psidev-ms-dev — Mass spectroscopy standard development

Re: [Psidev-ms-dev] Native source path CV param

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

Hi Matt, this seems reasonable to me. I don't think we've ever change the
mzML version when we updated the mapping file, but it doesn't seem
unreasonable.

I vaguely recall we had some other desired mapping file changes that have
been mentioned but not executed, although I can't recall them right now. I
think they were related to the recent CV additions. Maybe compensation
voltage and similar.

Perhaps if we have several mapping file changes, we can take care of them
all at once.

Let's compile a list of desirable mapping file changes. Everyone, please
email them here.

thanks,
Eric



> -----Original Message-----
> From: Matthew Chambers [mailto:mat...@gm...]
> Sent: Monday, June 11, 2012 9:04 AM
> To: psi...@li...; Mass spectrometry standard
> development
> Subject: [Psidev-ms-dev] Native source path CV param
>
> I've encountered a difficulty in deriving the original source path used
> for directory-based sources
> (Agilent, Waters, Bruker). I think it's great that our sourceFiles are
> actually files but when I
> need to actually find the original directory (which is what their APIs
> take), they're quite tricky
> to use. I'd like to add a term like "native source path" and be able to
> put it in every sourceFile.
> I'd put it in every sourceFile just in case some people check the last
> one and some check the first one.
>
> It would take a string value obviously. I'm not sure that this could be
> done without editing the
> mapping/validator though. The Java validator uses:
> http://psidev.svn.sourceforge.net/viewvc/psidev/psi/mzml/validator/src/
> main/java/psidev/psi/ms/object_rules/MassSpectraOrParameterFileInSource
> FileListObjectRule.java
>
> What would we do about bumping the schema version since it's
> theoretically a mapping file change?
>
> -Matt
>
> -----------------------------------------------------------------------
> -------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond.
> Discussions
> will include endpoint security, mobile security and the latest in
> malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
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> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

[Psidev-ms-dev] Native source path CV param

[Matthew C. <mat...@gm...>]

I've encountered a difficulty in deriving the original source path used for directory-based sources 
(Agilent, Waters, Bruker). I think it's great that our sourceFiles are actually files but when I 
need to actually find the original directory (which is what their APIs take), they're quite tricky 
to use. I'd like to add a term like "native source path" and be able to put it in every sourceFile. 
I'd put it in every sourceFile just in case some people check the last one and some check the first one.

It would take a string value obviously. I'm not sure that this could be done without editing the 
mapping/validator though. The Java validator uses:
http://psidev.svn.sourceforge.net/viewvc/psidev/psi/mzml/validator/src/main/java/psidev/psi/ms/object_rules/MassSpectraOrParameterFileInSourceFileListObjectRule.java

What would we do about bumping the schema version since it's theoretically a mapping file change?

-Matt

[Psidev-ms-dev] Release Candidate psi-ms.obo v.3.28.0_rc1

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

Dear proteomics community,

attached there's the release candidate 3.28.0_rc1 of the psi-ms.obo.

Newly added CV terms in version 3.28.0_rc1 of psi-ms.obo:
=========================================================
[Term]
id: MS:1002038
name: unlabeled sample
def: "A sample that has not been labelled or modified. This is often 
referred to as \"light\" to distinguish from \"heavy\"." [PSI:PI]
synonym: "light labeled sample" EXACT []
is_a: MS:1002018 ! MS1 label-based analysis

[Term]
id: MS:1002039
name: inlet attribute
def: "Inlet properties that are associated with a value." [PSI:MS]
is_a: MS:1000547 ! object attribute
relationship: part_of MS:1000458 ! source

[Term]
id: MS:1002040
name: inlet temperature
def: "The temperature of the inlet of a mass spectrometer." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000482 ! source attribute
is_a: MS:1002039 ! inlet attribute
relationship: has_units UO:0000012 ! kelvin
relationship: has_units UO:0000027 ! degree celsius

[Term]
id: MS:1002041
name: source temperature
def: "The temperature of the source of a mass spectrometer." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000482 ! source attribute
relationship: has_units UO:0000012 ! kelvin
relationship: has_units UO:0000027 ! degree celsius

[Term]
id: MS:1002042
name: modulation time
def: "The duration of a complete cycle of modulation in a comprehensive 
two-dimensional separation system, equals the length of a second 
dimension chromatogram, i.e., the time between two successive injections 
into the second column." 
[http://chromatographyonline.findanalytichem.com/lcgc/Column:+Coupling+Matters/Nomenclature-and-Conventions-in-Comprehensive-Mult/ArticleStandard/Article/detail/58429 
""]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000857 ! run attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum

Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] psi-ms controlled vocabulary psi-ms.obo v.3.27.0 released

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

Dear proteomics community,

attached there's the version 3.27.0 of the psi-ms.obo.

It contains terms used for mzQuantML validation, three new terms for 
nucleic acid base substitution proposed by Ville,
some new terms proposed by Eric for ProteomeXchange datasets.

Changed CV terms in version 3.27.0 of psi-ms.obo:
=================================================
************ The following four terms changed the case from MS1 
Label-based ... to MS1 label-based ... and
************ have the is_a: MS:1002018 ! MS1 label-based analysis relation
[Term]
id: MS:1002001
name: MS1 label-based raw feature quantitation
def: "MS1 label-based raw feature quantitation." [PSI:PI]
is_a: MS:1002018 ! MS1 label-based analysis

[Term]
id: MS:1002002
name: MS1 label-based peptide level quantitation
def: "MS1 label-based peptide level quantitation." [PSI:PI]
is_a: MS:1002018 ! MS1 label-based analysis

[Term]
id: MS:1002003
name: MS1 label-based protein level quantitation
def: "MS1 label-based protein level quantitation." [PSI:PI]
is_a: MS:1002018 ! MS1 label-based analysis

[Term]
id: MS:1002004
name: MS1 label-based proteingroup level quantitation
def: "MS1 label-based proteingroup level quantitation." [PSI:PI]
is_a: MS:1002018 ! MS1 label-based analysis

************ The following term has now an additional publication reference
[Term]
id: MS:1002005
name: iRT retention time normalization standard
def: "A de facto standard providing the retention times at which a 
specific set of 10 reference peptides exit the reference chromatographic 
column. The kit may be obtain from Biognosys." 
[DOI:10.1002/pmic.201100463, 
http://www.biognosys.ch/products/rt-kit.html ""]
is_a: MS:1000901 ! retention time normalization standard

************ Changed the following two terms from ... quantification ... 
to ... quantitation ...
[Term]
id: MS:1002009
name: isobaric label quantitation analysis
def: "Quantitation analysis using an isobaric labeling workflow." [PSI:PI]
is_a: MS:1001833 ! quantitation analysis summary

[Term]
id: MS:1002010
name: TMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher tandem mass tag 
(TMT) labeling workflow." [PSI:PI]
is_a: MS:1001833 ! quantitation analysis summary

************ The following term has now a has_units relationship
[Term]
id: MS:1002012
name: Mascot:PTM site assignment confidence
def: "Relative probability that PTM site assignment is correct, derived 
from the Mascot score difference between matches to the same spectrum 
(Mascot Delta Score)." 
[http://www.matrixscience.com/help/pt_mods_help.html#SITE ""]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001405 ! spectrum identification result details
is_a: MS:1001968 ! PTM localization score
relationship: has_units UO:0000187 ! percent


Newly added CV terms in version 3.27.0 of psi-ms.obo:
=====================================================
[Term]
id: MS:1002015
name: spectral count peptide level quantitation
def: "Spectral count peptide level quantitation." [PSI:PI]
is_a: MS:1001836 ! spectral counting quantitation analysis

[Term]
id: MS:1002016
name: spectral count protein level quantitation
def: "Spectral count protein level quantitation." [PSI:PI]
is_a: MS:1001836 ! spectral counting quantitation analysis

[Term]
id: MS:1002017
name: spectral count proteingroup level quantitation
def: "Spectral count proteingroup level quantitation." [PSI:PI]
is_a: MS:1001836 ! spectral counting quantitation analysis

[Term]
id: MS:1002018
name: MS1 label-based analysis
def: "MS1 label-based analysis." [PSI:PI]
is_a: MS:1001833 ! quantitation analysis summary

[Term]
id: MS:1002019
name: label-free raw feature quantitation
def: "Label-free raw feature quantitation." [PSI:PI]
is_a: MS:1001834 ! LC-MS label-free quantitation analysis

[Term]
id: MS:1002020
name: label-free peptide level quantitation
def: "Label-free peptide level quantitation." [PSI:PI]
is_a: MS:1001834 ! LC-MS label-free quantitation analysis

[Term]
id: MS:1002021
name: label-free protein level quantitation
def: "Label-free protein level quantitation." [PSI:PI]
is_a: MS:1001834 ! LC-MS label-free quantitation analysis

[Term]
id: MS:1002022
name: label-free proteingroup level quantitation
def: "Label-free proteingroup level quantitation." [PSI:PI]
is_a: MS:1001834 ! LC-MS label-free quantitation analysis

[Term]
id: MS:1002023
name: MS2 tag-based analysis
def: "MS2 tag-based analysis." [PSI:PI]
is_a: MS:1001833 ! quantitation analysis summary

[Term]
id: MS:1002024
name: MS2 tag-based feature level quantitation
def: "MS2 tag-based feature level quantitation." [PSI:PI]
is_a: MS:1002023 ! MS2 tag-based analysis

[Term]
id: MS:1002025
name: MS2 tag-based peptide level quantitation
def: "MS2 tag-based peptide level quantitation." [PSI:PI]
is_a: MS:1002023 ! MS2 tag-based analysis

[Term]
id: MS:1002026
name: MS2 tag-based protein level quantitation
def: "MS2 tag-based protein level quantitation." [PSI:PI]
is_a: MS:1002023 ! MS2 tag-based analysis

[Term]
id: MS:1002027
name: MS2 tag-based proteingroup level quantitation
def: "MS2 tag-based proteingroup level quantitation." [PSI:PI]
is_a: MS:1002023 ! MS2 tag-based analysis

[Term]
id: MS:1002028
name: nucleic acid base modification
def: "Nucleic acid base modification (substitution, insertion or 
deletion)." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001471 ! peptide modification details

[Term]
id: MS:1002029
name: original nucleic acid sequence
def: "Original nucleic acid sequence before a nucleic acid base 
modification." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001471 ! peptide modification details

[Term]
id: MS:1002030
name: modified nucleic acid sequence
def: "Modified nucleic acid sequence after a nucleic acid base 
modification." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001471 ! peptide modification details

[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]
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]
is_a: MS:1000878 ! external reference identifier

[Term]
id: MS:1002033
name: contact role
def: "Role of the contact person." [PSI:PI]
is_a: MS:1000585 ! contact attribute

[Term]
id: MS:1002034
name: first author
def: "The first of a set of authors associated with a publication or 
release. There may be more than one first author in cases where several 
authors share primary attribution." [PSI:MS]
is_a: MS:1002033 ! contact role

[Term]
id: MS:1002035
name: senior author
def: "The last of a set of authors associated with a publication or 
release. There may be more than one senior author in cases where several 
authors share senior attribution." [PSI:MS]
is_a: MS:1002033 ! contact role

[Term]
id: MS:1002036
name: co-author
def: "One of a set of authors associated with a publication or release." 
[PSI:MS]
is_a: MS:1002033 ! contact role

[Term]
id: MS:1002037
name: dataset submitter
def: "A person who submits a dataset to a repository." [PSI:MS]
is_a: MS:1002033 ! contact role

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum

Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] mzML for GCxGC/MS ?

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

Hi Steffen, thanks for the input. Yes, this has bothered me for a while
that we use "part_of" in an questionable way. We really need some sort of
relationship "is_attribute_of". Seems like there should be some kind of
relationship like this already. Anyone know?

Thanks,
Eric


> -----Original Message-----
> From: Steffen Neumann [mailto:sne...@ip...]
> Sent: Monday, May 28, 2012 12:48 PM
> To: psi...@li...
> Subject: Re: [Psidev-ms-dev] mzML for GCxGC/MS ?
>
> Hi,
>
> On Thu, 2012-05-24 at 18:10 +0200, Gerhard Mayer wrote:
> > should we also define something like an inlet attribute (referenced
> by
> > inlet temperature)?
>
> Yes, and they were part of the call notes from
> Tue, 1 Nov 2011 "[Psidev-pi-dev] PSI MSS WG call notes"
>
> where the "inlet attribute" had a
>
> 	relationship: part_of MS:1000458 ! source
>
> I don't recall that we wanted to get rid of "object attribute",
> my gut feeling is that from an ontology point of view
> it makes sense to define attributes as such,
> but we should keep the source and inlet attributes in sync
> w.r.t. the "object attribute", which currently lacks
> the "object attribute". OTOH, an attribute such as a temperature
> is hardly a PART_OF a physical device such as an inlet or source.
>
> Yours,
> Steffen
>
> For reference:
>
> [Term]
> id: MS:1000482
> name: source attribute
> def: "Property of a source device that need a value." [PSI:MS]
> relationship: part_of MS:1000458 ! source
>
> --
> IPB Halle                    AG Massenspektrometrie & Bioinformatik
> Dr. Steffen Neumann          http://www.IPB-Halle.DE
> Weinberg 3                   http://msbi.bic-gh.de
> 06120 Halle                  Tel. +49 (0) 345 5582 - 1470
>                                   +49 (0) 345 5582 - 0
> sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409
>
>
>
> -----------------------------------------------------------------------
> -------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond.
> Discussions
> will include endpoint security, mobile security and the latest in
> malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] mzML for GCxGC/MS ?

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

Hi,

On Thu, 2012-05-24 at 18:10 +0200, Gerhard Mayer wrote:
> should we also define something like an inlet attribute (referenced by 
> inlet temperature)?

Yes, and they were part of the call notes from 
Tue, 1 Nov 2011 "[Psidev-pi-dev] PSI MSS WG call notes"

where the "inlet attribute" had a 

	relationship: part_of MS:1000458 ! source
 
I don't recall that we wanted to get rid of "object attribute",
my gut feeling is that from an ontology point of view
it makes sense to define attributes as such,
but we should keep the source and inlet attributes in sync 
w.r.t. the "object attribute", which currently lacks 
the "object attribute". OTOH, an attribute such as a temperature 
is hardly a PART_OF a physical device such as an inlet or source.

Yours,
Steffen

For reference:

[Term]
id: MS:1000482
name: source attribute
def: "Property of a source device that need a value." [PSI:MS]
relationship: part_of MS:1000458 ! source

-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409

Re: [Psidev-ms-dev] mzML for GCxGC/MS ?

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

Hi,

On Thu, 2012-05-24 at 18:10 +0200, Gerhard Mayer wrote:
> should we also define something like an inlet attribute (referenced by 
> inlet temperature)?

We had been discussing this back when I had started the thread. 
I will dig back and suggest the terms again. Stay tuned.

Yours,
Steffen


-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409

Re: [Psidev-ms-dev] mzML for GCxGC/MS ?

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

Hi Gerhard, yes, I think this is probably the right thing to do. I have this
vague recollection that we were trying to do away with "object attribute"
since we introduced data types for each term. But maybe I'm
misremembering...

Thanks,
Eric


> -----Original Message-----
> From: Gerhard Mayer [mailto:Ger...@ru...]
> Sent: Thursday, May 24, 2012 9:11 AM
> To: Mass spectrometry standard development
> Subject: Re: [Psidev-ms-dev] mzML for GCxGC/MS ?
>
> Hi Eric,
>
> should we also define something like an inlet attribute (referenced by
> inlet temperature)?
>
> [Term]
> id: MS:1002039
> name: inlet attribute
> def: "Inlet properties that are associated with a value." [PSI:MS]
> is_a: MS:1000547 ! object attribute
>
> Best,
> Gerhard
>
>
> Am 24.05.2012 01:17, schrieb Eric Deutsch:
> > Hi everyone, I think this issue fell by the wayside a while back. I
> spoke
> > with Nils Hoffmann as ASMS and he urged that we get these in the CV
> so he
> > can use them. So I propose that we add the following terms.
> >
> > Unless there are objections, would you add these at the next
> interval,
> > Gerhard?
> >
> > Thanks!
> > Eric
> >
> > [Term]
> > id: MS:1000XXX
> > name: inlet temperaturedef:
> > "The temperature of the inlet of a mass spectrometer." [PSI:MS]
> > xref: value-type:xsd\:float "The allowed value-type for this CV
> term."
> > is_a: MS:1000482 ! source attribute
> > is_a: MS:1000XXX ! inlet attribute
> > relationship: has_units UO:0000012 ! kelvin
> > relationship: has_units UO:0000027 ! degree celsius
> >
> > [Term]
> > id: MS:1000XXX
> > name: source temperature
> > def: "The temperature of the source of a mass spectrometer." [PSI:MS]
> > xref: value-type:xsd\:float "The allowed value-type for this CV
> term."
> > is_a: MS:1000482 ! source attribute
> > relationship: has_units UO:0000012 ! kelvin
> > relationship: has_units UO:0000027 ! degree celsius
> >
> >   [Term]
> > id: MS:1000XXX
> > name: modulation time
> > def: "The duration of a complete cycle of modulation in a
> comprehensive
> > two-dimensional separation system, equals the length of a second
> dimension
> > chromatogram, i.e., the time between two successive injections into
> the
> > second column."
> >
> [http://chromatographyonline.findanalytichem.com/lcgc/Column:+Coupling+
> Matters/Nomenclature-and-Conventions-in-Comprehensive-
> Mult/ArticleStandard/Article/detail/58429]
> > xref: value-type:xsd\:string "The allowed value-type for this CV
> term."
> > is_a: MS:1000857 ! run attribute
> > relationship: has_units UO:0000010 ! second
> > relationship: has_units UO:0000031 ! minute
> >
> >
> >
> >> -----Original Message-----
> >> From: Steffen Neumann [mailto:sne...@ip...]
> >> Sent: Friday, May 27, 2011 12:46 AM
> >> To: Mass spectrometry standard development
> >> Subject: Re: [Psidev-ms-dev] mzML for GCxGC/MS ?
> >>
> >> Hi,
> >>
> >> On Sun, 2011-03-20 at 19:00 +0100, Oliver Kohlbacher wrote:
> >> ...
> >>> Conceptually, I would consider those just a single {L|G}C-MS run.
> >>> Information on how the 1D RT should be mapped to 2D coordinates
> >>> should be provided in addition to that. We could basically
> >>> store a relation assigning each scan two or more retention
> >>> coordinates (retention times or an index for the primary
> separation,
> >>> which would also make it comparable to offline fractionation).
> >> I now got my hands on some example data from Nils Hoffmann
> >> http://www.cebitec.uni-bielefeld.de/~hoffmann/files/GCxGC-MS-
> >> LECO.tar.bz2
> >> which I converted with the OpenMS-1.8 FileConverter
> >> http://msbi.ipb-halle.de/~sneumann/GCxGC_leco.mzML.bz2
> >>
> >> 1) OpenMS is already able to extract some information from the
> netCDF
> >>     where we lack the proper cvTerms. I would suggest
> >>     (also see separate mail on "inlet attribute")
> >>
> >> [Term]
> >> id: MS:1000XXX
> >> name: inlet temperature
> >> def: "Inlet temperature." [PSI:MS]
> >> xref: value-type:xsd\:float "The allowed value-type for this CV
> term."
> >> is_a: MS:1000482 ! source attribute
> >> is_a: MS:1000XXX ! inlet attribute
> >> relationship: has_units UO:0000012 ! kelvin
> >> relationship: has_units UO:0000027 ! degree celsius
> >>
> >> [Term]
> >> id: MS:1000XXX
> >> name: source temperature
> >> def: "Source temperature ... ." [PSI:MS]
> >> xref: value-type:xsd\:float "The allowed value-type for this CV
> term."
> >> is_a: MS:1000482 ! source attribute
> >> relationship: has_units UO:0000012 ! kelvin
> >> relationship: has_units UO:0000027 ! degree celsius
> >>
> >> 2a) For GCxGC, we need to specify the 2D coordinate / time system.
> >>     I would minimally suggest a new "run attribute":
> >>
> >> [Term]
> >> id: MS:1000XXX
> >> name: modulation time
> >> def: "The duration of a complete cycle of modulation in a
> comprehensive
> >> two-dimensional separation system, equals the length of a second
> >> dimension chromatogram, i.e., the time between two successive
> >> injections
> >> into the second column." [not PSI:MS ?]
> >> xref: value-type:xsd\:string "The allowed value-type for this CV
> term."
> >> is_a: MS:1000857 ! run attribute
> >> relationship: has_units UO:0000010 ! second
> >> relationship: has_units UO:0000031 ! minute
> >>
> >>     BTW: how do we "cite" the definition ? I it took from
> >>
> >>
> http://chromatographyonline.findanalytichem.com/lcgc/Column:+Coupling+M
> >> atters/Nomenclature-and-Conventions-in-Comprehensive-
> >> Mult/ArticleStandard/Article/detail/58429
> >>     There are tons more terms in this paper.
> >>
> >> 2b) Alternatively/additionally, we'd need to be able to add
> >>      several dimensions to the scan attribute "elution time".
> >>
> >>       MS:1000503 ! scan attribute
> >>       + MS:1000826 ! elution time
> >>         + MS:1000XXX ! first column elution time (def: Retention
> time of
> >> a
> >>                                     peak in the first dimension of a
> >>                                     comprehensive two-dimensional
> >> system)
> >>         + MS:1000XXX ! second column elution time (def: ... second
> ...)
> >>         + MS:1000XXX ! third column elution time
> >>         ...
> >>         + MS:1000XXX ! seventh column elution time (you get the idea
> >> ...)
> >>
> >>       Does anyone have a better idea ? Please ? Or is this
> reasonable
> >>       with current (and anticipated) seperation techniques ?
> >>       The paper above also lists GCϫGCϫGC, LC–GCϫGC or ...
> >>       I don't like the ordering in the name, but anything else would
> >>       rather be in the scope of sepML, and we still need to
> reference
> >>       several elution times.
> >>
> >> Usually, the 2a) modulation time is the "run attribute" that is
> >> programmed
> >> into the GCxGC-MS system when you run your samples. The actual
> elution
> >> times for each scan could be 2b) adjusted / corrected if there are
> any
> >> shifts/deviations (for whatever reason) within the run.
> >>
> >> Thoughts ?
> >>
> >> Yours,
> >> Steffen
> >>
> >> Just for reference, here is the netCDF metadata from above file(s):
> >>
> >> netcdf header information GCxGC {
> >> dimensions:
> >> ...
> >> 	point_number = UNLIMITED ; // (43969157 currently)
> >> 	scan_number = 100001 ;
> >> variables:
> >> ...
> >> // global attributes:
> >> 		:netcdf_file_date_time_stamp = "20090325161325+0100" ;
> >> 		:experiment_date_time_stamp = "20090306200015+0100" ;
> >> 		:experiment_type = "Centroided Mass Spectrum" ;
> >> 		:test_separation_type = "Gas-Liquid Chromatography" ;
> >> 		:test_ms_inlet = "Capillary Direct" ;
> >> 		:test_ms_inlet_temperature = 275.f ;
> >> 		:test_ionization_mode = "Electron Impact" ;
> >> 		:test_ionization_polarity = "Positive Polarity" ;
> >> 		:test_source_temperature = 200.f ;
> >> 		:test_accelerating_potential = -600.f ;
> >> 		:test_detector_type = "Electron Multiplier" ;
> >> 		:test_detector_potential = -1600.f ;
> >> 		:test_resolution_type = "Constant Resolution" ;
> >> 		:test_scan_function = "Mass Scan" ;
> >> 		:test_scan_direction = "Up" ;
> >> 		:test_scan_law = "Linear" ;
> >> 		:test_scan_time = 0.0002f ;
> >> ...
> >> }
> >>
> >>
> >> --
> >> IPB Halle                    AG Massenspektrometrie&  Bioinformatik
> >> Dr. Steffen Neumann          http://www.IPB-Halle.DE
> >> Weinberg 3                   http://msbi.bic-gh.de
> >> 06120 Halle                  Tel. +49 (0) 345 5582 - 1470
> >>                                    +49 (0) 345 5582 - 0
> >> sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409
> >>
> >>
> >>
> >> --------------------------------------------------------------------
> ---
> >> -------
> >> vRanger cuts backup time in half-while increasing security.
> >> With the market-leading solution for virtual backup and recovery,
> >> you get blazing-fast, flexible, and affordable data protection.
> >> Download your free trial now.
> >> http://p.sf.net/sfu/quest-d2dcopy1
> >> _______________________________________________
> >> Psidev-ms-dev mailing list
> >> Psi...@li...
> >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> > ---------------------------------------------------------------------
> ---------
> > Live Security Virtual Conference
> > Exclusive live event will cover all the ways today's security and
> > threat landscape has changed and how IT managers can respond.
> Discussions
> > will include endpoint security, mobile security and the latest in
> malware
> > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> > _______________________________________________
> > Psidev-ms-dev mailing list
> > Psi...@li...
> > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>
>
> --
> ---
> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> BioInformatik
> Medizinisches-Proteom-Center (MPC)
> Ruhr-Universität Bochum
> Zentrum für klinische Forschung I (ZKF I)
> E.042
> Universitätsstrasse 150
> D-44801 Bochum
>
> Phone:	+49(0)234/32-29836
> Fax:	+49(0)234/32-14554
> Email:	Ger...@ru...
> Web:	http://www.medizinisches-proteom-center.de
>
>
> -----------------------------------------------------------------------
> -------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond.
> Discussions
> will include endpoint security, mobile security and the latest in
> malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] mzML for GCxGC/MS ?

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

Hi Eric,

should we also define something like an inlet attribute (referenced by 
inlet temperature)?

[Term]
id: MS:1002039
name: inlet attribute
def: "Inlet properties that are associated with a value." [PSI:MS]
is_a: MS:1000547 ! object attribute

Best,
Gerhard


Am 24.05.2012 01:17, schrieb Eric Deutsch:
> Hi everyone, I think this issue fell by the wayside a while back. I spoke
> with Nils Hoffmann as ASMS and he urged that we get these in the CV so he
> can use them. So I propose that we add the following terms.
>
> Unless there are objections, would you add these at the next interval,
> Gerhard?
>
> Thanks!
> Eric
>
> [Term]
> id: MS:1000XXX
> name: inlet temperaturedef:
> "The temperature of the inlet of a mass spectrometer." [PSI:MS]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000482 ! source attribute
> is_a: MS:1000XXX ! inlet attribute
> relationship: has_units UO:0000012 ! kelvin
> relationship: has_units UO:0000027 ! degree celsius
>
> [Term]
> id: MS:1000XXX
> name: source temperature
> def: "The temperature of the source of a mass spectrometer." [PSI:MS]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000482 ! source attribute
> relationship: has_units UO:0000012 ! kelvin
> relationship: has_units UO:0000027 ! degree celsius
>
>   [Term]
> id: MS:1000XXX
> name: modulation time
> def: "The duration of a complete cycle of modulation in a comprehensive
> two-dimensional separation system, equals the length of a second dimension
> chromatogram, i.e., the time between two successive injections into the
> second column."
> [http://chromatographyonline.findanalytichem.com/lcgc/Column:+Coupling+Matters/Nomenclature-and-Conventions-in-Comprehensive-Mult/ArticleStandard/Article/detail/58429]
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1000857 ! run attribute
> relationship: has_units UO:0000010 ! second
> relationship: has_units UO:0000031 ! minute
>
>
>
>> -----Original Message-----
>> From: Steffen Neumann [mailto:sne...@ip...]
>> Sent: Friday, May 27, 2011 12:46 AM
>> To: Mass spectrometry standard development
>> Subject: Re: [Psidev-ms-dev] mzML for GCxGC/MS ?
>>
>> Hi,
>>
>> On Sun, 2011-03-20 at 19:00 +0100, Oliver Kohlbacher wrote:
>> ...
>>> Conceptually, I would consider those just a single {L|G}C-MS run.
>>> Information on how the 1D RT should be mapped to 2D coordinates
>>> should be provided in addition to that. We could basically
>>> store a relation assigning each scan two or more retention
>>> coordinates (retention times or an index for the primary separation,
>>> which would also make it comparable to offline fractionation).
>> I now got my hands on some example data from Nils Hoffmann
>> http://www.cebitec.uni-bielefeld.de/~hoffmann/files/GCxGC-MS-
>> LECO.tar.bz2
>> which I converted with the OpenMS-1.8 FileConverter
>> http://msbi.ipb-halle.de/~sneumann/GCxGC_leco.mzML.bz2
>>
>> 1) OpenMS is already able to extract some information from the netCDF
>>     where we lack the proper cvTerms. I would suggest
>>     (also see separate mail on "inlet attribute")
>>
>> [Term]
>> id: MS:1000XXX
>> name: inlet temperature
>> def: "Inlet temperature." [PSI:MS]
>> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>> is_a: MS:1000482 ! source attribute
>> is_a: MS:1000XXX ! inlet attribute
>> relationship: has_units UO:0000012 ! kelvin
>> relationship: has_units UO:0000027 ! degree celsius
>>
>> [Term]
>> id: MS:1000XXX
>> name: source temperature
>> def: "Source temperature ... ." [PSI:MS]
>> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>> is_a: MS:1000482 ! source attribute
>> relationship: has_units UO:0000012 ! kelvin
>> relationship: has_units UO:0000027 ! degree celsius
>>
>> 2a) For GCxGC, we need to specify the 2D coordinate / time system.
>>     I would minimally suggest a new "run attribute":
>>
>> [Term]
>> id: MS:1000XXX
>> name: modulation time
>> def: "The duration of a complete cycle of modulation in a comprehensive
>> two-dimensional separation system, equals the length of a second
>> dimension chromatogram, i.e., the time between two successive
>> injections
>> into the second column." [not PSI:MS ?]
>> xref: value-type:xsd\:string "The allowed value-type for this CV term."
>> is_a: MS:1000857 ! run attribute
>> relationship: has_units UO:0000010 ! second
>> relationship: has_units UO:0000031 ! minute
>>
>>     BTW: how do we "cite" the definition ? I it took from
>>
>> http://chromatographyonline.findanalytichem.com/lcgc/Column:+Coupling+M
>> atters/Nomenclature-and-Conventions-in-Comprehensive-
>> Mult/ArticleStandard/Article/detail/58429
>>     There are tons more terms in this paper.
>>
>> 2b) Alternatively/additionally, we'd need to be able to add
>>      several dimensions to the scan attribute "elution time".
>>
>>       MS:1000503 ! scan attribute
>>       + MS:1000826 ! elution time
>>         + MS:1000XXX ! first column elution time (def: Retention time of
>> a
>>                                     peak in the first dimension of a
>>                                     comprehensive two-dimensional
>> system)
>>         + MS:1000XXX ! second column elution time (def: ... second ...)
>>         + MS:1000XXX ! third column elution time
>>         ...
>>         + MS:1000XXX ! seventh column elution time (you get the idea
>> ...)
>>
>>       Does anyone have a better idea ? Please ? Or is this reasonable
>>       with current (and anticipated) seperation techniques ?
>>       The paper above also lists GCϫGCϫGC, LC–GCϫGC or ...
>>       I don't like the ordering in the name, but anything else would
>>       rather be in the scope of sepML, and we still need to reference
>>       several elution times.
>>
>> Usually, the 2a) modulation time is the "run attribute" that is
>> programmed
>> into the GCxGC-MS system when you run your samples. The actual elution
>> times for each scan could be 2b) adjusted / corrected if there are any
>> shifts/deviations (for whatever reason) within the run.
>>
>> Thoughts ?
>>
>> Yours,
>> Steffen
>>
>> Just for reference, here is the netCDF metadata from above file(s):
>>
>> netcdf header information GCxGC {
>> dimensions:
>> ...
>> 	point_number = UNLIMITED ; // (43969157 currently)
>> 	scan_number = 100001 ;
>> variables:
>> ...
>> // global attributes:
>> 		:netcdf_file_date_time_stamp = "20090325161325+0100" ;
>> 		:experiment_date_time_stamp = "20090306200015+0100" ;
>> 		:experiment_type = "Centroided Mass Spectrum" ;
>> 		:test_separation_type = "Gas-Liquid Chromatography" ;
>> 		:test_ms_inlet = "Capillary Direct" ;
>> 		:test_ms_inlet_temperature = 275.f ;
>> 		:test_ionization_mode = "Electron Impact" ;
>> 		:test_ionization_polarity = "Positive Polarity" ;
>> 		:test_source_temperature = 200.f ;
>> 		:test_accelerating_potential = -600.f ;
>> 		:test_detector_type = "Electron Multiplier" ;
>> 		:test_detector_potential = -1600.f ;
>> 		:test_resolution_type = "Constant Resolution" ;
>> 		:test_scan_function = "Mass Scan" ;
>> 		:test_scan_direction = "Up" ;
>> 		:test_scan_law = "Linear" ;
>> 		:test_scan_time = 0.0002f ;
>> ...
>> }
>>
>>
>> --
>> IPB Halle                    AG Massenspektrometrie&  Bioinformatik
>> Dr. Steffen Neumann          http://www.IPB-Halle.DE
>> Weinberg 3                   http://msbi.bic-gh.de
>> 06120 Halle                  Tel. +49 (0) 345 5582 - 1470
>>                                    +49 (0) 345 5582 - 0
>> sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409
>>
>>
>>
>> -----------------------------------------------------------------------
>> -------
>> vRanger cuts backup time in half-while increasing security.
>> With the market-leading solution for virtual backup and recovery,
>> you get blazing-fast, flexible, and affordable data protection.
>> Download your free trial now.
>> http://p.sf.net/sfu/quest-d2dcopy1
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev


-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum

Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] mzML for GCxGC/MS ?

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

Hi everyone, I think this issue fell by the wayside a while back. I spoke
with Nils Hoffmann as ASMS and he urged that we get these in the CV so he
can use them. So I propose that we add the following terms.

Unless there are objections, would you add these at the next interval,
Gerhard?

Thanks!
Eric

[Term]
id: MS:1000XXX
name: inlet temperaturedef:
"The temperature of the inlet of a mass spectrometer." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000482 ! source attribute
is_a: MS:1000XXX ! inlet attribute
relationship: has_units UO:0000012 ! kelvin
relationship: has_units UO:0000027 ! degree celsius

[Term]
id: MS:1000XXX
name: source temperature
def: "The temperature of the source of a mass spectrometer." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000482 ! source attribute
relationship: has_units UO:0000012 ! kelvin
relationship: has_units UO:0000027 ! degree celsius

 [Term]
id: MS:1000XXX
name: modulation time
def: "The duration of a complete cycle of modulation in a comprehensive
two-dimensional separation system, equals the length of a second dimension
chromatogram, i.e., the time between two successive injections into the
second column."
[http://chromatographyonline.findanalytichem.com/lcgc/Column:+Coupling+Matters/Nomenclature-and-Conventions-in-Comprehensive-Mult/ArticleStandard/Article/detail/58429]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000857 ! run attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute



> -----Original Message-----
> From: Steffen Neumann [mailto:sne...@ip...]
> Sent: Friday, May 27, 2011 12:46 AM
> To: Mass spectrometry standard development
> Subject: Re: [Psidev-ms-dev] mzML for GCxGC/MS ?
>
> Hi,
>
> On Sun, 2011-03-20 at 19:00 +0100, Oliver Kohlbacher wrote:
> ...
> > Conceptually, I would consider those just a single {L|G}C-MS run.
> > Information on how the 1D RT should be mapped to 2D coordinates
> > should be provided in addition to that. We could basically
> > store a relation assigning each scan two or more retention
> > coordinates (retention times or an index for the primary separation,
> > which would also make it comparable to offline fractionation).
>
> I now got my hands on some example data from Nils Hoffmann
> http://www.cebitec.uni-bielefeld.de/~hoffmann/files/GCxGC-MS-
> LECO.tar.bz2
> which I converted with the OpenMS-1.8 FileConverter
> http://msbi.ipb-halle.de/~sneumann/GCxGC_leco.mzML.bz2
>
> 1) OpenMS is already able to extract some information from the netCDF
>    where we lack the proper cvTerms. I would suggest
>    (also see separate mail on "inlet attribute")
>
> [Term]
> id: MS:1000XXX
> name: inlet temperature
> def: "Inlet temperature." [PSI:MS]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000482 ! source attribute
> is_a: MS:1000XXX ! inlet attribute
> relationship: has_units UO:0000012 ! kelvin
> relationship: has_units UO:0000027 ! degree celsius
>
> [Term]
> id: MS:1000XXX
> name: source temperature
> def: "Source temperature ... ." [PSI:MS]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000482 ! source attribute
> relationship: has_units UO:0000012 ! kelvin
> relationship: has_units UO:0000027 ! degree celsius
>
> 2a) For GCxGC, we need to specify the 2D coordinate / time system.
>    I would minimally suggest a new "run attribute":
>
> [Term]
> id: MS:1000XXX
> name: modulation time
> def: "The duration of a complete cycle of modulation in a comprehensive
> two-dimensional separation system, equals the length of a second
> dimension chromatogram, i.e., the time between two successive
> injections
> into the second column." [not PSI:MS ?]
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1000857 ! run attribute
> relationship: has_units UO:0000010 ! second
> relationship: has_units UO:0000031 ! minute
>
>    BTW: how do we "cite" the definition ? I it took from
>
> http://chromatographyonline.findanalytichem.com/lcgc/Column:+Coupling+M
> atters/Nomenclature-and-Conventions-in-Comprehensive-
> Mult/ArticleStandard/Article/detail/58429
>    There are tons more terms in this paper.
>
> 2b) Alternatively/additionally, we'd need to be able to add
>     several dimensions to the scan attribute "elution time".
>
>      MS:1000503 ! scan attribute
>      + MS:1000826 ! elution time
>        + MS:1000XXX ! first column elution time (def: Retention time of
> a
>                                    peak in the first dimension of a
>                                    comprehensive two-dimensional
> system)
>        + MS:1000XXX ! second column elution time (def: ... second ...)
>        + MS:1000XXX ! third column elution time
>        ...
>        + MS:1000XXX ! seventh column elution time (you get the idea
> ...)
>
>      Does anyone have a better idea ? Please ? Or is this reasonable
>      with current (and anticipated) seperation techniques ?
>      The paper above also lists GCϫGCϫGC, LC–GCϫGC or ...
>      I don't like the ordering in the name, but anything else would
>      rather be in the scope of sepML, and we still need to reference
>      several elution times.
>
> Usually, the 2a) modulation time is the "run attribute" that is
> programmed
> into the GCxGC-MS system when you run your samples. The actual elution
> times for each scan could be 2b) adjusted / corrected if there are any
> shifts/deviations (for whatever reason) within the run.
>
> Thoughts ?
>
> Yours,
> Steffen
>
> Just for reference, here is the netCDF metadata from above file(s):
>
> netcdf header information GCxGC {
> dimensions:
> ...
> 	point_number = UNLIMITED ; // (43969157 currently)
> 	scan_number = 100001 ;
> variables:
> ...
> // global attributes:
> 		:netcdf_file_date_time_stamp = "20090325161325+0100" ;
> 		:experiment_date_time_stamp = "20090306200015+0100" ;
> 		:experiment_type = "Centroided Mass Spectrum" ;
> 		:test_separation_type = "Gas-Liquid Chromatography" ;
> 		:test_ms_inlet = "Capillary Direct" ;
> 		:test_ms_inlet_temperature = 275.f ;
> 		:test_ionization_mode = "Electron Impact" ;
> 		:test_ionization_polarity = "Positive Polarity" ;
> 		:test_source_temperature = 200.f ;
> 		:test_accelerating_potential = -600.f ;
> 		:test_detector_type = "Electron Multiplier" ;
> 		:test_detector_potential = -1600.f ;
> 		:test_resolution_type = "Constant Resolution" ;
> 		:test_scan_function = "Mass Scan" ;
> 		:test_scan_direction = "Up" ;
> 		:test_scan_law = "Linear" ;
> 		:test_scan_time = 0.0002f ;
> ...
> }
>
>
> --
> IPB Halle                    AG Massenspektrometrie & Bioinformatik
> Dr. Steffen Neumann          http://www.IPB-Halle.DE
> Weinberg 3                   http://msbi.bic-gh.de
> 06120 Halle                  Tel. +49 (0) 345 5582 - 1470
>                                   +49 (0) 345 5582 - 0
> sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409
>
>
>
> -----------------------------------------------------------------------
> -------
> vRanger cuts backup time in half-while increasing security.
> With the market-leading solution for virtual backup and recovery,
> you get blazing-fast, flexible, and affordable data protection.
> Download your free trial now.
> http://p.sf.net/sfu/quest-d2dcopy1
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] Gettings started with the MS Standard

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

Hi Gerhard, thank you for forwarding the communication. I presented our
work on mzML and related at one of their telecons a few years ago.

Regards,
Eric


> -----Original Message-----
> From: Gerhard Mayer [mailto:Ger...@ru...]
> Sent: Thursday, May 10, 2012 2:24 AM
> To: psi...@li...; psidev-pi-
> de...@li...; Mass spectrometry standard development
> Subject: Re: [Psidev-ms-dev] Gettings started with the MS Standard
>
> Hello proteomics community,
>
> just for information I forward you the mail from Mark Bean from the
> AnIML group.
>
> Best Regards,
> Gerhard
>
> Am 09.05.2012 18:24, schrieb Mark Bean:
> > Dear Gerhard
> >
> > In that case, I am pleased to establish contact!  Thank you for the
> links.  I have subscribed silently to Psidev-pi-dev mailings for ages,
> but haven't kept up.  I should have, and now it is a bit harder to get
> started.
> >
> > AnIML has been going a long time (encapsulating all of analytical
> chemistry through volunteer efforts isn't the fastest car on the
> highway), perhaps too long.  Our web presence has been intentionally
> small because one or two of the major analytical companies started
> selling products that "supported AnIML" long before we had a standard.
> However, we do have the beginnings of a useful website at
> http://animl.sourceforge.net/ (or http://www.animl.org/ which is the
> same).
> >
> > The AnIML schemas are locked, undergoing a final punch-list review
> prior to documentation (we have funds for this from various instrument
> and pharmaceutical companies).  There are two schemas:  one constrains
> all AnIML data files and is immutable, the other constrains the
> Technique Definitions or Technique Extensions that the committee or
> other people create.  The Technique Definitions in turn also constrain
> the AnIML files for terminology, units, content for each Technique
> used.  And herein is a bit of an oddity in that xml AnIML files are
> constrained by another xml Technique Definition, which is not a schema,
> forcing us to create our own validator.
> >
> > So far we have UV-Vis, Chromatography techniques completed, and are
> currently working on NMR and MS.  When those are completed, we will
> ballot the standard and make it public through ASTM.  Originally we
> were working in collaboration with IUPAC, but I'm not sure how active
> their participation is these days.
> >
> > The chief architect of AnIML is Burkhard Schaefer (his father is a
> computer science professor in your country), based on work Burkhard did
> at the National Institute of Standards (NIST) in Washington, DC.  His
> e-mail is b.s...@bs...
> >
> > Best regards, and thanks for the fast response!  I hope to have more
> discussions in the future.
> >
> > Mark
> >
> >
> > -----Original Message-----
> > From: Gerhard Mayer [mailto:Ger...@ru...]
> > Sent: Wednesday, May 09, 2012 11:59 AM
> > To: Mark Bean
> > Subject: Re: Gettings started with the MS Standard
> >
> > Hello Mark,
> >
> > I think we didn't met or talked before, but of course any cooperation
> > between AnIML and psi-ms is always welcome.
> > As I understood AnIML is about spectroscopy of small molecules. Is
> that
> > correct?
> > Can you please send me back an official link to the AnIML?
> >
> > Since this year I am coordinating the psi-ms.obo ontology.
> > You can find it at
> > http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-
> ms/mzML/controlledVocabulary/psi-ms.obo
> > You can open the .obo file in any text editor or by use of OBO-Edit
> > http://oboedit.org/
> >
> > We have also a mailing list, which you can subscribe, so that you
> stay
> > informed with the latest developments of psi-ms.obo:
> > psi...@li...
> >
> > Best Regards,
> > Gerhard
> >
> > Am 09.05.2012 17:19, schrieb Mark Bean:
> >> ASTM E13 Committee on Analytical Data Standards (AnIML)
> --
> ---
> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> BioInformatik
> Medizinisches-Proteom-Center (MPC)
> Ruhr-Universität Bochum
> Zentrum für klinische Forschung I (ZKF I)
> E.042
> Universitätsstrasse 150
> D-44801 Bochum
>
> Phone:	+49(0)234/32-29836
> Fax:	+49(0)234/32-14554
> Email:	Ger...@ru...
> Web:	http://www.medizinisches-proteom-center.de
>
>
> -----------------------------------------------------------------------
> -------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond.
> Discussions
> will include endpoint security, mobile security and the latest in
> malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] Gettings started with the MS Standard

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

Hello proteomics community,

just for information I forward you the mail from Mark Bean from the 
AnIML group.

Best Regards,
Gerhard

Am 09.05.2012 18:24, schrieb Mark Bean:
> Dear Gerhard
>
> In that case, I am pleased to establish contact!  Thank you for the links.  I have subscribed silently to Psidev-pi-dev mailings for ages, but haven't kept up.  I should have, and now it is a bit harder to get started.
>
> AnIML has been going a long time (encapsulating all of analytical chemistry through volunteer efforts isn't the fastest car on the highway), perhaps too long.  Our web presence has been intentionally small because one or two of the major analytical companies started selling products that "supported AnIML" long before we had a standard.  However, we do have the beginnings of a useful website at http://animl.sourceforge.net/ (or http://www.animl.org/ which is the same).
>
> The AnIML schemas are locked, undergoing a final punch-list review prior to documentation (we have funds for this from various instrument and pharmaceutical companies).  There are two schemas:  one constrains all AnIML data files and is immutable, the other constrains the Technique Definitions or Technique Extensions that the committee or other people create.  The Technique Definitions in turn also constrain the AnIML files for terminology, units, content for each Technique used.  And herein is a bit of an oddity in that xml AnIML files are constrained by another xml Technique Definition, which is not a schema, forcing us to create our own validator.
>
> So far we have UV-Vis, Chromatography techniques completed, and are currently working on NMR and MS.  When those are completed, we will ballot the standard and make it public through ASTM.  Originally we were working in collaboration with IUPAC, but I'm not sure how active their participation is these days.
>
> The chief architect of AnIML is Burkhard Schaefer (his father is a computer science professor in your country), based on work Burkhard did at the National Institute of Standards (NIST) in Washington, DC.  His e-mail is b.s...@bs...
>
> Best regards, and thanks for the fast response!  I hope to have more discussions in the future.
>
> Mark
>
>
> -----Original Message-----
> From: Gerhard Mayer [mailto:Ger...@ru...]
> Sent: Wednesday, May 09, 2012 11:59 AM
> To: Mark Bean
> Subject: Re: Gettings started with the MS Standard
>
> Hello Mark,
>
> I think we didn't met or talked before, but of course any cooperation
> between AnIML and psi-ms is always welcome.
> As I understood AnIML is about spectroscopy of small molecules. Is that
> correct?
> Can you please send me back an official link to the AnIML?
>
> Since this year I am coordinating the psi-ms.obo ontology.
> You can find it at
> http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo
> You can open the .obo file in any text editor or by use of OBO-Edit
> http://oboedit.org/
>
> We have also a mailing list, which you can subscribe, so that you stay
> informed with the latest developments of psi-ms.obo:
> psi...@li...
>
> Best Regards,
> Gerhard
>
> Am 09.05.2012 17:19, schrieb Mark Bean:
>> ASTM E13 Committee on Analytical Data Standards (AnIML)
-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum

Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Release candidate psi-ms.obo v.3.26.0_rc1

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

Dear proteomics community,

attached there's the release candidate 3.26.0_rc1 of the psi-ms.obo.

It contains terms used for mzQuantML validation.
We can discuss them during our mzQuantML teleconference today.

Comments and further proposals are as always welcome.


We have already defined the following terms for use in AnalysisSummary 
of mzQuantML:
====================================================================================
MS:1001833 quantitation analysis summary
MS:1001834 LC-MS label-free quantitation analysis
MS:1001835 SILAC quantitation analysis
MS:1001836 spectral counting quantitation analysis
MS:1001837 iTRAQ quantitation analysis
MS:1001838 SRM quantitation analysis
MS:1001839 metabolic labeling 14N / 15N quantitation analysis
MS:1002001 MS1 Label-based raw feature quantitation
MS:1002002 MS1 Label-based peptide level quantitation
MS:1002003 MS1 Label-based protein level quantitation
MS:1002004 MS1 Label-based proteinGroup level quantitation
MS:1002009 isobaric label quantification analysis
MS:1002010 TMT quantification analysis


Newly added CV terms in version 3.26.0_rc1 of psi-ms.obo:
==========================================================
[Term]
id: MS:1002015
name: spectral count peptide level quantitation
def: "Spectral count peptide level quantitation." [PSI:PI]
is_a: MS:1001836 ! spectral counting quantitation analysis

[Term]
id: MS:1002016
name: spectral count protein level quantitation
def: "Spectral count protein level quantitation." [PSI:PI]
is_a: MS:1001836 ! spectral counting quantitation analysis

[Term]
id: MS:1002017
name: spectral count proteingroup level quantitation
def: "Spectral count proteingroup level quantitation." [PSI:PI]
is_a: MS:1001836 ! spectral counting quantitation analysis

[Term]
id: MS:1002018
name: MS1 label-based analysis
def: "MS1 label-based analysis." [PSI:PI]
is_a: MS:1001833 ! quantitation analysis summary

[Term]
id: MS:1002019
name: label-free raw feature quantitation
def: "Label-free raw feature quantitation." [PSI:PI]
is_a: MS:1001834 ! LC-MS label-free quantitation analysis

[Term]
id: MS:1002020
name: label-free peptide level quantitation
def: "Label-free peptide level quantitation." [PSI:PI]
is_a: MS:1001834 ! LC-MS label-free quantitation analysis

[Term]
id: MS:1002021
name: label-free protein level quantitation
def: "Label-free protein level quantitation." [PSI:PI]
is_a: MS:1001834 ! LC-MS label-free quantitation analysis

[Term]
id: MS:1002022
name: label-free proteingroup level quantitation
def: "Label-free proteingroup level quantitation." [PSI:PI]
is_a: MS:1001834 ! LC-MS label-free quantitation analysis

[Term]
id: MS:1002023
name: MS2 tag-based analysis
def: "MS2 tag-based analysis." [PSI:PI]
is_a: MS:1001833 ! quantitation analysis summary

[Term]
id: MS:1002024
name: MS2 tag-based feature level quantitation
def: "MS2 tag-based feature level quantitation." [PSI:PI]
is_a: MS:1002023 ! MS2 tag-based analysis

[Term]
id: MS:1002025
name: MS2 tag-based peptide level quantitation
def: "MS2 tag-based peptide level quantitation." [PSI:PI]
is_a: MS:1002023 ! MS2 tag-based analysis

[Term]
id: MS:1002026
name: MS2 tag-based protein level quantitation
def: "MS2 tag-based protein level quantitation." [PSI:PI]
is_a: MS:1002023 ! MS2 tag-based analysis

[Term]
id: MS:1002027
name: MS2 tag-based proteingroup level quantitation
def: "MS2 tag-based proteingroup level quantitation." [PSI:PI]
is_a: MS:1002023 ! MS2 tag-based analysis


Changed CV terms in version 3.26.0_rc1 of psi-ms.obo:
=====================================================
************ The following terms changed the case from MS1 Label-based 
... to MS1 label-based ... and
************ have the is_a: MS:1002018 ! MS1 label-based analysis relation
[Term]
id: MS:1002001
name: MS1 label-based raw feature quantitation
def: "MS1 label-based raw feature quantitation." [PSI:PI]
is_a: MS:1002018 ! MS1 label-based analysis

[Term]
id: MS:1002002
name: MS1 label-based peptide level quantitation
def: "MS1 label-based peptide level quantitation." [PSI:PI]
is_a: MS:1002018 ! MS1 label-based analysis

[Term]
id: MS:1002003
name: MS1 label-based protein level quantitation
def: "MS1 label-based protein level quantitation." [PSI:PI]
is_a: MS:1002018 ! MS1 label-based analysis

[Term]
id: MS:1002004
name: MS1 label-based proteingroup level quantitation
def: "MS1 label-based proteingroup level quantitation." [PSI:PI]
is_a: MS:1002018 ! MS1 label-based analysis


Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum

Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] Malware in the PSI web site

[Laurent G. <lg...@ca...>]

Hi Juan,

The following link [1], references in the mzTab specs, still points
towards an infected page.

Best wishes,

Laurent

[1] http://psidev.sourceforge.net/mod/data/PSI-MOD.obo


On 17 April 2012 08:01, Juan Antonio Vizcaino <ju...@eb...> wrote:
> Dear all,
>
> Sorry I could not reply to your e-mails individually. Since Sunday, I am attending a meeting in Spain and it has been quite busy here.
>
> I received the notification on Friday evening from Google. At the moment I am afraid there is not much we can do. The problem is that the drupal version in the old site is too old and I don't think it makes much sense try to 'fix' the old page.
>
> The alternative is then to move to the new web page that Henning introduced briefly in San Diego. However, there are a few issues. One of the main ones is how to maintain the links that have been included in the related publications. We will do our best but at the moment we don't have anyone who can especifically do the work so this will need to go on top of everything else for a couple of people. The content will not be as updated as in the old site and that means that the content will need to be enriched gradually in time. But that should not be a problem.
>
> Something that could help is that you send me the links you think have been included in your PSI related publications. That way we can try to create aliases for them.
>
> Best regards,
>
> Juan Antonio
>
>
>
>
> ------------------------------------------------------------------------------
> Better than sec? Nothing is better than sec when it comes to
> monitoring Big Data applications. Try Boundary one-second
> resolution app monitoring today. Free.
> http://p.sf.net/sfu/Boundary-dev2dev
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev



-- 
Laurent Gatto
- http://proteome.sysbiol.cam.ac.uk/lgatto/
Cambridge Centre for Proteomics
- http://www.bio.cam.ac.uk/proteomics

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate psi-ms.obo v.3.25.0_rc2

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

Hi Gerhard, this all looks good to me. Thank you for your continued
diligent efforts!

May I ask that you make one additional change in the upcoming commit?

Would you change all instances of "parts per notation unit" to just "parts
per notation"? This is a (rather dubious IMHO) change in the unit ontology
that we'll just follow. We have a few units that use this as a parent.

Thank you!
Eric


> -----Original Message-----
> From: Gerhard Mayer [mailto:Ger...@ru...]
> Sent: Friday, May 04, 2012 4:32 AM
> To: psi...@li...; Mass spectrometry standard
> development; psi...@li...
> Subject: [Psidev-ms-vocab] Release candidate psi-ms.obo v.3.25.0_rc2
>
> Dear proteomics community,
>
> attached there's the release candidate 3.25.0_rc2 of the psi-ms.obo.
>
> It contains some terms with added synonyms resp. changed datatype.
> Also a lot of the ProteomeDiscoverer terms were obsoleted in order to
> avoid the use of duplicate terms.
>
> In addition two new terms proposed by Eric for labeled quantification
> analyses, a term for DESI and
> two terms for specifying a collision energy ramp were added.
>
> Comments and proposals are as always welcome.
> If there are no objections it's planned to release the new version on
> 9th May.
>
>
> Changed CV terms in version 3.25.0-rc2 of psi-ms.obo:
> =====================================================
> ************ Added synonym "collision activated dissociation" and CAD
> [Term]
> id: MS:1000133
> name: collision-induced dissociation
> def: "The dissociation of an ion after collisional excitation. The term
> collisional-activated dissociation is not recommended." [PSI:MS]
> synonym: "CID" EXACT []
> synonym: "CAD" EXACT []
> synonym: "collision activated dissociation" EXACT []
> is_a: MS:1000044 ! dissociation method
>
> ************ Added synonym "HCD"
> [Term]
> id: MS:1000422
> name: high-energy collision-induced dissociation
> def: "A collision-induced dissociation process wherein the projectile
> ion has the translational energy higher than approximately 1000 eV."
> [PSI:MS]
> synonym: "HCD" EXACT []
> is_a: MS:1000044 ! dissociation method
>
> ************ Added synonym "MPD"
> [Term]
> id: MS:1000435
> name: photodissociation
> def: "A process wherein the reactant ion is dissociated as a result of
> absorption of one or more photons." [PSI:MS]
> synonym: "multiphoton dissociation" EXACT []
> synonym: "MPD" EXACT []
> is_a: MS:1000044 ! dissociation method
>
> ************ Changed the datatype to xsd:nonNegativeInteger
> [Term]
> id: MS:1001962
> name: Mascot:C13 counts
> def: "C13 peaks to use in peak detection." [PSI:MS]
> xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for
> this CV term."
> is_a: MS:1001302 ! search engine specific input parameter
>
> ************ Changed the is_a relation according to new hierarchy (see
> 'Newly added CV terms')
> [Term]
> id: MS:1001837
> name: iTRAQ quantitation analysis
> def: "Quantification analysis using the AB SCIEX iTRAQ isobaric
> labeling
> workflow, wherein 2-8 reporter ions are measured in MS/MS spectra near
> 114 m/z." [PSI:PI]
> is_a: MS:1002009 ! isobaric label quantification analysis
>
> ************ Obsoleted the term Mascot:use MudPIT scoring
> [Term]
> id: MS:1001667
> name: Mascot:use MudPIT scoring
> def: "OBSOLETE Determines whether to use MudPIT or normal scoring."
> [PSI:MS]
> comment: This term was made obsolete because it's recommended to use
> Mascot:ProteinScoringMethod (MS:1001318) instead.
> xref: value-type:xsd\:boolean "The allowed value-type for this CV
> term."
> is_a: MS:1001302 ! search engine specific input parameter
> is_obsolete: true
>
>
>
> The following ProteomeDiscoverer terms are now made obsolete:
> =============================================================
> *************************************************************
> [Term]
> id: MS:1001601
> name: ProteomeDiscoverer:Spectrum Files:Raw File names
> def: "OBSOLETE Name and location of the .raw file or files." [PSI:MS]
> comment: This term was made obsolete because it's recommended to use
> one
> of the 'mass spectrometer file format' terms (MS:1000560) instead.
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001302 ! search engine specific input parameter
> is_obsolete: true
>
> [Term]
> id: MS:1001602
> name: ProteomeDiscoverer:SRF File Selector:SRF File Path
> def: "OBSOLETE Path and name of the .srf (Sequest Result Format) file."
> [PSI:MS]
> comment: This term was made obsolete. Use attribute in mzIdentML /
> mzQuantML instead.
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001302 ! search engine specific input parameter
> is_obsolete: true
>
> [Term]
> id: MS:1001603
> name: ProteomeDiscoverer:Spectrum Selector:Ionization Source
> def: "OBSOLETE Ionization source (electro-, nano-, thermospray,
> electron
> impact, APCI, MALDI, FAB etc)." [PSI:MS]
> comment: This term was made obsolete because it's recommended to use
> one
> of the 'inlet type' (MS:1000007)or 'ionization type' (MS:1000008) terms
> instead.
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001302 ! search engine specific input parameter
> is_obsolete: true
>
> [Term]
> id: MS:1001604
> name: ProteomeDiscoverer:Activation Type
> def: "OBSOLETE Fragmentation method used (CID, MPD, ECD, PQD, ETD, HCD,
> Any)." [PSI:MS]
> comment: This term was made obsolete because it's recommended to use
> one
> of the 'ionization type' terms (MS:1000008) instead.
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001302 ! search engine specific input parameter
> is_obsolete: true
>
> [Term]
> id: MS:1001606
> name: ProteomeDiscoverer:Mass Analyzer
> def: "OBSOLETE Type of mass spectrometer used (ITMS, FTMS, TOFMS, SQMS,
> TQMS, SectorMS)." [PSI:MS]
> comment: This term was made obsolete because it's recommended to use
> mass analyzer type (MS:1000443) instead.
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001302 ! search engine specific input parameter
> is_obsolete: true
>
> [Term]
> id: MS:1001610
> name: ProteomeDiscoverer:MS Order
> def: "OBSOLETE Level of the mass spectrum (MS/MS=MS2 ... MS10)."
> [PSI:MS]
> comment: This term was made obsolete because it's recommended to use
> MS1
> spectrum (MS:1000579) or MSn spectrum (MS:1000580) instead.
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001302 ! search engine specific input parameter
> is_obsolete: true
>
> [Term]
> id: MS:1001611
> name: ProteomeDiscoverer:Polarity Mode
> def: "OBSOLETE Polarity mode (positive or negative)." [PSI:MS]
> comment: This term was made obsolete because it's recommended to use
> scan polarity (MS:1000465) instead.
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001302 ! search engine specific input parameter
> is_obsolete: true
>
> [Term]
> id: MS:1001614
> name: ProteomeDiscoverer:Scan Type
> def: "OBSOLETE Scan type for the precursor ion (full, Single Ion
> Monitoring (SIM), Single Reaction Monitoring (SRM))." [PSI:MS]
> comment: This term was made obsolete because it's recommended to use
> MS1
> spectrum (MS:1000579), MSn spectrum (MS:1000580), CRM spectrum
> (MS:1000581), SIM spectrum (MS:1000582) or SRM spectrum (MS:1000583)
> instead.
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001302 ! search engine specific input parameter
> is_obsolete: true
>
> [Term]
> id: MS:1001631
> name: ProteomeDiscoverer:Spectrum Grouper:Max RT Difference
> def: "OBSOLETE Chromatographic window where precursors to be grouped
> must reside to be considered the same species." [PSI:MS]
> comment: This term was made obsolete because it's recommended to use
> retention time window width (MS:1001907) instead.
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1001302 ! search engine specific input parameter
> is_obsolete: true
>
> [Term]
> id: MS:1001634
> name: ProteomeDiscoverer:Xtract:Highest MZ
> def: "OBSOLETE Highest mass-to-charge (mz) value for spectral peaks in
> the measured spectrum that are considered for Xtract." [PSI:MS]
> comment: This term was made obsolete because it's recommended to use
> scan window upper limit (MS:1000500) instead.
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1001302 ! search engine specific input parameter
> is_obsolete: true
>
> [Term]
> id: MS:1001636
> name: ProteomeDiscoverer:Xtract:Lowest MZ
> def: "OBSOLETE Lowest mass-to-charge (mz) value for spectral peaks in
> the measured spectrum that are considered for Xtract." [PSI:MS]
> comment: This term was made obsolete because it's recommended to use
> scan window lower limit (MS:1000501) instead.
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1001302 ! search engine specific input parameter
> is_obsolete: true
>
> [Term]
> id: MS:1001646
> name: ProteomeDiscoverer:Mascot:Decoy Search
> def: "OBSOLETE Determines whether the Proteome Discoverer application
> searches an additional decoy database." [PSI:MS]
> comment: This term was made obsolete because it's recommended to use
> quality estimation with decoy database (MS:1001194) instead.
> xref: value-type:xsd\:boolean "The allowed value-type for this CV
> term."
> is_a: MS:1001302 ! search engine specific input parameter
> is_obsolete: true
>
> [Term]
> id: MS:1001652
> name: ProteomeDiscoverer:Mascot:User Name
> def: "OBSOLETE Name of the user submitting the Mascot search." [PSI:MS]
> comment: This term was made obsolete because it's recommended to use
> researcher (MS:1001271) instead.
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001302 ! search engine specific input parameter
> is_obsolete: true
>
> [Term]
> id: MS:1001654
> name: ProteomeDiscoverer:Enzyme Name
> def: "OBSOLETE Specifies the enzyme reagent used for protein
> digestion."
> [PSI:MS]
> comment: This term was made obsolete because it's recommended to use
> cleavage agent name (MS:1001045) instead.
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001302 ! search engine specific input parameter
> is_obsolete: true
>
> [Term]
> id: MS:1001655
> name: ProteomeDiscoverer:Fragment Mass Tolerance
> def: "OBSOLETE Mass tolerance used for matching fragment peaks in Da or
> mmu." [PSI:MS]
> comment: This term was made obsolete because it's recommended to use
> search tolerance minus value (MS:1001413) or search tolerance plus
> value
> (MS:1001412) instead.
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1001302 ! search engine specific input parameter
> is_obsolete: true
>
> [Term]
> id: MS:1001659
> name: ProteomeDiscoverer:Precursor Mass Tolerance
> def: "OBSOLETE Mass window for which precursor ions are considered to
> be
> the same species." [PSI:MS]
> comment: This term was made obsolete because it's recommended to use
> search tolerance minus value (MS:1001413) or search tolerance plus
> value
> (MS:1001412) instead.
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1001302 ! search engine specific input parameter
> is_obsolete: true
>
> [Term]
> id: MS:1001661
> name: ProteomeDiscoverer:Protein Database
> def: "OBSOLETE Database to use in the search (configured on the Mascot
> server)." [PSI:MS]
> comment: This term was made obsolete because it's recommended to use
> database name (MS:1001013) instead.
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001302 ! search engine specific input parameter
> is_obsolete: true
>
> [Term]
> id: MS:1001665
> name: ProteomeDiscoverer:Mascot:Taxonomy
> def: "OBSOLETE Limits searches to entries from a particular species or
> group of species." [PSI:MS]
> comment: This term was made obsolete because it's recommended to use
> taxonomy: scientific name (MS:1001469) instead.
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001302 ! search engine specific input parameter
> is_obsolete: true
>
> [Term]
> id: MS:1001666
> name: ProteomeDiscoverer:Use Average Precursor Mass
> def: "OBSOLETE Use average mass for the precursor." [PSI:MS]
> comment: This term was made obsolete because it's recommended to use
> parent mass type average (MS:1001212) instead.
> xref: value-type:xsd\:boolean "The allowed value-type for this CV
> term."
> is_a: MS:1001302 ! search engine specific input parameter
> is_obsolete: true
>
> [Term]
> id: MS:1001682
> name: ProteomeDiscoverer:Search Against Decoy Database
> def: "OBSOLETE Determines whether the Proteome Discoverer application
> searches against a decoy database." [PSI:MS]
> comment: This term was made obsolete because it's recommended to use
> quality estimation with decoy database (MS:1001194) instead.
> xref: value-type:xsd\:boolean "The allowed value-type for this CV
> term."
> is_a: MS:1001302 ! search engine specific input parameter
> is_obsolete: true
>
> [Term]
> id: MS:1001701
> name: ProteomeDiscoverer:Spectrum Exporter:Export Format
> def: "OBSOLETE Format of the exported spectra (dta, mgf or mzData)."
> [PSI:MS]
> comment: This term was made obsolete because it's recommended to use
> one
> of the 'mass spectrometer file format' terms (MS:1000560) instead.
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001302 ! search engine specific input parameter
> is_obsolete: true
>
> [Term]
> id: MS:1001734
> name: ProteomeDiscoverer:Organism
> def: "OBSOLETE Sample organism (used for annotation purposes)."
> [PSI:MS]
> comment: This term was made obsolete because it's recommended to use
> taxonomy: scientific name (MS:1001469) instead.
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001302 ! search engine specific input parameter
> is_obsolete: true
>
> [Term]
> id: MS:1001735
> name: ProteomeDiscoverer:Reference Database
> def: "OBSOLETE Full path database name." [PSI:MS]
> comment: This term was made obsolete. Use attribute in mzIdentML /
> mzQuantML instead.
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001302 ! search engine specific input parameter
> is_obsolete: true
>
> [Term]
> id: MS:1001737
> name: ProteomeDiscoverer:Source file extension
> def: "OBSOLETE File type (if not pepXML)." [PSI:MS]
> comment: This term was made obsolete because it's recommended to use
> mass spectrometer file format (MS:1000560) instead.
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001302 ! search engine specific input parameter
> is_obsolete: true
>
> [Term]
> id: MS:1001738
> name: ProteomeDiscoverer:Source Files
> def: "OBSOLETE Input pepXML files." [PSI:MS]
> comment: This term was made obsolete because it's recommended to use
> pepXML file (MS:1001421) instead.
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001302 ! search engine specific input parameter
> is_obsolete: true
>
> [Term]
> id: MS:1001739
> name: ProteomeDiscoverer:Source Files old
> def: "OBSOLETE Input pepXML files (old)." [PSI:MS]
> comment: This term was made obsolete because it's recommended to use
> pepXML file (MS:1001421) instead.
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001302 ! search engine specific input parameter
> is_obsolete: true
>
>
>
> Newly added CV terms in version 3.25.0-rc2 of psi-ms.obo:
> =========================================================
> [Term]
> id: MS:1002009
> name: isobaric label quantification analysis
> def: "Quantification analysis using an isobaric labeling workflow."
> [PSI:PI]
> is_a: MS:1001833 ! quantitation analysis summary
>
> [Term]
> id: MS:1002010
> name: TMT quantification analysis
> def: "Quantification analysis using the Thermo Fisher tandem mass tag
> (TMT) labeling workflow." [PSI:PI]
> is_a: MS:1001833 ! quantitation analysis summary
>
> [Term]
> id: MS:1002011
> name: desorption electrospray ionization
> def: "Combination of electrospray and desorption ionization method that
> ionizes gases, liquids and solids in open air under atmospheric
> pressure." [DOI:10.1126/science.1104404, PMID:15486296]
> synonym: "DESI" EXACT []
> is_a: MS:1000240 ! atmospheric pressure ionization
>
> [Term]
> id: MS:1002012
> name: Mascot:PTM site assignment confidence
> def: "Relative probability that PTM site assignment is correct, derived
> from the Mascot score difference between matches to the same spectrum
> (Mascot Delta Score)."
> [http://www.matrixscience.com/help/pt_mods_help.html#SITE ""]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1001153 ! search engine specific score
> is_a: MS:1001143 ! search engine specific score for peptides
> is_a: MS:1001405 ! spectrum identification result details
> is_a: MS:1001968 ! PTM localization score
>
> [Term]
> id: MS:1002013
> name: collision energy ramp start
> def: "Collision energy at the start of the collision energy ramp."
> [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000045 ! collision energy
> relationship: has_units UO:0000266 ! electronvolt
>
> [Term]
> id: MS:1002014
> name: collision energy ramp end
> def: "Collision energy at the end of the collision energy ramp."
> [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000045 ! collision energy
> relationship: has_units UO:0000266 ! electronvolt
>
> Best Regards,
> Gerhard
>
> --
> ---
> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> BioInformatik
> Medizinisches-Proteom-Center (MPC)
> Ruhr-Universität Bochum
> Zentrum für klinische Forschung I (ZKF I)
> E.042
> Universitätsstrasse 150
> D-44801 Bochum
>
> Phone:	+49(0)234/32-29836
> Fax:	+49(0)234/32-14554
> Email:	Ger...@ru...
> Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Release candidate psi-ms.obo v.3.25.0_rc2

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

Dear proteomics community,

attached there's the release candidate 3.25.0_rc2 of the psi-ms.obo.

It contains some terms with added synonyms resp. changed datatype.
Also a lot of the ProteomeDiscoverer terms were obsoleted in order to 
avoid the use of duplicate terms.

In addition two new terms proposed by Eric for labeled quantification 
analyses, a term for DESI and
two terms for specifying a collision energy ramp were added.

Comments and proposals are as always welcome.
If there are no objections it's planned to release the new version on 
9th May.


Changed CV terms in version 3.25.0-rc2 of psi-ms.obo:
=====================================================
************ Added synonym "collision activated dissociation" and CAD
[Term]
id: MS:1000133
name: collision-induced dissociation
def: "The dissociation of an ion after collisional excitation. The term 
collisional-activated dissociation is not recommended." [PSI:MS]
synonym: "CID" EXACT []
synonym: "CAD" EXACT []
synonym: "collision activated dissociation" EXACT []
is_a: MS:1000044 ! dissociation method

************ Added synonym "HCD"
[Term]
id: MS:1000422
name: high-energy collision-induced dissociation
def: "A collision-induced dissociation process wherein the projectile 
ion has the translational energy higher than approximately 1000 eV." 
[PSI:MS]
synonym: "HCD" EXACT []
is_a: MS:1000044 ! dissociation method

************ Added synonym "MPD"
[Term]
id: MS:1000435
name: photodissociation
def: "A process wherein the reactant ion is dissociated as a result of 
absorption of one or more photons." [PSI:MS]
synonym: "multiphoton dissociation" EXACT []
synonym: "MPD" EXACT []
is_a: MS:1000044 ! dissociation method

************ Changed the datatype to xsd:nonNegativeInteger
[Term]
id: MS:1001962
name: Mascot:C13 counts
def: "C13 peaks to use in peak detection." [PSI:MS]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for 
this CV term."
is_a: MS:1001302 ! search engine specific input parameter

************ Changed the is_a relation according to new hierarchy (see 
'Newly added CV terms')
[Term]
id: MS:1001837
name: iTRAQ quantitation analysis
def: "Quantification analysis using the AB SCIEX iTRAQ isobaric labeling 
workflow, wherein 2-8 reporter ions are measured in MS/MS spectra near 
114 m/z." [PSI:PI]
is_a: MS:1002009 ! isobaric label quantification analysis

************ Obsoleted the term Mascot:use MudPIT scoring
[Term]
id: MS:1001667
name: Mascot:use MudPIT scoring
def: "OBSOLETE Determines whether to use MudPIT or normal scoring." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
Mascot:ProteinScoringMethod (MS:1001318) instead.
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true



The following ProteomeDiscoverer terms are now made obsolete:
=============================================================
*************************************************************
[Term]
id: MS:1001601
name: ProteomeDiscoverer:Spectrum Files:Raw File names
def: "OBSOLETE Name and location of the .raw file or files." [PSI:MS]
comment: This term was made obsolete because it's recommended to use one 
of the 'mass spectrometer file format' terms (MS:1000560) instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001602
name: ProteomeDiscoverer:SRF File Selector:SRF File Path
def: "OBSOLETE Path and name of the .srf (Sequest Result Format) file." 
[PSI:MS]
comment: This term was made obsolete. Use attribute in mzIdentML / 
mzQuantML instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001603
name: ProteomeDiscoverer:Spectrum Selector:Ionization Source
def: "OBSOLETE Ionization source (electro-, nano-, thermospray, electron 
impact, APCI, MALDI, FAB etc)." [PSI:MS]
comment: This term was made obsolete because it's recommended to use one 
of the 'inlet type' (MS:1000007)or 'ionization type' (MS:1000008) terms  
instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001604
name: ProteomeDiscoverer:Activation Type
def: "OBSOLETE Fragmentation method used (CID, MPD, ECD, PQD, ETD, HCD, 
Any)." [PSI:MS]
comment: This term was made obsolete because it's recommended to use one 
of the 'ionization type' terms (MS:1000008) instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001606
name: ProteomeDiscoverer:Mass Analyzer
def: "OBSOLETE Type of mass spectrometer used (ITMS, FTMS, TOFMS, SQMS, 
TQMS, SectorMS)." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
mass analyzer type (MS:1000443) instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001610
name: ProteomeDiscoverer:MS Order
def: "OBSOLETE Level of the mass spectrum (MS/MS=MS2 ... MS10)." [PSI:MS]
comment: This term was made obsolete because it's recommended to use MS1 
spectrum (MS:1000579) or MSn spectrum (MS:1000580) instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001611
name: ProteomeDiscoverer:Polarity Mode
def: "OBSOLETE Polarity mode (positive or negative)." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
scan polarity (MS:1000465) instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001614
name: ProteomeDiscoverer:Scan Type
def: "OBSOLETE Scan type for the precursor ion (full, Single Ion 
Monitoring (SIM), Single Reaction Monitoring (SRM))." [PSI:MS]
comment: This term was made obsolete because it's recommended to use MS1 
spectrum (MS:1000579), MSn spectrum (MS:1000580), CRM spectrum 
(MS:1000581), SIM spectrum (MS:1000582) or SRM spectrum (MS:1000583) 
instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001631
name: ProteomeDiscoverer:Spectrum Grouper:Max RT Difference
def: "OBSOLETE Chromatographic window where precursors to be grouped 
must reside to be considered the same species." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
retention time window width (MS:1001907) instead.
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001634
name: ProteomeDiscoverer:Xtract:Highest MZ
def: "OBSOLETE Highest mass-to-charge (mz) value for spectral peaks in 
the measured spectrum that are considered for Xtract." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
scan window upper limit (MS:1000500) instead.
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001636
name: ProteomeDiscoverer:Xtract:Lowest MZ
def: "OBSOLETE Lowest mass-to-charge (mz) value for spectral peaks in 
the measured spectrum that are considered for Xtract." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
scan window lower limit (MS:1000501) instead.
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001646
name: ProteomeDiscoverer:Mascot:Decoy Search
def: "OBSOLETE Determines whether the Proteome Discoverer application 
searches an additional decoy database." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
quality estimation with decoy database (MS:1001194) instead.
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001652
name: ProteomeDiscoverer:Mascot:User Name
def: "OBSOLETE Name of the user submitting the Mascot search." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
researcher (MS:1001271) instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001654
name: ProteomeDiscoverer:Enzyme Name
def: "OBSOLETE Specifies the enzyme reagent used for protein digestion." 
[PSI:MS]
comment: This term was made obsolete because it's recommended to use 
cleavage agent name (MS:1001045) instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001655
name: ProteomeDiscoverer:Fragment Mass Tolerance
def: "OBSOLETE Mass tolerance used for matching fragment peaks in Da or 
mmu." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
search tolerance minus value (MS:1001413) or search tolerance plus value 
(MS:1001412) instead.
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001659
name: ProteomeDiscoverer:Precursor Mass Tolerance
def: "OBSOLETE Mass window for which precursor ions are considered to be 
the same species." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
search tolerance minus value (MS:1001413) or search tolerance plus value 
(MS:1001412) instead.
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001661
name: ProteomeDiscoverer:Protein Database
def: "OBSOLETE Database to use in the search (configured on the Mascot 
server)." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
database name (MS:1001013) instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001665
name: ProteomeDiscoverer:Mascot:Taxonomy
def: "OBSOLETE Limits searches to entries from a particular species or 
group of species." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
taxonomy: scientific name (MS:1001469) instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001666
name: ProteomeDiscoverer:Use Average Precursor Mass
def: "OBSOLETE Use average mass for the precursor." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
parent mass type average (MS:1001212) instead.
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001682
name: ProteomeDiscoverer:Search Against Decoy Database
def: "OBSOLETE Determines whether the Proteome Discoverer application 
searches against a decoy database." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
quality estimation with decoy database (MS:1001194) instead.
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001701
name: ProteomeDiscoverer:Spectrum Exporter:Export Format
def: "OBSOLETE Format of the exported spectra (dta, mgf or mzData)." 
[PSI:MS]
comment: This term was made obsolete because it's recommended to use one 
of the 'mass spectrometer file format' terms (MS:1000560) instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001734
name: ProteomeDiscoverer:Organism
def: "OBSOLETE Sample organism (used for annotation purposes)." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
taxonomy: scientific name (MS:1001469) instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001735
name: ProteomeDiscoverer:Reference Database
def: "OBSOLETE Full path database name." [PSI:MS]
comment: This term was made obsolete. Use attribute in mzIdentML / 
mzQuantML instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001737
name: ProteomeDiscoverer:Source file extension
def: "OBSOLETE File type (if not pepXML)." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
mass spectrometer file format (MS:1000560) instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001738
name: ProteomeDiscoverer:Source Files
def: "OBSOLETE Input pepXML files." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
pepXML file (MS:1001421) instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001739
name: ProteomeDiscoverer:Source Files old
def: "OBSOLETE Input pepXML files (old)." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
pepXML file (MS:1001421) instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true



Newly added CV terms in version 3.25.0-rc2 of psi-ms.obo:
=========================================================
[Term]
id: MS:1002009
name: isobaric label quantification analysis
def: "Quantification analysis using an isobaric labeling workflow." [PSI:PI]
is_a: MS:1001833 ! quantitation analysis summary

[Term]
id: MS:1002010
name: TMT quantification analysis
def: "Quantification analysis using the Thermo Fisher tandem mass tag 
(TMT) labeling workflow." [PSI:PI]
is_a: MS:1001833 ! quantitation analysis summary

[Term]
id: MS:1002011
name: desorption electrospray ionization
def: "Combination of electrospray and desorption ionization method that 
ionizes gases, liquids and solids in open air under atmospheric 
pressure." [DOI:10.1126/science.1104404, PMID:15486296]
synonym: "DESI" EXACT []
is_a: MS:1000240 ! atmospheric pressure ionization

[Term]
id: MS:1002012
name: Mascot:PTM site assignment confidence
def: "Relative probability that PTM site assignment is correct, derived 
from the Mascot score difference between matches to the same spectrum 
(Mascot Delta Score)." 
[http://www.matrixscience.com/help/pt_mods_help.html#SITE ""]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001405 ! spectrum identification result details
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1002013
name: collision energy ramp start
def: "Collision energy at the start of the collision energy ramp." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000045 ! collision energy
relationship: has_units UO:0000266 ! electronvolt

[Term]
id: MS:1002014
name: collision energy ramp end
def: "Collision energy at the end of the collision energy ramp." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000045 ! collision energy
relationship: has_units UO:0000266 ! electronvolt

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum

Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] Converting TripleTOF data to centroid mode ?

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

This is timely since we were discussing this earlier in the week. I think
it would be great to add "collision energy ramp start" and "collision
energy ramp end" values to the CV and allow them as an alternative to just
a plain collision energy. I guess the assumption is that the ramp is
linear. One would only need to know the dwell time to calculate the slope.
But the slope probably doesn't matter, really. Just knowing that the CE
went from X to Y during the dwell should be sufficient, I would think.

Objections to adding those two terms and updating the mapping file?

Thanks,
Eric


> -----Original Message-----
> From: Matthew Chambers [mailto:mat...@gm...]
> Sent: Wednesday, May 02, 2012 10:35 AM
> To: Ralf Tautenhahn; Mass spectrometry standard development
> Subject: Re: [Psidev-ms-dev] Converting TripleTOF data to centroid mode
> ?
>
> Hi Ralf,
>
> I'm forwarding this to the psidev-ms mailing list.
>
> mzML doesn't support ramped CEs, but we could add it somehow. Something
> like "collision energy ramp
> start" and another term for the end. It wouldn't define the kind of
> slope, but representing that
> would need an equation.
>
> -Matt
>
>
> On 5/2/2012 12:24 PM, Ralf Tautenhahn wrote:
> > I'm testing it at the moment converting Triple TOF data to centroid
> mode, everything works great so
> > far! I manually verified that the files are in centroid mode. I also
> like the <comment>ABI/Analyst peak
> > picking</comment>.
> >
> > I talked to AB/Sciex yesterday and it seems that they are also
> working on fixing the missing
> > collision energy issue. It looks like one of the problems they have
> is that they don't know how to represent their ramped
> > collision energy modes, e.g. 35 +/- 15 V
> > Do the *XML dialects support ramped CEs ?
> >
> > Thanks again,
> > Ralf
> >
> > On 05/02/2012 09:35 AM, Matthew Chambers wrote:
> >> Wow. You're on the ball! Yes, the build is running now:
> >>
> http://teamcity.labkey.org:8080/viewType.html?tab=buildTypeStatusDiv&bu
> ildTypeId=bt36
> >>
> >> -Matt
> >>
> >>
> >> On 5/2/2012 11:32 AM, Ralf Tautenhahn wrote:
> >>> Hi Matt,
> >>>
> >>> I noticed that you committed
> >>>
> >>> Rev. 3589 "- re-enabled vendor peak picking for the .NET 4 version
> of the WiffFile API"
> >>>
> >>> Thank you!
> >>>
> >>> The current d/l is 3.0.3569. I assume the new binary (3589) will be
> build automatically?
> >>> I am looking forward to try it!
> >>>
> >>> Regards,
> >>> Ralf
> >
>
> -----------------------------------------------------------------------
> -------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond.
> Discussions
> will include endpoint security, mobile security and the latest in
> malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] Converting TripleTOF data to centroid mode ?

[Matthew C. <mat...@gm...>]

Hi Ralf,

I'm forwarding this to the psidev-ms mailing list.

mzML doesn't support ramped CEs, but we could add it somehow. Something like "collision energy ramp 
start" and another term for the end. It wouldn't define the kind of slope, but representing that 
would need an equation.

-Matt


On 5/2/2012 12:24 PM, Ralf Tautenhahn wrote:
> I'm testing it at the moment converting Triple TOF data to centroid mode, everything works great so
> far! I manually verified that the files are in centroid mode. I also like the <comment>ABI/Analyst peak
> picking</comment>.
>
> I talked to AB/Sciex yesterday and it seems that they are also working on fixing the missing
> collision energy issue. It looks like one of the problems they have is that they don't know how to represent their ramped
> collision energy modes, e.g. 35 +/- 15 V
> Do the *XML dialects support ramped CEs ?
>
> Thanks again,
> Ralf
>
> On 05/02/2012 09:35 AM, Matthew Chambers wrote:
>> Wow. You're on the ball! Yes, the build is running now:
>> http://teamcity.labkey.org:8080/viewType.html?tab=buildTypeStatusDiv&buildTypeId=bt36
>>
>> -Matt
>>
>>
>> On 5/2/2012 11:32 AM, Ralf Tautenhahn wrote:
>>> Hi Matt,
>>>
>>> I noticed that you committed
>>>
>>> Rev. 3589 "- re-enabled vendor peak picking for the .NET 4 version of the WiffFile API"
>>>
>>> Thank you!
>>>
>>> The current d/l is 3.0.3569. I assume the new binary (3589) will be build automatically?
>>> I am looking forward to try it!
>>>
>>> Regards,
>>> Ralf
>

[Psidev-ms-dev] psi-ms controlled vocabulary psi-ms.obo v.3.25.0_rc1

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

Dear proteomics community,

attached there's the release candidate 3.25.0_rc1 of the psi-ms.obo.

It contains some terms with added synonyms resp. changed datatype.
Also a lot of the ProteomeDiscoverer terms were obsoleted in order to 
avoid the use of duplicate terms.
In addition two new terms proposed by Eric for labeled quantification 
analyses and a term for DESI were added.

Comments and proposals are as always welcome.
If there are no objections it's planned to release the new version on 
9th May.


Changed CV terms in version 3.25.0-rc1 of psi-ms.obo:
=====================================================
************ Added synonym "collision activated dissociation" and "CAD"
[Term]
id: MS:1000133
name: collision-induced dissociation
def: "The dissociation of an ion after collisional excitation. The term 
collisional-activated dissociation is not recommended." [PSI:MS]
synonym: "CID" EXACT []
synonym: "CAD" EXACT []
synonym: "collision activated dissociation" EXACT []
is_a: MS:1000044 ! dissociation method

************ Added synonym "HCD"
[Term]
id: MS:1000422
name: high-energy collision-induced dissociation
def: "A collision-induced dissociation process wherein the projectile 
ion has the translational energy higher than approximately 1000 eV." 
[PSI:MS]
synonym: "HCD" EXACT []
is_a: MS:1000044 ! dissociation method

************ Added synonym "MPD"
[Term]
id: MS:1000435
name: photodissociation
def: "A process wherein the reactant ion is dissociated as a result of 
absorption of one or more photons." [PSI:MS]
synonym: "Multiphoton Dissociation" EXACT []
synonym: "MPD" EXACT []
is_a: MS:1000044 ! dissociation method

************ Added the datatype xsd:nonNegativeInteger 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." [PSI:MS]
synonym: "multiple-stage mass spectrometry spectrum" EXACT []
synonym: "nth generation product ion spectrum" EXACT []
synonym: "product ion spectrum" EXACT []
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for 
this CV term."
is_a: MS:1000294 ! mass spectrum
is_a: MS:1000524 ! data file content

************ Changed the datatype to xsd:nonNegativeInteger
[Term]
id: MS:1001962
name: Mascot:C13 counts
def: "C13 peaks to use in peak detection." [PSI:MS]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for 
this CV term."
is_a: MS:1001302 ! search engine specific input parameter

************ Changed the is_a relation according to new hierarchy (see 
'Newly added CV terms')
[Term]
id: MS:1001837
name: iTRAQ quantitation analysis
def: "Quantification analysis using the AB SCIEX iTRAQ isobaric labeling 
workflow, wherein 2-8 reporter ions are measured in MS/MS spectra near 
114 m/z." [PSI:PI]
is_a: MS:1002009 ! isobaric label quantification analysis



The following ProteomeDiscoverer terms are now made obsolete:
=============================================================
*************************************************************
[Term]
id: MS:1001601
name: ProteomeDiscoverer:Spectrum Files:Raw File names
def: "OBSOLETE Name and location of the .raw file or files." [PSI:MS]
comment: This term was made obsolete because it's recommended to use one 
of the 'mass spectrometer file format' terms (MS:1000560) instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001602
name: ProteomeDiscoverer:SRF File Selector:SRF File Path
def: "OBSOLETE Path and name of the .srf (Sequest Result Format) file." 
[PSI:MS]
comment: This term was made obsolete. Use attribute in mzIdentML / 
mzQuantML instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001603
name: ProteomeDiscoverer:Spectrum Selector:Ionization Source
def: "OBSOLETE Ionization source (electro-, nano-, thermospray, electron 
impact, APCI, MALDI, FAB etc)." [PSI:MS]
comment: This term was made obsolete because it's recommended to use one 
of the 'inlet type' (MS:1000007)or 'ionization type' (MS:1000008) terms  
instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001604
name: ProteomeDiscoverer:Activation Type
def: "OBSOLETE Fragmentation method used (CID, MPD, ECD, PQD, ETD, HCD, 
Any)." [PSI:MS]
comment: This term was made obsolete because it's recommended to use one 
of the 'ionization type' terms (MS:1000008) instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001606
name: ProteomeDiscoverer:Mass Analyzer
def: "OBSOLETE Type of mass spectrometer used (ITMS, FTMS, TOFMS, SQMS, 
TQMS, SectorMS)." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
mass analyzer type (MS:1000443) instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001610
name: ProteomeDiscoverer:MS Order
def: "OBSOLETE Level of the mass spectrum (MS/MS=MS2 ... MS10)." [PSI:MS]
comment: This term was made obsolete because it's recommended to use MS1 
spectrum (MS:1000579) or MSn spectrum (MS:1000580) instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001611
name: ProteomeDiscoverer:Polarity Mode
def: "OBSOLETE Polarity mode (positive or negative)." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
scan polarity (MS:1000465) instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001614
name: ProteomeDiscoverer:Scan Type
def: "OBSOLETE Scan type for the precursor ion (full, Single Ion 
Monitoring (SIM), Single Reaction Monitoring (SRM))." [PSI:MS]
comment: This term was made obsolete because it's recommended to use MS1 
spectrum (MS:1000579), MSn spectrum (MS:1000580), CRM spectrum 
(MS:1000581), SIM spectrum (MS:1000582) or SRM spectrum (MS:1000583) 
instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001631
name: ProteomeDiscoverer:Spectrum Grouper:Max RT Difference
def: "OBSOLETE Chromatographic window where precursors to be grouped 
must reside to be considered the same species." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
retention time window width (MS:1001907) instead.
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001634
name: ProteomeDiscoverer:Xtract:Highest MZ
def: "OBSOLETE Highest mass-to-charge (mz) value for spectral peaks in 
the measured spectrum that are considered for Xtract." [PSI:MS]
comment: This term was made obsolete because it's recommended to use one 
of the scan window upper limit (MS:1000500) instead.
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001636
name: ProteomeDiscoverer:Xtract:Lowest MZ
def: "OBSOLETE Lowest mass-to-charge (mz) value for spectral peaks in 
the measured spectrum that are considered for Xtract." [PSI:MS]
comment: This term was made obsolete because it's recommended to use one 
of the scan window lower limit (MS:1000501) instead.
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001646
name: ProteomeDiscoverer:Mascot:Decoy Search
def: "OBSOLETE Determines whether the Proteome Discoverer application 
searches an additional decoy database." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
quality estimation with decoy database (MS:1001194) instead.
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001652
name: ProteomeDiscoverer:Mascot:User Name
def: "OBSOLETE Name of the user submitting the Mascot search." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
researcher (MS:1001271) instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001654
name: ProteomeDiscoverer:Enzyme Name
def: "OBSOLETE Specifies the enzyme reagent used for protein digestion." 
[PSI:MS]
comment: This term was made obsolete because it's recommended to use 
cleavage agent name (MS:1001045) instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001655
name: ProteomeDiscoverer:Fragment Mass Tolerance
def: "OBSOLETE Mass tolerance used for matching fragment peaks in Da or 
mmu." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
search tolerance minus value (MS:1001413) or search tolerance plus value 
(MS:1001412) instead.
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001659
name: ProteomeDiscoverer:Precursor Mass Tolerance
def: "OBSOLETE Mass window for which precursor ions are considered to be 
the same species." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
search tolerance minus value (MS:1001413) or search tolerance plus value 
(MS:1001412) instead.
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001661
name: ProteomeDiscoverer:Protein Database
def: "OBSOLETE Database to use in the search (configured on the Mascot 
server)." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
database name (MS:1001013) instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001665
name: ProteomeDiscoverer:Mascot:Taxonomy
def: "OBSOLETE Limits searches to entries from a particular species or 
group of species." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
taxonomy: scientific name (MS:1001469) instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001666
name: ProteomeDiscoverer:Use Average Precursor Mass
def: "OBSOLETE Use average mass for the precursor." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
parent mass type average (MS:1001212) instead.
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001682
name: ProteomeDiscoverer:Search Against Decoy Database
def: "OBSOLETE Determines whether the Proteome Discoverer application 
searches against a decoy database." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
quality estimation with decoy database (MS:1001194) instead.
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001701
name: ProteomeDiscoverer:Spectrum Exporter:Export Format
def: "OBSOLETE Format of the exported spectra (dta, mgf or mzData)." 
[PSI:MS]
comment: This term was made obsolete because it's recommended to use one 
of the 'mass spectrometer file format' terms (MS:1000560) instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001734
name: ProteomeDiscoverer:Organism
def: "OBSOLETE Sample organism (used for annotation purposes)." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
taxonomy: scientific name (MS:1001469) instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001735
name: ProteomeDiscoverer:Reference Database
def: "OBSOLETE Full path database name." [PSI:MS]
comment: This term was made obsolete. Use attribute in mzIdentML / 
mzQuantML instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001737
name: ProteomeDiscoverer:Source file extension
def: "OBSOLETE File type (if not pepXML)." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
mass spectrometer file format (MS:1000560) instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001738
name: ProteomeDiscoverer:Source Files
def: "OBSOLETE Input pepXML files." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
pepXML file (MS:1001421) instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true

[Term]
id: MS:1001739
name: ProteomeDiscoverer:Source Files old
def: "OBSOLETE Input pepXML files (old)." [PSI:MS]
comment: This term was made obsolete because it's recommended to use 
pepXML file (MS:1001421) instead.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter
is_obsolete: true


Newly added CV terms in version 3.25.0-rc1 of psi-ms.obo:
=========================================================
[Term]
id: MS:1002009
name: isobaric label quantification analysis
def: "Quantification analysis using an isobaric labeling workflow." [PSI:PI]
is_a: MS:1001833 ! quantitation analysis summary

[Term]
id: MS:1002010
name: TMT quantification analysis
def: "Quantification analysis using the Thermo Fisher tandem mass tag 
(TMT) labeling workflow." [PSI:PI]
is_a: MS:1001833 ! quantitation analysis summary

[Term]
id: MS:1002011
name: desorption electrospray ionization
def: "Combination of electrospray and desorption ionization method that 
ionizes gases, liquids and solids in open air under atmospheric 
pressure." [DOI:10.1126/science.1104404, PMID:15486296]
synonym: "DESI" EXACT []
is_a: MS:1000240 ! atmospheric pressure ionization

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum

Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] I am unable to locate my mzML files that were uploaded on 20 Mar 2012

[pierre-alain b. <pie...@is...>]

Dear Emilie,

I could find your files on the page you mentioned.
One issue might be that the psidev.info website has recently been 
classified as being attacked by malware and your browser or firewall 
might not give access to the page. The EBI has prepared a new website 
and we should migrate asap to this one.

Best regards
Pierre-Alain






On 24.04.2012 20:39, Zehr, Emilie wrote:
>
> Dear Sirs:
>
> I am unable to locate my mzML files that were uploaded on 20 Mar 
> 2012.  There are 4 jpeg files but the 19 mzML files have the following 
> error message:
>
> *Page not found*
>
> The page you requested was not found on this web server. This could be 
> for a variety of reasons, including:
>
>   * You followed a broken or out-of-date link.
>   * You entered the URL for the page incorrectly.
>   * The page no longer exists.
>
> If you followed a broken link, please inform the owner of the 
> referring page.
>
> If you have any queries about this error, please e-mail 
> web...@th...main <mailto:web...@th...main>.
>
> ------------------------------------------------------------------------
>
> Back to *MailScanner has detected a possible fraud attempt from 
> "www.psidev.info" claiming to be* www.psidev.info homepage 
> <http://www.psidev.info/>
>
> I am using the URL that printed with the attachment list as my file 
> locator (http://www.psidev.info/index.php?q=node/461).
>
> Please advise,
>
> Emilie Zehr
>
>
>
>
>
> This electronic message contains information generated by the USDA 
> solely for the intended recipients. Any unauthorized interception of 
> this message or the use or disclosure of the information it contains 
> may violate the law and subject the violator to civil or criminal 
> penalties. If you believe you have received this message in error, 
> please notify the sender and delete the email immediately.
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>
>
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

[Psidev-ms-dev] I am unable to locate my mzML files that were uploaded on 20 Mar 2012

[Zehr, E. <Emi...@AR...>]

Dear Sirs:

I am unable to locate my mzML files that were uploaded on 20 Mar 2012.  There are 4 jpeg files but the 19 mzML files have the following error message:
Page not found
The page you requested was not found on this web server. This could be for a variety of reasons, including:

  *   You followed a broken or out-of-date link.
  *   You entered the URL for the page incorrectly.
  *   The page no longer exists.
If you followed a broken link, please inform the owner of the referring page.
If you have any queries about this error, please e-mail web...@th...main<mailto:web...@th...main>.
________________________________
Back to www.psidev.info homepage<http://www.psidev.info/>

I am using the URL that printed with the attachment list as my file locator (http://www.psidev.info/index.php?q=node/461).

Please advise,
Emilie Zehr





This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

[Psidev-ms-dev] Proposed new terms for TraML

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

Hi everyone, I’d like to propose some new terms for TraML. Comments on
these?



[Term]

id: MS:100????

name: iRT retention time normalization standard

def: "A de facto standard providing the retention times at which a specific
set of 10 reference peptides exit the reference chromatographic column. The
kit may be obtain from Biognosys.ch at
http://www.biognosys.ch/products/rt-kit.html" [PSI:MS]

is_a: MS:1000901 ! retention time normalization standard



[Term]

id: MS:100????

name: transition type

def: "The type of the transitions, e.g. target or decoy." [PSI:MS]

relationship: part_of MS:1000908 ! transition



[Term]

id: MS:100????

name: target transition

def: "A transition used to target a specific compound that may be in the
sample." [PSI:MS]

is_a: MS:100???? ! transition type



[Term]

id: MS:100????

name: decoy transition

def: "A transition not expected to be present in the sample and used to
calculate statistical confidence of target transition detections in some
workflows."

[PSI:MS]

is_a: MS:100???? ! transition type

[Psidev-ms-dev] psi-ms controlled vocabulary v.3.23.0 released

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

Dear proteomics community,

attached there's the the new version 3.23.0 of the psi-ms.obo.
It contains the newly proposed terms concerning mzQuantML validation 
from the San Diego meeting.

Changed CV terms in version 3.23.0 of psi-ms.obo:
=================================================
For MS:1001837 the name changed from iTraq ... to iTRAQ ...:

[Term]
id: MS:1001837
name: iTRAQ quantitation analysis
def: "iTRAQ workflow (reporter ions on MS/MS level)." [PSI:PI]
is_a: MS:1001833 ! quantitation analysis summary


Newly added CV terms in version 3.23.0 of psi-ms.obo:
=====================================================
[Term]
id: MS:1002001
name: MS1 Label-based raw feature quantitation
def: "MS1 Label-based raw feature quantitation (FeatureQuantLayer MUST 
be present)." [PSI:PI]
is_a: MS:1001833 ! quantitation analysis summary

[Term]
id: MS:1002002
name: MS1 Label-based peptide level quantitation
def: "MS1 Label-based peptide level quantitation 
(PeptideConsensusQuantLayer MUST be present)." [PSI:PI]
is_a: MS:1001833 ! quantitation analysis summary

[Term]
id: MS:1002003
name: MS1 Label-based protein level quantitation
def: "MS1 Label-based protein level quantitation (ProteinQuantLayer MUST 
be present)." [PSI:PI]
is_a: MS:1001833 ! quantitation analysis summary

[Term]
id: MS:1002004
name: MS1 Label-based proteinGroup level quantitation
def: "MS1 Label-based proteinGroup level quantitation 
(ProteinGroupQuantLayer MUST be present)." [PSI:PI]
is_a: MS:1001833 ! quantitation analysis summary

Best regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum

Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] [Psidev-pi-dev] Malware in the PSI web site

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

Hi Juanan, I did mostly understand, but I did not respond so clearly. I
think the main node numbers we need to worry about are the ones that we
created aliases for. So I would say the node numbers below are the key
ones. The aliases are quite recent, so their corresponding node numbers
are already out there, especially in Google.

Regards,
Eric


> -----Original Message-----
> From: Juan Antonio Vizcaino [mailto:ju...@eb...]
> Sent: Tuesday, April 17, 2012 8:45 AM
> To: Eric Deutsch
> Cc: psi...@li...; Mass spectrometry standard
> development
> Subject: Re: [Psidev-pi-dev] Malware in the PSI web site
>
> Hi Eric,
>
> Thanks a lot for this. I was aware of these ones. I have realized I did
> not explained myself very well before so I will explain here what the
> problem is.
>
> Let's take for instance the page, www.psidev.info/index.php?q=node/454.
> Before we created the aliases cited by Eric, I guess this URL could
> have potentially been used in previous publications.
>
> If that is the case, what it is impossible to set up in the new web
> page (also based on Drupal) is that the node numbers of the new
> generated pages are exactly the same than the ones in the old web page
> and present in those publications (the node numbers are generated by
> order ot creation, and the final number also depends on other things).
> So in the new site node 454 will appear as a different node number.
>
> We will need to set up aliases from node 454 page
> (www.psidev.info/index.php?q=node/454) into the new node number and
> that means that the links in the  publications will not work properly.
>
> For the aliases like www.psidev.info/mzml there will be no problem
> since they would be redirected to the new node number in the page
> anyway.
>
> If you can think of any case like the explained here, please let me
> know.
>
> Cheers,
>
> Juanan
>
>
>
>
> On 17 Apr 2012, at 17:12, Eric Deutsch wrote:
>
> > Hi Juanan, we tried to create aliases for all the major formats:
> >
> > www.psidev.info/traml
> > should point to:
> > http://www.psidev.info/index.php?q=node/405
> >
> > www.psidev.info/mzml
> >  should point to:
> > http://www.psidev.info/index.php?q=node/257
> >
> > And then we had:
> >
> > www.psidev.info/mzidentml
> > www.psidev.info/mzquantml
> >
> > I don't recall which numbers these pointed to. But Google has all
> this
> > information. Look slike mzIdentML was:
> >
> > www.psidev.info/index.php?q=node/454
> >
> > and mzQuantML:
> >
> > www.psidev.info/index.php?q=node/457
> >
> > And then I think we also has MIAPE:
> >
> > www.psidev.info/miape
> > Pointing to:
> > www.psidev.info/index.php?q=node/91
> >
> >
> >
> >> -----Original Message-----
> >> From: Juan Antonio Vizcaino [mailto:ju...@eb...]
> >> Sent: Tuesday, April 17, 2012 12:02 AM
> >> To: psi...@li...; Mass spectrometry standard
> >> development
> >> Subject: [Psidev-pi-dev] Malware in the PSI web site
> >>
> >> Dear all,
> >>
> >> Sorry I could not reply to your e-mails individually. Since Sunday,
> I
> >> am attending a meeting in Spain and it has been quite busy here.
> >>
> >> I received the notification on Friday evening from Google. At the
> >> moment I am afraid there is not much we can do. The problem is that
> the
> >> drupal version in the old site is too old and I don't think it makes
> >> much sense try to 'fix' the old page.
> >>
> >> The alternative is then to move to the new web page that Henning
> >> introduced briefly in San Diego. However, there are a few issues.
> One
> >> of the main ones is how to maintain the links that have been
> included
> >> in the related publications. We will do our best but at the moment
> we
> >> don't have anyone who can especifically do the work so this will
> need
> >> to go on top of everything else for a couple of people. The content
> >> will not be as updated as in the old site and that means that the
> >> content will need to be enriched gradually in time. But that should
> not
> >> be a problem.
> >>
> >> Something that could help is that you send me the links you think
> have
> >> been included in your PSI related publications. That way we can try
> to
> >> create aliases for them.
> >>
> >> Best regards,
> >>
> >> Juan Antonio
> >>
> >>
> >>
> >>
> >> --------------------------------------------------------------------
> ---
> >> -------
> >> Better than sec? Nothing is better than sec when it comes to
> >> monitoring Big Data applications. Try Boundary one-second
> >> resolution app monitoring today. Free.
> >> http://p.sf.net/sfu/Boundary-dev2dev
> >> _______________________________________________
> >> Psidev-pi-dev mailing list
> >> Psi...@li...
> >> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev

Re: [Psidev-ms-dev] [Psidev-pi-dev] Malware in the PSI web site

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

Hi Eric,

Thanks a lot for this. I was aware of these ones. I have realized I did not explained myself very well before so I will explain here what the problem is.

Let's take for instance the page, www.psidev.info/index.php?q=node/454. Before we created the aliases cited by Eric, I guess this URL could have potentially been used in previous publications.

If that is the case, what it is impossible to set up in the new web page (also based on Drupal) is that the node numbers of the new generated pages are exactly the same than the ones in the old web page and present in those publications (the node numbers are generated by order ot creation, and the final number also depends on other things). So in the new site node 454 will appear as a different node number.

We will need to set up aliases from node 454 page (www.psidev.info/index.php?q=node/454) into the new node number and that means that the links in the  publications will not work properly.

For the aliases like www.psidev.info/mzml there will be no problem since they would be redirected to the new node number in the page anyway.

If you can think of any case like the explained here, please let me know.

Cheers,

Juanan




On 17 Apr 2012, at 17:12, Eric Deutsch wrote:

> Hi Juanan, we tried to create aliases for all the major formats:
> 
> www.psidev.info/traml
> should point to:
> http://www.psidev.info/index.php?q=node/405
> 
> www.psidev.info/mzml
>  should point to:
> http://www.psidev.info/index.php?q=node/257
> 
> And then we had:
> 
> www.psidev.info/mzidentml
> www.psidev.info/mzquantml
> 
> I don't recall which numbers these pointed to. But Google has all this
> information. Look slike mzIdentML was:
> 
> www.psidev.info/index.php?q=node/454
> 
> and mzQuantML:
> 
> www.psidev.info/index.php?q=node/457
> 
> And then I think we also has MIAPE:
> 
> www.psidev.info/miape
> Pointing to:
> www.psidev.info/index.php?q=node/91
> 
> 
> 
>> -----Original Message-----
>> From: Juan Antonio Vizcaino [mailto:ju...@eb...]
>> Sent: Tuesday, April 17, 2012 12:02 AM
>> To: psi...@li...; Mass spectrometry standard
>> development
>> Subject: [Psidev-pi-dev] Malware in the PSI web site
>> 
>> Dear all,
>> 
>> Sorry I could not reply to your e-mails individually. Since Sunday, I
>> am attending a meeting in Spain and it has been quite busy here.
>> 
>> I received the notification on Friday evening from Google. At the
>> moment I am afraid there is not much we can do. The problem is that the
>> drupal version in the old site is too old and I don't think it makes
>> much sense try to 'fix' the old page.
>> 
>> The alternative is then to move to the new web page that Henning
>> introduced briefly in San Diego. However, there are a few issues. One
>> of the main ones is how to maintain the links that have been included
>> in the related publications. We will do our best but at the moment we
>> don't have anyone who can especifically do the work so this will need
>> to go on top of everything else for a couple of people. The content
>> will not be as updated as in the old site and that means that the
>> content will need to be enriched gradually in time. But that should not
>> be a problem.
>> 
>> Something that could help is that you send me the links you think have
>> been included in your PSI related publications. That way we can try to
>> create aliases for them.
>> 
>> Best regards,
>> 
>> Juan Antonio
>> 
>> 
>> 
>> 
>> -----------------------------------------------------------------------
>> -------
>> Better than sec? Nothing is better than sec when it comes to
>> monitoring Big Data applications. Try Boundary one-second
>> resolution app monitoring today. Free.
>> http://p.sf.net/sfu/Boundary-dev2dev
>> _______________________________________________
>> Psidev-pi-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev