MS:1002031
name: PASSEL transition group browser URI
def: "URI to retrieve transition group data for a PASSEL (PeptideAtlas
SRM Experiment Library) experiment." [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:1002032
name: PeptideAtlas dataset URI
def: "URI that allows access to a PeptideAtlas dataset." [PSI:PI]
xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier

************ PIA is now a postprocessing software
[Term]
id: MS:1002387
name: PIA
def: "PIA - Protein Inference Algorithms, a toolbox for protein
inference and identification analysis." [PSI:PI,
http://www.medizinisches-proteom-center.de/pia]
is_a: MS:1002415 ! postprocessing software


New CV terms in version 3.58.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002401
name: leading protein
def: "At least one protein within each group should be annotated as a
leading protein to indicate it has the strongest evidence (or
approximately equal) evidence other group members." [PSI:PI]
is_a: MS:1001101 ! protein group or subset relationship

[Term]
id: MS:1002402
name: non-leading protein
def: "Zero to many proteins within each group should be annotated as
non-leading to indicate that other proteins have stronger evidence."
[PSI:PI]
is_a: MS:1001101 ! protein group or subset relationship

[Term]
id: MS:1002403
name: group representative
def: "An arbitrary and optional flag applied to exactly one protein per
group to indicate it can serve as the representative of the group,
amongst leading proteins, in effect serving as a tiebreaker for
approaches that require exactly one group representative." [PSI:PI]
is_a: MS:1001101 ! protein group or subset relationship

[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

[Term]
id: MS:1002405
name: protein cluster details
def: "Details describing a protein cluster." [PSI:PI]
is_a: MS:1001085 ! protein result details

[Term]
id: MS:1002406
name: count of identified clusters
def: "The number of protein clusters that have been identified, which
must match the number of clusters 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:1002405 ! protein cluster details

[Term]
id: MS:1002407
name: cluster identifier
def: "An identifier applied to protein groups to indicate that they are
linked by shared peptides." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1001147 ! protein ambiguity group result details

[Term]
id: MS:1002408
name: number of distinct protein sequences
def: "The number of protein clusters that have been identified, which
must match the number of clusters 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:1002405 ! protein cluster details

[Term]
id: MS:1002409
name: Marginally distinguished protein
def: "Assigned to a non-leading protein that has some independent
evidence to support its presence relative to the leading protein(s),
e.g. the protein may have a unique peptide but not sufficient to be
promoted as a leading protein of another a group." [PSI:PI]
is_a: MS:1001101 ! protein group or subset relationship

[Term]
id: MS:1002410
name: Anubis
def: "Anubis software for selected reaction monitoring data." [PSI:PI,
http://quantitativeproteomics.org/anubis]
is_a: MS:1000871 ! SRM software
is_a: MS:1001139 ! quantitation software name

[Term]
id: MS:1002411
name: method file format
def: "Method specific file format." [PSI:PI]
is_a: MS:1001459 ! file format

[Term]
id: MS:1002412
name: TraML file
def: "The PSI TraML format." [PSI:PI,  http://www.psidev.info/traml]
is_a: MS:1002411 ! method file format

[Term]
id: MS:1002413
name: total XIC area
def: "Summed area of all the extracted ion chromatogram for the peptide
(e.g. of all the transitions in SRM)." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002414
name: product background
def: "The background area for the quantified transition." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002415
name: postprocessing software
def: "Postprocessing software." [PSI:MS]
is_a: MS:1001457 ! data processing software

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.049a
Universitätsstraße 150
D-44801 Bochum

Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] New version 3.57.0 of psi-ms.obo

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

Dear proteomics community,

attached there's the new version 3.57.0 of
the psi-ms.obo file.

It contains three new terms related to the SCiLS software and
new terms for PID, the Protein Inference Algorithm.


Changed CV terms in version 3.57.0 of psi-ms.obo:
=================================================
************ Corrected: removed the value-type tag
************ (Use the term ms level (MS:1000511) for specifying n)
[Term]
id: MS:1000580
name: MSn spectrum
def: "MSn refers to multi-stage MS/MS experiments designed to record
product ion spectra where n is the number of product ion stages (progeny
ions). For ion traps, sequential MS/MS experiments can be undertaken
where n > 2 whereas for a simple triple quadrupole system n=2. Use the
term ms level (MS:1000511) for specifying n." [PSI:MS]
synonym: "multiple-stage mass spectrometry spectrum" EXACT []
synonym: "nth generation product ion spectrum" EXACT []
synonym: "product ion spectrum" EXACT []
is_a: MS:1000294 ! mass spectrum
is_a: MS:1000524 ! data file content

************ Renamed contact organization --> contact affiliation
[Term]
id: MS:1000590
name: contact affiliation
def: "Home institution of the contact person." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000585 ! contact attribute

************ Changed the definition
************ Conversion software --> Data processing software
[Term]
id: MS:1001457
name: data processing software
def: "Data processing software." [PSI:MS]
is_a: MS:1000531 ! software


New CV terms in version 3.57.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002383
name: SCiLS software
def: "SCiLS software for data acquisition and analysis." [PSI:MS]
is_a: MS:1000531 ! software

[Term]
id: MS:1002384
name: SCiLS Lab
def: "SCiLS Lab software." [PSI:MS]
is_a: MS:1002383 ! SCiLS software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002385
name: SCiLS Lab file
def: "SCiLS Lab file format." [PSI:MS]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1002386
name: preprocessing software
def: "Preprocessing software." [PSI:MS]
is_a: MS:1000531 ! software

[Term]
id: MS:1002387
name: PIA
def: "PIA - Protein Inference Algorithms, a toolbox for protein
inference and identification analysis." [PSI:PI,
http://www.medizinisches-proteom-center.de/pia]
is_a: MS:1002386 ! preprocessing software

[Term]
id: MS:1002388
name: PIA XML file
def: "A compilation of search engine results in the PIA XML format."
[PSI:PI]
is_a: MS:1001040 ! intermediate analysis format

[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

[Term]
id: MS:1002390
name: PIA:FDRScore calculated
def: "Indicates whether the FDR score was calculated for the input
file." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002389 ! PIA workflow parameter

[Term]
id: MS:1002391
name: PIA:Combined FDRScore calculated
def: "Indicates whether the combined FDR score was calculated for the
PIA compilation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002389 ! PIA workflow parameter

[Term]
id: MS:1002392
name: PIA:PSM sets created
def: "Indicates whether PSM sets were created." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002389 ! PIA workflow parameter

[Term]
id: MS:1002393
name: PIA:used top identifications for FDR
def: "The number of top identifications per spectrum used for the FDR
calculation, 0 means all." [PSI:PI]
xref: value-type:xsd\:positiveInteger "The allowed value-type for this
CV term."
is_a: MS:1002389 ! PIA workflow parameter

[Term]
id: MS:1002394
name: PIA:protein score
def: "The score given to a protein by any protein inference." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details

[Term]
id: MS:1002395
name: PIA:protein inference
def: "The used algorithm for the protein inference using PIA." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002389 ! PIA workflow parameter

[Term]
id: MS:1002396
name: PIA:protein inference filter
def: "A filter used by PIA for the protein inference." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002389 ! PIA workflow parameter

[Term]
id: MS:1002397
name: PIA:protein inference scoring
def: "The used scoring method for the protein inference using PIA." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002389 ! PIA workflow parameter

[Term]
id: MS:1002398
name: PIA:protein inference used score
def: "The used base score for the protein inference using PIA." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002389 ! PIA workflow parameter

[Term]
id: MS:1002399
name: PIA:protein inference used PSMs
def: "The method to determine the PSMs used for scoring by the protein
inference." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002389 ! PIA workflow parameter

[Term]
id: MS:1002400
name: PIA:filter
def: "A filter used for the report generation." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002389 ! PIA workflow parameter

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.049a
Universitätsstraße 150
D-44801 Bochum

Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Invitation to a one-day workshop on mzTab for Metabolomics on March 6th 2014 in Tübingen, Germany

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

[This is a re-send, as the first attempt didn't make it to psidev-ms-dev,
 apologies if you have received it now multiple times.]

Dear all, this is an invitation to a one-day workshop on

             mzTab for Metabolomics

Date & Time:
============ 
Thursday, March 6th 2014 from 9:00-17:00

Location:
=========
University of Tübingen, Sand 1, Link to Maps: http://goo.gl/dljE7K . 
For further travel information to “Sand” Area see
http://www.uni-tuebingen.de/en/faculties/faculty-of-science/faculty/directions.html 

Programme: 
==========
We will have a few short presentations about the mzTab
background from proteomics and the UseCases in metabolomics 
and small molecules in general. The workshop participants 
will discuss/finalise the specification of mzTab for metabolomics,
create examples and determine the required PSI-MS controlled vocabulary terms.
Further details on the program can be expected in early 2014 
when the registration is closed.

Registration:
=============
Please fill out the google form at http://goo.gl/qsmQRR before Jan. 17th 2014.

Accommodation:
==============
Self organised, check out the Tübingen tourist information
http://tuebingen-info.de/index.php?id=768 for hotels.

Workshop Dinner(s):
===================
We will have a workshop dinner for the evening before, on 5th of March
at a local restaurant, sponsored by the EU FP7 project COSMOS. 
In addition, we will book a table in a local restaurant on March 6th 
for self-paid dinner for those leaving the following day.

We are looking forward to see you in Tübingen,

Yours,
Oliver Kohlbacher 
and Steffen Neumann

Re: [Psidev-ms-dev] Proposal for implementing ion mobility MS in mzML

[Monroe, M. E <Mat...@pn...>]

The one caveat that I will add is that we acquire ion mobility MS data using an LC front end, so it would be great if the format updates support that.  We call all of the spectra acquired from a given LC elution time a single "frame".  All of the mass spectra in that frame have the same LC elution time, but have their own (incrementing) ion mobility drift times, similar to the mode 1 (Full profile data) use-case discussed below.  We should be able to store this data in mzML format provided we can attach an LC elution time tag to each profile-mode mass spectrum (likely accession="MS:1000016" name="scan start time"), plus also an ion mobility drift time.  Ideally we would also like to tag each mass spectrum with a frame number (integer), which will make it obvious that a set of mass spectra all come from the same frame.  Without this frame number tag, the only way to group the related spectra together would be using the LC elution time.

Here's how each spectrum entry might look if we encode frame and scan in the "id" attribute:
<spectrum index="0" id="frame=1 scan=0"
<spectrum index="1" id="frame=1 scan=1"
<spectrum index="2" id="frame=1 scan=2"
<spectrum index="3" id="frame=1 scan=3"
...
<spectrum index="358" id="frame=1 scan=358"
<spectrum index="359" id="frame=1 scan=359"
<spectrum index="360" id="frame=2 scan=0"
<spectrum index="361" id="frame=2 scan=1"
<spectrum index="362" id="frame=2 scan=2"
...

The alternative is to encode the frame and scan info in explicit cvParam entries.

Matt Monroe

From: Eric Deutsch [mailto:ede...@sy...]
Sent: Friday, December 06, 2013 6:11 AM
To: Mass spectrometry standard development; Han...@wa...; David L. Tabb; Matt Chambers; Brendan MacLean
Cc: Eric Deutsch
Subject: Re: [Psidev-ms-dev] Proposal for implementing ion mobility MS in mzML

Hi everyone, in chatting with Brendan here in Dagstuhl, I learned that Matt is teetering on the brink of implementing proper support for ion mobility MS in ProteoWizard. I would like to refresh this thread with a proposal on how to implement IM-MS in mzML. This proposal was unencumbered by any actual implementation attempts, and we expected there would have to be refinements when someone actually performed the implementation. Since it seems that this is nigh, please examine this, and I hope it can be a useful guide. Perhaps Matt can study this and comment on whether this is useful, or if he will do things differently, or if this is not relevant. Please let me know if a telecall chat is warranted.

Thank you!
Eric


From: Eric Deutsch [mailto:ede...@sy...<mailto:ede...@sy...>]
Sent: Saturday, April 20, 2013 3:32 AM
To: Mass spectrometry standard development; Han...@wa...<mailto:Han...@wa...>; David L. Tabb
Cc: Eric Deutsch
Subject: Proposal for implementing ion mobility MS in mzML

Hi everyone, here follows a proposal for implementing ion mobility MS in mzML, which does not currently explicitly support IM-MS. This is based on a discussion with Waters representatives at the HUPO PSI workshop in Liverpool last week.

First for FAIMS, each spectrum should be tagged with the cvParam "FAIMS compensation voltage" MS:1001581: The DC potential applied to the asymmetric waveform in FAIMS that compensates for the difference between high and low field mobility of an ion. This appears to be complete and stable.

TODO: Verify that msconvert indeed supports this
TODO: Verify that the mapping file explicitly provides for this optional cvParam

Now for the traditional IM-MS, there appear to be two modes:
1) Full profile data (i.e. no post-processing or peak picking)
2) Processed, peak-picked data

For mode 1) The data will be encoded in a series of full profile scans, one for each profile spectrum and each profile spectrum will be tagged with its drift time. The only current suitable term in the CV is "product ion drift time" MS:1001967: The ion drift time of an MS2 product ion. After some discussion, it was concluded that there is no reason to distinguish between a product or precursor or other ion when providing its drift time. So I propose we obsolete this term and add the term "ion mobility drift time", which would store the drift time as a float with units milliseconds. Each spectrum would be tagged with its drift time in this way.

TODO: Obsolete "product ion drift time" MS:1001967 as unneeded and replaced with more generic term
TODO: Create new term "ion mobility drift time" with definition "Drift time of an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This time might refer to the central value of a bin into which all ions within a narrow range of drift time have been aggregated."

Re: [Psidev-ms-dev] Proposal for implementing ion mobility MS in mzML

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

Hi everyone, in chatting with Brendan here in Dagstuhl, I learned that Matt
is teetering on the brink of implementing proper support for ion mobility
MS in ProteoWizard. I would like to refresh this thread with a proposal on
how to implement IM-MS in mzML. This proposal was unencumbered by any
actual implementation attempts, and we expected there would have to be
refinements when someone actually performed the implementation. Since it
seems that this is nigh, please examine this, and I hope it can be a useful
guide. Perhaps Matt can study this and comment on whether this is useful,
or if he will do things differently, or if this is not relevant. Please let
me know if a telecall chat is warranted.



Thank you!

Eric





*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Saturday, April 20, 2013 3:32 AM
*To:* Mass spectrometry standard development; Han...@wa...;
David L. Tabb
*Cc:* Eric Deutsch
*Subject:* Proposal for implementing ion mobility MS in mzML



Hi everyone, here follows a proposal for implementing ion mobility MS in
mzML, which does not currently explicitly support IM-MS. This is based on a
discussion with Waters representatives at the HUPO PSI workshop in
Liverpool last week.



First for FAIMS, each spectrum should be tagged with the cvParam “FAIMS
compensation voltage” MS:1001581: The DC potential applied to the
asymmetric waveform in FAIMS that compensates for the difference between
high and low field mobility of an ion. This appears to be complete and
stable.



TODO: Verify that msconvert indeed supports this

TODO: Verify that the mapping file explicitly provides for this optional
cvParam



Now for the traditional IM-MS, there appear to be two modes:

1) Full profile data (i.e. no post-processing or peak picking)

2) Processed, peak-picked data



For mode 1) The data will be encoded in a series of full profile scans, one
for each profile spectrum and each profile spectrum will be tagged with its
drift time. The only current suitable term in the CV is “product ion drift
time” MS:1001967: The ion drift time of an MS2 product ion. After some
discussion, it was concluded that there is no reason to distinguish between
a product or precursor or other ion when providing its drift time. So I
propose we obsolete this term and add the term “ion mobility drift time”,
which would store the drift time as a float with units milliseconds. Each
spectrum would be tagged with its drift time in this way.



TODO: Obsolete “product ion drift time” MS:1001967 as unneeded and replaced
with more generic term

TODO: Create new term “ion mobility drift time” with definition “Drift time
of an ion or spectrum of ions as measured in an ion mobility mass
spectrometer. This time might refer to the central value of a bin into
which all ions within a narrow range of drift time have been aggregated.”



Therefore, if an instrument collected either MS1 or MS2 ions using the ion
mobility device, it would produce a series of profile-mode spectra, each
labeled with this new CV term containing the central drift time of ions
aggregated into that spectrum.



For mode 2) where some software has taken this series of profile spectra
with different drift times and produced a simplified peak-picked spectrum
with peaks centroided across m/z and drift time, the data will be encoded
into a single spectrum with an extra data array for mean drift time.



Currently supported data arrays are:

- m/z array

- intensity array

- charge array

- wavelength array        (this is for E-M radiation spectra)

- signal to noise array

- time array                    (envisioned for some time-domain spectrum,
not otherwise suitable for <Chromatogram>)

- et al.



TODO: Add term “mean drift time array”: Array of drift times, averaged from
a matrix of binned m/z and drift time values, corresponding to spectrum of
individual peaks encoded with an m/z array.



So, something else that Waters does upon processing the raw data into a
processed single spectrum is reducing the charge to 1. i.e. if the product
ion spectrum contains z=2 and z=3 peaks, this would be de-isotoped and
transformed to z=1 equivalent. This is customarily not done in mzML until
now. Although it should be noted in passing that msconvert CAN and DOES do
this for some instruments at least when converting from a raw format to
MGF, but not to mzML. How should this be encoded? Option 1 is to continue
to use the “m/z array” cvParam, but add another parameter on the
binarydataarray that indicates that the “m/z array” has been charge reduced
to z=1. Option 2 is to introduce a separate term “charge-reduced m/z array”
where we define it to mean that all m/z values have been transformed to
z=1. What do you think? I think I’m leaning to Option 2. This would mean
that existing software would not know how to access this new array. But it
is probably the case that existing software should not be accessing the
charge reduced data without explicit code changes to handle this case. Or
maybe it is friendlier to just reuse the original “m/z array” with a
modifier. Existing software would not know about the modified, but it could
access the reduced m/z values and presumably do something pretty reasonable
with them anyway. Most search engines should not be too dismayed as
receiving all z=1 peaks. And some are known to prefer it.



TODO: Decide how to implement this and add the appropriate new CV term.



And one final, similar item during the above processing the Waters software
calculates an average charge. So suppose that if during acquisition both a
charge 2+ precursor at 300 m/z and 3+ precursor ion at 200 m/z were present
in equal amounts (with the same drift time), then there would be a final,
combined charge reduced peak at 600 m/z and an average charge of 2.5. We
could consider using the current “charge array” term with a modifier that
it is an average, but the current datatype is integer, so we would have to
change that to a float. Otherwise, we would need to add a new term “mean
charge array” with a definition like “Array of mean charge values where the
mean charge is calculated as a weighted mean of the charges of individual
peaks that are aggregated into a processed spectrum.” Or similar.



TODO: Decide whether we reuse “charge array” with a modifier CV term and
change its datatype to integer, or introduced a new term for “mean charge”.



What do you think?



If we can decide this via email, this would be great. Else we’ll schedule a
telecall to hash it out and decide. Clearly we most need the opinions of
those familiar with IM-MS data and those that will be implementing tools to
process it.



Thanks,

Eric

[Psidev-ms-dev] Release candidate 3.57.0_rc2 of psi-ms.obo

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

Dear proteomics community,

attached there's the release candidate 3.57.0_rc2 of
the psi-ms.obo file.

It contains three new terms related to the SCiLS software and
new terms for PID, the Protein Inference Algorithm.


Changed CV terms in version 3.57.0_rc2 of psi-ms.obo:
=====================================================
************ Corrected: removed the value-type tag
************ (Use the term ms level (MS:1000511) for specifying n)
[Term]
id: MS:1000580
name: MSn spectrum
def: "MSn refers to multi-stage MS/MS experiments designed to record
product ion spectra where n is the number of product ion stages (progeny
ions). For ion traps, sequential MS/MS experiments can be undertaken
where n > 2 whereas for a simple triple quadrupole system n=2. Use the
term ms level (MS:1000511) for specifying n." [PSI:MS]
synonym: "multiple-stage mass spectrometry spectrum" EXACT []
synonym: "nth generation product ion spectrum" EXACT []
synonym: "product ion spectrum" EXACT []
is_a: MS:1000294 ! mass spectrum
is_a: MS:1000524 ! data file content

************ Renamed contact organization --> contact affiliation
[Term]
id: MS:1000590
name: contact affiliation
def: "Home institution of the contact person." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000585 ! contact attribute

************ Changed the definition
************ Conversion software --> Data processing software
[Term]
id: MS:1001457
name: data processing software
def: "Data processing software." [PSI:MS]
is_a: MS:1000531 ! software


New CV terms in version 3.57.0_rc2 of psi-ms.obo:
=================================================
[Term]
id: MS:1002383
name: SCiLS software
def: "SCiLS software for data acquisition and analysis." [PSI:MS]
is_a: MS:1000531 ! software

[Term]
id: MS:1002384
name: SCiLS Lab
def: "SCiLS Lab software." [PSI:MS]
is_a: MS:1002383 ! SCiLS software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002385
name: SCiLS Lab file
def: "SCiLS Lab file format." [PSI:MS]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1002386
name: preprocessing software
def: "Preprocessing software." [PSI:MS]
is_a: MS:1000531 ! software

[Term]
id: MS:1002387
name: PIA
def: "PIA - Protein Inference Algorithms, a toolbox for protein
inference and identification analysis." [PSI:PI,
http://www.medizinisches-proteom-center.de/pia]
is_a: MS:1002386 ! preprocessing software

[Term]
id: MS:1002388
name: PIA XML file
def: "A compilation of search engine results in the PIA XML format."
[PSI:PI]
is_a: MS:1001040 ! intermediate analysis format

[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

[Term]
id: MS:1002390
name: PIA:FDRScore calculated
def: "Indicates whether the FDR score was calculated for the input
file." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002389 ! PIA workflow parameter

[Term]
id: MS:1002391
name: PIA:Combined FDRScore calculated
def: "Indicates whether the combined FDR score was calculated for the
PIA compilation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002389 ! PIA workflow parameter

[Term]
id: MS:1002392
name: PIA:PSM sets created
def: "Indicates whether PSM sets were created." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002389 ! PIA workflow parameter

[Term]
id: MS:1002393
name: PIA:used top identifications for FDR
def: "The number of top identifications per spectrum used for the FDR
calculation, 0 means all." [PSI:PI]
xref: value-type:xsd\:positiveInteger "The allowed value-type for this
CV term."
is_a: MS:1002389 ! PIA workflow parameter

[Term]
id: MS:1002394
name: PIA:protein score
def: "The score given to a protein by any protein inference." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details

[Term]
id: MS:1002395
name: PIA:protein inference
def: "The used algorithm for the protein inference using PIA." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002389 ! PIA workflow parameter

[Term]
id: MS:1002396
name: PIA:protein inference filter
def: "A filter used by PIA for the protein inference." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002389 ! PIA workflow parameter

[Term]
id: MS:1002397
name: PIA:protein inference scoring
def: "The used scoring method for the protein inference using PIA." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002389 ! PIA workflow parameter

[Term]
id: MS:1002398
name: PIA:protein inference used score
def: "The used base score for the protein inference using PIA." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002389 ! PIA workflow parameter

[Term]
id: MS:1002399
name: PIA:protein inference used PSMs
def: "The method to determine the PSMs used for scoring by the protein
inference." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002389 ! PIA workflow parameter

[Term]
id: MS:1002400
name: PIA:filter
def: "A filter used for the report generation." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002389 ! PIA workflow parameter

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.049a
Universitätsstraße 150
D-44801 Bochum

Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Release candidate 3.57.0_rc1 of psi-ms.obo

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

Dear proteomics community,

attached there's the release candidate 3.57.0_rc1 of
the psi-ms.obo file.

It contains three new terms related to the SCiLS software.


Changed CV terms in version 3.57.0_rc1 of psi-ms.obo:
=====================================================
************ Corrected: removed the value-type tag
************ (Use the term ms level (MS:1000511) for specifying n)
[Term]
id: MS:1000580
name: MSn spectrum
def: "MSn refers to multi-stage MS/MS experiments designed to record
product ion spectra where n is the number of product ion stages (progeny
ions). For ion traps, sequential MS/MS experiments can be undertaken
where n > 2 whereas for a simple triple quadrupole system n=2. Use the
term ms level (MS:1000511) for specifying n." [PSI:MS]
synonym: "multiple-stage mass spectrometry spectrum" EXACT []
synonym: "nth generation product ion spectrum" EXACT []
synonym: "product ion spectrum" EXACT []
is_a: MS:1000294 ! mass spectrum
is_a: MS:1000524 ! data file content

************  Renamed contact organization --> contact affiliation
[Term]
id: MS:1000590
name: contact affiliation
def: "Home institution of the contact person." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000585 ! contact attribute



New CV terms in version 3.57.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002383
name: SCiLS software
def: "SCiLS software for data acquisition and analysis." [PSI:MS]
is_a: MS:1000531 ! software

[Term]
id: MS:1002384
name: SCiLS Lab
def: "SCiLS Lab software." [PSI:MS]
is_a: MS:1002383 ! SCiLS software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002385
name: SCiLS Lab file
def: "SCiLS Lab file format." [PSI:MS]
is_a: MS:1000560 ! mass spectrometer file format

Best Regards,
Gerhard
-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.049a
Universitätsstraße 150
D-44801 Bochum

Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] suggestions for MS term updates

[Florian R. <fl...@eb...>]

Hi Gerhard,

thanks for the clarifications!

I agree with your proposals.

In case 1) we'll try to map provided contact details to the given 
sub-terms and for the odd one that we cannot map we'll find an alternative.

In case 2) we will have to investigate all our cases, but I am almost 
certain you are right and we should use other terms in those cases.

Case 3) is a minor change and we'll go with the official version, 
whatever it'll be.


Thanks a lot!
Florian


On 20/11/2013 09:19, Gerhard Mayer wrote:
> Hi Florian, hi Tobias, hi all,
>
> 1) in case of MS:1000585 'contact attribute', I think this term was
> introduced only for grouping the more specialised sub-terms, which
> should be used in the concrete data files. These sub-terms like
> contact name
> contact address
> contact URL
> contact email
> ...
> have all string types defined for specifying the values. In the mapping
> files mzIdentML-mapping-1.1.0.xml and mzQuant-mapping-1.0.0.xml we also
> allow only these sub-terms.
>
>
> 2) The term MS:1000336: 'neutral loss' is currently defined as
> [Term]
> id: MS:1000336
> name: neutral loss
> def: "The loss of an uncharged species during a rearrangement process."
> [PSI:MS]
> is_a: MS:1000445 ! sequential m/z separation method
> is_a: MS:1001055 ! modification parameters
>
> I'm not sure what value to specify here for the MS:1000336 'neutral
> loss' term and what this value then describes.
>
> For specifying the m/z values we have the two terms MS:1001524 'fragment
> neutral loss' and MS:1001525 'precursor neutral loss'
>
> For describing the type of the ions with neutral losses we have terms like
> MS:1001146 'a ion-NH3',
> MS:1001148 'a ion-H2O'
> and so on
>
> In case of a MS:1000326 'constant neutral loss spectrum' one can specify
> the offset by using the term MS:1000803 'analyzer scan offset'
>
> I'm not an expert in all these things, maybe soemone else has an idea,
> what kind of value we should allow to specify for MS:1000336 'neutral loss'?
>
>
> 3) For the term MS:1000590 I agree that a renaming to 'contact
> affiliation' would be sensible.
>
> Best Regards,
> Gerhard
>
>
> Am 18.11.2013 17:39, schrieb Florian Reisinger:
>> Hi Gerhard,
>>
>> as you may know we are generating ProteomeXchange summaries for PX
>> datasets submitted to us, which we send to the ProteomeCentral
>> repository run by Eric.
>>
>> Eric has now started validating those summary messages more closely than
>> just applying syntactic checks. As part of that he checks the usage of
>> CV terms with respect to their definition in the MS CV.
>>
>> Tobias in our team (cc'ed) has looked at the issues reported by Eric's
>> checks and this has uncovered some issues/shortcomings in the CV term
>> definitions. Here are some cases that we have found so far (we'll
>> monitor the results of Eric's checks and of course let you know as soon
>> as we notice any new issues):
>>
>> MS:1000585: 'contact attribute', it does not define any allowed value,
>> but probably should do (I guess a generic string is the most flexible
>> option).
>>
>> MS:1000336: 'neutral loss', it does not specify any allowed value either
>> (but I am not sure if our use is correct, we'll look closer into the
>> users annotation to see if they make sense).
>>
>> MS:1000590: It's recommended name is 'contact organisation', but Eric
>> thinks 'contact affiliation' would be better (I guess a matter of taste).
>>
>> We would appreciate very much if you could have a look and update the CV
>> if you think it OK.
>>
>>
>> Thanks a lot!
>> Florian
>>
>>
>

Re: [Psidev-ms-dev] suggestions for MS term updates

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

Hi Florian, hi Tobias, hi all,

1) in case of MS:1000585 'contact attribute', I think this term was
introduced only for grouping the more specialised sub-terms, which
should be used in the concrete data files. These sub-terms like
contact name
contact address
contact URL
contact email
...
have all string types defined for specifying the values. In the mapping
files mzIdentML-mapping-1.1.0.xml and mzQuant-mapping-1.0.0.xml we also
allow only these sub-terms.


2) The term MS:1000336: 'neutral loss' is currently defined as
[Term]
id: MS:1000336
name: neutral loss
def: "The loss of an uncharged species during a rearrangement process."
[PSI:MS]
is_a: MS:1000445 ! sequential m/z separation method
is_a: MS:1001055 ! modification parameters

I'm not sure what value to specify here for the MS:1000336 'neutral
loss' term and what this value then describes.

For specifying the m/z values we have the two terms MS:1001524 'fragment
neutral loss' and MS:1001525 'precursor neutral loss'

For describing the type of the ions with neutral losses we have terms like
MS:1001146 'a ion-NH3',
MS:1001148 'a ion-H2O'
and so on

In case of a MS:1000326 'constant neutral loss spectrum' one can specify
the offset by using the term MS:1000803 'analyzer scan offset'

I'm not an expert in all these things, maybe soemone else has an idea,
what kind of value we should allow to specify for MS:1000336 'neutral loss'?


3) For the term MS:1000590 I agree that a renaming to 'contact
affiliation' would be sensible.

Best Regards,
Gerhard


Am 18.11.2013 17:39, schrieb Florian Reisinger:
> Hi Gerhard,
> 
> as you may know we are generating ProteomeXchange summaries for PX
> datasets submitted to us, which we send to the ProteomeCentral
> repository run by Eric.
> 
> Eric has now started validating those summary messages more closely than
> just applying syntactic checks. As part of that he checks the usage of
> CV terms with respect to their definition in the MS CV.
> 
> Tobias in our team (cc'ed) has looked at the issues reported by Eric's
> checks and this has uncovered some issues/shortcomings in the CV term
> definitions. Here are some cases that we have found so far (we'll
> monitor the results of Eric's checks and of course let you know as soon
> as we notice any new issues):
> 
> MS:1000585: 'contact attribute', it does not define any allowed value,
> but probably should do (I guess a generic string is the most flexible
> option).
> 
> MS:1000336: 'neutral loss', it does not specify any allowed value either
> (but I am not sure if our use is correct, we'll look closer into the
> users annotation to see if they make sense).
> 
> MS:1000590: It's recommended name is 'contact organisation', but Eric
> thinks 'contact affiliation' would be better (I guess a matter of taste).
> 
> We would appreciate very much if you could have a look and update the CV
> if you think it OK.
> 
> 
> Thanks a lot!
> Florian
> 
> 

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.049a
Universitätsstraße 150
D-44801 Bochum

Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] New mzML accession IDs

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

Hi Mike, this seems fine, then.



Thanks!

Eric





*From:* Mike Ashton [mailto:Mik...@kr...]
*Sent:* Thursday, November 14, 2013 4:08 AM
*To:* Eric Deutsch; Mass spectrometry standard development
*Subject:* RE: [Psidev-ms-dev] New mzML accession IDs



Hi Eric,



The top level term for Shimadzu’s instrument is actually MS:100124
(Shimadzu instrument model). I only wish to change the sub-term of
“Shimadzu Biotech instrument model”. This term was only used for our
MALDI-TOF line but we are gradually phasing this out and using the Shimadzu
name instead.



To ensure that we don’t have to rename the terms again I had a brief
conversation with our marketing manager. They have requested a small change
to my original request (removal of “Corporation” from one of the terms and
an instrument description of “MALDI-TOF-TOF”). So, to summarise, please
find my final request below:



Please rename:



MS:1000602 (Shimadzu Biotech instrument model”) to read “Shimadzu MALDI-TOF
instrument model”. The name and definition can both read the same.



MS:1001557 (Shimadzu Biotech software) to read “Shimadzu Corporation
software”. The name and definition can both read the same.




In addition to these modifications I would also like to create the
following accession IDs:



Name: MALDI Solutions LC-MALDI

Def: Software for automated LC-MALDI analysis and reporting

is_a: MS:1001455 ! acquisition software

is_a: MS:1001456 ! analysis software

is_a: MS:1001457 ! data processing software

is_a: MS:1001557 ! Shimadzu Corporation software



Name: Shimadzu MALDI-7090

Def: Shimadzu MALDI-7090: MALDI-TOF-TOF

is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model



Thanks,

*Mike*.



*From:* Eric Deutsch
[mailto:ede...@sy...<ede...@sy...>]

*Sent:* 13 November 2013 01:32
*To:* Mass spectrometry standard development; Mike Ashton
*Cc:* Eric Deutsch
*Subject:* RE: [Psidev-ms-dev] New mzML accession IDs



Hi Mike, thanks very much for helping to update our CV for Shimadzu
products. This seems all fine, with just one question: why have you limited
our most generic term:



Shimadzu Biotech instrument model

To

Shimadzu Corporation MALDI-TOF instrument model



Was/will there never be any kind of instrument but a MALDI-TOF from
Shimadzu?



Thanks,

Eric





*From:* Mike Ashton [mailto:Mik...@kr...]
*Sent:* Monday, November 11, 2013 10:45 AM
*To:* psi...@li...
*Subject:* [Psidev-ms-dev] New mzML accession IDs



Hi,



I would like to make a number of amendments to the mzML controlled
vocabulary for the Shimadzu products.



Please rename:



MS:1000602 (Shimadzu Biotech instrument model”) to read “Shimadzu
Corporation MALDI-TOF instrument model”. The name and definition can both
read the same.



MS:1001557 (Shimadzu Biotech software) to read “Shimadzu Corporation
software”. The name and definition can both read the same.




In addition to these modifications I would also like to create the
following accession IDs:



Name: MALDI Solutions LC-MALDI

Def: Software for automated LC-MALDI analysis and reporting

is_a: MS:1001455 ! acquisition software

is_a: MS:1001456 ! analysis software

is_a: MS:1001457 ! data processing software

is_a: MS:1001557 ! Shimadzu Corporation software



Name: Shimadzu MALDI-7090

Def: Shimadzu Corporation MALDI-7090: MALDI-TOF

is_a: MS:1000602 ! Shimadzu Corporation MALDI-TOF instrument model



Thanks,

*Mike*.



*Mike Ashton*

Head of Software



Kratos Analytical Ltd.

Wharfside, Trafford Wharf Road, Manchester M17 1GP.

Tel: +44 (0) 161 888 4400 Ext 329

Fax: +44 (0) 161 888 4401

Company Number 563161. Registered in England. Registered Offices as above.




________________________________________________________________________
This e-mail has been scanned for all viruses by Claranet. The
service is powered by MessageLabs. For more information on a proactive
anti-virus service working around the clock, around the globe, visit:
http://www.claranet.co.uk
________________________________________________________________________


________________________________________________________________________
This e-mail has been scanned for all viruses by Claranet. The
service is powered by MessageLabs. For more information on a proactive
anti-virus service working around the clock, around the globe, visit:
http://www.claranet.co.uk
________________________________________________________________________


________________________________________________________________________
This e-mail has been scanned for all viruses by Claranet. The
service is powered by MessageLabs. For more information on a proactive
anti-virus service working around the clock, around the globe, visit:
http://www.claranet.co.uk
________________________________________________________________________

Re: [Psidev-ms-dev] New mzML accession IDs

[Mike A. <Mik...@kr...>]

Hi Eric,

The top level term for Shimadzu's instrument is actually MS:100124 (Shimadzu instrument model). I only wish to change the sub-term of "Shimadzu Biotech instrument model". This term was only used for our MALDI-TOF line but we are gradually phasing this out and using the Shimadzu name instead.

To ensure that we don't have to rename the terms again I had a brief conversation with our marketing manager. They have requested a small change to my original request (removal of "Corporation" from one of the terms and an instrument description of "MALDI-TOF-TOF"). So, to summarise, please find my final request below:

Please rename:

MS:1000602 (Shimadzu Biotech instrument model") to read "Shimadzu MALDI-TOF instrument model". The name and definition can both read the same.

MS:1001557 (Shimadzu Biotech software) to read "Shimadzu Corporation software". The name and definition can both read the same.

In addition to these modifications I would also like to create the following accession IDs:

Name: MALDI Solutions LC-MALDI
Def: Software for automated LC-MALDI analysis and reporting
is_a: MS:1001455 ! acquisition software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software
is_a: MS:1001557 ! Shimadzu Corporation software

Name: Shimadzu MALDI-7090
Def: Shimadzu MALDI-7090: MALDI-TOF-TOF
is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model

Thanks,
Mike.

From: Eric Deutsch [mailto:ede...@sy...]
Sent: 13 November 2013 01:32
To: Mass spectrometry standard development; Mike Ashton
Cc: Eric Deutsch
Subject: RE: [Psidev-ms-dev] New mzML accession IDs

Hi Mike, thanks very much for helping to update our CV for Shimadzu products. This seems all fine, with just one question: why have you limited our most generic term:

Shimadzu Biotech instrument model
To
Shimadzu Corporation MALDI-TOF instrument model

Was/will there never be any kind of instrument but a MALDI-TOF from Shimadzu?

Thanks,
Eric


From: Mike Ashton [mailto:Mik...@kr...<mailto:Mik...@kr...>]
Sent: Monday, November 11, 2013 10:45 AM
To: psi...@li...<mailto:psi...@li...>
Subject: [Psidev-ms-dev] New mzML accession IDs

Hi,

I would like to make a number of amendments to the mzML controlled vocabulary for the Shimadzu products.

Please rename:

MS:1000602 (Shimadzu Biotech instrument model") to read "Shimadzu Corporation MALDI-TOF instrument model". The name and definition can both read the same.

MS:1001557 (Shimadzu Biotech software) to read "Shimadzu Corporation software". The name and definition can both read the same.

In addition to these modifications I would also like to create the following accession IDs:

Name: MALDI Solutions LC-MALDI
Def: Software for automated LC-MALDI analysis and reporting
is_a: MS:1001455 ! acquisition software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software
is_a: MS:1001557 ! Shimadzu Corporation software

Name: Shimadzu MALDI-7090
Def: Shimadzu Corporation MALDI-7090: MALDI-TOF
is_a: MS:1000602 ! Shimadzu Corporation MALDI-TOF instrument model

Thanks,
Mike.

Mike Ashton
Head of Software

Kratos Analytical Ltd.
Wharfside, Trafford Wharf Road, Manchester M17 1GP.
Tel: +44 (0) 161 888 4400 Ext 329
Fax: +44 (0) 161 888 4401
Company Number 563161. Registered in England. Registered Offices as above.


________________________________________________________________________
This e-mail has been scanned for all viruses by Claranet. The
service is powered by MessageLabs. For more information on a proactive
anti-virus service working around the clock, around the globe, visit:
http://www.claranet.co.uk
________________________________________________________________________

________________________________________________________________________
This e-mail has been scanned for all viruses by Claranet. The
service is powered by MessageLabs. For more information on a proactive
anti-virus service working around the clock, around the globe, visit:
http://www.claranet.co.uk
________________________________________________________________________

________________________________________________________________________
This e-mail has been scanned for all viruses by Claranet. The
service is powered by MessageLabs. For more information on a proactive
anti-virus service working around the clock, around the globe, visit:
http://www.claranet.co.uk
________________________________________________________________________

Re: [Psidev-ms-dev] New mzML accession IDs

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

Hi Mike, thanks very much for helping to update our CV for Shimadzu
products. This seems all fine, with just one question: why have you limited
our most generic term:



Shimadzu Biotech instrument model

To

Shimadzu Corporation MALDI-TOF instrument model



Was/will there never be any kind of instrument but a MALDI-TOF from
Shimadzu?



Thanks,

Eric





*From:* Mike Ashton [mailto:Mik...@kr...]
*Sent:* Monday, November 11, 2013 10:45 AM
*To:* psi...@li...
*Subject:* [Psidev-ms-dev] New mzML accession IDs



Hi,



I would like to make a number of amendments to the mzML controlled
vocabulary for the Shimadzu products.



Please rename:



MS:1000602 (Shimadzu Biotech instrument model”) to read “Shimadzu
Corporation MALDI-TOF instrument model”. The name and definition can both
read the same.



MS:1001557 (Shimadzu Biotech software) to read “Shimadzu Corporation
software”. The name and definition can both read the same.




In addition to these modifications I would also like to create the
following accession IDs:



Name: MALDI Solutions LC-MALDI

Def: Software for automated LC-MALDI analysis and reporting

is_a: MS:1001455 ! acquisition software

is_a: MS:1001456 ! analysis software

is_a: MS:1001457 ! data processing software

is_a: MS:1001557 ! Shimadzu Corporation software



Name: Shimadzu MALDI-7090

Def: Shimadzu Corporation MALDI-7090: MALDI-TOF

is_a: MS:1000602 ! Shimadzu Corporation MALDI-TOF instrument model



Thanks,

*Mike*.



*Mike Ashton*

Head of Software



Kratos Analytical Ltd.

Wharfside, Trafford Wharf Road, Manchester M17 1GP.

Tel: +44 (0) 161 888 4400 Ext 329

Fax: +44 (0) 161 888 4401

Company Number 563161. Registered in England. Registered Offices as above.




________________________________________________________________________
This e-mail has been scanned for all viruses by Claranet. The
service is powered by MessageLabs. For more information on a proactive
anti-virus service working around the clock, around the globe, visit:
http://www.claranet.co.uk
________________________________________________________________________