psidev-ms-dev — Mass spectroscopy standard development

Re: [Psidev-ms-dev] Release candidate 3.55.0_rc1 of psi-ms.obo

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

Hi Gerhard, many thanks for working on this. This is a big step toward
tidying up the CV. I think this is all good, except I'm a little nervous
about the units. However, I checked recent TraML and mzML files and they
don't seem to be using any of the units in the MS CV. They're all using
the UO, so that's good. I'm a little concerned, but have not reason to
stop this step.

Would someone check some recent mzIdentML and mzQuantML files to make sure
we're not still using these unit terms in the MS CV while producing these
documents?

Thanks,
Eric


> -----Original Message-----
> From: Gerhard Mayer [mailto:Ger...@ru...]
> Sent: Friday, September 27, 2013 5:09 AM
> To: psi...@li...; psidev-pi-
> de...@li...; Mass spectrometry standard development
> Subject: [Psidev-ms-dev] Release candidate 3.55.0_rc1 of psi-ms.obo
>
> Dear proteomics community,
>
> attached there's the release candidate 3.55.0_rc1 of
> the psi-ms.obo file. It contains one new term for
> the MZmine framework.
>
> In addition most of the purgatory terms are obsoleted
> now, but 10 terms are still left in the purgatory branch,
> because these terms are referenced by other terms.
>
>
> Changed CV terms in version 3.55.0_rc1 of psi-ms.obo:
> =====================================================
> ************ OBSOLETED PURGATORY TERMS
> MS:1000002	sample name
> MS:1000010	analyzer type
> MS:1000023	isolation width
> MS:1000054	chromatography
> MS:1000097	constant neutral mass loss
> MS:1000098	multiple ion monitoring
> MS:1000100	precursor ion scan
> MS:1000101	product ion scan
> MS:1000155	ELEMENT2
> MS:1000205	selected ion monitoring
> MS:1000206	selected reaction monitoring
> MS:1000214	electron energy obsolete
> MS:1000244	consecutive reaction monitoring
> MS:1000292	mass spectrograph obsolete
> MS:1000295	mattauch-herzog geometry
> MS:1000296	nier-johnson geometry
> MS:1000297	paul ion trap
> MS:1000299	quistor
> MS:1000313	scan m/z range?
> MS:1000323	constant neutral loss scan
> MS:1000324	constant neutral gain scan
> MS:1000338	nth generation product ion scan
> MS:1000352	secondary electron
> MS:1000368	metastable ion
> MS:1000378	stable ion
> MS:1000379	unstable ion
> MS:1000425	ion energy loss spectrum
> MS:1000454	instrument additional description
> MS:1000461	additional description
> MS:1000479	purgatory
> MS:1000552	maldi spot identifier
> MS:1001051	multiple enzyme combination rules
> MS:1001115	scan number(s)
> MS:1001213	search result details
> MS:1001326	add_others
>
>
> ************************************************************
> ************ TERMS STILL IN THE PURGATORY BRANCH
> The following 10 terms are still in the purgatory branch.
> It was not possible to obsolete them, because other terms
> still refer to them:
>
> ID			name
referenced
> by
> =============================================================
> MS:1000268 mass spectrometry				MS:1000020
scanning
> method
>
> 	MS:1000263 isotope ratio mass spectrometry
> MS:1000293 mass spectrometer				MS:1000226
molecular
> beam mass spectrometry
>
> 	MS:1000238 accelerator mass spectrometry
>
> 	MS:1000256 high-field asymmetric waveform ion mobility
> spectrometry
>
> 	MS:1000260 ion kinetic energy spectrometry
>
> 	MS:1000261 ion mobility spectrometry
>
> 	MS:1000267 mass analyzed ion kinetic energy spectrometry
>
> 	MS:1000269 mass spectrometry/mass spectrometry
>
> 	MS:1000277 residual gas analyzer
>
> 	MS:1000287 time-of-flight mass spectrometer
>
> 	MS:1000289 double-focusing mass spectrometer
>
> 	MS:1000290 hybrid mass spectrometer
>
> 	MS:1000298 prolate traochoidal mass spectrometer
>
> 	MS:1000301 sector mass spectrometer
>
> 	MS:1000302 tandem mass spectrometer
>
> 	MS:1000303 transmission quadrupole mass spectrometer
>
> 	MS:1000306 dynamic mass spectrometry
> MS:1000329 linked scan
MS:1000330 linked
> scan at constant b/e
>
> 	MS:1000331 Linked Scan at Constant E2/V
>
> 	MS:1000332 Linked Scan at Constant B2/E
>
> 	MS:1000333 Linked Scan at Constant B[1-(E/E0)]^1/2 / E
> MS:1000365 ion?
MS:1000437
> ion reaction
>
> 	MS:1000506 ion role
>
> 	MS:1000507 ion attribute
>
> 	MS:1000508 ion chemical type
> MS:1000444 m/z Separation Method			MS:1000234 mass
> resolving power
> (already obsolete)
>
> 	MS:1000305 cyclotron motion
>
> 	MS:1000314 mass selective axial ejection
>
> 	MS:1000315 mass selective instability
>
> 	MS:1000316 mathieu stability diagram
>
> 	MS:1000317 orthogonal extraction
>
> 	MS:1000318 resonance ion ejection
> MS:1000445 sequential m/z separation method	MS:1000270 multiple
> stage
> mass spectrometry
>
> 	MS:1000321 2E Mass Spectrum
>
> 	MS:1000334 MS/MS in Time
>
> 	MS:1000335 MS/MS in Space
>
> 	MS:1000336 neutral loss
> MS:1000459 spectrum instrument description	MS:1000037 polarity
> 		(already
> obsolete)
> MS:1000013 resolution type					MS:1000088
> constant
>
> 	MS:1000089 proportional
> MS:1000017 scan function					MS:1000090
mass
> scan
>
> 	MS:1000091 selected ion detection
> MS:1000020 scanning method					MS:1000498
full
> scan
>
> 	MS:1000791 enhanced resolution scan		(already obsolete)
>
>
> ************************************************************
> ************ TERMS OVERLAPPING WITH INCLUDED ONTOLOGIES
> B. In order to ensure non-orthogonality (redundancy)
>    between the CV terms and its imports, the following
>    terms in psi-ms.obo were made obsolete. Please use
>    the corresponding terms from the unit.obo resp.
>    PATO.obo instead.
>
> ID in psi-ms.obo name in unit.obo ID in unit.obo name in unit.obo
> =================================================================
> MS:1000212       dalton           UO:0000221     dalton
> MS:1000137       electron volt    UO:0000266     electronvolt
>
> MS:1000046       energy unit      UO:0000111     energy unit
>
> MS:1000464       mass unit        UO:0000002     mass unit
> MS:1000038       minute           UO:0000031     minute
> MS:1000039       second           UO:0000010     second
> MS:1000550       time unit        UO:0000003     time unit
> MS:1000460       unit             UO:0000000     unit
>
> ID in psi-ms.obo name in unit.obo ID in PATO.obo name in PATO.obo
> =================================================================
> MS:1000048       gas              PATO:0001737   gaseus configuration
> MS:1000095       linear           PATO:0001199   linear
> MS:1000049       liquid           PATO:0001735   liquid configuration
> MS:1000037       polarity         PATO:0002186   polarity
> MS:1000050       solid            PATO:0001736   solid configuration
> MS:1000843       wavelength       PATO:0001242   wavelength
>
>
> New CV terms in version 3.55.0_rc1 of psi-ms.obo:
> =================================================
> [Term]
> id: MS:1002342
> name: MZmine
> def: "A framework for differential analysis of mass spectrometry data."
> [PMID:16403790, PMID:20650010]
> is_a: MS:1001456 ! analysis software
> is_a: MS:1001457 ! data processing software
>
> Best Regards,
> Gerhard
> --
> ---
> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> Bioinformatics / Biostatistics
> Medizinisches-Proteom-Center (MPC)
> Ruhr-Universität Bochum
> Zentrum für klinische Forschung I (ZKF I)
> E.049a
> Universitätsstraße 150
> D-44801 Bochum
>
> Phone:	+49(0)234/32-21006
> Fax:	+49(0)234/32-14554
> Email:	Ger...@ru...
> Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Release candidate 3.55.0_rc1 of psi-ms.obo

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

Dear proteomics community,

attached there's the release candidate 3.55.0_rc1 of
the psi-ms.obo file. It contains one new term for
the MZmine framework.

In addition most of the purgatory terms are obsoleted
now, but 10 terms are still left in the purgatory branch,
because these terms are referenced by other terms.


Changed CV terms in version 3.55.0_rc1 of psi-ms.obo:
=====================================================
************ OBSOLETED PURGATORY TERMS
MS:1000002	sample name	
MS:1000010	analyzer type	
MS:1000023	isolation width	
MS:1000054	chromatography	
MS:1000097	constant neutral mass loss	
MS:1000098	multiple ion monitoring
MS:1000100	precursor ion scan	
MS:1000101	product ion scan	
MS:1000155	ELEMENT2	
MS:1000205	selected ion monitoring
MS:1000206	selected reaction monitoring
MS:1000214	electron energy obsolete	
MS:1000244	consecutive reaction monitoring	
MS:1000292	mass spectrograph obsolete
MS:1000295	mattauch-herzog geometry	
MS:1000296	nier-johnson geometry	
MS:1000297	paul ion trap
MS:1000299	quistor
MS:1000313	scan m/z range?	
MS:1000323	constant neutral loss scan	
MS:1000324	constant neutral gain scan	
MS:1000338	nth generation product ion scan	
MS:1000352	secondary electron	
MS:1000368	metastable ion	
MS:1000378	stable ion	
MS:1000379	unstable ion	
MS:1000425	ion energy loss spectrum	
MS:1000454	instrument additional description	
MS:1000461	additional description	
MS:1000479	purgatory	
MS:1000552	maldi spot identifier	
MS:1001051	multiple enzyme combination rules
MS:1001115	scan number(s)
MS:1001213	search result details
MS:1001326	add_others


************************************************************
************ TERMS STILL IN THE PURGATORY BRANCH
The following 10 terms are still in the purgatory branch.
It was not possible to obsolete them, because other terms
still refer to them:

ID			name							referenced by
=============================================================
MS:1000268 mass spectrometry				MS:1000020 scanning method
											MS:1000263 isotope ratio mass spectrometry
MS:1000293 mass spectrometer				MS:1000226 molecular beam mass spectrometry
											MS:1000238 accelerator mass spectrometry
											MS:1000256 high-field asymmetric waveform ion mobility
spectrometry
											MS:1000260 ion kinetic energy spectrometry
											MS:1000261 ion mobility spectrometry
											MS:1000267 mass analyzed ion kinetic energy spectrometry
											MS:1000269 mass spectrometry/mass spectrometry
											MS:1000277 residual gas analyzer
											MS:1000287 time-of-flight mass spectrometer
											MS:1000289 double-focusing mass spectrometer
											MS:1000290 hybrid mass spectrometer
											MS:1000298 prolate traochoidal mass spectrometer
											MS:1000301 sector mass spectrometer
											MS:1000302 tandem mass spectrometer
											MS:1000303 transmission quadrupole mass spectrometer
											MS:1000306 dynamic mass spectrometry
MS:1000329 linked scan						MS:1000330 linked scan at constant b/e
											MS:1000331 Linked Scan at Constant E2/V
											MS:1000332 Linked Scan at Constant B2/E
											MS:1000333 Linked Scan at Constant B[1-(E/E0)]^1/2 / E
MS:1000365 ion?								MS:1000437 ion reaction
											MS:1000506 ion role
											MS:1000507 ion attribute
											MS:1000508 ion chemical type
MS:1000444 m/z Separation Method			MS:1000234 mass resolving power	
(already obsolete)
											MS:1000305 cyclotron motion
											MS:1000314 mass selective axial ejection
											MS:1000315 mass selective instability
											MS:1000316 mathieu stability diagram
											MS:1000317 orthogonal extraction
											MS:1000318 resonance ion ejection
MS:1000445 sequential m/z separation method	MS:1000270 multiple stage
mass spectrometry
											MS:1000321 2E Mass Spectrum
											MS:1000334 MS/MS in Time
											MS:1000335 MS/MS in Space
											MS:1000336 neutral loss
MS:1000459 spectrum instrument description	MS:1000037 polarity		(already
obsolete)
MS:1000013 resolution type					MS:1000088 constant
											MS:1000089 proportional
MS:1000017 scan function					MS:1000090 mass scan
											MS:1000091 selected ion detection
MS:1000020 scanning method					MS:1000498 full scan
											MS:1000791 enhanced resolution scan		(already obsolete)


************************************************************
************ TERMS OVERLAPPING WITH INCLUDED ONTOLOGIES
B. In order to ensure non-orthogonality (redundancy)
   between the CV terms and its imports, the following
   terms in psi-ms.obo were made obsolete. Please use
   the corresponding terms from the unit.obo resp.
   PATO.obo instead.

ID in psi-ms.obo name in unit.obo ID in unit.obo name in unit.obo
=================================================================
MS:1000212       dalton           UO:0000221     dalton		
MS:1000137       electron volt    UO:0000266     electronvolt		
MS:1000046       energy unit      UO:0000111     energy unit		
MS:1000464       mass unit        UO:0000002     mass unit		
MS:1000038       minute           UO:0000031     minute		
MS:1000039       second           UO:0000010     second		
MS:1000550       time unit        UO:0000003     time unit		
MS:1000460       unit             UO:0000000     unit

ID in psi-ms.obo name in unit.obo ID in PATO.obo name in PATO.obo
=================================================================
MS:1000048       gas              PATO:0001737   gaseus configuration
MS:1000095       linear           PATO:0001199   linear
MS:1000049       liquid           PATO:0001735   liquid configuration
MS:1000037       polarity         PATO:0002186   polarity
MS:1000050       solid            PATO:0001736   solid configuration
MS:1000843       wavelength       PATO:0001242   wavelength


New CV terms in version 3.55.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002342
name: MZmine
def: "A framework for differential analysis of mass spectrometry data."
[PMID:16403790, PMID:20650010]
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

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

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

[Psidev-ms-dev] ion chemical type in the CV

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

Hi,

I am currently looking at how to annotate ions, 
specifically in -- but not limited to -- metabolomics.

The CV already has a branch of terms:
http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MS&termId=MS%3A1000508&termName=ion%20chemical%20type#

1) Am I correct in that 

  MS:1000361 dimeric ion		is_a	MS:1000358 cluster ion
  MS:1000375 protonated molecule	is_a	MS:1000353 adduct ion

2) Am I correct that an [2M+Na]+ is both an MS:1000353 adduct ion
   and also a MS:1000361 dimeric ion ?

3) Would it be better to annotate the kind of Adduct as 
   <cvParam cvRef="MS" accession="MS:1000353" name="adduct ion" value="Na"/>
   or as a child term, maybe even with the mass difference:
   <cvParam cvRef="MS" accession="MS:1000XXX" name="Na+ adduct" value="22.989218"  unitName="Dalton" unitCvRef="UO" />

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

[Psidev-ms-dev] mzQuantML for Metabolomics, <AssayQuantLayer> without <SmallMoleculeList> ?

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

Hi,

a while ago I had implemented mzQuantML export for the XCMS software[1],
often used in metabolomics MS data processing. It really only needs 
a subset of the complexity in mzQuantML, but I still have 
a few questions I couldn't solve with the schema 
and the 20mins guide to mzQ:

The result of XCMS is a DataMatrix, where each row is 
a feature matched across all Assays [2] (Each column corresponds to 
an <Assay>, which in turn has references only a single RawFile). 

>From what I understood, this matrix can not be encoded 
as <FeatureQuantLayer>, because each FeatureQuantLayer corresponds 
to only to one <Assay> and I can't encode all my columns into one
FeatureQuantLayer. Or did I get this wrong ?

Instead, I probably want to use an <AssayQuantLayer>.
For this I had to fake a <SmallMoleculeList>, 
since the small molecules have not yet been identified.

Is there any way around faking that <SmallMoleculeList> ?
Or did I get something wrong in first place ?

Yours,
Steffen

[1] http://sourceforge.net/mailarchive/forum.php?thread_name=61E394A548E109409A04651B3D41E51A58417A30%40BHEXMBX2.livad.liv.ac.uk&forum_name=psidev-ms-dev
[2] http://msbi.ipb-halle.de/~sneumann/e25-zoom.png


-- 
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] [Psidev-ms-vocab] Proposals for version 3.55.0_rc1 of psi-ms.obo.

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

Hi Gerhard, thank you, this is a sobering look at how far we really still
need to go with the CV. I think all the changes you propose are fine with
me.

Thanks for tidying up!
Eric


-----Original Message-----
From: Gerhard Mayer [mailto:Ger...@ru...]
Sent: Thursday, September 19, 2013 1:04 AM
To: psi...@li...;
psi...@li...; Mass spectrometry standard development
Subject: [Psidev-ms-vocab] Proposals for version 3.55.0_rc1 of psi-ms.obo.

Dear proteomics community,

Daniel Schober from Halle pointed out to some problems in our psi-ms.obo
ontology (see attached paper), which he presented some days ago at the
GI-ODLS 2013 workshop in Koblenz, Germany
(https://wiki.imise.uni-leipzig.de/Gruppen/OBML/Workshops/2013-ODLS)

In the future I will by and by pick up these suggestions.
Today we propose the following CV term changes for the next version
3.55.0_rc1 of the psi-ms.obo file.

Changed CV terms in version 3.55.0_rc1 of psi-ms.obo:
=====================================================
************ PURGATORY TERMS
A. In the following there's the list of purgatory terms. I propose to
   obsolete them all.
   If you think a term of this list is furthermore needed and should
   not be obsoleted, then please response to our mailing list for
   further discussion.

MS:1000002	sample nameMS:1000010	analyzer
typeMS:1000013	resolution
typeMS:1000020	scanning
methodMS:1000023	isolation
widthMS:1000054	chromatography
MS:1000097	constant neutral mass lossMS:1000098	multiple
ion monitoring
MS:1000100	precursor ion scanMS:1000101	product
ion scanMS:1000155	ELEMENT2
MS:1000205	selected ion monitoring
MS:1000206	selected reaction monitoring
MS:1000214	electron energy obsoleteMS:1000244	consecutive
reaction monitoringMS:1000268	mass
spectrometryMS:1000292	mass
spectrograph obsolete
MS:1000293	mass spectrometerMS:1000295	mattauch-herzog
geometryMS:1000296	nier-johnson
geometryMS:1000297	paul
ion trap
MS:1000299	quistor
MS:1000313	scan m/z range?MS:1000323	constant
neutral loss scanMS:1000324	constant
neutral gain scanMS:1000329	linked
scanMS:1000338	nth
generation product ion scanMS:1000352	secondary
electronMS:1000365	ion?
MS:1000368	metastable ionMS:1000378	stable
ionMS:1000379	unstable
ionMS:1000425	ion
energy loss spectrumMS:1000444	m/z
Separation MethodMS:1000445	sequential
m/z separation methodMS:1000454	instrument
additional descriptionMS:1000459	spectrum
instrument descriptionMS:1000461	additional
descriptionMS:1000479	purgatory
MS:1000552	maldi spot identifierMS:1001051	multiple
enzyme combination rules
MS:1001115	scan number(s)
MS:1001213	search result details
MS:1001326	add_others


************ TERMS OVERLAPPING WITH INCLUDED ONTOLOGIES B. The following
terms of psi-ms.obo are already included in the
   unit.obo resp. PATO.obo ontologies, which we include in our
   psi-ms.obo. In order to enusre non-orthogonality (redundancy)
   between the CV terms and its imports, we should either obsolete
   these terms or make them more specific.

   For instance we can either obsolete the term MS:1000460 'unit' and
   consequently use the term UO:0000000 'unit' instead, or we can
   redefine our term to MS:1000460 'mass spectrometry specific unit'.

ID in psi-ms.obo name in unit.obo ID in unit.obo name in unit.obo
=================================================================
MS:1000212       dalton           UO:0000221     daltonMS:1000137
electron volt    UO:0000266     electronvoltMS:1000046
energy unit      UO:0000111     energy unitMS:1000464
mass unit        UO:0000002     mass unitMS:1000038
minute           UO:0000031     minuteMS:1000039
second           UO:0000010     secondMS:1000550
time unit        UO:0000003     time unitMS:1000460
unit             UO:0000000     unit

ID in psi-ms.obo name in unit.obo ID in PATO.obo name in PATO.obo
=================================================================
MS:1000048       gas              PATO:0001737   gaseus configuration
MS:1000095       linear           PATO:0001199   linear
MS:1000049       liquid           PATO:0001735   liquid configuration
MS:1000037       polarity         PATO:0002186   polarity
MS:1000050       solid            PATO:0001736   solid configuration
MS:1000460       unit             PATO:0000672   unit
MS:1000843       wavelength       PATO:0001242   wavelength

Proposed solution: made the MS:1000XYZ terms obsolete in order to
                   ensure orthogonal (non-overlapping) CV’s.


New CV terms in version 3.55.0_rc1 of psi-ms.obo:
=================================================
No new terms in version 3.55_rc1.


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

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

[Psidev-ms-dev] Proposals for version 3.55.0_rc1 of psi-ms.obo.

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

Dear proteomics community,

Daniel Schober from Halle pointed out to some problems in
our psi-ms.obo ontology (see attached paper), which he presented
some days ago at the GI-ODLS 2013 workshop in Koblenz, Germany
(https://wiki.imise.uni-leipzig.de/Gruppen/OBML/Workshops/2013-ODLS)

In the future I will by and by pick up these suggestions.
Today we propose the following CV term changes for the next
version 3.55.0_rc1 of the psi-ms.obo file.

Changed CV terms in version 3.55.0_rc1 of psi-ms.obo:
=====================================================
************ PURGATORY TERMS
A. In the following there's the list of purgatory terms. I propose to
   obsolete them all.
   If you think a term of this list is furthermore needed and should
   not be obsoleted, then please response to our mailing list for
   further discussion.

MS:1000002	sample name	
MS:1000010	analyzer type	
MS:1000013	resolution type	
MS:1000020	scanning method	
MS:1000023	isolation width	
MS:1000054	chromatography	
MS:1000097	constant neutral mass loss	
MS:1000098	multiple ion monitoring
MS:1000100	precursor ion scan	
MS:1000101	product ion scan	
MS:1000155	ELEMENT2	
MS:1000205	selected ion monitoring
MS:1000206	selected reaction monitoring
MS:1000214	electron energy obsolete	
MS:1000244	consecutive reaction monitoring	
MS:1000268	mass spectrometry	
MS:1000292	mass spectrograph obsolete
MS:1000293	mass spectrometer	
MS:1000295	mattauch-herzog geometry	
MS:1000296	nier-johnson geometry	
MS:1000297	paul ion trap
MS:1000299	quistor
MS:1000313	scan m/z range?	
MS:1000323	constant neutral loss scan	
MS:1000324	constant neutral gain scan	
MS:1000329	linked scan	
MS:1000338	nth generation product ion scan	
MS:1000352	secondary electron	
MS:1000365	ion?	
MS:1000368	metastable ion	
MS:1000378	stable ion	
MS:1000379	unstable ion	
MS:1000425	ion energy loss spectrum	
MS:1000444	m/z Separation Method	
MS:1000445	sequential m/z separation method	
MS:1000454	instrument additional description	
MS:1000459	spectrum instrument description	
MS:1000461	additional description	
MS:1000479	purgatory	
MS:1000552	maldi spot identifier	
MS:1001051	multiple enzyme combination rules
MS:1001115	scan number(s)
MS:1001213	search result details
MS:1001326	add_others


************ TERMS OVERLAPPING WITH INCLUDED ONTOLOGIES
B. The following terms of psi-ms.obo are already included in the
   unit.obo resp. PATO.obo ontologies, which we include in our
   psi-ms.obo. In order to enusre non-orthogonality (redundancy)
   between the CV terms and its imports, we should either obsolete
   these terms or make them more specific.

   For instance we can either obsolete the term MS:1000460 'unit' and
   consequently use the term UO:0000000 'unit' instead, or we can
   redefine our term to MS:1000460 'mass spectrometry specific unit'.

ID in psi-ms.obo name in unit.obo ID in unit.obo name in unit.obo
=================================================================
MS:1000212       dalton           UO:0000221     dalton		
MS:1000137       electron volt    UO:0000266     electronvolt		
MS:1000046       energy unit      UO:0000111     energy unit		
MS:1000464       mass unit        UO:0000002     mass unit		
MS:1000038       minute           UO:0000031     minute		
MS:1000039       second           UO:0000010     second		
MS:1000550       time unit        UO:0000003     time unit		
MS:1000460       unit             UO:0000000     unit

ID in psi-ms.obo name in unit.obo ID in PATO.obo name in PATO.obo
=================================================================
MS:1000048       gas              PATO:0001737   gaseus configuration
MS:1000095       linear           PATO:0001199   linear
MS:1000049       liquid           PATO:0001735   liquid configuration
MS:1000037       polarity         PATO:0002186   polarity
MS:1000050       solid            PATO:0001736   solid configuration
MS:1000460       unit             PATO:0000672   unit
MS:1000843       wavelength       PATO:0001242   wavelength

Proposed solution: made the MS:1000XYZ terms obsolete in order to
                   ensure orthogonal (non-overlapping) CV’s.


New CV terms in version 3.55.0_rc1 of psi-ms.obo:
=================================================
No new terms in version 3.55_rc1.


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

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

[Psidev-ms-dev] New version 3.54.0 of psi-ms.obo

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

Dear proteomics community,

attached there's the new version 3.54.0 of the psi-ms.obo file.

The term 'translation frame' was de-obsoleted.
In addition a new term for second-pass peptide identifications was defined
(see http://www.matrixscience.com/help/error_tolerant_help.html)
and the definitions for the 'retention time' terms were changed.


Changed CV terms in version 3.54.0 of psi-ms.obo:
=================================================
************ de-obsoleted the following term, since useful in mzTab
[Term]
id: MS:1001024
name: translation frame
def: "The translated open reading frames from a nucleotide database
considered in the search (range: 1-6)." [PSI:PI]
is_a: MS:1001011 ! search database details

************ Changed the definitions of the various 'retention time' terms;
************ added value-type and units to the term MS:1000894
[Term]
id: MS:1000894
name: retention time
def: "A time interval from the start of chromatography when an analyte
exits a chromatographic column." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000887 ! peptide attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute

[Term]
id: MS:1000895
name: local retention time
def: "A time interval from the start of chromatography when an analyte
exits an unspecified local chromatographic column and instrumental
setup." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000894 ! retention time
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute

[Term]
id: MS:1000896
name: normalized retention time
def: "A time interval from the start of chromatography when an analyte
exits a standardized reference chromatographic column and instrumental
setup." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000894 ! retention time
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute

[Term]
id: MS:1000897
name: predicted retention time
def: "A time interval from the start of chromatography when an analyte
exits a chromatographic column as predicted by a referenced software
application." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000894 ! retention time
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute


New CV terms in version 3.54.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002341
name: second-pass peptide identification
def: "A putative identified peptide found in a second-pass search of
protein sequences selected from a first-pass search." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide result details


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

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

Re: [Psidev-ms-dev] Release candidate 3.54.0_rc1 of psi-ms.obo

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

Hi Gerhard, many thanks for your continued efforts in handling the CV, and
thank you for including the changes to the retention time terms we
discussed on the list.

I also notice there is a new term "error tolerant peptide". This sounds
like a term from a search engine, but I would argue that this name does
not represent the definition well. Peptides are not inherently tolerant or
intolerant of errors. Only people or software can tolerate errors. Maybe
we need a term "error tolerant person"? ;-) Or since we all have to
tolerate errors at some level, maybe we only need the term for people who
are able to tolerate very high degrees of error?

Anyway, if we need a term for this definition, may I suggest "second-pass
peptide identification" or something similar?

What do you think?

Thanks,
Eric


-----Original Message-----
From: Gerhard Mayer [mailto:Ger...@ru...]
Sent: Thursday, September 05, 2013 12:05 AM
To: psi...@li...;
psi...@li...; Mass spectrometry standard
development
Subject: [Psidev-ms-dev] Release candidate 3.54.0_rc1 of psi-ms.obo

Dear proteomics community,

attached there's the release candidate version 3.54.0_rc1 of the
psi-ms.obo file.

The term 'translation frame' was de-obsoleted.
In addition a new term for error tolerant peptide matches was defined (see
http://www.matrixscience.com/help/error_tolerant_help.html)
and the definitions for the 'retention time' terms were changed.


Changed CV terms in version 3.54.0_rc1 of psi-ms.obo:
=====================================================
************ de-obsoleted the following term, since useful in mzTab [Term]
id: MS:1001024
name: translation frame
def: "The translated open reading frames from a nucleotide database
considered in the search (range: 1-6)." [PSI:PI]
is_a: MS:1001011 ! search database details

************ Changed the definitions of the various 'retention time'
terms;
************ added value-type and units to the term MS:1000894 [Term]
id: MS:1000894
name: retention time
def: "A time interval from the start of chromatography when an analyte
exits a chromatographic column." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000887 ! peptide attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute

[Term]
id: MS:1000895
name: local retention time
def: "A time interval from the start of chromatography when an analyte
exits an unspecified local chromatographic column and instrumental setup."
[PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000894 ! retention time
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute

[Term]
id: MS:1000896
name: normalized retention time
def: "A time interval from the start of chromatography when an analyte
exits a standardized reference chromatographic column and instrumental
setup." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000894 ! retention time
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute

[Term]
id: MS:1000897
name: predicted retention time
def: "A time interval from the start of chromatography when an analyte
exits a chromatographic column as predicted by a referenced software
application." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000894 ! retention time
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute


New CV terms in version 3.54.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002341
name: error tolerant peptide
def: "A putative identified peptide found in a second-pass search of
protein sequences selected from a first-pass search." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide result details


Best Regards,
Gerhard

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

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

[Psidev-ms-dev] Release candidate 3.54.0_rc1 of psi-ms.obo

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

Dear proteomics community,

attached there's the release candidate version 3.54.0_rc1 of the
psi-ms.obo file.

The term 'translation frame' was de-obsoleted.
In addition a new term for error tolerant peptide matches was defined
(see http://www.matrixscience.com/help/error_tolerant_help.html)
and the definitions for the 'retention time' terms were changed.


Changed CV terms in version 3.54.0_rc1 of psi-ms.obo:
=====================================================
************ de-obsoleted the following term, since useful in mzTab
[Term]
id: MS:1001024
name: translation frame
def: "The translated open reading frames from a nucleotide database
considered in the search (range: 1-6)." [PSI:PI]
is_a: MS:1001011 ! search database details

************ Changed the definitions of the various 'retention time' terms;
************ added value-type and units to the term MS:1000894
[Term]
id: MS:1000894
name: retention time
def: "A time interval from the start of chromatography when an analyte
exits a chromatographic column." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000887 ! peptide attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute

[Term]
id: MS:1000895
name: local retention time
def: "A time interval from the start of chromatography when an analyte
exits an unspecified local chromatographic column and instrumental
setup." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000894 ! retention time
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute

[Term]
id: MS:1000896
name: normalized retention time
def: "A time interval from the start of chromatography when an analyte
exits a standardized reference chromatographic column and instrumental
setup." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000894 ! retention time
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute

[Term]
id: MS:1000897
name: predicted retention time
def: "A time interval from the start of chromatography when an analyte
exits a chromatographic column as predicted by a referenced software
application." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000894 ! retention time
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute


New CV terms in version 3.54.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002341
name: error tolerant peptide
def: "A putative identified peptide found in a second-pass search of
protein sequences selected from a first-pass search." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide result details


Best Regards,
Gerhard

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

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

Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.50.0 of psi-ms.obo

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

Hi Nils, this is an excellent suggestion. So here is the revised list of
definitions:



id: MS:1000894

name: retention time

def: "A time interval from the start of chromatography when an analyte
exits a chromatographic column." [PSI:MS]

id: MS:1000895

name: local retention time

def: "A time interval from the start of chromatography when an analyte
exits an unspecified local chromatographic column and instrumental setup."
[PSI:MS]

id: MS:1000896

name: normalized retention time

def: "A time interval from the start of chromatography when an analyte
exits a standardized reference chromatographic column and instrumental
setup." [PSI:MS]

id: MS:1000897

name: predicted retention time

def: "A time interval from the start of chromatography when an analyte
exits a chromatographic column as predicted by a referenced software
application." [PSI:MS]



Brian, by “local” we mean “an unspecified local chromatographic column and
instrumental setup” as opposed to a standardized reference setup. Most
retention times will be local as calibrating to some standard still seems
to be rare.



Thanks,

Eric





*From:* Nils Hoffmann [mailto:nil...@ce...]
*Sent:* Wednesday, September 04, 2013 1:29 PM
*To:* Mass spectrometry standard development
*Cc:* Brian Pratt; Mass spectrometry standard development;
psi...@li...; psi...@li...;
pro...@li...; Eric Deutsch
*Subject:* Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.50.0 of
psi-ms.obo



Hi Eric and Brian,

would it make sense to replace the term 'peptide' with 'analyte' in the
terms below covering elution time? This would also make them more
compatible with the terminology used in metabolomics and analytical
chemistry. Or did I miss a direct connection of these terms to proteomics
experiments somewhere?

Regards,

Nils



-- 

Nils Hoffmann                               phone:    +49-521-106-4342

Bielefeld University                        room:             U10-144

Faculty of Technology, Genome Informatics

P.O. Box 10 01 31

33501 Bielefeld, Germany

http://www.cebitec.uni-bielefeld.de/~hoffmann


Am 04.09.2013 um 22:12 schrieb Eric Deutsch <Eri...@sy...
>:

Hi Brian, I agree, this is an improvement. I tweaked the language a little
so all the definitions are in the same tense and  added a “from”. How does
everyone like these improved definitions?



id: MS:1000894

name: retention time

def: "A time interval from the start of chromatography when a peptide exits
a chromatographic column." [PSI:MS]



id: MS:1000895

name: local retention time

def: "A time interval from the start of chromatography when a peptide exits
an unspecified local chromatographic column and instrumental setup."
[PSI:MS]



id: MS:1000896

name: normalized retention time

def: "A time interval from the start of chromatography when a peptide exits
a standardized reference chromatographic column and instrumental setup."
[PSI:MS]



id: MS:1000897

name: predicted retention time

def: "A time interval from the start of chromatography when a peptide exits
a chromatographic column as predicted by a referenced software
application." [PSI:MS]







*From:* Brian Pratt [mailto:bri...@in...]
*Sent:* Wednesday, September 04, 2013 11:50 AM
*To:* Eric Deutsch
*Cc:* Mass spectrometry standard development;
psi...@li...; psi...@li...
*Subject:* Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.50.0 of
psi-ms.obo



It's the "relative to the beginning of a mass spectrometric run"  part that
strikes me as misleading - it doesn't seem proper when the chromatography
may have taken place in a completely different time period than the mass
spec analysis (again, thinking MALDI but trying to be perfectly general and
futureproof).  It just seems inline-LCMS-centric where it should be more
general.



Overall I would think it should use language about the column's history
rather than the mass analyzer's.  So for example

    id: MS:1000897

    name: predicted retention time

should simply read:

    def: "A time interval when a peptide will exit a chromatographic column
as predicted by a referenced software application." [PSI:MS]



and
  id: MS:1000894
  name: retention time
should be
  def: "A time interval at which a peptide exited a chromatographic column."
[PSI:MS]



etc.



Perhaps I am revisiting an already settled issue, but this just isn't
intuitive to me as currently written.  And I might just be the target
audience, as a developer dipping into this on an occasional basis.



Helpfully,



Brian Pratt



On Wed, Sep 4, 2013 at 10:12 AM, Eric Deutsch <
Eri...@sy...> wrote:

Hi Brian, can you elaborate on what is misleading? I don’t see how
concurrent elution and scan are implied in these terms? Maybe the term
“mass spectrometric run” is the vague part? Perhaps “chromatography” should
replace “a mass spectrometric run” for terms 894-896?



For pepXML, you almost surely want “scan start time” since that’s what is
pulled from the raw/mzML files, right? The true retention time of the
peptide ion seen in that scan is far more complex and usually not known
very well. The scan start time is a precise and often sufficiently useful
proxy for the true retention time. Right?



Allowed units are specified in the term metadata, see below..



Eric



id: MS:1000016

name: scan start time

def: "The time that an analyzer started a scan, relative to the start of
the MS run." [PSI:MS]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1000503 ! scan attribute

is_a: MS:1001105 ! peptide result details

is_a: MS:1001405 ! spectrum identification result details

relationship: has_units UO:0000010 ! second

relationship: has_units UO:0000031 ! minute



id: MS:1000894

name: retention time

def: "A measure of the interval relative to the beginning of a mass
spectrometric run." [PSI:MS]

is_a: MS:1000887 ! peptide attribute



id: MS:1000895

name: local retention time

def: "A measure of the interval relative to the beginning of a mass
spectrometric run when a peptide will exit an unspecified local
chromatographic column and instrumental setup." [PSI:MS]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1000894 ! retention time

relationship: has_units UO:0000010 ! second

relationship: has_units UO:0000031 ! minute

id: MS:1000896

name: normalized retention time

def: "A measure of the interval relative to the beginning of a mass
spectrometric run when a peptide will exit a standardized reference
chromatographic column and instrumental setup." [PSI:MS]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1000894 ! retention time

relationship: has_units UO:0000010 ! second

relationship: has_units UO:0000031 ! minute

id: MS:1000897

name: predicted retention time

def: "A time interval relative to the beginning of a mass spectrometric run
when a peptide will exit a chromatographic column as predicted by a
referenced software application." [PSI:MS]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1000894 ! retention time

relationship: has_units UO:0000010 ! second

relationship: has_units UO:0000031 ! minute











*From:* Brian Pratt [mailto:bri...@in...]
*Sent:* Wednesday, September 04, 2013 9:56 AM
*To:* Mass spectrometry standard development
*Cc:* psi...@li...;
psi...@li...; Eric Deutsch
*Subject:* Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.50.0 of
psi-ms.obo



>> What do you think?



I completely agree that these are distinct concepts, and of course I'm not
surprised that everyone else thinks so too.  But the description is
misleading, I think, since it really seems to assume concurrent elution and
scan.  A quibble perhaps but probably worth cleaning up.



The use in question is actually in pepXML related code, so retention time
is the concept we want for sure.  But now I guess I have to think about
managing units?  Or is it defined as being in seconds?  (And if so, perhaps
the description should be enhanced to reflect that?)



Thanks,



Brian



On Wed, Sep 4, 2013 at 9:45 AM, <Eri...@sy...> wrote:

Hi Brian, I'm not certain if that answers your question, but I might add
that ProteoWizard's use of the obsolete retention time(s) should be
changed to either scan start time or retention time. We intend scan start
time to be used in cases where there is a time tag associated with a
definite mass spec acquisition (as is the case in mzML and mzIdentML). The
non-obsolete retention time term should be used as an attribute associated
with a peptide molecule in a chromatographic column independent of an
instrument acquisition event (as is the case in TraML). The MALDI case is
a little more tricky. In practice, a scan start time will likely be
recorded with the instrument and should be written into mzML et al. The
chromatographic retention time might be known and could be recorded
separately (as this will be a different time than the instrument scan
time), but often is not well known when the mzML is written. But as you
allude to, these are now different concepts with different terms, whereas
before it was more muddled.

What do you think?

Regards,
Eric


> -----Original Message-----
> From: Gerhard Mayer [mailto:Ger...@ru...]
> Sent: Tuesday, September 03, 2013 11:24 PM
> To: psi...@li...
> Subject: Re: [Psidev-ms-vocab] [Psidev-ms-dev] New version 3.50.0 of
> psi-ms.obo
>
> Hi Brian,
>
> yes we obsoletetd the retention time(s) term.
>
> Because we had two terms: retention time and retention time(s), we
> decided to obsolete one and add a term named scan start time for the
> SpectrumIdentificationResult annotation, see our discussion in Issue 74
> on google code:
>
> https://code.google.com/p/psi-pi/issues/detail?id=74&can=1
>
> Best Regards,
> Gerhard
>
>
> Am 04.09.2013 00:38, schrieb Brian Pratt:

> > I'm a little slow noticing this (just now updating ProteoWizard's
> OBO), but
> > I wonder about the now obsoleted
> > id: MS:1001114
> > name: retention time(s)
> > def: "Retention time of the spectrum from the source file." [PSI:PI]
> >
> > Surely chromatography and mass spec can happen in entirely different
> time
> > frames, as with MALDI - or am I misunderstanding something?
> >
> > And how is it different from
> > id: MS:1000894
> > name: retention time
> > def: "A measure of the interval relative to the beginning of a mass
> > spectrometric run when a peptide will exit the chromatographic
> column."
> > [PSI:MS]
> >
> > And doesn't that definition have the same assumption about the column
> being
> > hooked up directly to the mass spec?
> >
> > Cheers,
> > Brian Pratt
> >
> >
> > On Fri, May 31, 2013 at 12:10 AM, Gerhard Mayer <
> > Ger...@ru...> wrote:
> >
> >> Dear proteomics community,
> >>
> >> attached there's the new version 3.50.0 of the psi-ms.obo file.
> >>
> >> It contains the changes concerning the retention time terms (issue
> 74),
> >> changes for the waters instrument term definitions and 3 new terms
> for the
> >> Byonic search engine.
> >>
> >>
> >> Changed CV terms in version 3.50.0 of psi-ms.obo:

> >> ==============================**===================

> >> ************ added the two is_a relations 'is_a: MS:1001105 !
> peptide
> >> result details' and
> >> ************ 'is_a: MS:1001405 ! spectrum identification result
> details'
> >> [Term]
> >> id: MS:1000016
> >> name: scan start time
> >> def: "The time that an analyzer started a scan, relative to the
> start of
> >> the MS run." [PSI:MS]
> >> xref: value-type:xsd\:float "The allowed value-type for this CV
> term."
> >> is_a: MS:1000503 ! scan attribute
> >> is_a: MS:1001105 ! peptide result details
> >> is_a: MS:1001405 ! spectrum identification result details
> >> relationship: has_units UO:0000010 ! second
> >> relationship: has_units UO:0000031 ! minute
> >>
> >> ************ Made obsolete
> >> [Term]
> >> id: MS:1001114
> >> name: retention time(s)
> >> def: "OBSOLETE Retention time of the spectrum from the source file."
> >> [PSI:PI]
> >> comment: This term was made obsolete because scan start time
> (MS:1000016)
> >> should be used instead.
> >> xref: value-type:xsd\:double "The allowed value-type for this CV
> term."
> >> is_a: MS:1001105 ! peptide result details
> >> is_a: MS:1001405 ! spectrum identification result details
> >> relationship: has_units UO:0000010 ! second
> >> relationship: has_units UO:0000031 ! minute
> >> is_obsolete: true
> >>
> >> ************ Changed the definition (removed 'peptide ...').
> >> [Term]
> >> id: MS:1000894
> >> name: retention time
> >> def: "A measure of the interval relative to the beginning of a mass
> >> spectrometric run." [PSI:MS]
> >> is_a: MS:1000887 ! peptide attribute
> >>
> >> ************ Changed the is_a relationship from 'detector type' -->
> 'array
> >> detector' for the next two terms
> >> [Term]
> >> id: MS:1000114
> >> name: microchannel plate detector
> >> def: "A thin plate that contains a closely spaced array of channels
> that
> >> each act as a continuous dynode particle multiplier. A charged
> particle,
> >> fast neutral particle, or photon striking the plate causes a cascade
> of
> >> secondary electrons that ultimately exits the opposite side of the
> plate."
> >> [PSI:MS]
> >> synonym: "multichannel plate" EXACT []
> >> is_a: MS:1000345 ! array detector
> >>
> >> [Term]
> >> id: MS:1000621
> >> name: photodiode array detector
> >> def: "An array detector used to record spectra in the ultraviolet
> and
> >> visible region of light." [PSI:MS]
> >> synonym: "PDA" EXACT []
> >> is_a: MS:1000345 ! array detector
> >>
> >> ************ Added the 'is_a: MS:1000621 ! photodiode array
> detector'
> >> relationship
> >> [Term]
> >> id: MS:1000818
> >> name: Acquity UPLC PDA
> >> def: "Acquity UPLC Photodiode Array Detector." [PSI:MS]
> >> is_a: MS:1000126 ! Waters instrument model
> >> is_a: MS:1000621 ! photodiode array detector
> >>
> >> ************ Added the 'is_a: MS:1002308 ! fluorescence detector'
> >> relationship
> >> [Term]
> >> id: MS:1000819
> >> name: Acquity UPLC FLR
> >> def: "Acquity UPLC Fluorescence Detector." [PSI:MS]
> >> is_a: MS:1000126 ! Waters instrument model
> >> is_a: MS:1002308 ! fluorescence detector
> >>
> >> ************ Adapted the definitions for the following Waters
> instruments
> >> to be more specific and unambiguous:
> >> MS:1000159    GCT
> >> MS:1000170    M@LDI L
> >> MS:1000171    M@LDI LR
> >> MS:1000188    Q-Tof micro
> >> MS:1000189    Q-Tof ultima
> >> MS:1000191    quattro micro
> >> MS:1000192    Quattro UItima
> >> MS:1000632    Q-Tof Premier
> >> MS:1001761    ACQUITY UPLC
> >> MS:1001762    ACQUITY UPLC H-Class
> >> MS:1001763    ACQUITY UPLC H-Class Bio
> >> MS:1001764    ACQUITY UPLC I-Class
> >> MS:1001765    ACQUITY UPLC Systems with 2D Technology
> >> MS:1001766    nanoACQUITY UPLC
> >> MS:1001767    nanoACQUITY UPLC System with Technology
> >> MS:1001768    nanoACQUITY UPLC with HDX Technology
> >> MS:1001769    TRIZAIC UPLC nanoTile
> >> MS:1001770    GCT Premier
> >> MS:1001771    MALDI Synapt G2 HDMS
> >> MS:1001772    MALDI Synapt G2 MS
> >> MS:1001773    MALDI Synapt G2-S HDMS
> >> MS:1001774    MALDI Synapt G2-S MS
> >> MS:1001775    MALDI Synapt HDMS
> >> MS:1001776    MALDI Synapt MS
> >> MS:1001777    Synapt G2 HDMS
> >> MS:1001778    Synapt G2 MS
> >> MS:1001779    Synapt G2-S HDMS
> >> MS:1001780    Synapt G2-S MS
> >> MS:1001781    Synapt HDMS
> >> MS:1001782    Synapt MS
> >> MS:1001783    Xevo G2 Q-Tof
> >> MS:1001784    Xevo G2 Tof
> >> MS:1001785    Xevo Q-Tof
> >> MS:1001786    3100
> >> MS:1001787    Acquity SQD
> >> MS:1001788    Acquity TQD
> >> MS:1001789    Quattro micro GC
> >> MS:1001790    Xevo TQ MS
> >> MS:1001791    Xevo TQD
> >> MS:1001792    Xevo TQ-S
> >> MS:1001795    Empower
> >> MS:1001796    Unify
> >>
> >>
> >> New CV terms in version 3.50.0 of psi-ms.obo:

> >> ==============================**===============

> >> [Term]
> >> id: MS:1002308
> >> name: fluorescence detector
> >> def: "A detector using a fluorescent signal after excitation with
> light."
> >> [PSI:MS]
> >> is_a: MS:1000026 ! detector type
> >>
> >> [Term]
> >> id: MS:1002309
> >> name: Byonic: Peptide AbsLogProb
> >> def: "The absolute value of the log-base10 of the Byonic posterior
> error
> >> probability (PEP) of the PSM. " [PSI:PI]
> >> xref: value-type:xsd\:double "The allowed value-type for this CV
> term."
> >> is_a: MS:1001143 ! search engine specific score for PSMs
> >> is_a: MS:1001153 ! search engine specific score
> >> has_order: MS:1002108 ! higher score better
> >>
> >> [Term]
> >> id: MS:1002310
> >> name: Byonic: Protein AbsLogProb
> >> def: "The absolute value of the log-base10 of the Byonic posterior
> error
> >> probability (PEP) of the protein. " [PSI:PI]
> >> xref: value-type:xsd\:double "The allowed value-type for this CV
> term."
> >> is_a: MS:1001116 ! single protein result details
> >> is_a: MS:1001153 ! search engine specific score
> >> has_order: MS:1002108 ! higher score better
> >>
> >> [Term]
> >> id: MS:1002311
> >> name: Byonic: Peptide AbsLogProb2D
> >> def: "The absolute value of the log-base10 Byonic two-dimensional
> >> posterior error probability (PEP) of the PSM. The two-dimensional
> PEP takes
> >> into account protein ranking information as well as PSM
> information."
> >> [PSI:PI]
> >> xref: value-type:xsd\:double "The allowed value-type for this CV
> term."
> >> is_a: MS:1001143 ! search engine specific score for PSMs
> >> is_a: MS:1001153 ! search engine specific score
> >> has_order: MS:1002108 ! higher score better
> >>
> >> Best Regards,
> >> Gerhard
> >>
> >> --
> >> ---
> >> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> >> Bioinformatik / Biostatistik
> >> Medizinisches-Proteom-Center (MPC)
> >> Ruhr-Universität Bochum
> >> Zentrum für klinische Forschung I (ZKF I)
> >> E.049a
> >> Universitätsstraße 150
> >> D-44801 Bochum
> >>  Phone: +49(0)234/32-21006
> >> Fax:    +49(0)234/32-14554
> >> Email:  Ger...@ru...

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

> ----------
> >> Get 100% visibility into Java/.NET code with AppDynamics Lite
> >> It's a free troubleshooting tool designed for production
> >> Get down to code-level detail for bottlenecks, with <2% overhead.
> >> Download for free and get started troubleshooting in minutes.
> >> http://p.sf.net/sfu/appdyn_d2d_ap2
> >> _______________________________________________
> >> Psidev-ms-dev mailing list
> >> Psi...@li...
> >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> >>
> >>
> >
> >
> >

> > ---------------------------------------------------------------------
> ---------
> > Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012,
> more!
> > Discover the easy way to master current and previous Microsoft
> technologies
> > and advance your career. Get an incredible 1,500+ hours of step-by-
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> > Psi...@li...
> > https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab

> >
>
>
> --
> ---
> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> Bioinformatik / Biostatistik
> Medizinisches-Proteom-Center (MPC)
> Ruhr-Universität Bochum
> Zentrum für klinische Forschung I (ZKF I)
> E.049a
> Universitätsstraße 150
> D-44801 Bochum
>
> Phone:        +49(0)234/32-21006
> Fax:  +49(0)234/32-14554
> Email:        Ger...@ru...
> Web:  http://www.medizinisches-proteom-center.de
>
> -----------------------------------------------------------------------
> -------

> Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
> Discover the easy way to master current and previous Microsoft
> technologies
> and advance your career. Get an incredible 1,500+ hours of step-by-step
> tutorial videos with LearnDevNow. Subscribe today and save!
> http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.cl
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> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab

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Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.50.0 of psi-ms.obo

[Nils H. <nil...@ce...>]

Hi Eric and Brian,
would it make sense to replace the term 'peptide' with 'analyte' in the terms below covering elution time? This would also make them more compatible with the terminology used in metabolomics and analytical chemistry. Or did I miss a direct connection of these terms to proteomics experiments somewhere?

Regards,
Nils

-- 
Nils Hoffmann                               phone:    +49-521-106-4342
Bielefeld University                        room:             U10-144
Faculty of Technology, Genome Informatics
P.O. Box 10 01 31    
33501 Bielefeld, Germany
http://www.cebitec.uni-bielefeld.de/~hoffmann

Am 04.09.2013 um 22:12 schrieb Eric Deutsch <Eri...@sy...>:

> Hi Brian, I agree, this is an improvement. I tweaked the language a little so all the definitions are in the same tense and  added a “from”. How does everyone like these improved definitions?
>  
> id: MS:1000894
> name: retention time
> def: "A time interval from the start of chromatography when a peptide exits a chromatographic column." [PSI:MS]
>  
> id: MS:1000895
> name: local retention time
> def: "A time interval from the start of chromatography when a peptide exits an unspecified local chromatographic column and instrumental setup." [PSI:MS]
>  
> id: MS:1000896
> name: normalized retention time
> def: "A time interval from the start of chromatography when a peptide exits a standardized reference chromatographic column and instrumental setup." [PSI:MS]
>  
> id: MS:1000897
> name: predicted retention time
> def: "A time interval from the start of chromatography when a peptide exits a chromatographic column as predicted by a referenced software application." [PSI:MS]
>  
>  
>  
> From: Brian Pratt [mailto:bri...@in...] 
> Sent: Wednesday, September 04, 2013 11:50 AM
> To: Eric Deutsch
> Cc: Mass spectrometry standard development; psi...@li...; psi...@li...
> Subject: Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.50.0 of psi-ms.obo
>  
> It's the "relative to the beginning of a mass spectrometric run"  part that strikes me as misleading - it doesn't seem proper when the chromatography may have taken place in a completely different time period than the mass spec analysis (again, thinking MALDI but trying to be perfectly general and futureproof).  It just seems inline-LCMS-centric where it should be more general.
>  
> Overall I would think it should use language about the column's history rather than the mass analyzer's.  So for example
>     id: MS:1000897
>     name: predicted retention time
> should simply read:
>     def: "A time interval when a peptide will exit a chromatographic column as predicted by a referenced software application." [PSI:MS]
>  
> and
>   id: MS:1000894
>   name: retention time
> should be
>   def: "A time interval at which a peptide exited a chromatographic column." [PSI:MS]
>  
> etc.
>  
> Perhaps I am revisiting an already settled issue, but this just isn't intuitive to me as currently written.  And I might just be the target audience, as a developer dipping into this on an occasional basis.
>  
> Helpfully,
>  
> Brian Pratt
>  
> 
> On Wed, Sep 4, 2013 at 10:12 AM, Eric Deutsch <Eri...@sy...> wrote:
> Hi Brian, can you elaborate on what is misleading? I don’t see how concurrent elution and scan are implied in these terms? Maybe the term “mass spectrometric run” is the vague part? Perhaps “chromatography” should replace “a mass spectrometric run” for terms 894-896?
>  
> For pepXML, you almost surely want “scan start time” since that’s what is pulled from the raw/mzML files, right? The true retention time of the peptide ion seen in that scan is far more complex and usually not known very well. The scan start time is a precise and often sufficiently useful proxy for the true retention time. Right?
>  
> Allowed units are specified in the term metadata, see below..
>  
> Eric
>  
> id: MS:1000016
> name: scan start time
> def: "The time that an analyzer started a scan, relative to the start of the MS run." [PSI:MS]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000503 ! scan attribute
> is_a: MS:1001105 ! peptide result details
> is_a: MS:1001405 ! spectrum identification result details
> relationship: has_units UO:0000010 ! second
> relationship: has_units UO:0000031 ! minute
>  
> id: MS:1000894
> name: retention time
> def: "A measure of the interval relative to the beginning of a mass spectrometric run." [PSI:MS]
> is_a: MS:1000887 ! peptide attribute
>  
> id: MS:1000895
> name: local retention time
> def: "A measure of the interval relative to the beginning of a mass spectrometric run when a peptide will exit an unspecified local chromatographic column and instrumental setup." [PSI:MS]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000894 ! retention time
> relationship: has_units UO:0000010 ! second
> relationship: has_units UO:0000031 ! minute
> id: MS:1000896
> name: normalized retention time
> def: "A measure of the interval relative to the beginning of a mass spectrometric run when a peptide will exit a standardized reference chromatographic column and instrumental setup." [PSI:MS]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000894 ! retention time
> relationship: has_units UO:0000010 ! second
> relationship: has_units UO:0000031 ! minute
> id: MS:1000897
> name: predicted retention time
> def: "A time interval relative to the beginning of a mass spectrometric run when a peptide will exit a chromatographic column as predicted by a referenced software application." [PSI:MS]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000894 ! retention time
> relationship: has_units UO:0000010 ! second
> relationship: has_units UO:0000031 ! minute
>  
>  
>  
>  
>  
> From: Brian Pratt [mailto:bri...@in...] 
> Sent: Wednesday, September 04, 2013 9:56 AM
> To: Mass spectrometry standard development
> Cc: psi...@li...; psi...@li...; Eric Deutsch
> Subject: Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.50.0 of psi-ms.obo
>  
> >> What do you think?
>  
> I completely agree that these are distinct concepts, and of course I'm not surprised that everyone else thinks so too.  But the description is misleading, I think, since it really seems to assume concurrent elution and scan.  A quibble perhaps but probably worth cleaning up.
>  
> The use in question is actually in pepXML related code, so retention time is the concept we want for sure.  But now I guess I have to think about managing units?  Or is it defined as being in seconds?  (And if so, perhaps the description should be enhanced to reflect that?)
>  
> Thanks,
>  
> Brian
>  
> 
> On Wed, Sep 4, 2013 at 9:45 AM, <Eri...@sy...> wrote:
> Hi Brian, I'm not certain if that answers your question, but I might add
> that ProteoWizard's use of the obsolete retention time(s) should be
> changed to either scan start time or retention time. We intend scan start
> time to be used in cases where there is a time tag associated with a
> definite mass spec acquisition (as is the case in mzML and mzIdentML). The
> non-obsolete retention time term should be used as an attribute associated
> with a peptide molecule in a chromatographic column independent of an
> instrument acquisition event (as is the case in TraML). The MALDI case is
> a little more tricky. In practice, a scan start time will likely be
> recorded with the instrument and should be written into mzML et al. The
> chromatographic retention time might be known and could be recorded
> separately (as this will be a different time than the instrument scan
> time), but often is not well known when the mzML is written. But as you
> allude to, these are now different concepts with different terms, whereas
> before it was more muddled.
> 
> What do you think?
> 
> Regards,
> Eric
> 
> 
> > -----Original Message-----
> > From: Gerhard Mayer [mailto:Ger...@ru...]
> > Sent: Tuesday, September 03, 2013 11:24 PM
> > To: psi...@li...
> > Subject: Re: [Psidev-ms-vocab] [Psidev-ms-dev] New version 3.50.0 of
> > psi-ms.obo
> >
> > Hi Brian,
> >
> > yes we obsoletetd the retention time(s) term.
> >
> > Because we had two terms: retention time and retention time(s), we
> > decided to obsolete one and add a term named scan start time for the
> > SpectrumIdentificationResult annotation, see our discussion in Issue 74
> > on google code:
> >
> > https://code.google.com/p/psi-pi/issues/detail?id=74&can=1
> >
> > Best Regards,
> > Gerhard
> >
> >
> > Am 04.09.2013 00:38, schrieb Brian Pratt:
> > > I'm a little slow noticing this (just now updating ProteoWizard's
> > OBO), but
> > > I wonder about the now obsoleted
> > > id: MS:1001114
> > > name: retention time(s)
> > > def: "Retention time of the spectrum from the source file." [PSI:PI]
> > >
> > > Surely chromatography and mass spec can happen in entirely different
> > time
> > > frames, as with MALDI - or am I misunderstanding something?
> > >
> > > And how is it different from
> > > id: MS:1000894
> > > name: retention time
> > > def: "A measure of the interval relative to the beginning of a mass
> > > spectrometric run when a peptide will exit the chromatographic
> > column."
> > > [PSI:MS]
> > >
> > > And doesn't that definition have the same assumption about the column
> > being
> > > hooked up directly to the mass spec?
> > >
> > > Cheers,
> > > Brian Pratt
> > >
> > >
> > > On Fri, May 31, 2013 at 12:10 AM, Gerhard Mayer <
> > > Ger...@ru...> wrote:
> > >
> > >> Dear proteomics community,
> > >>
> > >> attached there's the new version 3.50.0 of the psi-ms.obo file.
> > >>
> > >> It contains the changes concerning the retention time terms (issue
> > 74),
> > >> changes for the waters instrument term definitions and 3 new terms
> > for the
> > >> Byonic search engine.
> > >>
> > >>
> > >> Changed CV terms in version 3.50.0 of psi-ms.obo:
> > >> ==============================**===================
> > >> ************ added the two is_a relations 'is_a: MS:1001105 !
> > peptide
> > >> result details' and
> > >> ************ 'is_a: MS:1001405 ! spectrum identification result
> > details'
> > >> [Term]
> > >> id: MS:1000016
> > >> name: scan start time
> > >> def: "The time that an analyzer started a scan, relative to the
> > start of
> > >> the MS run." [PSI:MS]
> > >> xref: value-type:xsd\:float "The allowed value-type for this CV
> > term."
> > >> is_a: MS:1000503 ! scan attribute
> > >> is_a: MS:1001105 ! peptide result details
> > >> is_a: MS:1001405 ! spectrum identification result details
> > >> relationship: has_units UO:0000010 ! second
> > >> relationship: has_units UO:0000031 ! minute
> > >>
> > >> ************ Made obsolete
> > >> [Term]
> > >> id: MS:1001114
> > >> name: retention time(s)
> > >> def: "OBSOLETE Retention time of the spectrum from the source file."
> > >> [PSI:PI]
> > >> comment: This term was made obsolete because scan start time
> > (MS:1000016)
> > >> should be used instead.
> > >> xref: value-type:xsd\:double "The allowed value-type for this CV
> > term."
> > >> is_a: MS:1001105 ! peptide result details
> > >> is_a: MS:1001405 ! spectrum identification result details
> > >> relationship: has_units UO:0000010 ! second
> > >> relationship: has_units UO:0000031 ! minute
> > >> is_obsolete: true
> > >>
> > >> ************ Changed the definition (removed 'peptide ...').
> > >> [Term]
> > >> id: MS:1000894
> > >> name: retention time
> > >> def: "A measure of the interval relative to the beginning of a mass
> > >> spectrometric run." [PSI:MS]
> > >> is_a: MS:1000887 ! peptide attribute
> > >>
> > >> ************ Changed the is_a relationship from 'detector type' -->
> > 'array
> > >> detector' for the next two terms
> > >> [Term]
> > >> id: MS:1000114
> > >> name: microchannel plate detector
> > >> def: "A thin plate that contains a closely spaced array of channels
> > that
> > >> each act as a continuous dynode particle multiplier. A charged
> > particle,
> > >> fast neutral particle, or photon striking the plate causes a cascade
> > of
> > >> secondary electrons that ultimately exits the opposite side of the
> > plate."
> > >> [PSI:MS]
> > >> synonym: "multichannel plate" EXACT []
> > >> is_a: MS:1000345 ! array detector
> > >>
> > >> [Term]
> > >> id: MS:1000621
> > >> name: photodiode array detector
> > >> def: "An array detector used to record spectra in the ultraviolet
> > and
> > >> visible region of light." [PSI:MS]
> > >> synonym: "PDA" EXACT []
> > >> is_a: MS:1000345 ! array detector
> > >>
> > >> ************ Added the 'is_a: MS:1000621 ! photodiode array
> > detector'
> > >> relationship
> > >> [Term]
> > >> id: MS:1000818
> > >> name: Acquity UPLC PDA
> > >> def: "Acquity UPLC Photodiode Array Detector." [PSI:MS]
> > >> is_a: MS:1000126 ! Waters instrument model
> > >> is_a: MS:1000621 ! photodiode array detector
> > >>
> > >> ************ Added the 'is_a: MS:1002308 ! fluorescence detector'
> > >> relationship
> > >> [Term]
> > >> id: MS:1000819
> > >> name: Acquity UPLC FLR
> > >> def: "Acquity UPLC Fluorescence Detector." [PSI:MS]
> > >> is_a: MS:1000126 ! Waters instrument model
> > >> is_a: MS:1002308 ! fluorescence detector
> > >>
> > >> ************ Adapted the definitions for the following Waters
> > instruments
> > >> to be more specific and unambiguous:
> > >> MS:1000159    GCT
> > >> MS:1000170    M@LDI L
> > >> MS:1000171    M@LDI LR
> > >> MS:1000188    Q-Tof micro
> > >> MS:1000189    Q-Tof ultima
> > >> MS:1000191    quattro micro
> > >> MS:1000192    Quattro UItima
> > >> MS:1000632    Q-Tof Premier
> > >> MS:1001761    ACQUITY UPLC
> > >> MS:1001762    ACQUITY UPLC H-Class
> > >> MS:1001763    ACQUITY UPLC H-Class Bio
> > >> MS:1001764    ACQUITY UPLC I-Class
> > >> MS:1001765    ACQUITY UPLC Systems with 2D Technology
> > >> MS:1001766    nanoACQUITY UPLC
> > >> MS:1001767    nanoACQUITY UPLC System with Technology
> > >> MS:1001768    nanoACQUITY UPLC with HDX Technology
> > >> MS:1001769    TRIZAIC UPLC nanoTile
> > >> MS:1001770    GCT Premier
> > >> MS:1001771    MALDI Synapt G2 HDMS
> > >> MS:1001772    MALDI Synapt G2 MS
> > >> MS:1001773    MALDI Synapt G2-S HDMS
> > >> MS:1001774    MALDI Synapt G2-S MS
> > >> MS:1001775    MALDI Synapt HDMS
> > >> MS:1001776    MALDI Synapt MS
> > >> MS:1001777    Synapt G2 HDMS
> > >> MS:1001778    Synapt G2 MS
> > >> MS:1001779    Synapt G2-S HDMS
> > >> MS:1001780    Synapt G2-S MS
> > >> MS:1001781    Synapt HDMS
> > >> MS:1001782    Synapt MS
> > >> MS:1001783    Xevo G2 Q-Tof
> > >> MS:1001784    Xevo G2 Tof
> > >> MS:1001785    Xevo Q-Tof
> > >> MS:1001786    3100
> > >> MS:1001787    Acquity SQD
> > >> MS:1001788    Acquity TQD
> > >> MS:1001789    Quattro micro GC
> > >> MS:1001790    Xevo TQ MS
> > >> MS:1001791    Xevo TQD
> > >> MS:1001792    Xevo TQ-S
> > >> MS:1001795    Empower
> > >> MS:1001796    Unify
> > >>
> > >>
> > >> New CV terms in version 3.50.0 of psi-ms.obo:
> > >> ==============================**===============
> > >> [Term]
> > >> id: MS:1002308
> > >> name: fluorescence detector
> > >> def: "A detector using a fluorescent signal after excitation with
> > light."
> > >> [PSI:MS]
> > >> is_a: MS:1000026 ! detector type
> > >>
> > >> [Term]
> > >> id: MS:1002309
> > >> name: Byonic: Peptide AbsLogProb
> > >> def: "The absolute value of the log-base10 of the Byonic posterior
> > error
> > >> probability (PEP) of the PSM. " [PSI:PI]
> > >> xref: value-type:xsd\:double "The allowed value-type for this CV
> > term."
> > >> is_a: MS:1001143 ! search engine specific score for PSMs
> > >> is_a: MS:1001153 ! search engine specific score
> > >> has_order: MS:1002108 ! higher score better
> > >>
> > >> [Term]
> > >> id: MS:1002310
> > >> name: Byonic: Protein AbsLogProb
> > >> def: "The absolute value of the log-base10 of the Byonic posterior
> > error
> > >> probability (PEP) of the protein. " [PSI:PI]
> > >> xref: value-type:xsd\:double "The allowed value-type for this CV
> > term."
> > >> is_a: MS:1001116 ! single protein result details
> > >> is_a: MS:1001153 ! search engine specific score
> > >> has_order: MS:1002108 ! higher score better
> > >>
> > >> [Term]
> > >> id: MS:1002311
> > >> name: Byonic: Peptide AbsLogProb2D
> > >> def: "The absolute value of the log-base10 Byonic two-dimensional
> > >> posterior error probability (PEP) of the PSM. The two-dimensional
> > PEP takes
> > >> into account protein ranking information as well as PSM
> > information."
> > >> [PSI:PI]
> > >> xref: value-type:xsd\:double "The allowed value-type for this CV
> > term."
> > >> is_a: MS:1001143 ! search engine specific score for PSMs
> > >> is_a: MS:1001153 ! search engine specific score
> > >> has_order: MS:1002108 ! higher score better
> > >>
> > >> Best Regards,
> > >> Gerhard
> > >>
> > >> --
> > >> ---
> > >> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> > >> Bioinformatik / Biostatistik
> > >> Medizinisches-Proteom-Center (MPC)
> > >> Ruhr-Universität Bochum
> > >> Zentrum für klinische Forschung I (ZKF I)
> > >> E.049a
> > >> Universitätsstraße 150
> > >> D-44801 Bochum
> > >>  Phone: +49(0)234/32-21006
> > >> Fax:    +49(0)234/32-14554
> > >> Email:  Ger...@ru...
> > >> Web:    http://www.medizinisches-**proteom-
> > center.de<http://www.medizinisches-proteom-center.de>
> > >>
> > >>
> > >>
> > >> --------------------------------------------------------------------
> > ----------
> > >> Get 100% visibility into Java/.NET code with AppDynamics Lite
> > >> It's a free troubleshooting tool designed for production
> > >> Get down to code-level detail for bottlenecks, with <2% overhead.
> > >> Download for free and get started troubleshooting in minutes.
> > >> http://p.sf.net/sfu/appdyn_d2d_ap2
> > >> _______________________________________________
> > >> Psidev-ms-dev mailing list
> > >> Psi...@li...
> > >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> > >>
> > >>
> > >
> > >
> > >
> > > ---------------------------------------------------------------------
> > ---------
> > > Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012,
> > more!
> > > Discover the easy way to master current and previous Microsoft
> > technologies
> > > and advance your career. Get an incredible 1,500+ hours of step-by-
> > step
> > > tutorial videos with LearnDevNow. Subscribe today and save!
> > >
> > http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.cl
> > ktrk
> > >
> > >
> > >
> > > _______________________________________________
> > > Psidev-ms-vocab mailing list
> > > Psi...@li...
> > > https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab
> > >
> >
> >
> > --
> > ---
> > Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> > Bioinformatik / Biostatistik
> > Medizinisches-Proteom-Center (MPC)
> > Ruhr-Universität Bochum
> > Zentrum für klinische Forschung I (ZKF I)
> > E.049a
> > Universitätsstraße 150
> > D-44801 Bochum
> >
> > Phone:        +49(0)234/32-21006
> > Fax:  +49(0)234/32-14554
> > Email:        Ger...@ru...
> > Web:  http://www.medizinisches-proteom-center.de
> >
> > -----------------------------------------------------------------------
> > -------
> > Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
> > Discover the easy way to master current and previous Microsoft
> > technologies
> > and advance your career. Get an incredible 1,500+ hours of step-by-step
> > tutorial videos with LearnDevNow. Subscribe today and save!
> > http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.cl
> > ktrk
> > _______________________________________________
> > Psidev-ms-vocab mailing list
> > Psi...@li...
> > https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab
> 
> ------------------------------------------------------------------------------
> Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
> Discover the easy way to master current and previous Microsoft technologies
> and advance your career. Get an incredible 1,500+ hours of step-by-step
> tutorial videos with LearnDevNow. Subscribe today and save!
> http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.clktrk
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>  
>  
> ------------------------------------------------------------------------------
> Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
> Discover the easy way to master current and previous Microsoft technologies
> and advance your career. Get an incredible 1,500+ hours of step-by-step
> tutorial videos with LearnDevNow. Subscribe today and save!
> http://pubads.g.doubleclick.net/gampad/clk?id=58041391&iu=/4140/ostg.clktrk
> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.50.0 of psi-ms.obo

[Brian P. <bri...@in...>]

Better, for sure. But I can't quite tell the difference between 1000894 and
1000895, or rather I don't know what "local" means.  Makes me think GMT vs
local but I'm guessing that's not it.


On Wed, Sep 4, 2013 at 1:12 PM, Eric Deutsch <
Eri...@sy...> wrote:

> Hi Brian, I agree, this is an improvement. I tweaked the language a little
> so all the definitions are in the same tense and  added a “from”. How does
> everyone like these improved definitions?
>
>
>
> id: MS:1000894
>
> name: retention time
>
> def: "A time interval from the start of chromatography when a peptide
> exits a chromatographic column." [PSI:MS]
>
>
>
> id: MS:1000895
>
> name: local retention time
>
> def: "A time interval from the start of chromatography when a peptide
> exits an unspecified local chromatographic column and instrumental setup."
> [PSI:MS]
>
>
>
> id: MS:1000896
>
> name: normalized retention time
>
> def: "A time interval from the start of chromatography when a peptide
> exits a standardized reference chromatographic column and instrumental
> setup." [PSI:MS]
>
>
>
> id: MS:1000897
>
> name: predicted retention time
>
> def: "A time interval from the start of chromatography when a peptide
> exits a chromatographic column as predicted by a referenced software
> application." [PSI:MS]
>
>
>
>
>
>
>
> *From:* Brian Pratt [mailto:bri...@in...]
> *Sent:* Wednesday, September 04, 2013 11:50 AM
> *To:* Eric Deutsch
> *Cc:* Mass spectrometry standard development;
> psi...@li...; psi...@li...
>
> *Subject:* Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.50.0 of
> psi-ms.obo
>
>
>
> It's the "relative to the beginning of a mass spectrometric run"  part
> that strikes me as misleading - it doesn't seem proper when the
> chromatography may have taken place in a completely different time period
> than the mass spec analysis (again, thinking MALDI but trying to be
> perfectly general and futureproof).  It just seems inline-LCMS-centric
> where it should be more general.
>
>
>
> Overall I would think it should use language about the column's history
> rather than the mass analyzer's.  So for example
>
>     id: MS:1000897
>
>     name: predicted retention time
>
> should simply read:
>
>     def: "A time interval when a peptide will exit a chromatographic
> column as predicted by a referenced software application." [PSI:MS]
>
>
>
> and
>   id: MS:1000894
>   name: retention time
> should be
>   def: "A time interval at which a peptide exited a chromatographic column."
> [PSI:MS]
>
>
>
> etc.
>
>
>
> Perhaps I am revisiting an already settled issue, but this just isn't
> intuitive to me as currently written.  And I might just be the target
> audience, as a developer dipping into this on an occasional basis.
>
>
>
> Helpfully,
>
>
>
> Brian Pratt
>
>
>
> On Wed, Sep 4, 2013 at 10:12 AM, Eric Deutsch <
> Eri...@sy...> wrote:
>
> Hi Brian, can you elaborate on what is misleading? I don’t see how
> concurrent elution and scan are implied in these terms? Maybe the term
> “mass spectrometric run” is the vague part? Perhaps “chromatography” should
> replace “a mass spectrometric run” for terms 894-896?
>
>
>
> For pepXML, you almost surely want “scan start time” since that’s what is
> pulled from the raw/mzML files, right? The true retention time of the
> peptide ion seen in that scan is far more complex and usually not known
> very well. The scan start time is a precise and often sufficiently useful
> proxy for the true retention time. Right?
>
>
>
> Allowed units are specified in the term metadata, see below..
>
>
>
> Eric
>
>
>
> id: MS:1000016
>
> name: scan start time
>
> def: "The time that an analyzer started a scan, relative to the start of
> the MS run." [PSI:MS]
>
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>
> is_a: MS:1000503 ! scan attribute
>
> is_a: MS:1001105 ! peptide result details
>
> is_a: MS:1001405 ! spectrum identification result details
>
> relationship: has_units UO:0000010 ! second
>
> relationship: has_units UO:0000031 ! minute
>
>
>
> id: MS:1000894
>
> name: retention time
>
> def: "A measure of the interval relative to the beginning of a mass
> spectrometric run." [PSI:MS]
>
> is_a: MS:1000887 ! peptide attribute
>
>
>
> id: MS:1000895
>
> name: local retention time
>
> def: "A measure of the interval relative to the beginning of a mass
> spectrometric run when a peptide will exit an unspecified local
> chromatographic column and instrumental setup." [PSI:MS]
>
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>
> is_a: MS:1000894 ! retention time
>
> relationship: has_units UO:0000010 ! second
>
> relationship: has_units UO:0000031 ! minute
>
> id: MS:1000896
>
> name: normalized retention time
>
> def: "A measure of the interval relative to the beginning of a mass
> spectrometric run when a peptide will exit a standardized reference
> chromatographic column and instrumental setup." [PSI:MS]
>
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>
> is_a: MS:1000894 ! retention time
>
> relationship: has_units UO:0000010 ! second
>
> relationship: has_units UO:0000031 ! minute
>
> id: MS:1000897
>
> name: predicted retention time
>
> def: "A time interval relative to the beginning of a mass spectrometric
> run when a peptide will exit a chromatographic column as predicted by a
> referenced software application." [PSI:MS]
>
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>
> is_a: MS:1000894 ! retention time
>
> relationship: has_units UO:0000010 ! second
>
> relationship: has_units UO:0000031 ! minute
>
>
>
>
>
>
>
>
>
>
>
> *From:* Brian Pratt [mailto:bri...@in...]
> *Sent:* Wednesday, September 04, 2013 9:56 AM
> *To:* Mass spectrometry standard development
> *Cc:* psi...@li...;
> psi...@li...; Eric Deutsch
> *Subject:* Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.50.0 of
> psi-ms.obo
>
>
>
> >> What do you think?
>
>
>
> I completely agree that these are distinct concepts, and of course I'm not
> surprised that everyone else thinks so too.  But the description is
> misleading, I think, since it really seems to assume concurrent elution and
> scan.  A quibble perhaps but probably worth cleaning up.
>
>
>
> The use in question is actually in pepXML related code, so retention time
> is the concept we want for sure.  But now I guess I have to think about
> managing units?  Or is it defined as being in seconds?  (And if so, perhaps
> the description should be enhanced to reflect that?)
>
>
>
> Thanks,
>
>
>
> Brian
>
>
>
> On Wed, Sep 4, 2013 at 9:45 AM, <Eri...@sy...> wrote:
>
> Hi Brian, I'm not certain if that answers your question, but I might add
> that ProteoWizard's use of the obsolete retention time(s) should be
> changed to either scan start time or retention time. We intend scan start
> time to be used in cases where there is a time tag associated with a
> definite mass spec acquisition (as is the case in mzML and mzIdentML). The
> non-obsolete retention time term should be used as an attribute associated
> with a peptide molecule in a chromatographic column independent of an
> instrument acquisition event (as is the case in TraML). The MALDI case is
> a little more tricky. In practice, a scan start time will likely be
> recorded with the instrument and should be written into mzML et al. The
> chromatographic retention time might be known and could be recorded
> separately (as this will be a different time than the instrument scan
> time), but often is not well known when the mzML is written. But as you
> allude to, these are now different concepts with different terms, whereas
> before it was more muddled.
>
> What do you think?
>
> Regards,
> Eric
>
>
> > -----Original Message-----
> > From: Gerhard Mayer [mailto:Ger...@ru...]
> > Sent: Tuesday, September 03, 2013 11:24 PM
> > To: psi...@li...
> > Subject: Re: [Psidev-ms-vocab] [Psidev-ms-dev] New version 3.50.0 of
> > psi-ms.obo
> >
> > Hi Brian,
> >
> > yes we obsoletetd the retention time(s) term.
> >
> > Because we had two terms: retention time and retention time(s), we
> > decided to obsolete one and add a term named scan start time for the
> > SpectrumIdentificationResult annotation, see our discussion in Issue 74
> > on google code:
> >
> > https://code.google.com/p/psi-pi/issues/detail?id=74&can=1
> >
> > Best Regards,
> > Gerhard
> >
> >
> > Am 04.09.2013 00:38, schrieb Brian Pratt:
>
> > > I'm a little slow noticing this (just now updating ProteoWizard's
> > OBO), but
> > > I wonder about the now obsoleted
> > > id: MS:1001114
> > > name: retention time(s)
> > > def: "Retention time of the spectrum from the source file." [PSI:PI]
> > >
> > > Surely chromatography and mass spec can happen in entirely different
> > time
> > > frames, as with MALDI - or am I misunderstanding something?
> > >
> > > And how is it different from
> > > id: MS:1000894
> > > name: retention time
> > > def: "A measure of the interval relative to the beginning of a mass
> > > spectrometric run when a peptide will exit the chromatographic
> > column."
> > > [PSI:MS]
> > >
> > > And doesn't that definition have the same assumption about the column
> > being
> > > hooked up directly to the mass spec?
> > >
> > > Cheers,
> > > Brian Pratt
> > >
> > >
> > > On Fri, May 31, 2013 at 12:10 AM, Gerhard Mayer <
> > > Ger...@ru...> wrote:
> > >
> > >> Dear proteomics community,
> > >>
> > >> attached there's the new version 3.50.0 of the psi-ms.obo file.
> > >>
> > >> It contains the changes concerning the retention time terms (issue
> > 74),
> > >> changes for the waters instrument term definitions and 3 new terms
> > for the
> > >> Byonic search engine.
> > >>
> > >>
> > >> Changed CV terms in version 3.50.0 of psi-ms.obo:
>
> > >> ==============================**===================
>
> > >> ************ added the two is_a relations 'is_a: MS:1001105 !
> > peptide
> > >> result details' and
> > >> ************ 'is_a: MS:1001405 ! spectrum identification result
> > details'
> > >> [Term]
> > >> id: MS:1000016
> > >> name: scan start time
> > >> def: "The time that an analyzer started a scan, relative to the
> > start of
> > >> the MS run." [PSI:MS]
> > >> xref: value-type:xsd\:float "The allowed value-type for this CV
> > term."
> > >> is_a: MS:1000503 ! scan attribute
> > >> is_a: MS:1001105 ! peptide result details
> > >> is_a: MS:1001405 ! spectrum identification result details
> > >> relationship: has_units UO:0000010 ! second
> > >> relationship: has_units UO:0000031 ! minute
> > >>
> > >> ************ Made obsolete
> > >> [Term]
> > >> id: MS:1001114
> > >> name: retention time(s)
> > >> def: "OBSOLETE Retention time of the spectrum from the source file."
> > >> [PSI:PI]
> > >> comment: This term was made obsolete because scan start time
> > (MS:1000016)
> > >> should be used instead.
> > >> xref: value-type:xsd\:double "The allowed value-type for this CV
> > term."
> > >> is_a: MS:1001105 ! peptide result details
> > >> is_a: MS:1001405 ! spectrum identification result details
> > >> relationship: has_units UO:0000010 ! second
> > >> relationship: has_units UO:0000031 ! minute
> > >> is_obsolete: true
> > >>
> > >> ************ Changed the definition (removed 'peptide ...').
> > >> [Term]
> > >> id: MS:1000894
> > >> name: retention time
> > >> def: "A measure of the interval relative to the beginning of a mass
> > >> spectrometric run." [PSI:MS]
> > >> is_a: MS:1000887 ! peptide attribute
> > >>
> > >> ************ Changed the is_a relationship from 'detector type' -->
> > 'array
> > >> detector' for the next two terms
> > >> [Term]
> > >> id: MS:1000114
> > >> name: microchannel plate detector
> > >> def: "A thin plate that contains a closely spaced array of channels
> > that
> > >> each act as a continuous dynode particle multiplier. A charged
> > particle,
> > >> fast neutral particle, or photon striking the plate causes a cascade
> > of
> > >> secondary electrons that ultimately exits the opposite side of the
> > plate."
> > >> [PSI:MS]
> > >> synonym: "multichannel plate" EXACT []
> > >> is_a: MS:1000345 ! array detector
> > >>
> > >> [Term]
> > >> id: MS:1000621
> > >> name: photodiode array detector
> > >> def: "An array detector used to record spectra in the ultraviolet
> > and
> > >> visible region of light." [PSI:MS]
> > >> synonym: "PDA" EXACT []
> > >> is_a: MS:1000345 ! array detector
> > >>
> > >> ************ Added the 'is_a: MS:1000621 ! photodiode array
> > detector'
> > >> relationship
> > >> [Term]
> > >> id: MS:1000818
> > >> name: Acquity UPLC PDA
> > >> def: "Acquity UPLC Photodiode Array Detector." [PSI:MS]
> > >> is_a: MS:1000126 ! Waters instrument model
> > >> is_a: MS:1000621 ! photodiode array detector
> > >>
> > >> ************ Added the 'is_a: MS:1002308 ! fluorescence detector'
> > >> relationship
> > >> [Term]
> > >> id: MS:1000819
> > >> name: Acquity UPLC FLR
> > >> def: "Acquity UPLC Fluorescence Detector." [PSI:MS]
> > >> is_a: MS:1000126 ! Waters instrument model
> > >> is_a: MS:1002308 ! fluorescence detector
> > >>
> > >> ************ Adapted the definitions for the following Waters
> > instruments
> > >> to be more specific and unambiguous:
> > >> MS:1000159    GCT
> > >> MS:1000170    M@LDI L
> > >> MS:1000171    M@LDI LR
> > >> MS:1000188    Q-Tof micro
> > >> MS:1000189    Q-Tof ultima
> > >> MS:1000191    quattro micro
> > >> MS:1000192    Quattro UItima
> > >> MS:1000632    Q-Tof Premier
> > >> MS:1001761    ACQUITY UPLC
> > >> MS:1001762    ACQUITY UPLC H-Class
> > >> MS:1001763    ACQUITY UPLC H-Class Bio
> > >> MS:1001764    ACQUITY UPLC I-Class
> > >> MS:1001765    ACQUITY UPLC Systems with 2D Technology
> > >> MS:1001766    nanoACQUITY UPLC
> > >> MS:1001767    nanoACQUITY UPLC System with Technology
> > >> MS:1001768    nanoACQUITY UPLC with HDX Technology
> > >> MS:1001769    TRIZAIC UPLC nanoTile
> > >> MS:1001770    GCT Premier
> > >> MS:1001771    MALDI Synapt G2 HDMS
> > >> MS:1001772    MALDI Synapt G2 MS
> > >> MS:1001773    MALDI Synapt G2-S HDMS
> > >> MS:1001774    MALDI Synapt G2-S MS
> > >> MS:1001775    MALDI Synapt HDMS
> > >> MS:1001776    MALDI Synapt MS
> > >> MS:1001777    Synapt G2 HDMS
> > >> MS:1001778    Synapt G2 MS
> > >> MS:1001779    Synapt G2-S HDMS
> > >> MS:1001780    Synapt G2-S MS
> > >> MS:1001781    Synapt HDMS
> > >> MS:1001782    Synapt MS
> > >> MS:1001783    Xevo G2 Q-Tof
> > >> MS:1001784    Xevo G2 Tof
> > >> MS:1001785    Xevo Q-Tof
> > >> MS:1001786    3100
> > >> MS:1001787    Acquity SQD
> > >> MS:1001788    Acquity TQD
> > >> MS:1001789    Quattro micro GC
> > >> MS:1001790    Xevo TQ MS
> > >> MS:1001791    Xevo TQD
> > >> MS:1001792    Xevo TQ-S
> > >> MS:1001795    Empower
> > >> MS:1001796    Unify
> > >>
> > >>
> > >> New CV terms in version 3.50.0 of psi-ms.obo:
>
> > >> ==============================**===============
>
> > >> [Term]
> > >> id: MS:1002308
> > >> name: fluorescence detector
> > >> def: "A detector using a fluorescent signal after excitation with
> > light."
> > >> [PSI:MS]
> > >> is_a: MS:1000026 ! detector type
> > >>
> > >> [Term]
> > >> id: MS:1002309
> > >> name: Byonic: Peptide AbsLogProb
> > >> def: "The absolute value of the log-base10 of the Byonic posterior
> > error
> > >> probability (PEP) of the PSM. " [PSI:PI]
> > >> xref: value-type:xsd\:double "The allowed value-type for this CV
> > term."
> > >> is_a: MS:1001143 ! search engine specific score for PSMs
> > >> is_a: MS:1001153 ! search engine specific score
> > >> has_order: MS:1002108 ! higher score better
> > >>
> > >> [Term]
> > >> id: MS:1002310
> > >> name: Byonic: Protein AbsLogProb
> > >> def: "The absolute value of the log-base10 of the Byonic posterior
> > error
> > >> probability (PEP) of the protein. " [PSI:PI]
> > >> xref: value-type:xsd\:double "The allowed value-type for this CV
> > term."
> > >> is_a: MS:1001116 ! single protein result details
> > >> is_a: MS:1001153 ! search engine specific score
> > >> has_order: MS:1002108 ! higher score better
> > >>
> > >> [Term]
> > >> id: MS:1002311
> > >> name: Byonic: Peptide AbsLogProb2D
> > >> def: "The absolute value of the log-base10 Byonic two-dimensional
> > >> posterior error probability (PEP) of the PSM. The two-dimensional
> > PEP takes
> > >> into account protein ranking information as well as PSM
> > information."
> > >> [PSI:PI]
> > >> xref: value-type:xsd\:double "The allowed value-type for this CV
> > term."
> > >> is_a: MS:1001143 ! search engine specific score for PSMs
> > >> is_a: MS:1001153 ! search engine specific score
> > >> has_order: MS:1002108 ! higher score better
> > >>
> > >> Best Regards,
> > >> Gerhard
> > >>
> > >> --
> > >> ---
> > >> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> > >> Bioinformatik / Biostatistik
> > >> Medizinisches-Proteom-Center (MPC)
> > >> Ruhr-Universität Bochum
> > >> Zentrum für klinische Forschung I (ZKF I)
> > >> E.049a
> > >> Universitätsstraße 150
> > >> D-44801 Bochum
> > >>  Phone: +49(0)234/32-21006
> > >> Fax:    +49(0)234/32-14554
> > >> Email:  Ger...@ru...
>
> > >> Web:    http://www.medizinisches-**proteom-
> > center.de<http://www.medizinisches-proteom-center.de>
> > >>
> > >>
> > >>
> > >> --------------------------------------------------------------------
>
> > ----------
> > >> Get 100% visibility into Java/.NET code with AppDynamics Lite
> > >> It's a free troubleshooting tool designed for production
> > >> Get down to code-level detail for bottlenecks, with <2% overhead.
> > >> Download for free and get started troubleshooting in minutes.
> > >> http://p.sf.net/sfu/appdyn_d2d_ap2
> > >> _______________________________________________
> > >> Psidev-ms-dev mailing list
> > >> Psi...@li...
> > >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> > >>
> > >>
> > >
> > >
> > >
>
> > > ---------------------------------------------------------------------
> > ---------
> > > Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012,
> > more!
> > > Discover the easy way to master current and previous Microsoft
> > technologies
> > > and advance your career. Get an incredible 1,500+ hours of step-by-
> > step
> > > tutorial videos with LearnDevNow. Subscribe today and save!
> > >
> > http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.cl
> > ktrk
> > >
> > >
> > >
> > > _______________________________________________
> > > Psidev-ms-vocab mailing list
> > > Psi...@li...
> > > https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab
>
> > >
> >
> >
> > --
> > ---
> > Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> > Bioinformatik / Biostatistik
> > Medizinisches-Proteom-Center (MPC)
> > Ruhr-Universität Bochum
> > Zentrum für klinische Forschung I (ZKF I)
> > E.049a
> > Universitätsstraße 150
> > D-44801 Bochum
> >
> > Phone:        +49(0)234/32-21006
> > Fax:  +49(0)234/32-14554
> > Email:        Ger...@ru...
> > Web:  http://www.medizinisches-proteom-center.de
> >
> > -----------------------------------------------------------------------
> > -------
>
> > Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
> > Discover the easy way to master current and previous Microsoft
> > technologies
> > and advance your career. Get an incredible 1,500+ hours of step-by-step
> > tutorial videos with LearnDevNow. Subscribe today and save!
> > http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.cl
> > ktrk
> > _______________________________________________
> > Psidev-ms-vocab mailing list
> > Psi...@li...
> > https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab
>
>
> ------------------------------------------------------------------------------
> Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
> Discover the easy way to master current and previous Microsoft technologies
> and advance your career. Get an incredible 1,500+ hours of step-by-step
> tutorial videos with LearnDevNow. Subscribe today and save!
> http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.clktrk
>
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>
>
>
>
>

Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.50.0 of psi-ms.obo

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

Hi Brian, I agree, this is an improvement. I tweaked the language a little
so all the definitions are in the same tense and  added a “from”. How does
everyone like these improved definitions?



id: MS:1000894

name: retention time

def: "A time interval from the start of chromatography when a peptide exits
a chromatographic column." [PSI:MS]



id: MS:1000895

name: local retention time

def: "A time interval from the start of chromatography when a peptide exits
an unspecified local chromatographic column and instrumental setup."
[PSI:MS]



id: MS:1000896

name: normalized retention time

def: "A time interval from the start of chromatography when a peptide exits
a standardized reference chromatographic column and instrumental setup."
[PSI:MS]



id: MS:1000897

name: predicted retention time

def: "A time interval from the start of chromatography when a peptide exits
a chromatographic column as predicted by a referenced software
application." [PSI:MS]







*From:* Brian Pratt [mailto:bri...@in...]
*Sent:* Wednesday, September 04, 2013 11:50 AM
*To:* Eric Deutsch
*Cc:* Mass spectrometry standard development;
psi...@li...; psi...@li...
*Subject:* Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.50.0 of
psi-ms.obo



It's the "relative to the beginning of a mass spectrometric run"  part that
strikes me as misleading - it doesn't seem proper when the chromatography
may have taken place in a completely different time period than the mass
spec analysis (again, thinking MALDI but trying to be perfectly general and
futureproof).  It just seems inline-LCMS-centric where it should be more
general.



Overall I would think it should use language about the column's history
rather than the mass analyzer's.  So for example

    id: MS:1000897

    name: predicted retention time

should simply read:

    def: "A time interval when a peptide will exit a chromatographic column
as predicted by a referenced software application." [PSI:MS]



and
  id: MS:1000894
  name: retention time
should be
  def: "A time interval at which a peptide exited a chromatographic column."
[PSI:MS]



etc.



Perhaps I am revisiting an already settled issue, but this just isn't
intuitive to me as currently written.  And I might just be the target
audience, as a developer dipping into this on an occasional basis.



Helpfully,



Brian Pratt



On Wed, Sep 4, 2013 at 10:12 AM, Eric Deutsch <
Eri...@sy...> wrote:

Hi Brian, can you elaborate on what is misleading? I don’t see how
concurrent elution and scan are implied in these terms? Maybe the term
“mass spectrometric run” is the vague part? Perhaps “chromatography” should
replace “a mass spectrometric run” for terms 894-896?



For pepXML, you almost surely want “scan start time” since that’s what is
pulled from the raw/mzML files, right? The true retention time of the
peptide ion seen in that scan is far more complex and usually not known
very well. The scan start time is a precise and often sufficiently useful
proxy for the true retention time. Right?



Allowed units are specified in the term metadata, see below..



Eric



id: MS:1000016

name: scan start time

def: "The time that an analyzer started a scan, relative to the start of
the MS run." [PSI:MS]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1000503 ! scan attribute

is_a: MS:1001105 ! peptide result details

is_a: MS:1001405 ! spectrum identification result details

relationship: has_units UO:0000010 ! second

relationship: has_units UO:0000031 ! minute



id: MS:1000894

name: retention time

def: "A measure of the interval relative to the beginning of a mass
spectrometric run." [PSI:MS]

is_a: MS:1000887 ! peptide attribute



id: MS:1000895

name: local retention time

def: "A measure of the interval relative to the beginning of a mass
spectrometric run when a peptide will exit an unspecified local
chromatographic column and instrumental setup." [PSI:MS]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1000894 ! retention time

relationship: has_units UO:0000010 ! second

relationship: has_units UO:0000031 ! minute

id: MS:1000896

name: normalized retention time

def: "A measure of the interval relative to the beginning of a mass
spectrometric run when a peptide will exit a standardized reference
chromatographic column and instrumental setup." [PSI:MS]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1000894 ! retention time

relationship: has_units UO:0000010 ! second

relationship: has_units UO:0000031 ! minute

id: MS:1000897

name: predicted retention time

def: "A time interval relative to the beginning of a mass spectrometric run
when a peptide will exit a chromatographic column as predicted by a
referenced software application." [PSI:MS]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1000894 ! retention time

relationship: has_units UO:0000010 ! second

relationship: has_units UO:0000031 ! minute











*From:* Brian Pratt [mailto:bri...@in...]
*Sent:* Wednesday, September 04, 2013 9:56 AM
*To:* Mass spectrometry standard development
*Cc:* psi...@li...;
psi...@li...; Eric Deutsch
*Subject:* Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.50.0 of
psi-ms.obo



>> What do you think?



I completely agree that these are distinct concepts, and of course I'm not
surprised that everyone else thinks so too.  But the description is
misleading, I think, since it really seems to assume concurrent elution and
scan.  A quibble perhaps but probably worth cleaning up.



The use in question is actually in pepXML related code, so retention time
is the concept we want for sure.  But now I guess I have to think about
managing units?  Or is it defined as being in seconds?  (And if so, perhaps
the description should be enhanced to reflect that?)



Thanks,



Brian



On Wed, Sep 4, 2013 at 9:45 AM, <Eri...@sy...> wrote:

Hi Brian, I'm not certain if that answers your question, but I might add
that ProteoWizard's use of the obsolete retention time(s) should be
changed to either scan start time or retention time. We intend scan start
time to be used in cases where there is a time tag associated with a
definite mass spec acquisition (as is the case in mzML and mzIdentML). The
non-obsolete retention time term should be used as an attribute associated
with a peptide molecule in a chromatographic column independent of an
instrument acquisition event (as is the case in TraML). The MALDI case is
a little more tricky. In practice, a scan start time will likely be
recorded with the instrument and should be written into mzML et al. The
chromatographic retention time might be known and could be recorded
separately (as this will be a different time than the instrument scan
time), but often is not well known when the mzML is written. But as you
allude to, these are now different concepts with different terms, whereas
before it was more muddled.

What do you think?

Regards,
Eric


> -----Original Message-----
> From: Gerhard Mayer [mailto:Ger...@ru...]
> Sent: Tuesday, September 03, 2013 11:24 PM
> To: psi...@li...
> Subject: Re: [Psidev-ms-vocab] [Psidev-ms-dev] New version 3.50.0 of
> psi-ms.obo
>
> Hi Brian,
>
> yes we obsoletetd the retention time(s) term.
>
> Because we had two terms: retention time and retention time(s), we
> decided to obsolete one and add a term named scan start time for the
> SpectrumIdentificationResult annotation, see our discussion in Issue 74
> on google code:
>
> https://code.google.com/p/psi-pi/issues/detail?id=74&can=1
>
> Best Regards,
> Gerhard
>
>
> Am 04.09.2013 00:38, schrieb Brian Pratt:

> > I'm a little slow noticing this (just now updating ProteoWizard's
> OBO), but
> > I wonder about the now obsoleted
> > id: MS:1001114
> > name: retention time(s)
> > def: "Retention time of the spectrum from the source file." [PSI:PI]
> >
> > Surely chromatography and mass spec can happen in entirely different
> time
> > frames, as with MALDI - or am I misunderstanding something?
> >
> > And how is it different from
> > id: MS:1000894
> > name: retention time
> > def: "A measure of the interval relative to the beginning of a mass
> > spectrometric run when a peptide will exit the chromatographic
> column."
> > [PSI:MS]
> >
> > And doesn't that definition have the same assumption about the column
> being
> > hooked up directly to the mass spec?
> >
> > Cheers,
> > Brian Pratt
> >
> >
> > On Fri, May 31, 2013 at 12:10 AM, Gerhard Mayer <
> > Ger...@ru...> wrote:
> >
> >> Dear proteomics community,
> >>
> >> attached there's the new version 3.50.0 of the psi-ms.obo file.
> >>
> >> It contains the changes concerning the retention time terms (issue
> 74),
> >> changes for the waters instrument term definitions and 3 new terms
> for the
> >> Byonic search engine.
> >>
> >>
> >> Changed CV terms in version 3.50.0 of psi-ms.obo:

> >> ==============================**===================

> >> ************ added the two is_a relations 'is_a: MS:1001105 !
> peptide
> >> result details' and
> >> ************ 'is_a: MS:1001405 ! spectrum identification result
> details'
> >> [Term]
> >> id: MS:1000016
> >> name: scan start time
> >> def: "The time that an analyzer started a scan, relative to the
> start of
> >> the MS run." [PSI:MS]
> >> xref: value-type:xsd\:float "The allowed value-type for this CV
> term."
> >> is_a: MS:1000503 ! scan attribute
> >> is_a: MS:1001105 ! peptide result details
> >> is_a: MS:1001405 ! spectrum identification result details
> >> relationship: has_units UO:0000010 ! second
> >> relationship: has_units UO:0000031 ! minute
> >>
> >> ************ Made obsolete
> >> [Term]
> >> id: MS:1001114
> >> name: retention time(s)
> >> def: "OBSOLETE Retention time of the spectrum from the source file."
> >> [PSI:PI]
> >> comment: This term was made obsolete because scan start time
> (MS:1000016)
> >> should be used instead.
> >> xref: value-type:xsd\:double "The allowed value-type for this CV
> term."
> >> is_a: MS:1001105 ! peptide result details
> >> is_a: MS:1001405 ! spectrum identification result details
> >> relationship: has_units UO:0000010 ! second
> >> relationship: has_units UO:0000031 ! minute
> >> is_obsolete: true
> >>
> >> ************ Changed the definition (removed 'peptide ...').
> >> [Term]
> >> id: MS:1000894
> >> name: retention time
> >> def: "A measure of the interval relative to the beginning of a mass
> >> spectrometric run." [PSI:MS]
> >> is_a: MS:1000887 ! peptide attribute
> >>
> >> ************ Changed the is_a relationship from 'detector type' -->
> 'array
> >> detector' for the next two terms
> >> [Term]
> >> id: MS:1000114
> >> name: microchannel plate detector
> >> def: "A thin plate that contains a closely spaced array of channels
> that
> >> each act as a continuous dynode particle multiplier. A charged
> particle,
> >> fast neutral particle, or photon striking the plate causes a cascade
> of
> >> secondary electrons that ultimately exits the opposite side of the
> plate."
> >> [PSI:MS]
> >> synonym: "multichannel plate" EXACT []
> >> is_a: MS:1000345 ! array detector
> >>
> >> [Term]
> >> id: MS:1000621
> >> name: photodiode array detector
> >> def: "An array detector used to record spectra in the ultraviolet
> and
> >> visible region of light." [PSI:MS]
> >> synonym: "PDA" EXACT []
> >> is_a: MS:1000345 ! array detector
> >>
> >> ************ Added the 'is_a: MS:1000621 ! photodiode array
> detector'
> >> relationship
> >> [Term]
> >> id: MS:1000818
> >> name: Acquity UPLC PDA
> >> def: "Acquity UPLC Photodiode Array Detector." [PSI:MS]
> >> is_a: MS:1000126 ! Waters instrument model
> >> is_a: MS:1000621 ! photodiode array detector
> >>
> >> ************ Added the 'is_a: MS:1002308 ! fluorescence detector'
> >> relationship
> >> [Term]
> >> id: MS:1000819
> >> name: Acquity UPLC FLR
> >> def: "Acquity UPLC Fluorescence Detector." [PSI:MS]
> >> is_a: MS:1000126 ! Waters instrument model
> >> is_a: MS:1002308 ! fluorescence detector
> >>
> >> ************ Adapted the definitions for the following Waters
> instruments
> >> to be more specific and unambiguous:
> >> MS:1000159    GCT
> >> MS:1000170    M@LDI L
> >> MS:1000171    M@LDI LR
> >> MS:1000188    Q-Tof micro
> >> MS:1000189    Q-Tof ultima
> >> MS:1000191    quattro micro
> >> MS:1000192    Quattro UItima
> >> MS:1000632    Q-Tof Premier
> >> MS:1001761    ACQUITY UPLC
> >> MS:1001762    ACQUITY UPLC H-Class
> >> MS:1001763    ACQUITY UPLC H-Class Bio
> >> MS:1001764    ACQUITY UPLC I-Class
> >> MS:1001765    ACQUITY UPLC Systems with 2D Technology
> >> MS:1001766    nanoACQUITY UPLC
> >> MS:1001767    nanoACQUITY UPLC System with Technology
> >> MS:1001768    nanoACQUITY UPLC with HDX Technology
> >> MS:1001769    TRIZAIC UPLC nanoTile
> >> MS:1001770    GCT Premier
> >> MS:1001771    MALDI Synapt G2 HDMS
> >> MS:1001772    MALDI Synapt G2 MS
> >> MS:1001773    MALDI Synapt G2-S HDMS
> >> MS:1001774    MALDI Synapt G2-S MS
> >> MS:1001775    MALDI Synapt HDMS
> >> MS:1001776    MALDI Synapt MS
> >> MS:1001777    Synapt G2 HDMS
> >> MS:1001778    Synapt G2 MS
> >> MS:1001779    Synapt G2-S HDMS
> >> MS:1001780    Synapt G2-S MS
> >> MS:1001781    Synapt HDMS
> >> MS:1001782    Synapt MS
> >> MS:1001783    Xevo G2 Q-Tof
> >> MS:1001784    Xevo G2 Tof
> >> MS:1001785    Xevo Q-Tof
> >> MS:1001786    3100
> >> MS:1001787    Acquity SQD
> >> MS:1001788    Acquity TQD
> >> MS:1001789    Quattro micro GC
> >> MS:1001790    Xevo TQ MS
> >> MS:1001791    Xevo TQD
> >> MS:1001792    Xevo TQ-S
> >> MS:1001795    Empower
> >> MS:1001796    Unify
> >>
> >>
> >> New CV terms in version 3.50.0 of psi-ms.obo:

> >> ==============================**===============

> >> [Term]
> >> id: MS:1002308
> >> name: fluorescence detector
> >> def: "A detector using a fluorescent signal after excitation with
> light."
> >> [PSI:MS]
> >> is_a: MS:1000026 ! detector type
> >>
> >> [Term]
> >> id: MS:1002309
> >> name: Byonic: Peptide AbsLogProb
> >> def: "The absolute value of the log-base10 of the Byonic posterior
> error
> >> probability (PEP) of the PSM. " [PSI:PI]
> >> xref: value-type:xsd\:double "The allowed value-type for this CV
> term."
> >> is_a: MS:1001143 ! search engine specific score for PSMs
> >> is_a: MS:1001153 ! search engine specific score
> >> has_order: MS:1002108 ! higher score better
> >>
> >> [Term]
> >> id: MS:1002310
> >> name: Byonic: Protein AbsLogProb
> >> def: "The absolute value of the log-base10 of the Byonic posterior
> error
> >> probability (PEP) of the protein. " [PSI:PI]
> >> xref: value-type:xsd\:double "The allowed value-type for this CV
> term."
> >> is_a: MS:1001116 ! single protein result details
> >> is_a: MS:1001153 ! search engine specific score
> >> has_order: MS:1002108 ! higher score better
> >>
> >> [Term]
> >> id: MS:1002311
> >> name: Byonic: Peptide AbsLogProb2D
> >> def: "The absolute value of the log-base10 Byonic two-dimensional
> >> posterior error probability (PEP) of the PSM. The two-dimensional
> PEP takes
> >> into account protein ranking information as well as PSM
> information."
> >> [PSI:PI]
> >> xref: value-type:xsd\:double "The allowed value-type for this CV
> term."
> >> is_a: MS:1001143 ! search engine specific score for PSMs
> >> is_a: MS:1001153 ! search engine specific score
> >> has_order: MS:1002108 ! higher score better
> >>
> >> Best Regards,
> >> Gerhard
> >>
> >> --
> >> ---
> >> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> >> Bioinformatik / Biostatistik
> >> Medizinisches-Proteom-Center (MPC)
> >> Ruhr-Universität Bochum
> >> Zentrum für klinische Forschung I (ZKF I)
> >> E.049a
> >> Universitätsstraße 150
> >> D-44801 Bochum
> >>  Phone: +49(0)234/32-21006
> >> Fax:    +49(0)234/32-14554
> >> Email:  Ger...@ru...

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

> ----------
> >> Get 100% visibility into Java/.NET code with AppDynamics Lite
> >> It's a free troubleshooting tool designed for production
> >> Get down to code-level detail for bottlenecks, with <2% overhead.
> >> Download for free and get started troubleshooting in minutes.
> >> http://p.sf.net/sfu/appdyn_d2d_ap2
> >> _______________________________________________
> >> Psidev-ms-dev mailing list
> >> Psi...@li...
> >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> >>
> >>
> >
> >
> >

> > ---------------------------------------------------------------------
> ---------
> > Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012,
> more!
> > Discover the easy way to master current and previous Microsoft
> technologies
> > and advance your career. Get an incredible 1,500+ hours of step-by-
> step
> > tutorial videos with LearnDevNow. Subscribe today and save!
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.cl
> ktrk
> >
> >
> >
> > _______________________________________________
> > Psidev-ms-vocab mailing list
> > Psi...@li...
> > https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab

> >
>
>
> --
> ---
> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> Bioinformatik / Biostatistik
> Medizinisches-Proteom-Center (MPC)
> Ruhr-Universität Bochum
> Zentrum für klinische Forschung I (ZKF I)
> E.049a
> Universitätsstraße 150
> D-44801 Bochum
>
> Phone:        +49(0)234/32-21006
> Fax:  +49(0)234/32-14554
> Email:        Ger...@ru...
> Web:  http://www.medizinisches-proteom-center.de
>
> -----------------------------------------------------------------------
> -------

> Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
> Discover the easy way to master current and previous Microsoft
> technologies
> and advance your career. Get an incredible 1,500+ hours of step-by-step
> tutorial videos with LearnDevNow. Subscribe today and save!
> http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.cl
> ktrk
> _______________________________________________
> Psidev-ms-vocab mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab

------------------------------------------------------------------------------
Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
Discover the easy way to master current and previous Microsoft technologies
and advance your career. Get an incredible 1,500+ hours of step-by-step
tutorial videos with LearnDevNow. Subscribe today and save!
http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.clktrk

_______________________________________________
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https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.50.0 of psi-ms.obo

[Brian P. <bri...@in...>]

It's the "relative to the beginning of a mass spectrometric run"  part that
strikes me as misleading - it doesn't seem proper when the chromatography
may have taken place in a completely different time period than the mass
spec analysis (again, thinking MALDI but trying to be perfectly general and
futureproof).  It just seems inline-LCMS-centric where it should be more
general.

Overall I would think it should use language about the column's history
rather than the mass analyzer's.  So for example
    id: MS:1000897
    name: predicted retention time
should simply read:
    def: "A time interval when a peptide will exit a chromatographic column
as predicted by a referenced software application." [PSI:MS]

and
  id: MS:1000894
  name: retention time
should be
  def: "A time interval at which a peptide exited a chromatographic column."
[PSI:MS]

etc.

Perhaps I am revisiting an already settled issue, but this just isn't
intuitive to me as currently written.  And I might just be the target
audience, as a developer dipping into this on an occasional basis.

Helpfully,

Brian Pratt


On Wed, Sep 4, 2013 at 10:12 AM, Eric Deutsch <
Eri...@sy...> wrote:

> Hi Brian, can you elaborate on what is misleading? I don’t see how
> concurrent elution and scan are implied in these terms? Maybe the term
> “mass spectrometric run” is the vague part? Perhaps “chromatography” should
> replace “a mass spectrometric run” for terms 894-896?
>
>
>
> For pepXML, you almost surely want “scan start time” since that’s what is
> pulled from the raw/mzML files, right? The true retention time of the
> peptide ion seen in that scan is far more complex and usually not known
> very well. The scan start time is a precise and often sufficiently useful
> proxy for the true retention time. Right?
>
>
>
> Allowed units are specified in the term metadata, see below..
>
>
>
> Eric
>
>
>
> id: MS:1000016
>
> name: scan start time
>
> def: "The time that an analyzer started a scan, relative to the start of
> the MS run." [PSI:MS]
>
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>
> is_a: MS:1000503 ! scan attribute
>
> is_a: MS:1001105 ! peptide result details
>
> is_a: MS:1001405 ! spectrum identification result details
>
> relationship: has_units UO:0000010 ! second
>
> relationship: has_units UO:0000031 ! minute
>
>
>
> id: MS:1000894
>
> name: retention time
>
> def: "A measure of the interval relative to the beginning of a mass
> spectrometric run." [PSI:MS]
>
> is_a: MS:1000887 ! peptide attribute
>
>
>
> id: MS:1000895
>
> name: local retention time
>
> def: "A measure of the interval relative to the beginning of a mass
> spectrometric run when a peptide will exit an unspecified local
> chromatographic column and instrumental setup." [PSI:MS]
>
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>
> is_a: MS:1000894 ! retention time
>
> relationship: has_units UO:0000010 ! second
>
> relationship: has_units UO:0000031 ! minute
>
> id: MS:1000896
>
> name: normalized retention time
>
> def: "A measure of the interval relative to the beginning of a mass
> spectrometric run when a peptide will exit a standardized reference
> chromatographic column and instrumental setup." [PSI:MS]
>
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>
> is_a: MS:1000894 ! retention time
>
> relationship: has_units UO:0000010 ! second
>
> relationship: has_units UO:0000031 ! minute
>
> id: MS:1000897
>
> name: predicted retention time
>
> def: "A time interval relative to the beginning of a mass spectrometric
> run when a peptide will exit a chromatographic column as predicted by a
> referenced software application." [PSI:MS]
>
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>
> is_a: MS:1000894 ! retention time
>
> relationship: has_units UO:0000010 ! second
>
> relationship: has_units UO:0000031 ! minute
>
>
>
>
>
>
>
>
>
>
>
> *From:* Brian Pratt [mailto:bri...@in...]
> *Sent:* Wednesday, September 04, 2013 9:56 AM
> *To:* Mass spectrometry standard development
> *Cc:* psi...@li...;
> psi...@li...; Eric Deutsch
> *Subject:* Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.50.0 of
> psi-ms.obo
>
>
>
> >> What do you think?
>
>
>
> I completely agree that these are distinct concepts, and of course I'm not
> surprised that everyone else thinks so too.  But the description is
> misleading, I think, since it really seems to assume concurrent elution and
> scan.  A quibble perhaps but probably worth cleaning up.
>
>
>
> The use in question is actually in pepXML related code, so retention time
> is the concept we want for sure.  But now I guess I have to think about
> managing units?  Or is it defined as being in seconds?  (And if so, perhaps
> the description should be enhanced to reflect that?)
>
>
>
> Thanks,
>
>
>
> Brian
>
>
>
> On Wed, Sep 4, 2013 at 9:45 AM, <Eri...@sy...> wrote:
>
> Hi Brian, I'm not certain if that answers your question, but I might add
> that ProteoWizard's use of the obsolete retention time(s) should be
> changed to either scan start time or retention time. We intend scan start
> time to be used in cases where there is a time tag associated with a
> definite mass spec acquisition (as is the case in mzML and mzIdentML). The
> non-obsolete retention time term should be used as an attribute associated
> with a peptide molecule in a chromatographic column independent of an
> instrument acquisition event (as is the case in TraML). The MALDI case is
> a little more tricky. In practice, a scan start time will likely be
> recorded with the instrument and should be written into mzML et al. The
> chromatographic retention time might be known and could be recorded
> separately (as this will be a different time than the instrument scan
> time), but often is not well known when the mzML is written. But as you
> allude to, these are now different concepts with different terms, whereas
> before it was more muddled.
>
> What do you think?
>
> Regards,
> Eric
>
>
> > -----Original Message-----
> > From: Gerhard Mayer [mailto:Ger...@ru...]
> > Sent: Tuesday, September 03, 2013 11:24 PM
> > To: psi...@li...
> > Subject: Re: [Psidev-ms-vocab] [Psidev-ms-dev] New version 3.50.0 of
> > psi-ms.obo
> >
> > Hi Brian,
> >
> > yes we obsoletetd the retention time(s) term.
> >
> > Because we had two terms: retention time and retention time(s), we
> > decided to obsolete one and add a term named scan start time for the
> > SpectrumIdentificationResult annotation, see our discussion in Issue 74
> > on google code:
> >
> > https://code.google.com/p/psi-pi/issues/detail?id=74&can=1
> >
> > Best Regards,
> > Gerhard
> >
> >
> > Am 04.09.2013 00:38, schrieb Brian Pratt:
>
> > > I'm a little slow noticing this (just now updating ProteoWizard's
> > OBO), but
> > > I wonder about the now obsoleted
> > > id: MS:1001114
> > > name: retention time(s)
> > > def: "Retention time of the spectrum from the source file." [PSI:PI]
> > >
> > > Surely chromatography and mass spec can happen in entirely different
> > time
> > > frames, as with MALDI - or am I misunderstanding something?
> > >
> > > And how is it different from
> > > id: MS:1000894
> > > name: retention time
> > > def: "A measure of the interval relative to the beginning of a mass
> > > spectrometric run when a peptide will exit the chromatographic
> > column."
> > > [PSI:MS]
> > >
> > > And doesn't that definition have the same assumption about the column
> > being
> > > hooked up directly to the mass spec?
> > >
> > > Cheers,
> > > Brian Pratt
> > >
> > >
> > > On Fri, May 31, 2013 at 12:10 AM, Gerhard Mayer <
> > > Ger...@ru...> wrote:
> > >
> > >> Dear proteomics community,
> > >>
> > >> attached there's the new version 3.50.0 of the psi-ms.obo file.
> > >>
> > >> It contains the changes concerning the retention time terms (issue
> > 74),
> > >> changes for the waters instrument term definitions and 3 new terms
> > for the
> > >> Byonic search engine.
> > >>
> > >>
> > >> Changed CV terms in version 3.50.0 of psi-ms.obo:
>
> > >> ==============================**===================
>
> > >> ************ added the two is_a relations 'is_a: MS:1001105 !
> > peptide
> > >> result details' and
> > >> ************ 'is_a: MS:1001405 ! spectrum identification result
> > details'
> > >> [Term]
> > >> id: MS:1000016
> > >> name: scan start time
> > >> def: "The time that an analyzer started a scan, relative to the
> > start of
> > >> the MS run." [PSI:MS]
> > >> xref: value-type:xsd\:float "The allowed value-type for this CV
> > term."
> > >> is_a: MS:1000503 ! scan attribute
> > >> is_a: MS:1001105 ! peptide result details
> > >> is_a: MS:1001405 ! spectrum identification result details
> > >> relationship: has_units UO:0000010 ! second
> > >> relationship: has_units UO:0000031 ! minute
> > >>
> > >> ************ Made obsolete
> > >> [Term]
> > >> id: MS:1001114
> > >> name: retention time(s)
> > >> def: "OBSOLETE Retention time of the spectrum from the source file."
> > >> [PSI:PI]
> > >> comment: This term was made obsolete because scan start time
> > (MS:1000016)
> > >> should be used instead.
> > >> xref: value-type:xsd\:double "The allowed value-type for this CV
> > term."
> > >> is_a: MS:1001105 ! peptide result details
> > >> is_a: MS:1001405 ! spectrum identification result details
> > >> relationship: has_units UO:0000010 ! second
> > >> relationship: has_units UO:0000031 ! minute
> > >> is_obsolete: true
> > >>
> > >> ************ Changed the definition (removed 'peptide ...').
> > >> [Term]
> > >> id: MS:1000894
> > >> name: retention time
> > >> def: "A measure of the interval relative to the beginning of a mass
> > >> spectrometric run." [PSI:MS]
> > >> is_a: MS:1000887 ! peptide attribute
> > >>
> > >> ************ Changed the is_a relationship from 'detector type' -->
> > 'array
> > >> detector' for the next two terms
> > >> [Term]
> > >> id: MS:1000114
> > >> name: microchannel plate detector
> > >> def: "A thin plate that contains a closely spaced array of channels
> > that
> > >> each act as a continuous dynode particle multiplier. A charged
> > particle,
> > >> fast neutral particle, or photon striking the plate causes a cascade
> > of
> > >> secondary electrons that ultimately exits the opposite side of the
> > plate."
> > >> [PSI:MS]
> > >> synonym: "multichannel plate" EXACT []
> > >> is_a: MS:1000345 ! array detector
> > >>
> > >> [Term]
> > >> id: MS:1000621
> > >> name: photodiode array detector
> > >> def: "An array detector used to record spectra in the ultraviolet
> > and
> > >> visible region of light." [PSI:MS]
> > >> synonym: "PDA" EXACT []
> > >> is_a: MS:1000345 ! array detector
> > >>
> > >> ************ Added the 'is_a: MS:1000621 ! photodiode array
> > detector'
> > >> relationship
> > >> [Term]
> > >> id: MS:1000818
> > >> name: Acquity UPLC PDA
> > >> def: "Acquity UPLC Photodiode Array Detector." [PSI:MS]
> > >> is_a: MS:1000126 ! Waters instrument model
> > >> is_a: MS:1000621 ! photodiode array detector
> > >>
> > >> ************ Added the 'is_a: MS:1002308 ! fluorescence detector'
> > >> relationship
> > >> [Term]
> > >> id: MS:1000819
> > >> name: Acquity UPLC FLR
> > >> def: "Acquity UPLC Fluorescence Detector." [PSI:MS]
> > >> is_a: MS:1000126 ! Waters instrument model
> > >> is_a: MS:1002308 ! fluorescence detector
> > >>
> > >> ************ Adapted the definitions for the following Waters
> > instruments
> > >> to be more specific and unambiguous:
> > >> MS:1000159    GCT
> > >> MS:1000170    M@LDI L
> > >> MS:1000171    M@LDI LR
> > >> MS:1000188    Q-Tof micro
> > >> MS:1000189    Q-Tof ultima
> > >> MS:1000191    quattro micro
> > >> MS:1000192    Quattro UItima
> > >> MS:1000632    Q-Tof Premier
> > >> MS:1001761    ACQUITY UPLC
> > >> MS:1001762    ACQUITY UPLC H-Class
> > >> MS:1001763    ACQUITY UPLC H-Class Bio
> > >> MS:1001764    ACQUITY UPLC I-Class
> > >> MS:1001765    ACQUITY UPLC Systems with 2D Technology
> > >> MS:1001766    nanoACQUITY UPLC
> > >> MS:1001767    nanoACQUITY UPLC System with Technology
> > >> MS:1001768    nanoACQUITY UPLC with HDX Technology
> > >> MS:1001769    TRIZAIC UPLC nanoTile
> > >> MS:1001770    GCT Premier
> > >> MS:1001771    MALDI Synapt G2 HDMS
> > >> MS:1001772    MALDI Synapt G2 MS
> > >> MS:1001773    MALDI Synapt G2-S HDMS
> > >> MS:1001774    MALDI Synapt G2-S MS
> > >> MS:1001775    MALDI Synapt HDMS
> > >> MS:1001776    MALDI Synapt MS
> > >> MS:1001777    Synapt G2 HDMS
> > >> MS:1001778    Synapt G2 MS
> > >> MS:1001779    Synapt G2-S HDMS
> > >> MS:1001780    Synapt G2-S MS
> > >> MS:1001781    Synapt HDMS
> > >> MS:1001782    Synapt MS
> > >> MS:1001783    Xevo G2 Q-Tof
> > >> MS:1001784    Xevo G2 Tof
> > >> MS:1001785    Xevo Q-Tof
> > >> MS:1001786    3100
> > >> MS:1001787    Acquity SQD
> > >> MS:1001788    Acquity TQD
> > >> MS:1001789    Quattro micro GC
> > >> MS:1001790    Xevo TQ MS
> > >> MS:1001791    Xevo TQD
> > >> MS:1001792    Xevo TQ-S
> > >> MS:1001795    Empower
> > >> MS:1001796    Unify
> > >>
> > >>
> > >> New CV terms in version 3.50.0 of psi-ms.obo:
>
> > >> ==============================**===============
>
> > >> [Term]
> > >> id: MS:1002308
> > >> name: fluorescence detector
> > >> def: "A detector using a fluorescent signal after excitation with
> > light."
> > >> [PSI:MS]
> > >> is_a: MS:1000026 ! detector type
> > >>
> > >> [Term]
> > >> id: MS:1002309
> > >> name: Byonic: Peptide AbsLogProb
> > >> def: "The absolute value of the log-base10 of the Byonic posterior
> > error
> > >> probability (PEP) of the PSM. " [PSI:PI]
> > >> xref: value-type:xsd\:double "The allowed value-type for this CV
> > term."
> > >> is_a: MS:1001143 ! search engine specific score for PSMs
> > >> is_a: MS:1001153 ! search engine specific score
> > >> has_order: MS:1002108 ! higher score better
> > >>
> > >> [Term]
> > >> id: MS:1002310
> > >> name: Byonic: Protein AbsLogProb
> > >> def: "The absolute value of the log-base10 of the Byonic posterior
> > error
> > >> probability (PEP) of the protein. " [PSI:PI]
> > >> xref: value-type:xsd\:double "The allowed value-type for this CV
> > term."
> > >> is_a: MS:1001116 ! single protein result details
> > >> is_a: MS:1001153 ! search engine specific score
> > >> has_order: MS:1002108 ! higher score better
> > >>
> > >> [Term]
> > >> id: MS:1002311
> > >> name: Byonic: Peptide AbsLogProb2D
> > >> def: "The absolute value of the log-base10 Byonic two-dimensional
> > >> posterior error probability (PEP) of the PSM. The two-dimensional
> > PEP takes
> > >> into account protein ranking information as well as PSM
> > information."
> > >> [PSI:PI]
> > >> xref: value-type:xsd\:double "The allowed value-type for this CV
> > term."
> > >> is_a: MS:1001143 ! search engine specific score for PSMs
> > >> is_a: MS:1001153 ! search engine specific score
> > >> has_order: MS:1002108 ! higher score better
> > >>
> > >> Best Regards,
> > >> Gerhard
> > >>
> > >> --
> > >> ---
> > >> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> > >> Bioinformatik / Biostatistik
> > >> Medizinisches-Proteom-Center (MPC)
> > >> Ruhr-Universität Bochum
> > >> Zentrum für klinische Forschung I (ZKF I)
> > >> E.049a
> > >> Universitätsstraße 150
> > >> D-44801 Bochum
> > >>  Phone: +49(0)234/32-21006
> > >> Fax:    +49(0)234/32-14554
> > >> Email:  Ger...@ru...
>
> > >> Web:    http://www.medizinisches-**proteom-
> > center.de<http://www.medizinisches-proteom-center.de>
> > >>
> > >>
> > >>
> > >> --------------------------------------------------------------------
>
> > ----------
> > >> Get 100% visibility into Java/.NET code with AppDynamics Lite
> > >> It's a free troubleshooting tool designed for production
> > >> Get down to code-level detail for bottlenecks, with <2% overhead.
> > >> Download for free and get started troubleshooting in minutes.
> > >> http://p.sf.net/sfu/appdyn_d2d_ap2
> > >> _______________________________________________
> > >> Psidev-ms-dev mailing list
> > >> Psi...@li...
> > >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> > >>
> > >>
> > >
> > >
> > >
>
> > > ---------------------------------------------------------------------
> > ---------
> > > Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012,
> > more!
> > > Discover the easy way to master current and previous Microsoft
> > technologies
> > > and advance your career. Get an incredible 1,500+ hours of step-by-
> > step
> > > tutorial videos with LearnDevNow. Subscribe today and save!
> > >
> > http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.cl
> > ktrk
> > >
> > >
> > >
> > > _______________________________________________
> > > Psidev-ms-vocab mailing list
> > > Psi...@li...
> > > https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab
>
> > >
> >
> >
> > --
> > ---
> > Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> > Bioinformatik / Biostatistik
> > Medizinisches-Proteom-Center (MPC)
> > Ruhr-Universität Bochum
> > Zentrum für klinische Forschung I (ZKF I)
> > E.049a
> > Universitätsstraße 150
> > D-44801 Bochum
> >
> > Phone:        +49(0)234/32-21006
> > Fax:  +49(0)234/32-14554
> > Email:        Ger...@ru...
> > Web:  http://www.medizinisches-proteom-center.de
> >
> > -----------------------------------------------------------------------
> > -------
>
> > Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
> > Discover the easy way to master current and previous Microsoft
> > technologies
> > and advance your career. Get an incredible 1,500+ hours of step-by-step
> > tutorial videos with LearnDevNow. Subscribe today and save!
> > http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.cl
> > ktrk
> > _______________________________________________
> > Psidev-ms-vocab mailing list
> > Psi...@li...
> > https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab
>
>
> ------------------------------------------------------------------------------
> Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
> Discover the easy way to master current and previous Microsoft technologies
> and advance your career. Get an incredible 1,500+ hours of step-by-step
> tutorial videos with LearnDevNow. Subscribe today and save!
> http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.clktrk
>
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>
>
>

Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.50.0 of psi-ms.obo

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

Hi Brian, can you elaborate on what is misleading? I don’t see how
concurrent elution and scan are implied in these terms? Maybe the term
“mass spectrometric run” is the vague part? Perhaps “chromatography” should
replace “a mass spectrometric run” for terms 894-896?



For pepXML, you almost surely want “scan start time” since that’s what is
pulled from the raw/mzML files, right? The true retention time of the
peptide ion seen in that scan is far more complex and usually not known
very well. The scan start time is a precise and often sufficiently useful
proxy for the true retention time. Right?



Allowed units are specified in the term metadata, see below..



Eric



id: MS:1000016

name: scan start time

def: "The time that an analyzer started a scan, relative to the start of
the MS run." [PSI:MS]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1000503 ! scan attribute

is_a: MS:1001105 ! peptide result details

is_a: MS:1001405 ! spectrum identification result details

relationship: has_units UO:0000010 ! second

relationship: has_units UO:0000031 ! minute



id: MS:1000894

name: retention time

def: "A measure of the interval relative to the beginning of a mass
spectrometric run." [PSI:MS]

is_a: MS:1000887 ! peptide attribute



id: MS:1000895

name: local retention time

def: "A measure of the interval relative to the beginning of a mass
spectrometric run when a peptide will exit an unspecified local
chromatographic column and instrumental setup." [PSI:MS]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1000894 ! retention time

relationship: has_units UO:0000010 ! second

relationship: has_units UO:0000031 ! minute

id: MS:1000896

name: normalized retention time

def: "A measure of the interval relative to the beginning of a mass
spectrometric run when a peptide will exit a standardized reference
chromatographic column and instrumental setup." [PSI:MS]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1000894 ! retention time

relationship: has_units UO:0000010 ! second

relationship: has_units UO:0000031 ! minute

id: MS:1000897

name: predicted retention time

def: "A time interval relative to the beginning of a mass spectrometric run
when a peptide will exit a chromatographic column as predicted by a
referenced software application." [PSI:MS]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1000894 ! retention time

relationship: has_units UO:0000010 ! second

relationship: has_units UO:0000031 ! minute











*From:* Brian Pratt [mailto:bri...@in...]
*Sent:* Wednesday, September 04, 2013 9:56 AM
*To:* Mass spectrometry standard development
*Cc:* psi...@li...;
psi...@li...; Eric Deutsch
*Subject:* Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.50.0 of
psi-ms.obo



>> What do you think?



I completely agree that these are distinct concepts, and of course I'm not
surprised that everyone else thinks so too.  But the description is
misleading, I think, since it really seems to assume concurrent elution and
scan.  A quibble perhaps but probably worth cleaning up.



The use in question is actually in pepXML related code, so retention time
is the concept we want for sure.  But now I guess I have to think about
managing units?  Or is it defined as being in seconds?  (And if so, perhaps
the description should be enhanced to reflect that?)



Thanks,



Brian



On Wed, Sep 4, 2013 at 9:45 AM, <Eri...@sy...> wrote:

Hi Brian, I'm not certain if that answers your question, but I might add
that ProteoWizard's use of the obsolete retention time(s) should be
changed to either scan start time or retention time. We intend scan start
time to be used in cases where there is a time tag associated with a
definite mass spec acquisition (as is the case in mzML and mzIdentML). The
non-obsolete retention time term should be used as an attribute associated
with a peptide molecule in a chromatographic column independent of an
instrument acquisition event (as is the case in TraML). The MALDI case is
a little more tricky. In practice, a scan start time will likely be
recorded with the instrument and should be written into mzML et al. The
chromatographic retention time might be known and could be recorded
separately (as this will be a different time than the instrument scan
time), but often is not well known when the mzML is written. But as you
allude to, these are now different concepts with different terms, whereas
before it was more muddled.

What do you think?

Regards,
Eric


> -----Original Message-----
> From: Gerhard Mayer [mailto:Ger...@ru...]
> Sent: Tuesday, September 03, 2013 11:24 PM
> To: psi...@li...
> Subject: Re: [Psidev-ms-vocab] [Psidev-ms-dev] New version 3.50.0 of
> psi-ms.obo
>
> Hi Brian,
>
> yes we obsoletetd the retention time(s) term.
>
> Because we had two terms: retention time and retention time(s), we
> decided to obsolete one and add a term named scan start time for the
> SpectrumIdentificationResult annotation, see our discussion in Issue 74
> on google code:
>
> https://code.google.com/p/psi-pi/issues/detail?id=74&can=1
>
> Best Regards,
> Gerhard
>
>
> Am 04.09.2013 00:38, schrieb Brian Pratt:

> > I'm a little slow noticing this (just now updating ProteoWizard's
> OBO), but
> > I wonder about the now obsoleted
> > id: MS:1001114
> > name: retention time(s)
> > def: "Retention time of the spectrum from the source file." [PSI:PI]
> >
> > Surely chromatography and mass spec can happen in entirely different
> time
> > frames, as with MALDI - or am I misunderstanding something?
> >
> > And how is it different from
> > id: MS:1000894
> > name: retention time
> > def: "A measure of the interval relative to the beginning of a mass
> > spectrometric run when a peptide will exit the chromatographic
> column."
> > [PSI:MS]
> >
> > And doesn't that definition have the same assumption about the column
> being
> > hooked up directly to the mass spec?
> >
> > Cheers,
> > Brian Pratt
> >
> >
> > On Fri, May 31, 2013 at 12:10 AM, Gerhard Mayer <
> > Ger...@ru...> wrote:
> >
> >> Dear proteomics community,
> >>
> >> attached there's the new version 3.50.0 of the psi-ms.obo file.
> >>
> >> It contains the changes concerning the retention time terms (issue
> 74),
> >> changes for the waters instrument term definitions and 3 new terms
> for the
> >> Byonic search engine.
> >>
> >>
> >> Changed CV terms in version 3.50.0 of psi-ms.obo:

> >> ==============================**===================

> >> ************ added the two is_a relations 'is_a: MS:1001105 !
> peptide
> >> result details' and
> >> ************ 'is_a: MS:1001405 ! spectrum identification result
> details'
> >> [Term]
> >> id: MS:1000016
> >> name: scan start time
> >> def: "The time that an analyzer started a scan, relative to the
> start of
> >> the MS run." [PSI:MS]
> >> xref: value-type:xsd\:float "The allowed value-type for this CV
> term."
> >> is_a: MS:1000503 ! scan attribute
> >> is_a: MS:1001105 ! peptide result details
> >> is_a: MS:1001405 ! spectrum identification result details
> >> relationship: has_units UO:0000010 ! second
> >> relationship: has_units UO:0000031 ! minute
> >>
> >> ************ Made obsolete
> >> [Term]
> >> id: MS:1001114
> >> name: retention time(s)
> >> def: "OBSOLETE Retention time of the spectrum from the source file."
> >> [PSI:PI]
> >> comment: This term was made obsolete because scan start time
> (MS:1000016)
> >> should be used instead.
> >> xref: value-type:xsd\:double "The allowed value-type for this CV
> term."
> >> is_a: MS:1001105 ! peptide result details
> >> is_a: MS:1001405 ! spectrum identification result details
> >> relationship: has_units UO:0000010 ! second
> >> relationship: has_units UO:0000031 ! minute
> >> is_obsolete: true
> >>
> >> ************ Changed the definition (removed 'peptide ...').
> >> [Term]
> >> id: MS:1000894
> >> name: retention time
> >> def: "A measure of the interval relative to the beginning of a mass
> >> spectrometric run." [PSI:MS]
> >> is_a: MS:1000887 ! peptide attribute
> >>
> >> ************ Changed the is_a relationship from 'detector type' -->
> 'array
> >> detector' for the next two terms
> >> [Term]
> >> id: MS:1000114
> >> name: microchannel plate detector
> >> def: "A thin plate that contains a closely spaced array of channels
> that
> >> each act as a continuous dynode particle multiplier. A charged
> particle,
> >> fast neutral particle, or photon striking the plate causes a cascade
> of
> >> secondary electrons that ultimately exits the opposite side of the
> plate."
> >> [PSI:MS]
> >> synonym: "multichannel plate" EXACT []
> >> is_a: MS:1000345 ! array detector
> >>
> >> [Term]
> >> id: MS:1000621
> >> name: photodiode array detector
> >> def: "An array detector used to record spectra in the ultraviolet
> and
> >> visible region of light." [PSI:MS]
> >> synonym: "PDA" EXACT []
> >> is_a: MS:1000345 ! array detector
> >>
> >> ************ Added the 'is_a: MS:1000621 ! photodiode array
> detector'
> >> relationship
> >> [Term]
> >> id: MS:1000818
> >> name: Acquity UPLC PDA
> >> def: "Acquity UPLC Photodiode Array Detector." [PSI:MS]
> >> is_a: MS:1000126 ! Waters instrument model
> >> is_a: MS:1000621 ! photodiode array detector
> >>
> >> ************ Added the 'is_a: MS:1002308 ! fluorescence detector'
> >> relationship
> >> [Term]
> >> id: MS:1000819
> >> name: Acquity UPLC FLR
> >> def: "Acquity UPLC Fluorescence Detector." [PSI:MS]
> >> is_a: MS:1000126 ! Waters instrument model
> >> is_a: MS:1002308 ! fluorescence detector
> >>
> >> ************ Adapted the definitions for the following Waters
> instruments
> >> to be more specific and unambiguous:
> >> MS:1000159    GCT
> >> MS:1000170    M@LDI L
> >> MS:1000171    M@LDI LR
> >> MS:1000188    Q-Tof micro
> >> MS:1000189    Q-Tof ultima
> >> MS:1000191    quattro micro
> >> MS:1000192    Quattro UItima
> >> MS:1000632    Q-Tof Premier
> >> MS:1001761    ACQUITY UPLC
> >> MS:1001762    ACQUITY UPLC H-Class
> >> MS:1001763    ACQUITY UPLC H-Class Bio
> >> MS:1001764    ACQUITY UPLC I-Class
> >> MS:1001765    ACQUITY UPLC Systems with 2D Technology
> >> MS:1001766    nanoACQUITY UPLC
> >> MS:1001767    nanoACQUITY UPLC System with Technology
> >> MS:1001768    nanoACQUITY UPLC with HDX Technology
> >> MS:1001769    TRIZAIC UPLC nanoTile
> >> MS:1001770    GCT Premier
> >> MS:1001771    MALDI Synapt G2 HDMS
> >> MS:1001772    MALDI Synapt G2 MS
> >> MS:1001773    MALDI Synapt G2-S HDMS
> >> MS:1001774    MALDI Synapt G2-S MS
> >> MS:1001775    MALDI Synapt HDMS
> >> MS:1001776    MALDI Synapt MS
> >> MS:1001777    Synapt G2 HDMS
> >> MS:1001778    Synapt G2 MS
> >> MS:1001779    Synapt G2-S HDMS
> >> MS:1001780    Synapt G2-S MS
> >> MS:1001781    Synapt HDMS
> >> MS:1001782    Synapt MS
> >> MS:1001783    Xevo G2 Q-Tof
> >> MS:1001784    Xevo G2 Tof
> >> MS:1001785    Xevo Q-Tof
> >> MS:1001786    3100
> >> MS:1001787    Acquity SQD
> >> MS:1001788    Acquity TQD
> >> MS:1001789    Quattro micro GC
> >> MS:1001790    Xevo TQ MS
> >> MS:1001791    Xevo TQD
> >> MS:1001792    Xevo TQ-S
> >> MS:1001795    Empower
> >> MS:1001796    Unify
> >>
> >>
> >> New CV terms in version 3.50.0 of psi-ms.obo:

> >> ==============================**===============

> >> [Term]
> >> id: MS:1002308
> >> name: fluorescence detector
> >> def: "A detector using a fluorescent signal after excitation with
> light."
> >> [PSI:MS]
> >> is_a: MS:1000026 ! detector type
> >>
> >> [Term]
> >> id: MS:1002309
> >> name: Byonic: Peptide AbsLogProb
> >> def: "The absolute value of the log-base10 of the Byonic posterior
> error
> >> probability (PEP) of the PSM. " [PSI:PI]
> >> xref: value-type:xsd\:double "The allowed value-type for this CV
> term."
> >> is_a: MS:1001143 ! search engine specific score for PSMs
> >> is_a: MS:1001153 ! search engine specific score
> >> has_order: MS:1002108 ! higher score better
> >>
> >> [Term]
> >> id: MS:1002310
> >> name: Byonic: Protein AbsLogProb
> >> def: "The absolute value of the log-base10 of the Byonic posterior
> error
> >> probability (PEP) of the protein. " [PSI:PI]
> >> xref: value-type:xsd\:double "The allowed value-type for this CV
> term."
> >> is_a: MS:1001116 ! single protein result details
> >> is_a: MS:1001153 ! search engine specific score
> >> has_order: MS:1002108 ! higher score better
> >>
> >> [Term]
> >> id: MS:1002311
> >> name: Byonic: Peptide AbsLogProb2D
> >> def: "The absolute value of the log-base10 Byonic two-dimensional
> >> posterior error probability (PEP) of the PSM. The two-dimensional
> PEP takes
> >> into account protein ranking information as well as PSM
> information."
> >> [PSI:PI]
> >> xref: value-type:xsd\:double "The allowed value-type for this CV
> term."
> >> is_a: MS:1001143 ! search engine specific score for PSMs
> >> is_a: MS:1001153 ! search engine specific score
> >> has_order: MS:1002108 ! higher score better
> >>
> >> Best Regards,
> >> Gerhard
> >>
> >> --
> >> ---
> >> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> >> Bioinformatik / Biostatistik
> >> Medizinisches-Proteom-Center (MPC)
> >> Ruhr-Universität Bochum
> >> Zentrum für klinische Forschung I (ZKF I)
> >> E.049a
> >> Universitätsstraße 150
> >> D-44801 Bochum
> >>  Phone: +49(0)234/32-21006
> >> Fax:    +49(0)234/32-14554
> >> Email:  Ger...@ru...

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

> ----------
> >> Get 100% visibility into Java/.NET code with AppDynamics Lite
> >> It's a free troubleshooting tool designed for production
> >> Get down to code-level detail for bottlenecks, with <2% overhead.
> >> Download for free and get started troubleshooting in minutes.
> >> http://p.sf.net/sfu/appdyn_d2d_ap2
> >> _______________________________________________
> >> Psidev-ms-dev mailing list
> >> Psi...@li...
> >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> >>
> >>
> >
> >
> >

> > ---------------------------------------------------------------------
> ---------
> > Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012,
> more!
> > Discover the easy way to master current and previous Microsoft
> technologies
> > and advance your career. Get an incredible 1,500+ hours of step-by-
> step
> > tutorial videos with LearnDevNow. Subscribe today and save!
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.cl
> ktrk
> >
> >
> >
> > _______________________________________________
> > Psidev-ms-vocab mailing list
> > Psi...@li...
> > https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab

> >
>
>
> --
> ---
> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> Bioinformatik / Biostatistik
> Medizinisches-Proteom-Center (MPC)
> Ruhr-Universität Bochum
> Zentrum für klinische Forschung I (ZKF I)
> E.049a
> Universitätsstraße 150
> D-44801 Bochum
>
> Phone:        +49(0)234/32-21006
> Fax:  +49(0)234/32-14554
> Email:        Ger...@ru...
> Web:  http://www.medizinisches-proteom-center.de
>
> -----------------------------------------------------------------------
> -------

> Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
> Discover the easy way to master current and previous Microsoft
> technologies
> and advance your career. Get an incredible 1,500+ hours of step-by-step
> tutorial videos with LearnDevNow. Subscribe today and save!
> http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.cl
> ktrk
> _______________________________________________
> Psidev-ms-vocab mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab

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Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.50.0 of psi-ms.obo

[Brian P. <bri...@in...>]

>> What do you think?

I completely agree that these are distinct concepts, and of course I'm not
surprised that everyone else thinks so too.  But the description is
misleading, I think, since it really seems to assume concurrent elution and
scan.  A quibble perhaps but probably worth cleaning up.

The use in question is actually in pepXML related code, so retention time
is the concept we want for sure.  But now I guess I have to think about
managing units?  Or is it defined as being in seconds?  (And if so, perhaps
the description should be enhanced to reflect that?)

Thanks,

Brian


On Wed, Sep 4, 2013 at 9:45 AM, <Eri...@sy...> wrote:

> Hi Brian, I'm not certain if that answers your question, but I might add
> that ProteoWizard's use of the obsolete retention time(s) should be
> changed to either scan start time or retention time. We intend scan start
> time to be used in cases where there is a time tag associated with a
> definite mass spec acquisition (as is the case in mzML and mzIdentML). The
> non-obsolete retention time term should be used as an attribute associated
> with a peptide molecule in a chromatographic column independent of an
> instrument acquisition event (as is the case in TraML). The MALDI case is
> a little more tricky. In practice, a scan start time will likely be
> recorded with the instrument and should be written into mzML et al. The
> chromatographic retention time might be known and could be recorded
> separately (as this will be a different time than the instrument scan
> time), but often is not well known when the mzML is written. But as you
> allude to, these are now different concepts with different terms, whereas
> before it was more muddled.
>
> What do you think?
>
> Regards,
> Eric
>
>
> > -----Original Message-----
> > From: Gerhard Mayer [mailto:Ger...@ru...]
> > Sent: Tuesday, September 03, 2013 11:24 PM
> > To: psi...@li...
> > Subject: Re: [Psidev-ms-vocab] [Psidev-ms-dev] New version 3.50.0 of
> > psi-ms.obo
> >
> > Hi Brian,
> >
> > yes we obsoletetd the retention time(s) term.
> >
> > Because we had two terms: retention time and retention time(s), we
> > decided to obsolete one and add a term named scan start time for the
> > SpectrumIdentificationResult annotation, see our discussion in Issue 74
> > on google code:
> >
> > https://code.google.com/p/psi-pi/issues/detail?id=74&can=1
> >
> > Best Regards,
> > Gerhard
> >
> >
> > Am 04.09.2013 00:38, schrieb Brian Pratt:
> > > I'm a little slow noticing this (just now updating ProteoWizard's
> > OBO), but
> > > I wonder about the now obsoleted
> > > id: MS:1001114
> > > name: retention time(s)
> > > def: "Retention time of the spectrum from the source file." [PSI:PI]
> > >
> > > Surely chromatography and mass spec can happen in entirely different
> > time
> > > frames, as with MALDI - or am I misunderstanding something?
> > >
> > > And how is it different from
> > > id: MS:1000894
> > > name: retention time
> > > def: "A measure of the interval relative to the beginning of a mass
> > > spectrometric run when a peptide will exit the chromatographic
> > column."
> > > [PSI:MS]
> > >
> > > And doesn't that definition have the same assumption about the column
> > being
> > > hooked up directly to the mass spec?
> > >
> > > Cheers,
> > > Brian Pratt
> > >
> > >
> > > On Fri, May 31, 2013 at 12:10 AM, Gerhard Mayer <
> > > Ger...@ru...> wrote:
> > >
> > >> Dear proteomics community,
> > >>
> > >> attached there's the new version 3.50.0 of the psi-ms.obo file.
> > >>
> > >> It contains the changes concerning the retention time terms (issue
> > 74),
> > >> changes for the waters instrument term definitions and 3 new terms
> > for the
> > >> Byonic search engine.
> > >>
> > >>
> > >> Changed CV terms in version 3.50.0 of psi-ms.obo:
> > >> ==============================**===================
> > >> ************ added the two is_a relations 'is_a: MS:1001105 !
> > peptide
> > >> result details' and
> > >> ************ 'is_a: MS:1001405 ! spectrum identification result
> > details'
> > >> [Term]
> > >> id: MS:1000016
> > >> name: scan start time
> > >> def: "The time that an analyzer started a scan, relative to the
> > start of
> > >> the MS run." [PSI:MS]
> > >> xref: value-type:xsd\:float "The allowed value-type for this CV
> > term."
> > >> is_a: MS:1000503 ! scan attribute
> > >> is_a: MS:1001105 ! peptide result details
> > >> is_a: MS:1001405 ! spectrum identification result details
> > >> relationship: has_units UO:0000010 ! second
> > >> relationship: has_units UO:0000031 ! minute
> > >>
> > >> ************ Made obsolete
> > >> [Term]
> > >> id: MS:1001114
> > >> name: retention time(s)
> > >> def: "OBSOLETE Retention time of the spectrum from the source file."
> > >> [PSI:PI]
> > >> comment: This term was made obsolete because scan start time
> > (MS:1000016)
> > >> should be used instead.
> > >> xref: value-type:xsd\:double "The allowed value-type for this CV
> > term."
> > >> is_a: MS:1001105 ! peptide result details
> > >> is_a: MS:1001405 ! spectrum identification result details
> > >> relationship: has_units UO:0000010 ! second
> > >> relationship: has_units UO:0000031 ! minute
> > >> is_obsolete: true
> > >>
> > >> ************ Changed the definition (removed 'peptide ...').
> > >> [Term]
> > >> id: MS:1000894
> > >> name: retention time
> > >> def: "A measure of the interval relative to the beginning of a mass
> > >> spectrometric run." [PSI:MS]
> > >> is_a: MS:1000887 ! peptide attribute
> > >>
> > >> ************ Changed the is_a relationship from 'detector type' -->
> > 'array
> > >> detector' for the next two terms
> > >> [Term]
> > >> id: MS:1000114
> > >> name: microchannel plate detector
> > >> def: "A thin plate that contains a closely spaced array of channels
> > that
> > >> each act as a continuous dynode particle multiplier. A charged
> > particle,
> > >> fast neutral particle, or photon striking the plate causes a cascade
> > of
> > >> secondary electrons that ultimately exits the opposite side of the
> > plate."
> > >> [PSI:MS]
> > >> synonym: "multichannel plate" EXACT []
> > >> is_a: MS:1000345 ! array detector
> > >>
> > >> [Term]
> > >> id: MS:1000621
> > >> name: photodiode array detector
> > >> def: "An array detector used to record spectra in the ultraviolet
> > and
> > >> visible region of light." [PSI:MS]
> > >> synonym: "PDA" EXACT []
> > >> is_a: MS:1000345 ! array detector
> > >>
> > >> ************ Added the 'is_a: MS:1000621 ! photodiode array
> > detector'
> > >> relationship
> > >> [Term]
> > >> id: MS:1000818
> > >> name: Acquity UPLC PDA
> > >> def: "Acquity UPLC Photodiode Array Detector." [PSI:MS]
> > >> is_a: MS:1000126 ! Waters instrument model
> > >> is_a: MS:1000621 ! photodiode array detector
> > >>
> > >> ************ Added the 'is_a: MS:1002308 ! fluorescence detector'
> > >> relationship
> > >> [Term]
> > >> id: MS:1000819
> > >> name: Acquity UPLC FLR
> > >> def: "Acquity UPLC Fluorescence Detector." [PSI:MS]
> > >> is_a: MS:1000126 ! Waters instrument model
> > >> is_a: MS:1002308 ! fluorescence detector
> > >>
> > >> ************ Adapted the definitions for the following Waters
> > instruments
> > >> to be more specific and unambiguous:
> > >> MS:1000159    GCT
> > >> MS:1000170    M@LDI L
> > >> MS:1000171    M@LDI LR
> > >> MS:1000188    Q-Tof micro
> > >> MS:1000189    Q-Tof ultima
> > >> MS:1000191    quattro micro
> > >> MS:1000192    Quattro UItima
> > >> MS:1000632    Q-Tof Premier
> > >> MS:1001761    ACQUITY UPLC
> > >> MS:1001762    ACQUITY UPLC H-Class
> > >> MS:1001763    ACQUITY UPLC H-Class Bio
> > >> MS:1001764    ACQUITY UPLC I-Class
> > >> MS:1001765    ACQUITY UPLC Systems with 2D Technology
> > >> MS:1001766    nanoACQUITY UPLC
> > >> MS:1001767    nanoACQUITY UPLC System with Technology
> > >> MS:1001768    nanoACQUITY UPLC with HDX Technology
> > >> MS:1001769    TRIZAIC UPLC nanoTile
> > >> MS:1001770    GCT Premier
> > >> MS:1001771    MALDI Synapt G2 HDMS
> > >> MS:1001772    MALDI Synapt G2 MS
> > >> MS:1001773    MALDI Synapt G2-S HDMS
> > >> MS:1001774    MALDI Synapt G2-S MS
> > >> MS:1001775    MALDI Synapt HDMS
> > >> MS:1001776    MALDI Synapt MS
> > >> MS:1001777    Synapt G2 HDMS
> > >> MS:1001778    Synapt G2 MS
> > >> MS:1001779    Synapt G2-S HDMS
> > >> MS:1001780    Synapt G2-S MS
> > >> MS:1001781    Synapt HDMS
> > >> MS:1001782    Synapt MS
> > >> MS:1001783    Xevo G2 Q-Tof
> > >> MS:1001784    Xevo G2 Tof
> > >> MS:1001785    Xevo Q-Tof
> > >> MS:1001786    3100
> > >> MS:1001787    Acquity SQD
> > >> MS:1001788    Acquity TQD
> > >> MS:1001789    Quattro micro GC
> > >> MS:1001790    Xevo TQ MS
> > >> MS:1001791    Xevo TQD
> > >> MS:1001792    Xevo TQ-S
> > >> MS:1001795    Empower
> > >> MS:1001796    Unify
> > >>
> > >>
> > >> New CV terms in version 3.50.0 of psi-ms.obo:
> > >> ==============================**===============
> > >> [Term]
> > >> id: MS:1002308
> > >> name: fluorescence detector
> > >> def: "A detector using a fluorescent signal after excitation with
> > light."
> > >> [PSI:MS]
> > >> is_a: MS:1000026 ! detector type
> > >>
> > >> [Term]
> > >> id: MS:1002309
> > >> name: Byonic: Peptide AbsLogProb
> > >> def: "The absolute value of the log-base10 of the Byonic posterior
> > error
> > >> probability (PEP) of the PSM. " [PSI:PI]
> > >> xref: value-type:xsd\:double "The allowed value-type for this CV
> > term."
> > >> is_a: MS:1001143 ! search engine specific score for PSMs
> > >> is_a: MS:1001153 ! search engine specific score
> > >> has_order: MS:1002108 ! higher score better
> > >>
> > >> [Term]
> > >> id: MS:1002310
> > >> name: Byonic: Protein AbsLogProb
> > >> def: "The absolute value of the log-base10 of the Byonic posterior
> > error
> > >> probability (PEP) of the protein. " [PSI:PI]
> > >> xref: value-type:xsd\:double "The allowed value-type for this CV
> > term."
> > >> is_a: MS:1001116 ! single protein result details
> > >> is_a: MS:1001153 ! search engine specific score
> > >> has_order: MS:1002108 ! higher score better
> > >>
> > >> [Term]
> > >> id: MS:1002311
> > >> name: Byonic: Peptide AbsLogProb2D
> > >> def: "The absolute value of the log-base10 Byonic two-dimensional
> > >> posterior error probability (PEP) of the PSM. The two-dimensional
> > PEP takes
> > >> into account protein ranking information as well as PSM
> > information."
> > >> [PSI:PI]
> > >> xref: value-type:xsd\:double "The allowed value-type for this CV
> > term."
> > >> is_a: MS:1001143 ! search engine specific score for PSMs
> > >> is_a: MS:1001153 ! search engine specific score
> > >> has_order: MS:1002108 ! higher score better
> > >>
> > >> Best Regards,
> > >> Gerhard
> > >>
> > >> --
> > >> ---
> > >> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> > >> Bioinformatik / Biostatistik
> > >> Medizinisches-Proteom-Center (MPC)
> > >> Ruhr-Universität Bochum
> > >> Zentrum für klinische Forschung I (ZKF I)
> > >> E.049a
> > >> Universitätsstraße 150
> > >> D-44801 Bochum
> > >>  Phone: +49(0)234/32-21006
> > >> Fax:    +49(0)234/32-14554
> > >> Email:  Ger...@ru...
> > >> Web:    http://www.medizinisches-**proteom-
> > center.de<http://www.medizinisches-proteom-center.de>
> > >>
> > >>
> > >>
> > >> --------------------------------------------------------------------
> > ----------
> > >> Get 100% visibility into Java/.NET code with AppDynamics Lite
> > >> It's a free troubleshooting tool designed for production
> > >> Get down to code-level detail for bottlenecks, with <2% overhead.
> > >> Download for free and get started troubleshooting in minutes.
> > >> http://p.sf.net/sfu/appdyn_d2d_ap2
> > >> _______________________________________________
> > >> Psidev-ms-dev mailing list
> > >> Psi...@li...
> > >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> > >>
> > >>
> > >
> > >
> > >
> > > ---------------------------------------------------------------------
> > ---------
> > > Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012,
> > more!
> > > Discover the easy way to master current and previous Microsoft
> > technologies
> > > and advance your career. Get an incredible 1,500+ hours of step-by-
> > step
> > > tutorial videos with LearnDevNow. Subscribe today and save!
> > >
> > http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.cl
> > ktrk
> > >
> > >
> > >
> > > _______________________________________________
> > > Psidev-ms-vocab mailing list
> > > Psi...@li...
> > > https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab
> > >
> >
> >
> > --
> > ---
> > Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> > Bioinformatik / Biostatistik
> > Medizinisches-Proteom-Center (MPC)
> > Ruhr-Universität Bochum
> > Zentrum für klinische Forschung I (ZKF I)
> > E.049a
> > Universitätsstraße 150
> > D-44801 Bochum
> >
> > Phone:        +49(0)234/32-21006
> > Fax:  +49(0)234/32-14554
> > Email:        Ger...@ru...
> > Web:  http://www.medizinisches-proteom-center.de
> >
> > -----------------------------------------------------------------------
> > -------
> > Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
> > Discover the easy way to master current and previous Microsoft
> > technologies
> > and advance your career. Get an incredible 1,500+ hours of step-by-step
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> > https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab
>
>
> ------------------------------------------------------------------------------
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>

Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.50.0 of psi-ms.obo

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

Hi Brian, I'm not certain if that answers your question, but I might add
that ProteoWizard's use of the obsolete retention time(s) should be
changed to either scan start time or retention time. We intend scan start
time to be used in cases where there is a time tag associated with a
definite mass spec acquisition (as is the case in mzML and mzIdentML). The
non-obsolete retention time term should be used as an attribute associated
with a peptide molecule in a chromatographic column independent of an
instrument acquisition event (as is the case in TraML). The MALDI case is
a little more tricky. In practice, a scan start time will likely be
recorded with the instrument and should be written into mzML et al. The
chromatographic retention time might be known and could be recorded
separately (as this will be a different time than the instrument scan
time), but often is not well known when the mzML is written. But as you
allude to, these are now different concepts with different terms, whereas
before it was more muddled.

What do you think?

Regards,
Eric


> -----Original Message-----
> From: Gerhard Mayer [mailto:Ger...@ru...]
> Sent: Tuesday, September 03, 2013 11:24 PM
> To: psi...@li...
> Subject: Re: [Psidev-ms-vocab] [Psidev-ms-dev] New version 3.50.0 of
> psi-ms.obo
>
> Hi Brian,
>
> yes we obsoletetd the retention time(s) term.
>
> Because we had two terms: retention time and retention time(s), we
> decided to obsolete one and add a term named scan start time for the
> SpectrumIdentificationResult annotation, see our discussion in Issue 74
> on google code:
>
> https://code.google.com/p/psi-pi/issues/detail?id=74&can=1
>
> Best Regards,
> Gerhard
>
>
> Am 04.09.2013 00:38, schrieb Brian Pratt:
> > I'm a little slow noticing this (just now updating ProteoWizard's
> OBO), but
> > I wonder about the now obsoleted
> > id: MS:1001114
> > name: retention time(s)
> > def: "Retention time of the spectrum from the source file." [PSI:PI]
> >
> > Surely chromatography and mass spec can happen in entirely different
> time
> > frames, as with MALDI - or am I misunderstanding something?
> >
> > And how is it different from
> > id: MS:1000894
> > name: retention time
> > def: "A measure of the interval relative to the beginning of a mass
> > spectrometric run when a peptide will exit the chromatographic
> column."
> > [PSI:MS]
> >
> > And doesn't that definition have the same assumption about the column
> being
> > hooked up directly to the mass spec?
> >
> > Cheers,
> > Brian Pratt
> >
> >
> > On Fri, May 31, 2013 at 12:10 AM, Gerhard Mayer <
> > Ger...@ru...> wrote:
> >
> >> Dear proteomics community,
> >>
> >> attached there's the new version 3.50.0 of the psi-ms.obo file.
> >>
> >> It contains the changes concerning the retention time terms (issue
> 74),
> >> changes for the waters instrument term definitions and 3 new terms
> for the
> >> Byonic search engine.
> >>
> >>
> >> Changed CV terms in version 3.50.0 of psi-ms.obo:
> >> ==============================**===================
> >> ************ added the two is_a relations 'is_a: MS:1001105 !
> peptide
> >> result details' and
> >> ************ 'is_a: MS:1001405 ! spectrum identification result
> details'
> >> [Term]
> >> id: MS:1000016
> >> name: scan start time
> >> def: "The time that an analyzer started a scan, relative to the
> start of
> >> the MS run." [PSI:MS]
> >> xref: value-type:xsd\:float "The allowed value-type for this CV
> term."
> >> is_a: MS:1000503 ! scan attribute
> >> is_a: MS:1001105 ! peptide result details
> >> is_a: MS:1001405 ! spectrum identification result details
> >> relationship: has_units UO:0000010 ! second
> >> relationship: has_units UO:0000031 ! minute
> >>
> >> ************ Made obsolete
> >> [Term]
> >> id: MS:1001114
> >> name: retention time(s)
> >> def: "OBSOLETE Retention time of the spectrum from the source file."
> >> [PSI:PI]
> >> comment: This term was made obsolete because scan start time
> (MS:1000016)
> >> should be used instead.
> >> xref: value-type:xsd\:double "The allowed value-type for this CV
> term."
> >> is_a: MS:1001105 ! peptide result details
> >> is_a: MS:1001405 ! spectrum identification result details
> >> relationship: has_units UO:0000010 ! second
> >> relationship: has_units UO:0000031 ! minute
> >> is_obsolete: true
> >>
> >> ************ Changed the definition (removed 'peptide ...').
> >> [Term]
> >> id: MS:1000894
> >> name: retention time
> >> def: "A measure of the interval relative to the beginning of a mass
> >> spectrometric run." [PSI:MS]
> >> is_a: MS:1000887 ! peptide attribute
> >>
> >> ************ Changed the is_a relationship from 'detector type' -->
> 'array
> >> detector' for the next two terms
> >> [Term]
> >> id: MS:1000114
> >> name: microchannel plate detector
> >> def: "A thin plate that contains a closely spaced array of channels
> that
> >> each act as a continuous dynode particle multiplier. A charged
> particle,
> >> fast neutral particle, or photon striking the plate causes a cascade
> of
> >> secondary electrons that ultimately exits the opposite side of the
> plate."
> >> [PSI:MS]
> >> synonym: "multichannel plate" EXACT []
> >> is_a: MS:1000345 ! array detector
> >>
> >> [Term]
> >> id: MS:1000621
> >> name: photodiode array detector
> >> def: "An array detector used to record spectra in the ultraviolet
> and
> >> visible region of light." [PSI:MS]
> >> synonym: "PDA" EXACT []
> >> is_a: MS:1000345 ! array detector
> >>
> >> ************ Added the 'is_a: MS:1000621 ! photodiode array
> detector'
> >> relationship
> >> [Term]
> >> id: MS:1000818
> >> name: Acquity UPLC PDA
> >> def: "Acquity UPLC Photodiode Array Detector." [PSI:MS]
> >> is_a: MS:1000126 ! Waters instrument model
> >> is_a: MS:1000621 ! photodiode array detector
> >>
> >> ************ Added the 'is_a: MS:1002308 ! fluorescence detector'
> >> relationship
> >> [Term]
> >> id: MS:1000819
> >> name: Acquity UPLC FLR
> >> def: "Acquity UPLC Fluorescence Detector." [PSI:MS]
> >> is_a: MS:1000126 ! Waters instrument model
> >> is_a: MS:1002308 ! fluorescence detector
> >>
> >> ************ Adapted the definitions for the following Waters
> instruments
> >> to be more specific and unambiguous:
> >> MS:1000159    GCT
> >> MS:1000170    M@LDI L
> >> MS:1000171    M@LDI LR
> >> MS:1000188    Q-Tof micro
> >> MS:1000189    Q-Tof ultima
> >> MS:1000191    quattro micro
> >> MS:1000192    Quattro UItima
> >> MS:1000632    Q-Tof Premier
> >> MS:1001761    ACQUITY UPLC
> >> MS:1001762    ACQUITY UPLC H-Class
> >> MS:1001763    ACQUITY UPLC H-Class Bio
> >> MS:1001764    ACQUITY UPLC I-Class
> >> MS:1001765    ACQUITY UPLC Systems with 2D Technology
> >> MS:1001766    nanoACQUITY UPLC
> >> MS:1001767    nanoACQUITY UPLC System with Technology
> >> MS:1001768    nanoACQUITY UPLC with HDX Technology
> >> MS:1001769    TRIZAIC UPLC nanoTile
> >> MS:1001770    GCT Premier
> >> MS:1001771    MALDI Synapt G2 HDMS
> >> MS:1001772    MALDI Synapt G2 MS
> >> MS:1001773    MALDI Synapt G2-S HDMS
> >> MS:1001774    MALDI Synapt G2-S MS
> >> MS:1001775    MALDI Synapt HDMS
> >> MS:1001776    MALDI Synapt MS
> >> MS:1001777    Synapt G2 HDMS
> >> MS:1001778    Synapt G2 MS
> >> MS:1001779    Synapt G2-S HDMS
> >> MS:1001780    Synapt G2-S MS
> >> MS:1001781    Synapt HDMS
> >> MS:1001782    Synapt MS
> >> MS:1001783    Xevo G2 Q-Tof
> >> MS:1001784    Xevo G2 Tof
> >> MS:1001785    Xevo Q-Tof
> >> MS:1001786    3100
> >> MS:1001787    Acquity SQD
> >> MS:1001788    Acquity TQD
> >> MS:1001789    Quattro micro GC
> >> MS:1001790    Xevo TQ MS
> >> MS:1001791    Xevo TQD
> >> MS:1001792    Xevo TQ-S
> >> MS:1001795    Empower
> >> MS:1001796    Unify
> >>
> >>
> >> New CV terms in version 3.50.0 of psi-ms.obo:
> >> ==============================**===============
> >> [Term]
> >> id: MS:1002308
> >> name: fluorescence detector
> >> def: "A detector using a fluorescent signal after excitation with
> light."
> >> [PSI:MS]
> >> is_a: MS:1000026 ! detector type
> >>
> >> [Term]
> >> id: MS:1002309
> >> name: Byonic: Peptide AbsLogProb
> >> def: "The absolute value of the log-base10 of the Byonic posterior
> error
> >> probability (PEP) of the PSM. " [PSI:PI]
> >> xref: value-type:xsd\:double "The allowed value-type for this CV
> term."
> >> is_a: MS:1001143 ! search engine specific score for PSMs
> >> is_a: MS:1001153 ! search engine specific score
> >> has_order: MS:1002108 ! higher score better
> >>
> >> [Term]
> >> id: MS:1002310
> >> name: Byonic: Protein AbsLogProb
> >> def: "The absolute value of the log-base10 of the Byonic posterior
> error
> >> probability (PEP) of the protein. " [PSI:PI]
> >> xref: value-type:xsd\:double "The allowed value-type for this CV
> term."
> >> is_a: MS:1001116 ! single protein result details
> >> is_a: MS:1001153 ! search engine specific score
> >> has_order: MS:1002108 ! higher score better
> >>
> >> [Term]
> >> id: MS:1002311
> >> name: Byonic: Peptide AbsLogProb2D
> >> def: "The absolute value of the log-base10 Byonic two-dimensional
> >> posterior error probability (PEP) of the PSM. The two-dimensional
> PEP takes
> >> into account protein ranking information as well as PSM
> information."
> >> [PSI:PI]
> >> xref: value-type:xsd\:double "The allowed value-type for this CV
> term."
> >> is_a: MS:1001143 ! search engine specific score for PSMs
> >> is_a: MS:1001153 ! search engine specific score
> >> has_order: MS:1002108 ! higher score better
> >>
> >> Best Regards,
> >> Gerhard
> >>
> >> --
> >> ---
> >> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> >> Bioinformatik / Biostatistik
> >> Medizinisches-Proteom-Center (MPC)
> >> Ruhr-Universität Bochum
> >> Zentrum für klinische Forschung I (ZKF I)
> >> E.049a
> >> Universitätsstraße 150
> >> D-44801 Bochum
> >>  Phone: +49(0)234/32-21006
> >> Fax:    +49(0)234/32-14554
> >> Email:  Ger...@ru...
> >> Web:    http://www.medizinisches-**proteom-
> center.de<http://www.medizinisches-proteom-center.de>
> >>
> >>
> >>
> >> --------------------------------------------------------------------
> ----------
> >> Get 100% visibility into Java/.NET code with AppDynamics Lite
> >> It's a free troubleshooting tool designed for production
> >> Get down to code-level detail for bottlenecks, with <2% overhead.
> >> Download for free and get started troubleshooting in minutes.
> >> http://p.sf.net/sfu/appdyn_d2d_ap2
> >> _______________________________________________
> >> Psidev-ms-dev mailing list
> >> Psi...@li...
> >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> >>
> >>
> >
> >
> >
> > ---------------------------------------------------------------------
> ---------
> > Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012,
> more!
> > Discover the easy way to master current and previous Microsoft
> technologies
> > and advance your career. Get an incredible 1,500+ hours of step-by-
> step
> > tutorial videos with LearnDevNow. Subscribe today and save!
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.cl
> ktrk
> >
> >
> >
> > _______________________________________________
> > Psidev-ms-vocab mailing list
> > Psi...@li...
> > https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab
> >
>
>
> --
> ---
> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> Bioinformatik / Biostatistik
> Medizinisches-Proteom-Center (MPC)
> Ruhr-Universität Bochum
> Zentrum für klinische Forschung I (ZKF I)
> E.049a
> Universitätsstraße 150
> D-44801 Bochum
>
> Phone:	+49(0)234/32-21006
> Fax:	+49(0)234/32-14554
> Email:	Ger...@ru...
> Web:	http://www.medizinisches-proteom-center.de
>
> -----------------------------------------------------------------------
> -------
> Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
> Discover the easy way to master current and previous Microsoft
> technologies
> and advance your career. Get an incredible 1,500+ hours of step-by-step
> tutorial videos with LearnDevNow. Subscribe today and save!
> http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.cl
> ktrk
> _______________________________________________
> Psidev-ms-vocab mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab

Re: [Psidev-ms-dev] New version 3.50.0 of psi-ms.obo

[Brian P. <bri...@in...>]

I'm a little slow noticing this (just now updating ProteoWizard's OBO), but
I wonder about the now obsoleted
id: MS:1001114
name: retention time(s)
def: "Retention time of the spectrum from the source file." [PSI:PI]

Surely chromatography and mass spec can happen in entirely different time
frames, as with MALDI - or am I misunderstanding something?

And how is it different from
id: MS:1000894
name: retention time
def: "A measure of the interval relative to the beginning of a mass
spectrometric run when a peptide will exit the chromatographic column."
[PSI:MS]

And doesn't that definition have the same assumption about the column being
hooked up directly to the mass spec?

Cheers,
Brian Pratt


On Fri, May 31, 2013 at 12:10 AM, Gerhard Mayer <
Ger...@ru...> wrote:

> Dear proteomics community,
>
> attached there's the new version 3.50.0 of the psi-ms.obo file.
>
> It contains the changes concerning the retention time terms (issue 74),
> changes for the waters instrument term definitions and 3 new terms for the
> Byonic search engine.
>
>
> Changed CV terms in version 3.50.0 of psi-ms.obo:
> ==============================**===================
> ************ added the two is_a relations 'is_a: MS:1001105 ! peptide
> result details' and
> ************ 'is_a: MS:1001405 ! spectrum identification result details'
> [Term]
> id: MS:1000016
> name: scan start time
> def: "The time that an analyzer started a scan, relative to the start of
> the MS run." [PSI:MS]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000503 ! scan attribute
> is_a: MS:1001105 ! peptide result details
> is_a: MS:1001405 ! spectrum identification result details
> relationship: has_units UO:0000010 ! second
> relationship: has_units UO:0000031 ! minute
>
> ************ Made obsolete
> [Term]
> id: MS:1001114
> name: retention time(s)
> def: "OBSOLETE Retention time of the spectrum from the source file."
> [PSI:PI]
> comment: This term was made obsolete because scan start time (MS:1000016)
> should be used instead.
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1001105 ! peptide result details
> is_a: MS:1001405 ! spectrum identification result details
> relationship: has_units UO:0000010 ! second
> relationship: has_units UO:0000031 ! minute
> is_obsolete: true
>
> ************ Changed the definition (removed 'peptide ...').
> [Term]
> id: MS:1000894
> name: retention time
> def: "A measure of the interval relative to the beginning of a mass
> spectrometric run." [PSI:MS]
> is_a: MS:1000887 ! peptide attribute
>
> ************ Changed the is_a relationship from 'detector type' --> 'array
> detector' for the next two terms
> [Term]
> id: MS:1000114
> name: microchannel plate detector
> def: "A thin plate that contains a closely spaced array of channels that
> each act as a continuous dynode particle multiplier. A charged particle,
> fast neutral particle, or photon striking the plate causes a cascade of
> secondary electrons that ultimately exits the opposite side of the plate."
> [PSI:MS]
> synonym: "multichannel plate" EXACT []
> is_a: MS:1000345 ! array detector
>
> [Term]
> id: MS:1000621
> name: photodiode array detector
> def: "An array detector used to record spectra in the ultraviolet and
> visible region of light." [PSI:MS]
> synonym: "PDA" EXACT []
> is_a: MS:1000345 ! array detector
>
> ************ Added the 'is_a: MS:1000621 ! photodiode array detector'
> relationship
> [Term]
> id: MS:1000818
> name: Acquity UPLC PDA
> def: "Acquity UPLC Photodiode Array Detector." [PSI:MS]
> is_a: MS:1000126 ! Waters instrument model
> is_a: MS:1000621 ! photodiode array detector
>
> ************ Added the 'is_a: MS:1002308 ! fluorescence detector'
> relationship
> [Term]
> id: MS:1000819
> name: Acquity UPLC FLR
> def: "Acquity UPLC Fluorescence Detector." [PSI:MS]
> is_a: MS:1000126 ! Waters instrument model
> is_a: MS:1002308 ! fluorescence detector
>
> ************ Adapted the definitions for the following Waters instruments
> to be more specific and unambiguous:
> MS:1000159    GCT
> MS:1000170    M@LDI L
> MS:1000171    M@LDI LR
> MS:1000188    Q-Tof micro
> MS:1000189    Q-Tof ultima
> MS:1000191    quattro micro
> MS:1000192    Quattro UItima
> MS:1000632    Q-Tof Premier
> MS:1001761    ACQUITY UPLC
> MS:1001762    ACQUITY UPLC H-Class
> MS:1001763    ACQUITY UPLC H-Class Bio
> MS:1001764    ACQUITY UPLC I-Class
> MS:1001765    ACQUITY UPLC Systems with 2D Technology
> MS:1001766    nanoACQUITY UPLC
> MS:1001767    nanoACQUITY UPLC System with Technology
> MS:1001768    nanoACQUITY UPLC with HDX Technology
> MS:1001769    TRIZAIC UPLC nanoTile
> MS:1001770    GCT Premier
> MS:1001771    MALDI Synapt G2 HDMS
> MS:1001772    MALDI Synapt G2 MS
> MS:1001773    MALDI Synapt G2-S HDMS
> MS:1001774    MALDI Synapt G2-S MS
> MS:1001775    MALDI Synapt HDMS
> MS:1001776    MALDI Synapt MS
> MS:1001777    Synapt G2 HDMS
> MS:1001778    Synapt G2 MS
> MS:1001779    Synapt G2-S HDMS
> MS:1001780    Synapt G2-S MS
> MS:1001781    Synapt HDMS
> MS:1001782    Synapt MS
> MS:1001783    Xevo G2 Q-Tof
> MS:1001784    Xevo G2 Tof
> MS:1001785    Xevo Q-Tof
> MS:1001786    3100
> MS:1001787    Acquity SQD
> MS:1001788    Acquity TQD
> MS:1001789    Quattro micro GC
> MS:1001790    Xevo TQ MS
> MS:1001791    Xevo TQD
> MS:1001792    Xevo TQ-S
> MS:1001795    Empower
> MS:1001796    Unify
>
>
> New CV terms in version 3.50.0 of psi-ms.obo:
> ==============================**===============
> [Term]
> id: MS:1002308
> name: fluorescence detector
> def: "A detector using a fluorescent signal after excitation with light."
> [PSI:MS]
> is_a: MS:1000026 ! detector type
>
> [Term]
> id: MS:1002309
> name: Byonic: Peptide AbsLogProb
> def: "The absolute value of the log-base10 of the Byonic posterior error
> probability (PEP) of the PSM. " [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1001143 ! search engine specific score for PSMs
> is_a: MS:1001153 ! search engine specific score
> has_order: MS:1002108 ! higher score better
>
> [Term]
> id: MS:1002310
> name: Byonic: Protein AbsLogProb
> def: "The absolute value of the log-base10 of the Byonic posterior error
> probability (PEP) of the protein. " [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1001116 ! single protein result details
> is_a: MS:1001153 ! search engine specific score
> has_order: MS:1002108 ! higher score better
>
> [Term]
> id: MS:1002311
> name: Byonic: Peptide AbsLogProb2D
> def: "The absolute value of the log-base10 Byonic two-dimensional
> posterior error probability (PEP) of the PSM. The two-dimensional PEP takes
> into account protein ranking information as well as PSM information."
> [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1001143 ! search engine specific score for PSMs
> is_a: MS:1001153 ! search engine specific score
> has_order: MS:1002108 ! higher score better
>
> Best Regards,
> Gerhard
>
> --
> ---
> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> Bioinformatik / Biostatistik
> Medizinisches-Proteom-Center (MPC)
> Ruhr-Universität Bochum
> Zentrum für klinische Forschung I (ZKF I)
> E.049a
> Universitätsstraße 150
> D-44801 Bochum
>  Phone: +49(0)234/32-21006
> Fax:    +49(0)234/32-14554
> Email:  Ger...@ru...
> Web:    http://www.medizinisches-**proteom-center.de<http://www.medizinisches-proteom-center.de>
>
>
>
> ------------------------------------------------------------------------------
> Get 100% visibility into Java/.NET code with AppDynamics Lite
> It's a free troubleshooting tool designed for production
> Get down to code-level detail for bottlenecks, with <2% overhead.
> Download for free and get started troubleshooting in minutes.
> http://p.sf.net/sfu/appdyn_d2d_ap2
> _______________________________________________
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[Psidev-ms-dev] New version 3.53.0 of psi-ms.obo

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

Dear proteomics community,

attached there's the new version 3.53.0 of the psi-ms.obo file.

It contains a new term for a PreoteomeXchange project tag.


Changed CV terms in version 3.53.0 of psi-ms.obo:
=================================================
************ Added 'higher score better'
[Term]
id: MS:1002338
name: Andromeda:score
def: "The probability based score of the Andromeda search engine." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
has_order: MS:1002108 ! higher score better


New CV terms in version 3.53.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002340
name: ProteomeXchange project tag
def: "Tag that can be added to a ProteomeXchange dataset, to enable the
grouping of datasets. One tag can be used for indicating that a given
dataset is part of a bigger project, like e.g. the Human Proteome
Project." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier


Best Regards,
Gerhard

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

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

[Psidev-ms-dev] Release candidate 3.53.0_rc1 of psi-ms.obo

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

Dear proteomics community,

attached there's the release candidate 3.53.0_rc1 of the psi-ms.obo file.

It contains a new term for a PreoteomeXchange project tag.


Changed CV terms in version 3.53.0_rc1 of psi-ms.obo:
=====================================================
************ Added 'higher score better'
[Term]
id: MS:1002338
name: Andromeda:score
def: "The probability based score of the Andromeda search engine." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
has_order: MS:1002108 ! higher score better


New CV terms in version 3.53.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002340
name: ProteomeXchange project tag
def: "Tag that can be added to a ProteomeXchange dataset, to enable the
grouping of datasets. One tag can be used for indicating that a given
dataset is part of a bigger project, like e.g. the Human Proteome
Project." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier


Best Regards,
Gerhard

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

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

[Psidev-ms-dev] New version 3.52.0 of psi-ms.obo

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

Dear proteomics community,

attached there's the new version 3.52.0 of the psi-ms.obo file.

It contains scores and some new ProteomeDiscoverer 1.4 input parameters.
e.g. for MS Amanda.
In addition it defines some terms for conversion and analysis software.


Changed CV terms in version 3.52.0 of psi-ms.obo:
=================================================
************ Added boolean data type
[Term]
id: MS:1001194
name: quality estimation with decoy database
def: "Quality estimation by decoy database." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001060 ! quality estimation method details


New CV terms in version 3.52.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002316
name: ProteomeDiscoverer:Amanda:high confidence threshold
def: "Strict confidence probability score." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002317
name: ProteomeDiscoverer:Amanda:middle confidence threshold
def: "Relaxed confidence probability score." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002318
name: ProteomeDiscoverer:automatic workload
def: "Flag indicating automatic estimation of the workload level." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002319
name: Amanda:AmandaScore
def: "The Amanda score of the scoring function for a PSM." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1002320
name: ProteomeDiscoverer:max differential modifications
def: "Maximum dynamic modifications per PSM." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002321
name: ProteomeDiscoverer:max equal modifications
def: "Maximum equal modifications per PSM." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002322
name: ProteomeDiscoverer:min peptide length
def: "Minimum peptide length." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002323
name: ProteomeDiscoverer:max peptide length
def: "Maximum peptide length." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002324
name: ProteomeDiscoverer:max number neutral loss
def: "Maximum number of same neutral losses." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002325
name: ProteomeDiscoverer:max number neutral loss modifications
def: "Max number of same neutral losses of modifications." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002326
name: ProteomeDiscoverer:use flanking ions
def: "Flag for usage of flanking ions." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002327
name: ProteomeDiscoverer:max number of same modifs
def: "The maximum number of possible equal modifications per PSM." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002328
name: ProteomeDiscoverer:perform deisotoping
def: "Defines whether a simple deisotoping shall be performed." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002329
name: ProteomeDiscoverer:ion settings
def: "Specifies the fragment ions and neutral losses that are
calculated." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002330
name: ProteomeDiscoverer:3. Static Modification
def: "Determine 3rd static (fixed) post-translational modifications
(PTMs)." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002331
name: ProteomeDiscoverer:5. Dynamic Modification
def: "Determine 5th dynamic (variable) post-translational modifications
(PTMs)." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002332
name: lab head
def: "The scientist responsible for personnel, grants, and
instrumentation in a functional laboratory group." [PSI:PI]
is_a: MS:1002033 ! contact role

[Term]
id: MS:1002333
name: conversion software
def: "Computer software primarily designed to convert data represented
in one format to another format, sometimes with minor data alterations
in the process." [PSI:PI]
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002334
name: ProCon
def: "Java software designed to convert one of several proteomics
identification results formats into mzIdentML or PRIDE XML." [PSI:PI,
http://www.medizinisches-proteom-center.de/procon]
is_a: MS:1002333 ! conversion software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002335
name: PRIDE Converter2
def: "Java software designed to convert one of several proteomics
identification results formats into PRIDE XML." [PMID:22949509]
is_a: MS:1002333 ! conversion software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002336
name: Amanda
def: "Amanda scoring system for PSM identification." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002337
name: Andromeda
def: "Andromeda is a peptide search engine." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002338
name: Andromeda:score
def: "The probability based score of the Andromeda search engine." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1002339
name: site:global FDR
def: "Estimation of global false discovery rate of peptides with a
posttranslational modification." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001405 ! spectrum identification result details

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

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

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.52.0_rc3 of psi-ms.obo

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

May I suggest some enhancements?



[Term]

id: MS:1002332

name: lab head

def: "The scientist responsible for personnel, grants, and instrumentation
in a functional laboratory group." [PSI:PI]

is_a: MS:1002033 ! contact role



[Term]

id: MS:1002333

name: conversion software

def: "Computer software primarily designed to convert data represented in
one format to another format, sometimes with minor data alterations in the
process." [PSI:PI]

is_a: MS:1001457 ! data processing software



[Term]

id: MS:1002334

name: ProCon

def: "Java software designed to convert one of several proteomics
identification results formats into mzIdentML or PRIDE XML." [PSI:PI,
http://www.medizinisches-proteom-center.de/procon]

is_a: MS:1002333 ! conversion software



[Term]

id: MS:1002335

name: PRIDE Converter2

def: " Java software designed to convert one of several proteomics
identification results formats into PRIDE XML." [PMID:22949509]

is_a: MS:1002333 ! conversion software











-----Original Message-----
From: Gerhard Mayer [mailto:Ger...@ru...]
Sent: Sunday, August 18, 2013 11:47 PM
To: psi...@li...;
psi...@li...; Mass spectrometry standard development
Subject: [Psidev-ms-vocab] Release candidate 3.52.0_rc3 of psi-ms.obo



Dear proteomics community,



attached there's the release candidate 3.52.0_rc3 of the psi-ms.obo file.



It contains scores and some new ProteomeDiscoverer 1.4 input parameters.

e.g. for MS Amanda.

In addition it defines some terms for converter software.





Changed CV terms in version 3.52.0_rc3 of psi-ms.obo:

=====================================================

************ Added boolean data type

[Term]

id: MS:1001194

name: quality estimation with decoy database

def: "Quality estimation by decoy database." [PSI:PI]

xref: value-type:xsd\:boolean "The allowed value-type for this CV term."

is_a: MS:1001060 ! quality estimation method details





New CV terms in version 3.52.0_rc3 of psi-ms.obo:

=================================================

[Term]

id: MS:1002316

name: ProteomeDiscoverer:Amanda:high confidence threshold

def: "Strict confidence probability score." [PSI:PI]

xref: value-type:xsd\:int "The allowed value-type for this CV term."

is_a: MS:1002101 ! ProteomeDiscoverer input parameter



[Term]

id: MS:1002317

name: ProteomeDiscoverer:Amanda:middle confidence threshold

def: "Relaxed confidence probability score." [PSI:PI]

xref: value-type:xsd\:int "The allowed value-type for this CV term."

is_a: MS:1002101 ! ProteomeDiscoverer input parameter



[Term]

id: MS:1002318

name: ProteomeDiscoverer:automatic workload

def: "Flag indicating automatic estimation of the workload level." [PSI:PI]

xref: value-type:xsd\:boolean "The allowed value-type for this CV term."

is_a: MS:1002101 ! ProteomeDiscoverer input parameter



[Term]

id: MS:1002319

name: Amanda:AmandaScore

def: "The Amanda score of the scoring function for a PSM." [PSI:PI]

xref: value-type:xsd\:double "The allowed value-type for this CV term."

is_a: MS:1001143 ! search engine specific score for PSMs

is_a: MS:1001153 ! search engine specific score



[Term]

id: MS:1002320

name: ProteomeDiscoverer:max differential modifications

def: "Maximum dynamic modifications per PSM." [PSI:PI]

xref: value-type:xsd\:int "The allowed value-type for this CV term."

is_a: MS:1002101 ! ProteomeDiscoverer input parameter



[Term]

id: MS:1002321

name: ProteomeDiscoverer:max equal modifications

def: "Maximum equal modifications per PSM." [PSI:PI]

xref: value-type:xsd\:int "The allowed value-type for this CV term."

is_a: MS:1002101 ! ProteomeDiscoverer input parameter



[Term]

id: MS:1002322

name: ProteomeDiscoverer:min peptide length

def: "Minimum peptide length." [PSI:PI]

xref: value-type:xsd\:int "The allowed value-type for this CV term."

is_a: MS:1002101 ! ProteomeDiscoverer input parameter



[Term]

id: MS:1002323

name: ProteomeDiscoverer:max peptide length

def: "Maximum peptide length." [PSI:PI]

xref: value-type:xsd\:int "The allowed value-type for this CV term."

is_a: MS:1002101 ! ProteomeDiscoverer input parameter



[Term]

id: MS:1002324

name: ProteomeDiscoverer:max number neutral loss

def: "Maximum number of same neutral losses." [PSI:PI]

xref: value-type:xsd\:int "The allowed value-type for this CV term."

is_a: MS:1002101 ! ProteomeDiscoverer input parameter



[Term]

id: MS:1002325

name: ProteomeDiscoverer:max number neutral loss modifications

def: "Max number of same neutral losses of modifications." [PSI:PI]

xref: value-type:xsd\:int "The allowed value-type for this CV term."

is_a: MS:1002101 ! ProteomeDiscoverer input parameter



[Term]

id: MS:1002326

name: ProteomeDiscoverer:use flanking ions

def: "Flag for usage of flanking ions." [PSI:PI]

xref: value-type:xsd\:boolean "The allowed value-type for this CV term."

is_a: MS:1002101 ! ProteomeDiscoverer input parameter



[Term]

id: MS:1002327

name: ProteomeDiscoverer:max number of same modifs

def: "The maximum number of possible equal modifications per PSM." [PSI:PI]

xref: value-type:xsd\:int "The allowed value-type for this CV term."

is_a: MS:1002101 ! ProteomeDiscoverer input parameter



[Term]

id: MS:1002328

name: ProteomeDiscoverer:perform deisotoping

def: "Defines whether a simple deisotoping shall be performed." [PSI:PI]

xref: value-type:xsd\:boolean "The allowed value-type for this CV term."

is_a: MS:1002101 ! ProteomeDiscoverer input parameter



[Term]

id: MS:1002329

name: ProteomeDiscoverer:ion settings

def: "Specifies the fragment ions and neutral losses that are

calculated." [PSI:PI]

xref: value-type:xsd\:string "The allowed value-type for this CV term."

is_a: MS:1002101 ! ProteomeDiscoverer input parameter



[Term]

id: MS:1002330

name: ProteomeDiscoverer:3. Static Modification

def: "Determine 3rd static (fixed) post-translational modifications

(PTMs)." [PSI:PI]

xref: value-type:xsd\:string "The allowed value-type for this CV term."

is_a: MS:1002101 ! ProteomeDiscoverer input parameter



[Term]

id: MS:1002331

name: ProteomeDiscoverer:5. Dynamic Modification

def: "Determine 5th dynamic (variable) post-translational modifications

(PTMs)." [PSI:PI]

xref: value-type:xsd\:string "The allowed value-type for this CV term."

is_a: MS:1002101 ! ProteomeDiscoverer input parameter



[Term]

id: MS:1002332

name: lab head

def: "The laboratory head responsible for a submitted dataset." [PSI:PI]

is_a: MS:1002037 ! dataset submitter



[Term]

id: MS:1002333

name: converter software

def: "The used conversion software." [PSI:PI]

is_a: MS:1001457 ! data processing software



[Term]

id: MS:1002334

name: ProCon

def: "Proteomics Conversion tool." [PSI:PI,

http://www.medizinisches-proteom-center.de/procon]

is_a: MS:1002333 ! converter software



[Term]

id: MS:1002335

name: PRIDE Converter2

def: "Proteomics Conversion tool." [PMID:22949509]

is_a: MS:1002333 ! converter software



Best Regards,

Gerhard



-- 

---

Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer

Bioinformatik / Biostatistik

Medizinisches-Proteom-Center (MPC)

Ruhr-Universität Bochum

Zentrum für klinische Forschung I (ZKF I)

E.049a

Universitätsstraße 150

D-44801 Bochum



Phone: +49(0)234/32-21006

Fax:        +49(0)234/32-14554

Email:    Ger...@ru...

Web:     http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Release candidate 3.52.0_rc3 of psi-ms.obo

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

Dear proteomics community,

attached there's the release candidate 3.52.0_rc3 of the psi-ms.obo file.

It contains scores and some new ProteomeDiscoverer 1.4 input parameters.
e.g. for MS Amanda.
In addition it defines some terms for converter software.


Changed CV terms in version 3.52.0_rc3 of psi-ms.obo:
=====================================================
************ Added boolean data type
[Term]
id: MS:1001194
name: quality estimation with decoy database
def: "Quality estimation by decoy database." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001060 ! quality estimation method details


New CV terms in version 3.52.0_rc3 of psi-ms.obo:
=================================================
[Term]
id: MS:1002316
name: ProteomeDiscoverer:Amanda:high confidence threshold
def: "Strict confidence probability score." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002317
name: ProteomeDiscoverer:Amanda:middle confidence threshold
def: "Relaxed confidence probability score." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002318
name: ProteomeDiscoverer:automatic workload
def: "Flag indicating automatic estimation of the workload level." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002319
name: Amanda:AmandaScore
def: "The Amanda score of the scoring function for a PSM." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1002320
name: ProteomeDiscoverer:max differential modifications
def: "Maximum dynamic modifications per PSM." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002321
name: ProteomeDiscoverer:max equal modifications
def: "Maximum equal modifications per PSM." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002322
name: ProteomeDiscoverer:min peptide length
def: "Minimum peptide length." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002323
name: ProteomeDiscoverer:max peptide length
def: "Maximum peptide length." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002324
name: ProteomeDiscoverer:max number neutral loss
def: "Maximum number of same neutral losses." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002325
name: ProteomeDiscoverer:max number neutral loss modifications
def: "Max number of same neutral losses of modifications." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002326
name: ProteomeDiscoverer:use flanking ions
def: "Flag for usage of flanking ions." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002327
name: ProteomeDiscoverer:max number of same modifs
def: "The maximum number of possible equal modifications per PSM." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002328
name: ProteomeDiscoverer:perform deisotoping
def: "Defines whether a simple deisotoping shall be performed." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002329
name: ProteomeDiscoverer:ion settings
def: "Specifies the fragment ions and neutral losses that are
calculated." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002330
name: ProteomeDiscoverer:3. Static Modification
def: "Determine 3rd static (fixed) post-translational modifications
(PTMs)." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002331
name: ProteomeDiscoverer:5. Dynamic Modification
def: "Determine 5th dynamic (variable) post-translational modifications
(PTMs)." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002332
name: lab head
def: "The laboratory head responsible for a submitted dataset." [PSI:PI]
is_a: MS:1002037 ! dataset submitter

[Term]
id: MS:1002333
name: converter software
def: "The used conversion software." [PSI:PI]
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002334
name: ProCon
def: "Proteomics Conversion tool." [PSI:PI,
http://www.medizinisches-proteom-center.de/procon]
is_a: MS:1002333 ! converter software

[Term]
id: MS:1002335
name: PRIDE Converter2
def: "Proteomics Conversion tool." [PMID:22949509]
is_a: MS:1002333 ! converter software

Best Regards,
Gerhard

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

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

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.52.0_rc2 of psi-ms.obo

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

Hi Gerhard, many thanks for continuing to handle these new terms. They
look okay, although I see several cases where the word 'peptide' is used
where 'PSM' is almost surely meant, which doesn't set a good example for
precision in this area. Also, of course, I would think that reusing the
generic p-value and E-value would be preferable over inventing
Amanda-specific ones.

Cheers,
Eric


-----Original Message-----
From: Gerhard Mayer [mailto:Ger...@ru...]
Sent: Wednesday, July 31, 2013 11:59 PM
To: psi...@li...;
psi...@li...; Mass spectrometry standard
development
Subject: [Psidev-ms-vocab] Release candidate 3.52.0_rc2 of psi-ms.obo

Dear proteomics community,

attached there's the release candidate 3.52.0_rc2 of the psi-ms.obo file.

It contains scores and some new ProteomeDiscoverer 1.4 input parameters.
e.g. for MS Amanada.


Changed CV terms in version 3.52.0_rc2 of psi-ms.obo:
=====================================================
************ Added boolean data type
[Term]
id: MS:1001194
name: quality estimation with decoy database
def: "Quality estimation by decoy database." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001060 ! quality estimation method details


New CV terms in version 3.52.0_rc2 of psi-ms.obo:
=================================================
[Term]
id: MS:1002316
name: ProteomeDiscoverer:Amanda:high confidence threshold
def: "Strict confidence probability score." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002317
name: ProteomeDiscoverer:Amanda:middle confidence threshold
def: "Relaxed confidence probability score." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002318
name: ProteomeDiscoverer:automatic workload
def: "Flag indicating automatic estimation of the workload level."
[PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002319
name: Amanda:AmandaScore
def: "The Amanda score of the scoring function for an identified peptide."
[PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1002320
name: Amanda:evalue
def: "Amanda E-value (the expectValue that a peptide was identified by
chance)." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001872 ! E-value for peptides

[Term]
id: MS:1002321
name: Amanda:pvalue
def: "Amanda p-value (the probability that a peptide was identified by
chance)." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001870 ! p-value for peptides

[Term]
id: MS:1002322
name: ProteomeDiscoverer:max differential modifications
def: "Maximum dynamic modifications per peptide." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002323
name: ProteomeDiscoverer:max equal modifications
def: "Maximum equal modifications per peptide." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002324
name: ProteomeDiscoverer:min peptide length
def: "Minimum peptide length." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002325
name: ProteomeDiscoverer:max peptide length
def: "Maximum peptide length." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002326
name: ProteomeDiscoverer:max number neutral loss
def: "Maximum number of same neutral losses." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002327
name: ProteomeDiscoverer:max number neutral loss modifications
def: "Max number of same neutral losses of modifications." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002328
name: ProteomeDiscoverer:use flanking ions
def: "Flag for usage of flanking ions." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002329
name: ProteomeDiscoverer:max number of same modifs
def: "The maximum number of possible equal modifications per peptide."
[PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002330
name: ProteomeDiscoverer:perform deisotoping
def: "Defines whether a simple deisotoping shall be performed." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002331
name: ProteomeDiscoverer:ion settings
def: "Specifies the fragment ions and neutral losses that are calculated."
[PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002332
name: ProteomeDiscoverer:3. Static Modification
def: "Determine 3rd static (fixed) post-translational modifications
(PTMs)." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002333
name: ProteomeDiscoverer:5. Dynamic Modification
def: "Determine 5th dynamic (variable) post-translational modifications
(PTMs)." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

Best Regards,
Gerhard

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

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

[Psidev-ms-dev] Release candidate 3.52.0_rc2 of psi-ms.obo

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

Dear proteomics community,

attached there's the release candidate 3.52.0_rc2 of the psi-ms.obo file.

It contains scores and some new ProteomeDiscoverer 1.4 input parameters.
e.g. for MS Amanada.


Changed CV terms in version 3.52.0_rc2 of psi-ms.obo:
=====================================================
************ Added boolean data type
[Term]
id: MS:1001194
name: quality estimation with decoy database
def: "Quality estimation by decoy database." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001060 ! quality estimation method details


New CV terms in version 3.52.0_rc2 of psi-ms.obo:
=================================================
[Term]
id: MS:1002316
name: ProteomeDiscoverer:Amanda:high confidence threshold
def: "Strict confidence probability score." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002317
name: ProteomeDiscoverer:Amanda:middle confidence threshold
def: "Relaxed confidence probability score." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002318
name: ProteomeDiscoverer:automatic workload
def: "Flag indicating automatic estimation of the workload level." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002319
name: Amanda:AmandaScore
def: "The Amanda score of the scoring function for an identified
peptide." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1002320
name: Amanda:evalue
def: "Amanda E-value (the expectValue that a peptide was identified by
chance)." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001872 ! E-value for peptides

[Term]
id: MS:1002321
name: Amanda:pvalue
def: "Amanda p-value (the probability that a peptide was identified by
chance)." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001870 ! p-value for peptides

[Term]
id: MS:1002322
name: ProteomeDiscoverer:max differential modifications
def: "Maximum dynamic modifications per peptide." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002323
name: ProteomeDiscoverer:max equal modifications
def: "Maximum equal modifications per peptide." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002324
name: ProteomeDiscoverer:min peptide length
def: "Minimum peptide length." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002325
name: ProteomeDiscoverer:max peptide length
def: "Maximum peptide length." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002326
name: ProteomeDiscoverer:max number neutral loss
def: "Maximum number of same neutral losses." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002327
name: ProteomeDiscoverer:max number neutral loss modifications
def: "Max number of same neutral losses of modifications." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002328
name: ProteomeDiscoverer:use flanking ions
def: "Flag for usage of flanking ions." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002329
name: ProteomeDiscoverer:max number of same modifs
def: "The maximum number of possible equal modifications per peptide."
[PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002330
name: ProteomeDiscoverer:perform deisotoping
def: "Defines whether a simple deisotoping shall be performed." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002331
name: ProteomeDiscoverer:ion settings
def: "Specifies the fragment ions and neutral losses that are
calculated." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002332
name: ProteomeDiscoverer:3. Static Modification
def: "Determine 3rd static (fixed) post-translational modifications
(PTMs)." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002333
name: ProteomeDiscoverer:5. Dynamic Modification
def: "Determine 5th dynamic (variable) post-translational modifications
(PTMs)." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

Best Regards,
Gerhard

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

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