psidev-ms-dev — Mass spectroscopy standard development

[Psidev-ms-dev] Post-doc position

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

Hi all,

I'm currently looking for a postdoc to work on PSI standards and software: http://www.jobs.ac.uk/job/AGX034/bioinformatics-postdoctoral-research-associate-software-engineer/, please pass on to anyone who may be interested.

Best wishes
Andy

Re: [Psidev-ms-dev] Downstream tools accepting mzQuantML ?

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

Hi Nils and Steffen,

Thanks for your message, really pleased to see this work going on! I’ve copied this across to the PSI-PI list, since the PI group has led the development of mzQuantML. To get mzQuantML fully metabolomics compliant, we need to do three things:


1)      Work up some high-quality example files (as you are doing)

2)      Write some semantic rules for testing what a real file looks like – see examples here: http://code.google.com/p/mzquantml/source/browse/#svn%2Ftrunk%2Fschema

3)      Update the semantic validation software to check for a metabolomics mzQuantML file: http://code.google.com/p/mzquantml-validator/

a.       This is managed by Da Qi in my group

We are currently working on the SRM rules and converters, planning a short technical brief manuscript describing the work. This seems an appropriate route for the metabolomics “module” of mzQuantML as well. I would be happy to arrange a call in a few weeks to pull together interested people and coordinate this work.

To date, there are a few tools that can read mzQuantML files, but these are still under development:

http://www.proteosuite.org/
http://code.google.com/p/jmzquantml/
http://code.google.com/p/mzq-lib/  (contains a converter to CSV and HTML)

This reminds me that we need to build a webpage on the PSI site for tools implementing mzQuantML. Da – do you think you could set this up when you have a few spare minutes?

The plan is also to write a robust mzQuantML to mzTab converter, although mzTab is currently undergoing quite a lot of structural changes, and mzTab should be quite easy to read into stats packages. Also using the jmzquantml API, Java programmers could write their own file format converters or stats wrappers very easily,

Best wishes
Andy




From: Nils Hoffmann [mailto:nil...@ce...]
Sent: 15 July 2013 09:13
To: psi...@li...
Subject: Re: [Psidev-ms-dev] Downstream tools accepting mzQuantML ?

Hi Steffen,

I think the link should read:

https://github.com/sneumann/mtbls2/blob/master/mtbls2.mzq.xml

I will definitely put support for mzQuantML on my todo list.

Yours,
Nils

Am 15.07.2013 10:03, schrieb Steffen Neumann:

Hi,



I am currently writing some examples of (metabolomics) mzQuantML files [1],

and I am looking for consumers for these files:



Are there any (statistics) or other programs or visualisers, or ...

out there, which read mzQuantML and produce some result from it ?



This will also put to test the statement on the mzQ web site:

"...We expect that the format MAY also be able to cover

 ...Small molecule quantification (in metabolomics)",

and I'd love to help get check marked ;-)







Thanks in advance,

Yours,

Steffen



[1] https:/https://github.com/sneumann/mtbls2/blob/master/mtbls2.mzq.xml/github.com/sneumann/mtbls2/blob/master/mtbls2.mzq.xml<https://https:/github.com/sneumann/mtbls2/blob/master/mtbls2.mzq.xml/github.com/sneumann/mtbls2/blob/master/mtbls2.mzq.xml>










--

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

Re: [Psidev-ms-dev] Downstream tools accepting mzQuantML ?

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

Hi Steffen,

I think the link should read:

https://github.com/sneumann/mtbls2/blob/master/mtbls2.mzq.xml

I will definitely put support for mzQuantML on my todo list.

Yours,
Nils

Am 15.07.2013 10:03, schrieb Steffen Neumann:
> Hi,
>
> I am currently writing some examples of (metabolomics) mzQuantML files [1], 
> and I am looking for consumers for these files:
>
> Are there any (statistics) or other programs or visualisers, or ...
> out there, which read mzQuantML and produce some result from it ?
>
> This will also put to test the statement on the mzQ web site:
> "...We expect that the format MAY also be able to cover 
>  ...Small molecule quantification (in metabolomics)",
> and I'd love to help get check marked ;-)
>
>
> Thanks in advance,
> Yours,
> Steffen
>
> [1] https:/https://github.com/sneumann/mtbls2/blob/master/mtbls2.mzq.xml/github.com/sneumann/mtbls2/blob/master/mtbls2.mzq.xml
>
>
>


-- 
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

[Psidev-ms-dev] Downstream tools accepting mzQuantML ?

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

Hi,

I am currently writing some examples of (metabolomics) mzQuantML files [1], 
and I am looking for consumers for these files:

Are there any (statistics) or other programs or visualisers, or ...
out there, which read mzQuantML and produce some result from it ?

This will also put to test the statement on the mzQ web site:
"...We expect that the format MAY also be able to cover 
 ...Small molecule quantification (in metabolomics)",
and I'd love to help get check marked ;-)


Thanks in advance,
Yours,
Steffen

[1] https:/https://github.com/sneumann/mtbls2/blob/master/mtbls2.mzq.xml/github.com/sneumann/mtbls2/blob/master/mtbls2.mzq.xml



-- 
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] New version 3.51.0 of psi-ms.obo

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

Dear proteomics community,

attached there's the new release 3.51.0 of the psi-ms.obo file.

It contains some new terms for MS-Numpress and one new term for use in 
mzIdentML indicating
that a <SpectrumIdentificationList> containes the consensus result from 
several search engine runs.


Changed CV terms in version 3.51.0 of psi-ms.obo:
============================================
************ Inserted space after colon in the name row for:
[Term]
id: MS:1002287
name: PeptideProphet
def: "A program in the TPP that calculates PSM probabilities for MS/MS 
proteomics data searched with any of the supported sequence or spectral 
library search engines via the pepXML format." [PMID:12403597, 
PMID:23176103]
is_a: MS:1002286 ! Trans-Proteomic Pipeline software

[Term]
id: MS:1002291
name: Libra
def: "A program in the TPP that calculates PSM, peptide, and 
protein-level abundances based on N-channel isobaric label peptide data 
such as iTRAQ, TMT, etc." [PSI:PI]
is_a: MS:1002286 ! Trans-Proteomic Pipeline software


New CV terms in version 3.51.0 of psi-ms.obo:
=========================================
[Term]
id: MS:1002312
name: MS-Numpress linear prediction compression
def: "Compression using MS-Numpress linear prediction compression." 
[https://github.com/fickludd/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002313
name: MS-Numpress positive integer compression
def: "Compression using MS-Numpress positive integer compression." 
[https://github.com/fickludd/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002314
name: MS-Numpress short logged float compression
def: "Compression using MS-Numpress short logged float compression." 
[https://github.com/fickludd/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002315
name: consensus result
def: "Indicates a consensus result from several search engine runs." 
[PSI:PI]
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] Release candidate 3.51.0_rc1 of psi-ms.obo

[Johan T. <joh...@im...>]

Hi Gerhard,

Thanks for maintaining this vocabulary. The new terms are fine, but I noticed today that for some reason the PeptideProphet term (MS:1002287) and Libra term (MS:1002291) have no space after the colon in the name row. This messes with Proteowizard CV update scripts. I suggest adjusting this for consistency in these two terms.

Best,
Johan

Johan Teleman
Ph.D. student
Dept. of Immunotechnology
Lund University

________________________________________
Från: Gerhard Mayer [Ger...@ru...]
Skickat: den 20 juni 2013 09:13
Till: psi...@li...; psi...@li...; Mass spectrometry standard development
Ämne: [Psidev-ms-dev] Release candidate 3.51.0_rc1 of psi-ms.obo

Dear proteomics community,

attached there's the release candidate 3.51.0_rc1 of the psi-ms.obo file.

It contains some new terms for MS-Numpress.


Changed CV terms in version 3.51.0_rc1 of psi-ms.obo:
=====================================================
************ No changes


New CV terms in version 3.51.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002312
name: MS-Numpress linear prediction compression
def: "Compression using MS-Numpress linear prediction compression."
[https://github.com/fickludd/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002313
name: MS-Numpress positive integer compression
def: "Compression using MS-Numpress positive integer compression."
[https://github.com/fickludd/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002314
name: MS-Numpress short logged float compression
def: "Compression using MS-Numpress short logged float compression."
[https://github.com/fickludd/ms-numpress]
is_a: MS:1000572 ! binary data compression type

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 3.51.0_rc1 of psi-ms.obo

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

Dear proteomics community,

attached there's the release candidate 3.51.0_rc1 of the psi-ms.obo file.

It contains some new terms for MS-Numpress.


Changed CV terms in version 3.51.0_rc1 of psi-ms.obo:
=====================================================
************ No changes


New CV terms in version 3.51.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002312
name: MS-Numpress linear prediction compression
def: "Compression using MS-Numpress linear prediction compression." 
[https://github.com/fickludd/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002313
name: MS-Numpress positive integer compression
def: "Compression using MS-Numpress positive integer compression." 
[https://github.com/fickludd/ms-numpress]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1002314
name: MS-Numpress short logged float compression
def: "Compression using MS-Numpress short logged float compression." 
[https://github.com/fickludd/ms-numpress]
is_a: MS:1000572 ! binary data compression type

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] Ten minutes guide about requesting new CV terms

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

Hi Gerhard,

Thanks a lot for this.

I have made some minor edits.

Cheers,

Juan Antonio

Re: [Psidev-ms-dev] Ten minutes guide about requesting new CV terms

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

Hi Gerhard, this looks really great, many thanks for putting this
together. I have no further comments.

Regards,
Eric


-----Original Message-----
From: Gerhard Mayer [mailto:Ger...@ru...]
Sent: Friday, June 14, 2013 12:38 AM
To: psi...@li...; Mass spectrometry standard
development
Subject: [Psidev-ms-dev] Ten minutes guide about requesting new CV terms

Hi all,

actually I got some questions on how to use the CV terms and how in
general to proceed if one wants to convert search engine results into
mzIdentML. It seems that a lot of people out there are novices to the
concept of how to semantically annotate the data in our formats.

Therefore I propose to put a small ten minute guide (see attachment) on
the psidev.info CV web site.
If you want you can add other points of which you think they should be
included into this 10 minutes guide or have other proposals or comments,
please send them back to me, so that I can assemble a final version and
put it on the web site.

Best Regards,
Gerhard Mayer

--
---
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] Ten minutes guide about requesting new CV terms

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

Hi all,

actually I got some questions on how to use the CV terms and how in 
general to proceed if one
wants to convert search engine results into mzIdentML. It seems that a 
lot of people out there
are novices to the concept of how to semantically annotate the data in 
our formats.

Therefore I propose to put a small ten minute guide (see attachment) on 
the psidev.info CV web site.
If you want you can add other points of which you think they should be 
included into this 10 minutes guide
or have other proposals or comments, please send them back to me, so 
that I can assemble a final version
and put it on the web site.

Best Regards,
Gerhard Mayer

-- 
---
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 3.50.0 of psi-ms.obo

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

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

[Psidev-ms-dev] Release candidate 3.50.0_rc1 of psi-ms.obo

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

Dear proteomics community,

attached there's the new version 3.50.0_rc1 of the psi-ms.obo file.

It contains the changes concerning the retention time terms (issue 74)
and changes for the waters instrument terms.


Changed CV terms in version 3.50.0_rc1 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 
visable 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_rc1 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

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] mzML validation

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

Hi,
I have created a patched version of the validator with some
simplifications and user experience improvements that runs out of the box.

What would be the best way to contribute the changes?
Should I add may patches to a tracker under

https://sourceforge.net/tracker/?group_id=65472&atid=511100

for review?

Where can the ready to run jar archive be distributed for download?

Regards,
Nils

Am 02.05.2013 10:40, schrieb Jones, Andy:
> Thanks all - can anyone make a build of the Java tool - the source is only present from the link, seems a bit unreasonable to get users to compile it :-)
>
> -----Original Message-----
> From: 'Eric Deutsch' [mailto:Eri...@sy...] 
> Sent: 01 May 2013 19:11
> To: Mass spectrometry standard development
> Cc: Eric Deutsch
> Subject: Re: [Psidev-ms-dev] mzML validation
>
> Hi everyone, there is also a Java version available in SourceForge:
>
> https://psidev.svn.sourceforge.net/svnroot/psidev/psi/mzml/validator/
>
> regards,
> Eric
>
>
>> -----Original Message-----
>> From: Steffen Neumann [mailto:sne...@ip...]
>> Sent: Wednesday, May 01, 2013 9:49 AM
>> To: Mass spectrometry standard development
>> Subject: Re: [Psidev-ms-dev] mzML validation
>>
>> Hi,
>>
>> On Wed, 2013-05-01 at 15:28 +0000, Jones, Andy wrote:
>> ...
>>>  is purely an online validator so will presumably only work for 
>>> small files. I thought there was a downloadable Java app for doing 
>>> mzML validation, but I can’t see any obvious link to it,
>> Almost ;-) It's C++.
>>
>> The "mzML semantic validator created by Marc Sturm (OpenMS/TOPP)"
>> is based on the FileInfo Tool,
>> www-bs2.informatik.uni-tuebingen.de/services/OpenMS-
>> release/html/TOPP_FileInfo.html
>>
>> So download OpenMS and use it's FileInfo.
>>
>> 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
>>
>>
>> ----------------------------------------------------------------------
>> --
>> ------
>> Introducing AppDynamics Lite, a free troubleshooting tool for 
>> Java/.NET Get 100% visibility into your production application - at no cost.
>> Code-level diagnostics for performance bottlenecks with <2% overhead 
>> Download for free and get started troubleshooting in minutes.
>> http://p.sf.net/sfu/appdyn_d2d_ap1
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> ------------------------------------------------------------------------------
> Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost.
> Code-level diagnostics for performance bottlenecks with <2% overhead Download for free and get started troubleshooting in minutes.
> http://p.sf.net/sfu/appdyn_d2d_ap1
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>
> ------------------------------------------------------------------------------
> Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET
> Get 100% visibility into your production application - at no cost.
> Code-level diagnostics for performance bottlenecks with <2% overhead
> Download for free and get started troubleshooting in minutes.
> http://p.sf.net/sfu/appdyn_d2d_ap1
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev


-- 
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

[Psidev-ms-dev] Release candidate 3.49.0_rc1 of psi-ms.obo

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

Dear proteomics community,

attached there's the new version 3.49.0_rc1 of the psi-ms.obo file.

It contains new terms for Bruker instruments and the definition of 
domain ranges
for use in p-value and E-value terms.


Changed CV terms in version 3.49.0_rc1 of psi-ms.obo:
=====================================================
************ Added string value
[Term]
id: MS:1001875
name: modification motif
def: "The regular expression describing the sequence motif for a 
modification." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001056 ! modification specificity rule

************ Made obsolete
[Term]
id: MS:1001874
name: FDRScore
def: "OBSOLETE A smoothing of the distribution of q-values calculated 
for PSMs from individual search engines, such that ordering of result 
quality is maintained and all FDRScore values are guaranteed to have a 
value > 0." [PMID:19253293]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
comment: This term was made obsolete because it was replaced by combined 
FDRScore (MS:1002125).
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score
is_obsolete: true

************ Added relationship has_domain to the following terms
[Term]
id: MS:1001870
name: p-value for peptides
def: "Peptide identification confidence metric p-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001092 ! peptide identification confidence metric
has_domain: MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1001871
name: p-value for proteins
def: "Protein identification confidence metric p-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001198 ! protein identification confidence metric
has_domain: MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1001872
name: E-value for peptides
def: "Peptide identification confidence metric E-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001092 ! peptide identification confidence metric
has_domain: MS:1002306 ! value greater than zero

[Term]
id: MS:1001873
name: E-value for proteins
def: "Protein identification confidence metric E-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001198 ! protein identification confidence metric
has_domain: MS:1002306 ! value greater than zero

[Term]
id: MS:1002072
name: p-value
def: "P-value as result of one of the processing steps described. 
Specify in the description, which processing step it was." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype
has_domain: MS:1002305 ! value between 0 and 1 inclusive

************ Changed is_a from MS:1001805 ! quantification datatype --> 
MS:1002072 ! p-value
[Term]
id: MS:1001854
name: ANOVA p-value
def: "Global datatype: p-value of ANOVA of group means (e.g. 
Progenesis)." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002072 ! value

[Term]
id: MS:1001855
name: t-test p-value
def: "P-value of t-Test of two groups." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002072 ! p-value


New CV terms in version 3.49.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002302
name: Bruker Container file
def: "Bruker Container raw file format." [PSI:MS]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1002303
name: Bruker Container nativeID format
def: "Native identifier (UUID)." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000767 ! native spectrum identifier format

[Typedef]
id: has_domain
name: has_domain

[Term]
id: MS:1002304
name: domain range
def: "Domain range of a numerical value." [PSI:PI]
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass 
Spectrometry Vocabularies

[Term]
id: MS:1002305
name: value between 0 and 1 inclusive
def: "Value range for probabilities." [PSI:PI]
is_a: MS:1002304 ! domain range

[Term]
id: MS:1002306
name: value greater than zero
def: "Positive value range." [PSI:PI]
is_a: MS:1002304 ! domain range

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] mzML validation

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

Thanks all - can anyone make a build of the Java tool - the source is only present from the link, seems a bit unreasonable to get users to compile it :-)

-----Original Message-----
From: 'Eric Deutsch' [mailto:Eri...@sy...] 
Sent: 01 May 2013 19:11
To: Mass spectrometry standard development
Cc: Eric Deutsch
Subject: Re: [Psidev-ms-dev] mzML validation

Hi everyone, there is also a Java version available in SourceForge:

https://psidev.svn.sourceforge.net/svnroot/psidev/psi/mzml/validator/

regards,
Eric


> -----Original Message-----
> From: Steffen Neumann [mailto:sne...@ip...]
> Sent: Wednesday, May 01, 2013 9:49 AM
> To: Mass spectrometry standard development
> Subject: Re: [Psidev-ms-dev] mzML validation
>
> Hi,
>
> On Wed, 2013-05-01 at 15:28 +0000, Jones, Andy wrote:
> ...
> >  is purely an online validator so will presumably only work for 
> > small files. I thought there was a downloadable Java app for doing 
> > mzML validation, but I can’t see any obvious link to it,
>
> Almost ;-) It's C++.
>
> The "mzML semantic validator created by Marc Sturm (OpenMS/TOPP)"
> is based on the FileInfo Tool,
> www-bs2.informatik.uni-tuebingen.de/services/OpenMS-
> release/html/TOPP_FileInfo.html
>
> So download OpenMS and use it's FileInfo.
>
> 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
>
>
> ----------------------------------------------------------------------
> --
> ------
> Introducing AppDynamics Lite, a free troubleshooting tool for 
> Java/.NET Get 100% visibility into your production application - at no cost.
> Code-level diagnostics for performance bottlenecks with <2% overhead 
> Download for free and get started troubleshooting in minutes.
> http://p.sf.net/sfu/appdyn_d2d_ap1
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

------------------------------------------------------------------------------
Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost.
Code-level diagnostics for performance bottlenecks with <2% overhead Download for free and get started troubleshooting in minutes.
http://p.sf.net/sfu/appdyn_d2d_ap1
_______________________________________________
Psidev-ms-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] mzML validation

['Eric Deutsch' <Eri...@sy...>]

Hi everyone, there is also a Java version available in SourceForge:

https://psidev.svn.sourceforge.net/svnroot/psidev/psi/mzml/validator/

regards,
Eric


> -----Original Message-----
> From: Steffen Neumann [mailto:sne...@ip...]
> Sent: Wednesday, May 01, 2013 9:49 AM
> To: Mass spectrometry standard development
> Subject: Re: [Psidev-ms-dev] mzML validation
>
> Hi,
>
> On Wed, 2013-05-01 at 15:28 +0000, Jones, Andy wrote:
> ...
> >  is purely an online validator so will presumably only work for small
> > files. I thought there was a downloadable Java app for doing mzML
> > validation, but I can’t see any obvious link to it,
>
> Almost ;-) It's C++.
>
> The "mzML semantic validator created by Marc Sturm (OpenMS/TOPP)"
> is based on the FileInfo Tool,
> www-bs2.informatik.uni-tuebingen.de/services/OpenMS-
> release/html/TOPP_FileInfo.html
>
> So download OpenMS and use it's FileInfo.
>
> 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
>
>
> ------------------------------------------------------------------------
> ------
> Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET
> Get 100% visibility into your production application - at no cost.
> Code-level diagnostics for performance bottlenecks with <2% overhead
> Download for free and get started troubleshooting in minutes.
> http://p.sf.net/sfu/appdyn_d2d_ap1
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] mzML validation

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

Hi,

On Wed, 2013-05-01 at 15:28 +0000, Jones, Andy wrote:
...
>  is purely an online validator so will presumably only work for small
> files. I thought there was a downloadable Java app for doing mzML
> validation, but I can’t see any obvious link to it,

Almost ;-) It's C++.

The "mzML semantic validator created by Marc Sturm (OpenMS/TOPP)" 
is based on the FileInfo Tool,
www-bs2.informatik.uni-tuebingen.de/services/OpenMS-release/html/TOPP_FileInfo.html

So download OpenMS and use it's FileInfo.

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] mzML validation

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

Hi all,

Can someone tell me what the current status is of validation tools for mzML - the info on http://www.psidev.info/mzml/ points at two links:

 - mzML semantic validator<http://eddie.thep.lu.se/prodac_validator/validator.pl> at ProDaC

 - mzML semantic validator<http://www-bs2.informatik.uni-tuebingen.de/services/OpenMS/mzML/> created by Marc Sturm (OpenMS/TOPP<http://www.openms.de>)
The first link doesn't reach any server - I think this was supposed to be a Java web start app. The second link appears to be okay, but this is purely an online validator so will presumably only work for small files. I thought there was a downloadable Java app for doing mzML validation, but I can't see any obvious link to it,
Best wishes
Andy

[Psidev-ms-dev] Release candidate 3.48.0_rc3 of psi-ms.obo

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

Dear proteomics community,

attached there's the release candidate 3.48.0_rc3 of the psi-ms.obo file.

It contains new terms for LC and GC separation, detector potential, SRM 
quantitation analysis and
some Waters, LECO and Bruker instruments.
Maybe it's a compromise not to use apostrophes for the Bruker Daltonics' 
terms
in the name: tags, but leave them in the def: tags.


Changed CV terms in version 3.48.0_rc3 of psi-ms.obo:
=====================================================
************ Corrected spelling error in definition
[Term]
id: MS:1000873
name: peptide attribute calculation software
def: "Software used to predict or calculate numerical attributes of 
peptides." [PSI:MS]
is_a: MS:1000531 ! software

************ Changed name + def: maXis impact --> impact
************ Changed is_a relationship from MS:1001547 ! Bruker 
Daltonics maXis series --> MS:1001536 ! Bruker Daltonics micrOTOF series
[Term]
id: MS:1002077
name: impact
def: "Bruker Daltonics' impact: ESI Q-TOF, Nanospray, APCI, APPI, 
GC-APCI, CaptiveSpray." [PSI:MS]
is_a: MS:1001536 ! Bruker Daltonics micrOTOF series

************ Updated the definitions for the following two terms.
[Term]
id: MS:1002029
name: original nucleic acid sequence
def: "Specification of the original nucleic acid sequence, prior to a 
modification. The value slot should hold the DNA or RNA sequence." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001471 ! peptide modification details

[Term]
id: MS:1002030
name: modified nucleic acid sequence
def: "Specification of the modified nucleic acid sequence. The value 
slot should hold the DNA or RNA sequence." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001471 ! peptide modification details


New CV terms in version 3.48.0_rc3 of psi-ms.obo:
=================================================
[Term]
id: MS:1002270
name: chromatography separation
def: "A technique by which molecules are separated by chemical and 
physical properties such as hydrophobicity or vapor pressure." [PSI:MS]
is_a: MS:1000857 ! run attribute

[Term]
id: MS:1002271
name: liquid chromatography separation
def: "Liquid chromatography (LC) is a separation technique in which the 
mobile phase is a liquid." [PSI:MS]
is_a: MS:1002270 ! chromatography separation

[Term]
id: MS:1002272
name: gas chromatography separation
def: "Gas chromatography (GC) is a separation technique in which the 
mobile phase is a gas." [PSI:MS]
is_a: MS:1002270 ! chromatography separation

[Term]
id: MS:1002273
name: detector potential
def: "Detector potential difference in volts." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000481 ! detector attribute
relationship: has_units UO:0000218 ! volt

[Term]
id: MS:1002274
name: SQ Detector 2
def: "Waters quadrupole based SQ Detector 2." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1002275
name: Xevo G2-S Tof
def: "Waters oa-ToF based Xevo G2-S Tof." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1002276
name: Xevo G2-S QTof
def: "Waters oa-ToF based Xevo G2-S QTof." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1002277
name: AutoSpec Premier
def: "Waters AutoSpec Premier." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1002278
name: Pegasus III
def: "LECO nominal mass resolution time-of-flight GC mass spectrometer." 
[PSI:MS]
is_a: MS:1001800 ! LECO instrument model

[Term]
id: MS:1002279
name: maXis 4G
def: "Bruker Daltonics' maXis 4G: ESI Q-TOF, Nanospray, APCI, APPI, 
GC-APCI, CaptiveSpray." [PSI:MS]
is_a: MS:1001547 ! Bruker Daltonics maXis series

[Term]
id: MS:1002280
name: compact
def: "Bruker Daltonics' compact: ESI Q-TOF, Nanospray, APCI, APPI, 
GC-APCI, CaptiveSpray." [PSI:MS]
is_a: MS:1001536 ! Bruker Daltonics micrOTOF series

[Term]
id: MS:1002280
name: compact
def: "Bruker Daltonics' compact." [PSI:MS]
is_a: MS:1001536 ! Bruker Daltonics micrOTOF series

[Term]
id: MS:1002281
name: SRM feature level quantitation
def: "Selected Reaction Monitoring feature level quantitation." [PSI:PI]
is_a: MS:1001838 ! SRM quantitation analysis

[Term]
id: MS:1002282
name: SRM peptide level quantitation
def: "Selected Reaction Monitoring peptide level quantitation." [PSI:PI]
is_a: MS:1001838 ! SRM quantitation analysis

[Term]
id: MS:1002283
name: SRM protein level quantitation
def: "Selected Reaction Monitoring protein level quantitation." [PSI:PI]
is_a: MS:1001838 ! SRM quantitation analysis

[Term]
id: MS:1002284
name: SRM proteingroup level quantitation
def: "Selected Reaction Monitoring proteingroup level quantitation." 
[PSI:PI]
is_a: MS:1001838 ! SRM quantitation analysis

[Term]
id: MS:1002285
name: Trans-Proteomic Pipeline
def: "A suite of open source tools for the processing of MS/MS 
proteomics data developed by the Seattle Proteome Center at the 
Institute for Systems Biology." [PSI:PI]
synonym: "TPP" EXACT []
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002286
name: Trans-Proteomic Pipeline software
def: "A software program that is a component of the Trans-Proteomic 
Pipeline." [PSI:PI]
is_a: MS:1001456 ! analysis software
relationship: part_of MS:1002285 ! Trans-Proteomic Pipeline

[Term]
id: MS:1002287
name:PeptideProphet
def: "A program in the TPP that calculates PSM probabilities for MS/MS 
proteomics data searched with any of the supported sequence or spectral 
library search engines via the pepXML format." [PMID:12403597, 
PMID:23176103]
is_a: MS:1002286 ! Trans-Proteomic Pipeline software

[Term]
id: MS:1002288
name: iProphet
def: "A program in the TPP that calculates distinct peptide 
probabilities based on several lines of corroborating evidence including 
search results from multiple search engines via the pepXML format." 
[PMID:21876204]
is_a: MS:1002286 ! Trans-Proteomic Pipeline software

[Term]
id: MS:1002289
name: ProteinProphet
def: "A program in the TPP that calculates protein-level probabilities 
based on input PSM or peptide-level probabilities from PeptideProphet or 
iProphet. The output is written in the protXML format." [PMID:14632076]
is_a: MS:1002286 ! Trans-Proteomic Pipeline software

[Term]
id: MS:1002289
name: ASAPRatio
def: "A program in the TPP that calculates PSM, peptide, and 
protein-level abundances based on 2-channel isotope-labeled data such as 
ICAT, SILAC, etc." [PSI:PI]
is_a: MS:1002286 ! Trans-Proteomic Pipeline software

[Term]
id: MS:1002290
name: XPRESS
def: "A program in the TPP that calculates PSM-level abundances based on 
2-channel isotope-labeled data such as ICAT, SILAC, etc." [PSI:PI]
is_a: MS:1002286 ! Trans-Proteomic Pipeline software

[Term]
id: MS:1002291
name:Libra
def: "A program in the TPP that calculates PSM, peptide, and 
protein-level abundances based on N-channel isobaric label peptide data 
such as iTRAQ, TMT, etc." [PSI:PI]
is_a: MS:1002286 ! Trans-Proteomic Pipeline software

[Term]
id: MS:1002292
name: PTMProphet
def: "A program in the TPP that calculates PTM localization 
probabilities by re-analyzing the peaks that are available to 
distinguish between possible modification sites." [PSI:PI]
is_a: MS:1002286 ! Trans-Proteomic Pipeline software

[Term]
id: MS:1002293
name: Bruker Daltonics SCION series
def: "Bruker Daltonics' SCION series." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1002294
name: Bruker Daltonics EVOQ series
def: "Bruker Daltonics' EVOQ series." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1002295
name: SCION SQ
def: "Bruker Daltonics' SCION SQ: GC-single quadrupole" [PSI:MS]
is_a: MS:1000YYY ! Bruker Daltonics SCION series

[Term]
id: MS:1002296
name: SCION TQ
def: "Bruker Daltonics' SCION TQ: GC-triple quadrupole" [PSI:MS]
is_a: MS:1000YYY ! Bruker Daltonics SCION series

[Term]
id: MS:1002297
name: EVOQ Elite
def: "Bruker Daltonics' EVOQ Elite: LC-triple quadrupole" [PSI:MS]
is_a: MS:1000ZZZ ! Bruker Daltonics EVOQ series

[Term]
id: MS:1002298
name: EVOQ Qube
def: "Bruker Daltonics' EVOQ Qube: LC-triple quadrupole" [PSI:MS]
is_a: MS:1000ZZZ ! Bruker Daltonics EVOQ series

[Term]
id: MS:1002299
name: micrOTOF-Q III
def: "Bruker Daltonics' micrOTOF-Q III: ESI Q-TOF, Nanospray, APCI, 
APPI, GC-APCI, CaptiveSpray." [PSI:MS]
is_a: MS:1001536 ! Bruker Daltonics micrOTOF series

[Term]
id: MS:1002300
name: amaZon Speed ETD
def: "Bruker Daltonics' amaZon Speed ETD: ESI quadrupole ion trap, 
Nanospray, APCI, APPI, ETD, PTR, GC-APCI, CaptiveSpray." [PSI:MS]
is_a: MS:1001545 ! Bruker Daltonics amaZon series

[Term]
id: MS:1002301
name: amaZon Speed
def: "Bruker Daltonics' amaZon ETD: ESI quadrupole ion trap, Nanospray, 
APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS]
is_a: MS:1001545 ! Bruker Daltonics amaZon series

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 3.48.0_rc2 of psi-ms.obo

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

Hi,

I don't object the apostrophe-removal idea,
and can live with both ways.

Yours,
Steffen

On Wed, 2013-04-24 at 07:08 -0700, Eric Deutsch wrote:
> But none of other vendors have apostrophes to denote origin. I would suggest
> that the apostrophes are an unfortunate anomaly for the Brukers that would
> be best removed. I guess we can let Gerhard break the tie.



-- 
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] Release candidate 3.48.0_rc2 of psi-ms.obo

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

But none of other vendors have apostrophes to denote origin. I would suggest
that the apostrophes are an unfortunate anomaly for the Brukers that would
be best removed. I guess we can let Gerhard break the tie.

Cheers,
Eric


> -----Original Message-----
> From: Steffen Neumann [mailto:sne...@ip...]
> Sent: Wednesday, April 24, 2013 6:44 AM
> To: Mass spectrometry standard development
> Cc: psi...@li...; psidev-pi-
> de...@li...; Eric Deutsch
> Subject: Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate
> 3.48.0_rc2 of psi-ms.obo
>
> Hi,
>
> On Wed, 2013-04-24 at 06:12 -0700, 'Eric Deutsch' wrote:
> > The Steffen, looks great, many thanks. I would suggest going without
> the
> > apostrophe on all definitions for consistency.
>
> Hm, which variant is consist is debatable.
> In the existing psi-ms.obo all
>
> 	def: "Bruker Daltonics XXX series." [PSI:MS]
>
> are indeed without apostrophe. That's consistent with
> the two new series I just sent. Good.
>
> But I get all 40 of the actual instruments in psi-ms.obo
> with Apostrophe, and none without:
>
> 	grep "Daltonics'" psi-ms.obo | grep "^def"
> 	...
> 	def: "Bruker Daltonics' HCTultra ETD II: ESI Q-TOF, Nanospray,
> APCI,...
> 	def: "Bruker Daltonics' microflex LT: MALDI TOF." [PSI:MS]
> 	def: "Bruker Daltonics' micrOTOF: ESI TOF, APCI, APPI." [PSI:MS]
> 	...
>
> So it'd be consistent to keep them with apostrophe,
> even though the programmer in me jerks upon unmatched apostrophes :-)
>
> I'd suggest to keep the proposed list as-is.
>
> Yours,
> Steffen
>
>
> --
> IPB Halle                    AG Massenspektrometrie & Bioinformatik
> Dr. Steffen Neumann          http://www.IPB-Halle.DE
> Weinberg 3                   http://msbi.bic-gh.de
> 06120 Halle                  Tel. +49 (0) 345 5582 - 1470
>                                   +49 (0) 345 5582 - 0
> sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.48.0_rc2 of psi-ms.obo

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

Hi,

On Wed, 2013-04-24 at 06:12 -0700, 'Eric Deutsch' wrote:
> The Steffen, looks great, many thanks. I would suggest going without the
> apostrophe on all definitions for consistency.

Hm, which variant is consist is debatable. 
In the existing psi-ms.obo all 

	def: "Bruker Daltonics XXX series." [PSI:MS]

are indeed without apostrophe. That's consistent with 
the two new series I just sent. Good.

But I get all 40 of the actual instruments in psi-ms.obo 
with Apostrophe, and none without:

	grep "Daltonics'" psi-ms.obo | grep "^def" 
	...
	def: "Bruker Daltonics' HCTultra ETD II: ESI Q-TOF, Nanospray, APCI,... 
	def: "Bruker Daltonics' microflex LT: MALDI TOF." [PSI:MS]
	def: "Bruker Daltonics' micrOTOF: ESI TOF, APCI, APPI." [PSI:MS]
	...

So it'd be consistent to keep them with apostrophe, 
even though the programmer in me jerks upon unmatched apostrophes :-)

I'd suggest to keep the proposed list as-is.

Yours,
Steffen


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

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.48.0_rc2 of psi-ms.obo

['Eric Deutsch' <Eri...@sy...>]

The Steffen, looks great, many thanks. I would suggest going without the
apostrophe on all definitions for consistency.

Thanks,
Eric


> -----Original Message-----
> From: Steffen Neumann [mailto:sne...@ip...]
> Sent: Wednesday, April 24, 2013 6:04 AM
> To: Mass spectrometry standard development
> Cc: psi...@li...; psidev-ms-
> vo...@li...
> Subject: Re: [Psidev-ms-vocab] [Psidev-ms-dev] Release candidate
> 3.48.0_rc2 of psi-ms.obo
>
> Hi Gerhard and list,
>
> coincidentally I had another list of Bruker instruments
> which includes their GC-MS and also recent LC-MS instruments.
> The "def:" definitions include the available ion sources in many cases,
> because that's common for other Bruker models in psi-ms.obo .
>
> As discussed off-list, my additions don't need to go into 3.48.0
> if that'd delay the release too much.
>
> Yours,
> Steffen
>
> On Mon, 2013-04-22 at 15:06 +0200, Gerhard Mayer wrote:
> ...
> > Changed CV terms in version 3.48.0_rc2 of psi-ms.obo:
> > =====================================================
> > ************ Changed name + def: maXis impact --> impact
> > ************ Changed is_a relationship from MS:1001547 ! Bruker
> Daltonics maXis series --> MS:1001536 ! Bruker Daltonics micrOTOF
> series
>
> # Two new instrument series:
>
> [Term]
> id: MS:100YYY
> name: Bruker Daltonics SCION series
> def: "Bruker Daltonics SCION series." [PSI:MS]
> is_a: MS:1000122 ! Bruker Daltonics instrument model
>
> [Term]
> id: MS:100ZZZ
> name: Bruker Daltonics EVOQ series
> def: "Bruker Daltonics EVOQ series." [PSI:MS]
> is_a: MS:1000122 ! Bruker Daltonics instrument model
>
> # Two new GC instruments:
>
> [Term]
> id: MS:1000XXX
> name: SCION SQ
> def: "Bruker Daltonics' SCION SQ: GC-single quadrupole" [PSI:MS]
> is_a: MS:1000YYY ! Bruker Daltonics SCION series
>
> [Term]
> id: MS:1000XXX
> name: SCION TQ
> def: "Bruker Daltonics' SCION TQ: GC-triple quadrupole" [PSI:MS]
> is_a: MS:1000YYY ! Bruker Daltonics SCION series
>
> # Two new LC TQ instruments:
>
> [Term]
> id: MS:1000XXX
> name: EVOQ Elite
> def: "Bruker Daltonics' EVOQ Elite: LC-triple quadrupole" [PSI:MS]
> is_a: MS:1000ZZZ ! Bruker Daltonics EVOQ series
>
> [Term]
> id: MS:1000XXX
> name: EVOQ Qube
> def: "Bruker Daltonics' EVOQ Qube: LC-triple quadrupole" [PSI:MS]
> is_a: MS:1000ZZZ ! Bruker Daltonics EVOQ series
>
> # A new variant of the QTOF:
>
> [Term]
> id: MS:1000XXX
> name: micrOTOF-Q III
> def: "Bruker Daltonics' micrOTOF-Q III: ESI Q-TOF, Nanospray, APCI,
> APPI, GC-APCI, CaptiveSpray." [PSI:MS]
> is_a: MS:1001536 ! Bruker Daltonics micrOTOF series
>
> # Two new variants of the ion traps:
>
> [Term]
> id: MS:100XXX
> name: amaZon Speed ETD
> def: "Bruker Daltonics' amaZon Speed ETD: ESI quadrupole ion trap,
> Nanospray, APCI, APPI, ETD, PTR, GC-APCI, CaptiveSpray." [PSI:MS]
> is_a: MS:1001545 ! Bruker Daltonics amaZon series
>
> [Term]
> id: MS:100XXX
> name: amaZon Speed
> def: "Bruker Daltonics' amaZon ETD: ESI quadrupole ion trap, Nanospray,
> APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS]
> is_a: MS:1001545 ! Bruker Daltonics amaZon series
>
> # Already proposed for 3.48.0_rc2, but here with addition of available
> ion sources,
> # as already done for e.g. http://www.ebi.ac.uk/ontology-
> lookup/browse.do?ontName=MS&termId=MS%3A1000178&termName=microTOF%20LC
>
> [Term]
> id: MS:1002279
> name: maXis 4G
> #def: "Bruker Daltonics' maXis 4G." [PSI:MS]
> def: "Bruker Daltonics' maXis 4G: ESI Q-TOF, Nanospray, APCI, APPI, GC-
> APCI, CaptiveSpray." [PSI:MS]
> is_a: MS:1001547 ! Bruker Daltonics maXis series
>
> [Term]
> id: MS:1002280
> name: compact
> def: "Bruker Daltonics' compact: ESI Q-TOF, Nanospray, APCI, APPI, GC-
> APCI, CaptiveSpray." [PSI:MS]
> is_a: MS:1001536 ! Bruker Daltonics micrOTOF series
>
> [Term]
> id: MS:1002077
> name: impact
> def: "Bruker Daltonics' impact: ESI Q-TOF, Nanospray, APCI, APPI, GC-
> APCI, CaptiveSpray." [PSI:MS]
> is_a: MS:1001536 ! Bruker Daltonics micrOTOF series
>
>
>
> --
> 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
>
>
> -----------------------------------------------------------------------
> -------
> Try New Relic Now & We'll Send You this Cool Shirt
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> _______________________________________________
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> Psi...@li...
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Re: [Psidev-ms-dev] Release candidate 3.48.0_rc2 of psi-ms.obo

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

Hi Gerhard and list,

coincidentally I had another list of Bruker instruments
which includes their GC-MS and also recent LC-MS instruments.
The "def:" definitions include the available ion sources in many cases, 
because that's common for other Bruker models in psi-ms.obo .

As discussed off-list, my additions don't need to go into 3.48.0
if that'd delay the release too much.

Yours,
Steffen

On Mon, 2013-04-22 at 15:06 +0200, Gerhard Mayer wrote:
...
> Changed CV terms in version 3.48.0_rc2 of psi-ms.obo:
> =====================================================
> ************ Changed name + def: maXis impact --> impact
> ************ Changed is_a relationship from MS:1001547 ! Bruker Daltonics maXis series --> MS:1001536 ! Bruker Daltonics micrOTOF series

# Two new instrument series:

[Term]
id: MS:100YYY
name: Bruker Daltonics SCION series
def: "Bruker Daltonics SCION series." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:100ZZZ
name: Bruker Daltonics EVOQ series
def: "Bruker Daltonics EVOQ series." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

# Two new GC instruments:

[Term]
id: MS:1000XXX
name: SCION SQ
def: "Bruker Daltonics' SCION SQ: GC-single quadrupole" [PSI:MS]
is_a: MS:1000YYY ! Bruker Daltonics SCION series

[Term]
id: MS:1000XXX
name: SCION TQ
def: "Bruker Daltonics' SCION TQ: GC-triple quadrupole" [PSI:MS]
is_a: MS:1000YYY ! Bruker Daltonics SCION series

# Two new LC TQ instruments:

[Term]
id: MS:1000XXX
name: EVOQ Elite
def: "Bruker Daltonics' EVOQ Elite: LC-triple quadrupole" [PSI:MS]
is_a: MS:1000ZZZ ! Bruker Daltonics EVOQ series

[Term]
id: MS:1000XXX
name: EVOQ Qube
def: "Bruker Daltonics' EVOQ Qube: LC-triple quadrupole" [PSI:MS]
is_a: MS:1000ZZZ ! Bruker Daltonics EVOQ series

# A new variant of the QTOF:

[Term]
id: MS:1000XXX
name: micrOTOF-Q III
def: "Bruker Daltonics' micrOTOF-Q III: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS]
is_a: MS:1001536 ! Bruker Daltonics micrOTOF series

# Two new variants of the ion traps:

[Term]
id: MS:100XXX
name: amaZon Speed ETD
def: "Bruker Daltonics' amaZon Speed ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, ETD, PTR, GC-APCI, CaptiveSpray." [PSI:MS]
is_a: MS:1001545 ! Bruker Daltonics amaZon series

[Term]
id: MS:100XXX
name: amaZon Speed
def: "Bruker Daltonics' amaZon ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS]
is_a: MS:1001545 ! Bruker Daltonics amaZon series

# Already proposed for 3.48.0_rc2, but here with addition of available ion sources,
# as already done for e.g. http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MS&termId=MS%3A1000178&termName=microTOF%20LC

[Term]
id: MS:1002279
name: maXis 4G
#def: "Bruker Daltonics' maXis 4G." [PSI:MS]
def: "Bruker Daltonics' maXis 4G: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS]
is_a: MS:1001547 ! Bruker Daltonics maXis series

[Term]
id: MS:1002280
name: compact
def: "Bruker Daltonics' compact: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS]
is_a: MS:1001536 ! Bruker Daltonics micrOTOF series

[Term]
id: MS:1002077
name: impact
def: "Bruker Daltonics' impact: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS]
is_a: MS:1001536 ! Bruker Daltonics micrOTOF series



-- 
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] Close PSI-GPS list?

[Juan P. A. <jp...@cn...>]

Ok from my part

best wishes
Juan Pablo

El 22/04/2013 12:48, Jones, Andy escribió:
>
> Hi all,
>
> To my knowledge, the PSI GPS list is no longer used for any 
> discussion, but accumulates around 10 junk messages per day. Shall we 
> close the list to new posts?
>
> Best wishes
>
> Andy
>


-- 

/Dr. Juan Pablo Albar/

/ProteoRed//-ISCIII, Coordinator/

/HUPO Council Member/

/Centro Nacional de BiotecnologÌa/CSIC/

/UAM Campus Cantoblanco/

/Darwin, 3/

/Madrid E-28049 Spain/

//

/http://www.proteored.org//

/Telf//(+34) 91585-4696/

/Fax(+34) 91585-4506/

//

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