psidev-ms-dev — Mass spectroscopy standard development

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.84.0_rc2 of psi-ms.obo

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

Thanks Gerhard!


Sent from Samsung Mobile


-------- Original message --------
From: mayerg97
Date:01/04/2016 14:35 (GMT+00:00)
To: psi...@li...,psi...@li...,psi...@li...
Subject: [Psidev-ms-vocab] Release candidate 3.84.0_rc2 of psi-ms.obo

Dear proteomics community,


here's the release candidate 3.84.0_rc2 of the psi-ms.obo file.
It contains mainly new terms for proteogenomics searches.


New CV terms in version 3.84.0_rc2 of psi-ms.obo:
=================================================
************
[Term]
id: MS:1002631
name: Electron-Transfer/Higher-Energy Collision Dissociation (EThcD)
def: "A dissociation process combining electron-transfer and higher-energy collision dissociation (EThcD). It combines ETD (reaction time) followed by HCD (activation energy)." [PSI:PI]
synonym: "EThcD" EXACT []
is_a: MS:1000044 ! dissociation method

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

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

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

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

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

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

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

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

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

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

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

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

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


Changed CV terms in version 3.84.0_rc2 of psi-ms.obo:
=====================================================
************ added is_a: MS:1002489 ! special processing
[Term]
id: MS:1001031
name: spectral library search
def: "A search using a library of spectra." [PSI:PI]
is_a: MS:1001080 ! search type
is_a: MS:1002489 ! special processing

Best Regards,
Gerhard
--
--
Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER
PhD student
Medizinisches Proteom-Center
DEPARTMENT Medical Bioinformatics
Building ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum
Fon +49 (0)234 32-21006 | Fax +49 (0)234 32-14554
E-mail <mailto:ger...@ru...> ger...@ru...<mailto:ger...@ru...>
<http://www.medizinisches-proteom-center.de/>www.medizinisches-proteom-center.de<http://www.medizinisches-proteom-center.de>
[cid:par...@ru...]

[Psidev-ms-dev] Release candidate 3.84.0_rc2 of psi-ms.obo

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

Dear proteomics community,


here's the release candidate 3.84.0_rc2 of the psi-ms.obo file.
It contains mainly new terms for proteogenomics searches.


New CV terms in version 3.84.0_rc2 of psi-ms.obo:
=================================================
************
[Term]
id: MS:1002631
name: Electron-Transfer/Higher-Energy Collision Dissociation (EThcD)
def: "A dissociation process combining electron-transfer and 
higher-energy collision dissociation (EThcD). It combines ETD (reaction 
time) followed by HCD (activation energy)." [PSI:PI]
synonym: "EThcD" EXACT []
is_a: MS:1000044 ! dissociation method

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

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

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

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

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

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

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

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

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

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

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

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

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


Changed CV terms in version 3.84.0_rc2 of psi-ms.obo:
=====================================================
************ added is_a: MS:1002489 ! special processing
[Term]
id: MS:1001031
name: spectral library search
def: "A search using a library of spectra." [PSI:PI]
is_a: MS:1001080 ! search type
is_a: MS:1002489 ! special processing

Best Regards,
Gerhard
-- 

*--*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

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

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

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

Hi Andy, I fired up the schema generation script and refreshed everything
based on what’s in github now. You can see the current result here:



http://www.peptideatlas.org/PSI/schemas/mzIdentML/1.2/mzIdentML1.2.0.html



The schema seems pretty fine, but the example files have some issues. Here
are a few observations of things to fix:

- Examples files still have older CV URLS like:

<cv id="PSI-MS" uri="
http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"
version="3.73.0" fullName="PSI-MS"/>

<cv id="UO" uri="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"
fullName="UNIT-ONTOLOGY"/>

    <cv id="PRIDE"
uri="http://code.google.com/p/ebi-pride/source/browse/trunk/pride-core/schema/pride_cv.obo"
fullName="PRIDE"/>



I ran a few of the files through my validator and have the following things:

PeptideShaker_mzid_1_2_example.mzid

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

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

ERROR: cvParam Phospho has a value, but it should not!

ERROR: cvParam Oxidation has a value, but it should not!

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

ERROR: cvParam Carbamidomethyl has a value, but it should not!



combined_fdr_1.2.mzid

WARNING: MS:1001400 should be 'OMSSA xml format' instead of 'OMSSA xml file'

WARNING: MS:1001062 should be 'Mascot MGF format' instead of 'Mascot MGF
file'

ERROR: cvParam distinct peptide-level q-value should have units, but it
does not!



xiFDR-CrossLinkExample.mzid

WARNING: MS:1002543 should be 'xiFDR' instead of 'XiFDR'

ERROR: cvParam contact address should have a value, but it does not!

ERROR: cvParam contact name should have a value, but it does not!

ERROR: cvParam unknown modification should have a value, but it does not!



This is not exhaustive, but just some results from a first foray into this.



If someone is interested in fixing these things and checking them it, I can
push further and report other problems.



Regards,

Eric







*From:* Jones, Andy [mailto:And...@li...]
*Sent:* Tuesday, March 29, 2016 8:10 AM
*To:* psi...@li...
*Cc:* psi...@li...
*Subject:* Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev]
Proteogenomics update in mzid 1.2



Hi all,

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

Agenda:

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

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

3.       Any other business



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

Thanks

Andy







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



Fine for me too

Pierre-Alain



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



That works fine for me!



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



Hi all,

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

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

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

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

Does this work for everyone?

Best wishes

Andy







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



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

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

An hour earlier would be fine for the 24th.

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

Thanks,

Eric



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



Hi all,

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

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

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

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

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

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

Best wishes

Andy

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

[Mathias W. <wa...@in...>]

Hi all,

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

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

mzid ppxl issues: we will need many more CV entries. E.g. the types of cross-link. Be it a mono-link, loop-link or cross-link.
And there are only mono-link definitions in unimod (and only for DSS), so I guess we need more reagents used for crosslinking in one of the ontologies that define the pairs, 
Also, to my understanding, isotope labeling is often used as a measure of reassurance of the identified cross-links. I suppose that kind of detected pairing information would go in the SpectrumIdentificationResult?
And there seems to be ambiguous definition available on the pairing of the different SpectrumIdentificationItem elements in one SpectrumIdentificationResult as linked peptides. It is the value of cv term 'cross-link spectrum identification item', isn't it - so we can use rank for sorting?

best,
 Mathias

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





Dial-in details, call in 15 mins: 



Numbers: 

+ UK: 0808 109 5644 

+ US: 877-420-0272 

+ Belgium: 0800 509 80 

+ Germany: 0800 101 2079 

+ Switzerland: 0800 000 860 

+ Generic international: +44 (0) 20 8322 2500 (UK number) 



Access code: 297427 # 





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



Hi all, 

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

Agenda: 

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

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

3. Any other business 



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

Thanks 

Andy 









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



Fine for me too 

Pierre-Alain 





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



That works fine for me! 





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



Hi all, 

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

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

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

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

Does this work for everyone? 

Best wishes 

Andy 









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



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

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

An hour earlier would be fine for the 24 th . 

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

Thanks, 

Eric 





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



Hi all, 

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

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

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

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

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

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

Best wishes 

Andy 






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[Psidev-ms-dev] Request for new CV Term for MSDK

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

Hi everyone,
on behalf of the MSDK development team, I would like to request a new CV
term for the MSDK software development kit.

Our proposal is as follows, with the number still pending:

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

Best regards,
Nils

P.S.: Sorry for the accidental empty post yesterday.

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

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

Dial-in details, call in 15 mins:

Numbers:
+ UK: 0808 109 5644
+ US: 877-420-0272
+ Belgium: 0800 509 80
+ Germany: 0800 101 2079
+ Switzerland: 0800 000 860
+ Generic international: +44 (0) 20 8322 2500 (UK number)
Access code: 297427 #

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

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

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

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

3.       Any other business

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



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

Fine for me too
Pierre-Alain

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

That works fine for me!

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

Hi all,
I think the 24th is out for various people as an Easter-related holiday in some countries. Eric is correct, that time zones will be changing.
On the 31st, my preferred slot is actually 4pm British summer time:
http://www.timeanddate.com/worldclock/fixedtime.html?msg=mzid+1.2+call&iso=20160331T16&p1=301
This would be 8am in Seattle; 5pm Germany;  5pm Norway; (and 4pm in the independent nation state of the EBI)
Does this work for everyone?
Best wishes
Andy



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

Thanks, Andy, I like this idea. The times are not good for me, however. Normally 4pm London time is 8am Seattle time, but for these few weeks, 4pm London time is 9am Seattle time and I have a standing meeting I cannot change.
http://www.timeanddate.com/worldclock/fixedtime.html?iso=20160324T16&p1=1440
An hour earlier would be fine for the 24th.
I hope I’m not getting confused between 4pm GMT and London local time? I think on the 24th 16:00 GMT = 4pm local London, but on the 31st, 16:00 GMT is 5pm London time?
Thanks,
Eric

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

Hi all,
Over the coming weeks, I will be trying to get mzid 1.2 largely tied up for a final review in Ghent, before we submit the spec doc and associated manuscript. I have cross-posted this message (since PSI-PI has not been active lately), but probably will drop PSI-MS from the list in future. If you’re interested in mzid 1.2, please make sure to follow the PSI-PI list.
One feature I would like to add into mzid 1.2 is better support for proteogenomics approaches.  There are some parallel efforts to adapt genome formats BED and BAM for proteomics (and updates will be presented in Ghent I think). It would be nice if the info needed for proBed and proBAM was consistently expressed in mzid 1.2 files (mainly genome coordinates for peptides).
Along with Juan et al., we have come up with a proposal for how this might be done in mzid 1.2. Please see attached. Feel free to annotate any comments on the document, or email back to the list any parts you feel need adapting or comments for discussion.
It might be useful to have one or two conference calls on mzid 1.2 before Ghent. How would following dates suit:

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

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

Re: [Psidev-ms-dev] Release candidate 3.84.0_rc1 of psi-ms.obo

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

----- Nachricht beantworten -----
Von: "mayerg97" <ger...@ru...>
An: <psi...@li...>, <psi...@li...>, <psi...@li...>
Betreff: [Psidev-ms-dev] Release candidate 3.84.0_rc1 of psi-ms.obo
Datum: Mi., März 30, 2016 16:56

[Psidev-ms-dev] Release candidate 3.84.0_rc1 of psi-ms.obo

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

Dear proteomics community,

here's the release candidate 3.84.0_rc1 of the psi-ms.obo file.

New CV terms in version 3.84.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002631
name: Electron-Transfer/Higher-Energy Collision Dissociation (EThcD)
def: "A dissociation process combining electron-transfer and 
higher-energy collision dissociation (EThcD). It combines ETD (reaction 
time) followed by HCD (activation energy)." [PSI:PI]
synonym: "EThcD" EXACT []
is_a: MS:1000044 ! dissociation method

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

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

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


Best Regards,
Gerhard
-- 

*--*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

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

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

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

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

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

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

3.       Any other business

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



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

Fine for me too
Pierre-Alain

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

That works fine for me!

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

Hi all,
I think the 24th is out for various people as an Easter-related holiday in some countries. Eric is correct, that time zones will be changing.
On the 31st, my preferred slot is actually 4pm British summer time:
http://www.timeanddate.com/worldclock/fixedtime.html?msg=mzid+1.2+call&iso=20160331T16&p1=301
This would be 8am in Seattle; 5pm Germany;  5pm Norway; (and 4pm in the independent nation state of the EBI)
Does this work for everyone?
Best wishes
Andy



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

Thanks, Andy, I like this idea. The times are not good for me, however. Normally 4pm London time is 8am Seattle time, but for these few weeks, 4pm London time is 9am Seattle time and I have a standing meeting I cannot change.
http://www.timeanddate.com/worldclock/fixedtime.html?iso=20160324T16&p1=1440
An hour earlier would be fine for the 24th.
I hope I’m not getting confused between 4pm GMT and London local time? I think on the 24th 16:00 GMT = 4pm local London, but on the 31st, 16:00 GMT is 5pm London time?
Thanks,
Eric

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

Hi all,
Over the coming weeks, I will be trying to get mzid 1.2 largely tied up for a final review in Ghent, before we submit the spec doc and associated manuscript. I have cross-posted this message (since PSI-PI has not been active lately), but probably will drop PSI-MS from the list in future. If you’re interested in mzid 1.2, please make sure to follow the PSI-PI list.
One feature I would like to add into mzid 1.2 is better support for proteogenomics approaches.  There are some parallel efforts to adapt genome formats BED and BAM for proteomics (and updates will be presented in Ghent I think). It would be nice if the info needed for proBed and proBAM was consistently expressed in mzid 1.2 files (mainly genome coordinates for peptides).
Along with Juan et al., we have come up with a proposal for how this might be done in mzid 1.2. Please see attached. Feel free to annotate any comments on the document, or email back to the list any parts you feel need adapting or comments for discussion.
It might be useful to have one or two conference calls on mzid 1.2 before Ghent. How would following dates suit:

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

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

Re: [Psidev-ms-dev] Registration is open for PSI workshop April 18-20

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

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



I look forward to seeing you in Ghent!



Regards,

Eric





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



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



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



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



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



Please let me know if you have any questions.



I look forward to seeing you in Ghent!



Regards,

Eric

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

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

Hi Gerben,

Thanks for the input. In terms of novel event peptides, it would be nice to include these as optional CV terms for mzid 1.2 (or 1.1 for that matter).

I will take the proBAM 0.8 list as a starting point, and once we are happy with the list, get them added to the PSI-MS CV.
Best wishes
Andy

From: Gerben Menschaert [mailto:ger...@gm...]
Sent: 23 March 2016 14:00
To: Jones, Andy <jo...@li...>
Cc: psi...@li...; psi...@li...; psi...@li...
Subject: Re: [Psidev-pi-dev] Proteogenomics update in mzid 1.2

Hi Andy,

I won’t be able to join the 31st of March.
I looked into the CV term descriptions and these seem good to me.
I can provide you with a list of “novel event” peptides if necessary, or you can take the list from the proBAM format document.

All the best,
Gerben


On 21 Mar 2016, at 12:21, Jones, Andy <And...@li...<mailto:And...@li...>> wrote:

Hi all,
Over the coming weeks, I will be trying to get mzid 1.2 largely tied up for a final review in Ghent, before we submit the spec doc and associated manuscript. I have cross-posted this message (since PSI-PI has not been active lately), but probably will drop PSI-MS from the list in future. If you’re interested in mzid 1.2, please make sure to follow the PSI-PI list.
One feature I would like to add into mzid 1.2 is better support for proteogenomics approaches.  There are some parallel efforts to adapt genome formats BED and BAM for proteomics (and updates will be presented in Ghent I think). It would be nice if the info needed for proBed and proBAM was consistently expressed in mzid 1.2 files (mainly genome coordinates for peptides).
Along with Juan et al., we have come up with a proposal for how this might be done in mzid 1.2. Please see attached. Feel free to annotate any comments on the document, or email back to the list any parts you feel need adapting or comments for discussion.
It might be useful to have one or two conference calls on mzid 1.2 before Ghent. How would following dates suit:

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

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



<Proteogenomics_CV_terms.docx>------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785351&iu=/4140_______________________________________________
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Psi...@li...<mailto:Psi...@li...>
https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev

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

[Gerben M. <ger...@gm...>]

Hi Andy,

I won’t be able to join the 31st of March.
I looked into the CV term descriptions and these seem good to me.
I can provide you with a list of “novel event” peptides if necessary, or you can take the list from the proBAM format document. 

All the best,
Gerben



> On 21 Mar 2016, at 12:21, Jones, Andy <And...@li...> wrote:
> 
> Hi all,
> 
> Over the coming weeks, I will be trying to get mzid 1.2 largely tied up for a final review in Ghent, before we submit the spec doc and associated manuscript. I have cross-posted this message (since PSI-PI has not been active lately), but probably will drop PSI-MS from the list in future. If you’re interested in mzid 1.2, please make sure to follow the PSI-PI list.
> 
> One feature I would like to add into mzid 1.2 is better support for proteogenomics approaches.  There are some parallel efforts to adapt genome formats BED and BAM for proteomics (and updates will be presented in Ghent I think). It would be nice if the info needed for proBed and proBAM was consistently expressed in mzid 1.2 files (mainly genome coordinates for peptides).
> 
> Along with Juan et al., we have come up with a proposal for how this might be done in mzid 1.2. Please see attached. Feel free to annotate any comments on the document, or email back to the list any parts you feel need adapting or comments for discussion. 
> 
> It might be useful to have one or two conference calls on mzid 1.2 before Ghent. How would following dates suit:
> 
> -          This Thurs (24th March) at 4pm GMT
> 
> -          Next Thurs (31st March) at 4pm GMT
> 
> Best wishes
> 
> Andy 
> 
>  
> 
>  
> 
>  
> 
> <Proteogenomics_CV_terms.docx>------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785351&iu=/4140_______________________________________________ <http://pubads.g.doubleclick.net/gampad/clk?id=278785351&iu=/4140_______________________________________________>
> Psidev-pi-dev mailing list
> Psi...@li... <mailto:Psi...@li...>
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev <https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev>

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

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

Hi Eric,

The implementation of the BED format in that nice manuscript is done without "paying much attention" to the format itself (it is not their main focus), and considering only some of the possible use cases that one might encounter.

Cheers,

Juanan



> On 23 Mar 2016, at 03:03, Eric Deutsch <ede...@sy...> wrote:
> 
> Hi Mathias, the proBAM specification is undergoing some revisions beyond
> what was published. We have one more set of action items to apply to the
> spec and then we will be sending it around for inspection and comment. Soon
> and before the workshop I hope.
> 
> So that is the only published thing so far, but Xiaojing Wang and others are
> working within the PSI to enhance it.
> 
> But that reminds me that I recently saw this paper from David Fenyö and
> colleagues come out. I confess I haven't read it yet, but this may have some
> significant impact on the developing proBED format:
> http://pubs.acs.org/doi/abs/10.1021/acs.jproteome.5b00870
> http://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.5b00870
> 
> Regards,
> Eric
> 
> 
> -----Original Message-----
> From: Mathias Walzer [mailto:wa...@in...]
> Sent: Tuesday, March 22, 2016 6:57 AM
> To: Mass spectrometry standard development
> <psi...@li...>
> Subject: Re: [Psidev-ms-dev] Proteogenomics update in mzid 1.2
> 
> Hi all,
> 
> just a quick thought on the proteogenomics part, see attachment.
> 
> Is http://www.mcponline.org/content/15/3/1164.full#sec-1 the only source for
> an official definition of proBAM?
> 
> Best,
> Mathias
> 
> ----- Original Message -----
> From: "Andy Jones" <And...@li...>
> To: psi...@li...,
> psi...@li..., psi...@li...
> Sent: Monday, 21 March, 2016 12:21:29 PM
> Subject: [Psidev-ms-dev] Proteogenomics update in mzid 1.2
> 
> 
> 
> 
> 
> Hi all,
> 
> Over the coming weeks, I will be trying to get mzid 1.2 largely tied up for
> a final review in Ghent, before we submit the spec doc and associated
> manuscript. I have cross-posted this message (since PSI-PI has not been
> active lately), but probably will drop PSI-MS from the list in future. If
> you’re interested in mzid 1.2, please make sure to follow the PSI-PI list.
> 
> One feature I would like to add into mzid 1.2 is better support for
> proteogenomics approaches. There are some parallel efforts to adapt genome
> formats BED and BAM for proteomics (and updates will be presented in Ghent I
> think). It would be nice if the info needed for proBed and proBAM was
> consistently expressed in mzid 1.2 files (mainly genome coordinates for
> peptides).
> 
> Along with Juan et al., we have come up with a proposal for how this might
> be done in mzid 1.2. Please see attached. Feel free to annotate any comments
> on the document, or email back to the list any parts you feel need adapting
> or comments for discussion.
> 
> It might be useful to have one or two conference calls on mzid 1.2 before
> Ghent. How would following dates suit:
> 
> - This Thurs (24 th March) at 4pm GMT
> 
> - Next Thurs (31 st March) at 4pm GMT
> 
> Best wishes
> 
> Andy
> 
> 
> 
> 
> 
> 
> ------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with Intel Data Analytics
> Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785351&iu=/4140
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> 
> ------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785351&iu=/4140
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

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

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

Hi Mathias, the proBAM specification is undergoing some revisions beyond
what was published. We have one more set of action items to apply to the
spec and then we will be sending it around for inspection and comment. Soon
and before the workshop I hope.

So that is the only published thing so far, but Xiaojing Wang and others are
working within the PSI to enhance it.

But that reminds me that I recently saw this paper from David Fenyö and
colleagues come out. I confess I haven't read it yet, but this may have some
significant impact on the developing proBED format:
http://pubs.acs.org/doi/abs/10.1021/acs.jproteome.5b00870
http://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.5b00870

Regards,
Eric


-----Original Message-----
From: Mathias Walzer [mailto:wa...@in...]
Sent: Tuesday, March 22, 2016 6:57 AM
To: Mass spectrometry standard development
<psi...@li...>
Subject: Re: [Psidev-ms-dev] Proteogenomics update in mzid 1.2

Hi all,

just a quick thought on the proteogenomics part, see attachment.

Is http://www.mcponline.org/content/15/3/1164.full#sec-1 the only source for
an official definition of proBAM?

Best,
 Mathias

----- Original Message -----
From: "Andy Jones" <And...@li...>
To: psi...@li...,
psi...@li..., psi...@li...
Sent: Monday, 21 March, 2016 12:21:29 PM
Subject: [Psidev-ms-dev] Proteogenomics update in mzid 1.2





Hi all,

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

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

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

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

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

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

Best wishes

Andy






------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with Intel Data Analytics
Acceleration Library.
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Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

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

[Mathias W. <wa...@in...>]

Hi all,

just a quick thought on the proteogenomics part, see attachment.

Is http://www.mcponline.org/content/15/3/1164.full#sec-1 the only source for an official definition of proBAM?

Best,
 Mathias

----- Original Message -----
From: "Andy Jones" <And...@li...>
To: psi...@li..., psi...@li..., psi...@li...
Sent: Monday, 21 March, 2016 12:21:29 PM
Subject: [Psidev-ms-dev] Proteogenomics update in mzid 1.2





Hi all, 

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

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

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

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

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

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

Best wishes 

Andy 






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

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

That works fine for me!



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



Hi all,

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

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

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

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

Does this work for everyone?

Best wishes

Andy







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



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

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

An hour earlier would be fine for the 24th.

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

Thanks,

Eric



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



Hi all,

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

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

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

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

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

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

Best wishes

Andy

[Psidev-ms-dev] New version 3.83.0 of psi-ms.obo

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

Dear proteomics community,


here's the latest version 3.83.0 of the psi-ms.obo file.
It contains new terms for PRIDE XML, mzTab and labelling reagents, see

https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo


New CV terms in version 3.83.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002600
name: PRIDE XML
def: "Internal data and submission format of the PRIDE database." 
[http://ftp.pride.ebi.ac.uk/pride/resources/schema/pride/pride.xsd]
is_a: MS:1002130 ! identification file format

[Term]
id: MS:1002601
name: mzTab
def: "Tabular result format for proteomics and metabolomics 
experiments." [PMID:24980485, http://www.psidev.info/mztab/]
is_a: MS:1000914 ! tab delimited text format

[Term]
id: MS:1002602
name: quantification reagent
def: "Reagent used in labeled quantification methods." [PSI:PI]
is_a: MS:1002111 ! assay label attribute
is_a: MS:1000548 ! sample attribute

[Term]
id: MS:1002603
name: ICAT reagent
def: "Isotope coded affinity tag reagent." [PSI:PI]
is_a: MS:1002602 ! quantification reagent

[Term]
id: MS:1002604
name: ICAT heavy reagent
def: "The name of the sample labelled with the heavy ICAT label." [PSI:PI]
is_a: MS:1002603 ! ICAT reagent

[Term]
id: MS:1002605
name: ICAT light reagent
def: "The name of the sample labelled with the light ICAT label." [PSI:PI]
is_a: MS:1002603 ! ICAT reagent

[Term]
id: MS:1002606
name: ICPL reagent
def: "Isotope coded protein labeling reagent." [PSI:PI]
is_a: MS:1002602 ! quantification reagent

[Term]
id: MS:1002607
name: ICPL reagent 0
def: "The name of the sample labelled with the ICPL reagent 0." [PSI:PI]
is_a: MS:1002606 ! ICPL reagent

[Term]
id: MS:1002608
name: ICPL reagent 4
def: "The name of the sample labelled with the ICPL reagent 4." [PSI:PI]
is_a: MS:1002606 ! ICPL reagent

[Term]
id: MS:1002609
name: ICPL reagent 6
def: "The name of the sample labelled with the ICPL reagent 6." [PSI:PI]
is_a: MS:1002606 ! ICPL reagent

[Term]
id: MS:1002610
name: ICPL reagent 10
def: "The name of the sample labelled with the ICPL reagent 10." [PSI:PI]
is_a: MS:1002606 ! ICPL reagent

[Term]
id: MS:1002611
name: SILAC reagent
def: "Stable isotope labeling with amino acids in cell culture reagent." 
[PSI:PI]
is_a: MS:1002602 ! quantification reagent

[Term]
id: MS:1002612
name: SILAC heavy reagent
def: "The name of the sample labelled with the heavy SILAC label." [PSI:PI]
is_a: MS:1002611 ! SILAC reagent

[Term]
id: MS:1002613
name: SILAC medium reagent
def: "The name of the sample labelled with the medium SILAC label." [PSI:PI]
is_a: MS:1002611 ! SILAC reagent

[Term]
id: MS:1002614
name: SILAC light reagent
def: "The name of the sample labelled with the light SILAC label." [PSI:PI]
is_a: MS:1002611 ! SILAC reagent

[Term]
id: MS:1002615
name: TMT reagent
def: "Tandem mass tag reagent." [PSI:PI]
is_a: MS:1002602 ! quantification reagent

[Term]
id: MS:1002616
name: TMT reagent 126
def: "The name of the sample labelled with the TMT reagent 126." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002617
name: TMT reagent 127
def: "The name of the sample labelled with the TMT reagent 127." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002618
name: TMT reagent 128
def: "The name of the sample labelled with the TMT reagent 128." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002619
name: TMT reagent 129
def: "The name of the sample labelled with the TMT reagent 129." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002620
name: TMT reagent 130
def: "The name of the sample labelled with the TMT reagent 130." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002621
name: TMT reagent 131
def: "The name of the sample labelled with the TMT reagent 131." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002622
name: iTRAQ reagent
def: "Isobaric tag for relative and absolute quantitation reagent." [PSI:PI]
is_a: MS:1002602 ! quantification reagent

[Term]
id: MS:1002623
name: iTRAQ reagent 113
def: "The name of the sample labelled with the iTRAQ reagent 113." [PSI:PI]
is_a: MS:1002622 ! iTRAQ reagent

[Term]
id: MS:1002624
name: iTRAQ reagent 114
def: "The name of the sample labelled with the iTRAQ reagent 114." [PSI:PI]
is_a: MS:1002622 ! iTRAQ reagent

[Term]
id: MS:1002625
name: iTRAQ reagent 115
def: "The name of the sample labelled with the iTRAQ reagent 115." [PSI:PI]
is_a: MS:1002622 ! iTRAQ reagent

[Term]
id: MS:1002626
name: iTRAQ reagent 116
def: "The name of the sample labelled with the iTRAQ reagent 116." [PSI:PI]
is_a: MS:1002622 ! iTRAQ reagent

[Term]
id: MS:1002627
name: iTRAQ reagent 117
def: "The name of the sample labelled with the iTRAQ reagent 117." [PSI:PI]
is_a: MS:1002622 ! iTRAQ reagent

[Term]
id: MS:1002628
name: iTRAQ reagent 118
def: "The name of the sample labelled with the iTRAQ reagent 118." [PSI:PI]
is_a: MS:1002622 ! iTRAQ reagent

[Term]
id: MS:1002629
name: iTRAQ reagent 119
def: "The name of the sample labelled with the iTRAQ reagent 119." [PSI:PI]
is_a: MS:1002622 ! iTRAQ reagent

[Term]
id: MS:1002630
name: iTRAQ reagent 121
def: "The name of the sample labelled with the iTRAQ reagent 121." [PSI:PI]
is_a: MS:1002622 ! iTRAQ reagent


Changed CV terms in version 3.83.0 of psi-ms.obo:
=================================================
************ Renamed MS:1001984 from 'Ascore' to 'Ascore software' to 
avoid name clash with term
************ id: MS:1001985 (name: Ascore)
[Term]
id: MS:1001984
name: Ascore software
def: "Ascore software." [PSI:MS]
is_a: MS:1001456 ! analysis software


Best Regards,
Gerhard

-- 

*--*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

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

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

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

Hi all,
I think the 24th is out for various people as an Easter-related holiday in some countries. Eric is correct, that time zones will be changing.
On the 31st, my preferred slot is actually 4pm British summer time:
http://www.timeanddate.com/worldclock/fixedtime.html?msg=mzid+1.2+call&iso=20160331T16&p1=301
This would be 8am in Seattle; 5pm Germany;  5pm Norway; (and 4pm in the independent nation state of the EBI)
Does this work for everyone?
Best wishes
Andy



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

Thanks, Andy, I like this idea. The times are not good for me, however. Normally 4pm London time is 8am Seattle time, but for these few weeks, 4pm London time is 9am Seattle time and I have a standing meeting I cannot change.
http://www.timeanddate.com/worldclock/fixedtime.html?iso=20160324T16&p1=1440
An hour earlier would be fine for the 24th.
I hope I’m not getting confused between 4pm GMT and London local time? I think on the 24th 16:00 GMT = 4pm local London, but on the 31st, 16:00 GMT is 5pm London time?
Thanks,
Eric

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

Hi all,
Over the coming weeks, I will be trying to get mzid 1.2 largely tied up for a final review in Ghent, before we submit the spec doc and associated manuscript. I have cross-posted this message (since PSI-PI has not been active lately), but probably will drop PSI-MS from the list in future. If you’re interested in mzid 1.2, please make sure to follow the PSI-PI list.
One feature I would like to add into mzid 1.2 is better support for proteogenomics approaches.  There are some parallel efforts to adapt genome formats BED and BAM for proteomics (and updates will be presented in Ghent I think). It would be nice if the info needed for proBed and proBAM was consistently expressed in mzid 1.2 files (mainly genome coordinates for peptides).
Along with Juan et al., we have come up with a proposal for how this might be done in mzid 1.2. Please see attached. Feel free to annotate any comments on the document, or email back to the list any parts you feel need adapting or comments for discussion.
It might be useful to have one or two conference calls on mzid 1.2 before Ghent. How would following dates suit:

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

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

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

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

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

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

An hour earlier would be fine for the 24th.

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

Thanks,

Eric



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



Hi all,

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

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

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

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

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

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

Best wishes

Andy

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

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

Hi all,
Over the coming weeks, I will be trying to get mzid 1.2 largely tied up for a final review in Ghent, before we submit the spec doc and associated manuscript. I have cross-posted this message (since PSI-PI has not been active lately), but probably will drop PSI-MS from the list in future. If you’re interested in mzid 1.2, please make sure to follow the PSI-PI list.
One feature I would like to add into mzid 1.2 is better support for proteogenomics approaches.  There are some parallel efforts to adapt genome formats BED and BAM for proteomics (and updates will be presented in Ghent I think). It would be nice if the info needed for proBed and proBAM was consistently expressed in mzid 1.2 files (mainly genome coordinates for peptides).
Along with Juan et al., we have come up with a proposal for how this might be done in mzid 1.2. Please see attached. Feel free to annotate any comments on the document, or email back to the list any parts you feel need adapting or comments for discussion.
It might be useful to have one or two conference calls on mzid 1.2 before Ghent. How would following dates suit:

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

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

[Psidev-ms-dev] Release candidate 3.83.0_rc2 of psi-ms.obo

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

Dear proteomics community,

attached you find the release candidate 3.83.0_rc2 of the psi-ms.obo file.
It contains new terms for PRIDE XML, mzTab and labelling reagents.


New CV terms in version 3.83.0_rc2 of psi-ms.obo:
=================================================
[Term]
id: MS:1002600
name: PRIDE XML
def: "Internal data and submission format of the PRIDE database." 
[http://ftp.pride.ebi.ac.uk/pride/resources/schema/pride/pride.xsd]
is_a: MS:1002130 ! identification file format

[Term]
id: MS:1002601
name: mzTab
def: "Tabular result format for proteomics and metabolomics 
experiments." [PMID:24980485, http://www.psidev.info/mztab/]
is_a: MS:1000914 ! tab delimited text format

[Term]
id: MS:1002602
name: quantification reagent
def: "Reagent used in labeled quantification methods." [PSI:PI]
is_a: MS:1002111 ! assay label attribute
is_a: MS:1000548 ! sample attribute

[Term]
id: MS:1002603
name: ICAT reagent
def: "Isotope coded affinity tag reagent." [PSI:PI]
is_a: MS:1002602 ! quantification reagent

[Term]
id: MS:1002604
name: ICAT heavy reagent
def: "The name of the sample labelled with the heavy ICAT label." [PSI:PI]
is_a: MS:1002603 ! ICAT reagent

[Term]
id: MS:1002605
name: ICAT light reagent
def: "The name of the sample labelled with the light ICAT label." [PSI:PI]
is_a: MS:1002603 ! ICAT reagent

[Term]
id: MS:1002606
name: ICPL reagent
def: "Isotope coded protein labeling reagent." [PSI:PI]
is_a: MS:1002602 ! quantification reagent

[Term]
id: MS:1002607
name: ICPL reagent 0
def: "The name of the sample labelled with the ICPL reagent 0." [PSI:PI]
is_a: MS:1002606 ! ICPL reagent

[Term]
id: MS:1002608
name: ICPL reagent 4
def: "The name of the sample labelled with the ICPL reagent 4." [PSI:PI]
is_a: MS:1002606 ! ICPL reagent

[Term]
id: MS:1002609
name: ICPL reagent 6
def: "The name of the sample labelled with the ICPL reagent 6." [PSI:PI]
is_a: MS:1002606 ! ICPL reagent

[Term]
id: MS:1002610
name: ICPL reagent 10
def: "The name of the sample labelled with the ICPL reagent 10." [PSI:PI]
is_a: MS:1002606 ! ICPL reagent

[Term]
id: MS:1002611
name: SILAC reagent
def: "Stable isotope labeling with amino acids in cell culture reagent." 
[PSI:PI]
is_a: MS:1002602 ! quantification reagent

[Term]
id: MS:1002612
name: SILAC heavy reagent
def: "The name of the sample labelled with the heavy SILAC label." [PSI:PI]
is_a: MS:1002611 ! SILAC reagent

[Term]
id: MS:1002613
name: SILAC medium reagent
def: "The name of the sample labelled with the medium SILAC label." [PSI:PI]
is_a: MS:1002611 ! SILAC reagent

[Term]
id: MS:1002614
name: SILAC light reagent
def: "The name of the sample labelled with the light SILAC label." [PSI:PI]
is_a: MS:1002611 ! SILAC reagent

[Term]
id: MS:1002615
name: TMT reagent
def: "Tandem mass tag reagent." [PSI:PI]
is_a: MS:1002602 ! quantification reagent

[Term]
id: MS:1002616
name: TMT reagent 126
def: "The name of the sample labelled with the TMT reagent 126." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002617
name: TMT reagent 127
def: "The name of the sample labelled with the TMT reagent 127." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002618
name: TMT reagent 128
def: "The name of the sample labelled with the TMT reagent 128." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002619
name: TMT reagent 129
def: "The name of the sample labelled with the TMT reagent 129." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002620
name: TMT reagent 130
def: "The name of the sample labelled with the TMT reagent 130." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002621
name: TMT reagent 131
def: "The name of the sample labelled with the TMT reagent 131." [PSI:PI]
is_a: MS:1002615 ! TMT reagent

[Term]
id: MS:1002622
name: iTRAQ reagent
def: "Isobaric tag for relative and absolute quantitation reagent." [PSI:PI]
is_a: MS:1002602 ! quantification reagent

[Term]
id: MS:1002623
name: iTRAQ reagent 113
def: "The name of the sample labelled with the iTRAQ reagent 113." [PSI:PI]
is_a: MS:1002622 ! iTRAQ reagent

[Term]
id: MS:1002624
name: iTRAQ reagent 114
def: "The name of the sample labelled with the iTRAQ reagent 114." [PSI:PI]
is_a: MS:1002622 ! iTRAQ reagent

[Term]
id: MS:1002625
name: iTRAQ reagent 115
def: "The name of the sample labelled with the iTRAQ reagent 115." [PSI:PI]
is_a: MS:1002622 ! iTRAQ reagent

[Term]
id: MS:1002626
name: iTRAQ reagent 116
def: "The name of the sample labelled with the iTRAQ reagent 116." [PSI:PI]
is_a: MS:1002622 ! iTRAQ reagent

[Term]
id: MS:1002627
name: iTRAQ reagent 117
def: "The name of the sample labelled with the iTRAQ reagent 117." [PSI:PI]
is_a: MS:1002622 ! iTRAQ reagent

[Term]
id: MS:1002628
name: iTRAQ reagent 118
def: "The name of the sample labelled with the iTRAQ reagent 118." [PSI:PI]
is_a: MS:1002622 ! iTRAQ reagent

[Term]
id: MS:1002629
name: iTRAQ reagent 119
def: "The name of the sample labelled with the iTRAQ reagent 119." [PSI:PI]
is_a: MS:1002622 ! iTRAQ reagent

[Term]
id: MS:1002630
name: iTRAQ reagent 121
def: "The name of the sample labelled with the iTRAQ reagent 121." [PSI:PI]
is_a: MS:1002622 ! iTRAQ reagent


Changed CV terms in version 3.83.0_rc2 of psi-ms.obo:
=====================================================
************ Renamed MS:1001984 from 'Ascore' to 'Ascore software' to 
avoid name clash with term
************ id: MS:1001985 (name: Ascore)
[Term]
id: MS:1001984
name: Ascore software
def: "Ascore software." [PSI:MS]
is_a: MS:1001456 ! analysis software

Best Regards,
Gerhard
-- 

*--*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

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

[Psidev-ms-dev] Release candidate 3.83.0_rc1 od psi-ms.obo

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

Dear proteomics community,

attached you find the release candidate 3.83.0_rc1 of the psi-ms.obo file.

New CV terms in version 3.83.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002600
name: PRIDE XML
def: "Internal data and submission format of the PRIDE database." 
[http://ftp.pride.ebi.ac.uk/pride/resources/schema/pride/pride.xsd]
is_a: MS:1002130 ! identification file format

[Term]
id: MS:1002601
name: mzTab
def: "Tabular result format for proteomics and metabolomics 
experiments." [PMID:24980485, http://www.psidev.info/mztab/]
is_a: MS:1000914 ! tab delimited text format


Changed CV terms in version 3.83.0_rc1 of psi-ms.obo:
=====================================================
************ No changed terms


Best Regards,
Gerhard
-- 

*--*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

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

[Psidev-ms-dev] Registration is open for PSI workshop April 18-20

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

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



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



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



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



Please let me know if you have any questions.



I look forward to seeing you in Ghent!



Regards,

Eric

Re: [Psidev-ms-dev] HDF5-based mass spectrometry formats

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

Hi everyone, we can certainly make room for discussion about this and
other formats at the PSI workshop, yes. I will put it on the schedule.

However, we did discuss a highly similar topic at last year's workshop,
with respect to mzDB. There are now many formats for mass spec data that
are similar in many ways, including the major modern ones: mz5, mzDB, and
imzML plus older or niche ones like mzXML, YAMSF, etc.

After much discussion last year, we arrived at a PSI position on the
matter. However, I don't think we ever formalized this in a written public
way, which we probably should have done, just so it is clear. Here is what
I believe the position is:

In the effort to unify on a single standard format for mass spectrometer
output data, so that all workflows and tools may at least work with one
common format that can then be universally exchanged and archived, the PSI
will only endorse mzML as its official format. The mzML format is
information rich, standardized yet flexible, and transparent; it is not
the most efficient, but efficiency usually leads to other compromises in
readability, repairability, implementation ease, and sustainability. The
PSI will work with developers of other formats to ensure that the mzML
metadata model can be preserved in other formats so that all metadata can
be easily transformed to and from mzML without information loss or
ambiguity.

Therefore, I would highly encourage you to replicate the mzML metadata
model/schema. It is fine if you wish to persist the information in HDF5 in
whatever efficient manner you choose, but retaining the mzML metadata
model will allow for easy lossless transformation between mzML and your
format. This has been done for mz5, mzDB, and imzML, and would be
encouraged for all future versions as well.

Regards,
Eric


-----Original Message-----
From: jeleclai [mailto:jel...@un...]
Sent: Tuesday, January 26, 2016 7:42 AM
To: Mass spectrometry standard development
Subject: Re: [Psidev-ms-dev] HDF5-based mass spectrometry formats

Hi Andy,

I am using the c++ libraries but lately, we tried  HDF5's dotnet
framework with c# successfully to read and write HDF5 files. In case of
Java and Python, I currently have little experience, but as far as I
know most functionalities of HDF5 are supported in these languages, and
some datatypes (such as compound and variable length datatypes), which
were problematic some time ago are now supported by translation to
alternative datatypes. Concerning the Java interface, there are some
functions that are not supported, most of them connected to pointers.
See
(https://www.hdfgroup.org/products/java/JNI/jhi5/jhi5_unsupported_function
s.html)
for a complete list.

So far, we converted Waters HDMS data to our format without storing
empty scans. I will attend the PSI, so it would be great to discuss with
you about it.
Best,

Jenny


Am 26.01.2016 um 15:36 schrieb Jones, Andy:
> Hi Jenny,
>
> When we last evaluated mz5, one of the issues appeared to be lack of
good libraries beyond C++ for HDF5, so I would be interested to see if
Java and Python libraries have improved in the last few years - do you
know if much has changed? My recollection was that the Java methods only
worked by bridging into C++, and did not provide native support for all
reading and writing tasks that would be needed. As such, unless we took on
the job of building true HDF5 support into Java and other languages, it
seemed that other developers would be locked out. In the PSI we need to be
quite conservative about the technologies we build upon, and this was
certainly a concern at that time.
>
> All that said, I think there is still interest in the PSI for exploring
how data representations might evolve in the future. It is ultimately up
to Eric Deutsch who leads the PSI-MS part, but I would be keen to hear
about what you've been doing at the upcoming PSI meeting in Ghent (18-20th
April) if you can come along?
>
> Eric - what do you think, is there room on the agenda for this?
>
> I also have a few projects going with Waters, and I'm far from convinced
that mzML is the right solution for representing their HDMS (ion mobility)
data sets, at least without very specialised compression for all the empty
scans that result. Independently of progress within the PSI, I would be
interested to see what you've been developing.
> best wishes
> Andy
>
>
>
>
>
> ________________________________________
> From: jeleclai [jel...@un...]
> Sent: 26 January 2016 14:14
> To: psi...@li...
> Subject: Re: [Psidev-ms-dev] HDF5-based mass spectrometry formats
>
> Hi,
>
> thanks for your email.
>
> So far, the file format is implemented for ion mobility data but the
> design is applicable to non-IMS data as well. So the support for
> "regular" experiments is planned as well.
>
> We are aware of the mz5 implementation as it is a good example how mass
> spectrometry data can be transferred to a binary format in combination
> with the benefits from the mzML ontology. Nevertheless, it seems that
> mz5, although being available now for quite some time (2012),  it has
> not been extensively used. mz5 is more efficient in terms of file size
> and I/O compared to mzML. But this gain in performance alone didn't seem
> to convince the broad mass spectrometry community to change to a new
> file format.  I can see two reasons for that: First, never change a
> running system. Second, data was not "large enough" to push a change in
> using a different file format. But especially with the addition of ion
> mobility as an extra dimension of separation, data complexity is
> increasing and will continue to increase in the future with evolving
> techniques. Therefore, although it requires  the use of an additional
> library (HDF5) a binary format will become essential when working with
> large data. HDF5 is portable and has C, C++,  Java and python
> interfaces, so it should not be an obstacle.  In addition, it is
> well-established as scientific file format with many different tools
> including tools to inspect the file (HDF5View) and the hdf group offers
> good service ( detailed documentation, free email support, new release
> twice a year...).
>
> Numpress definitely sounds interesting and I will take a look at it. ;-)
>
> Best wishes,
>
> Jenny
>
>
>
> Am 25.01.2016 um 16:43 schrieb Johan Teleman:
>> Hi Jenny,
>>
>> Having access to a binary format could clearly benefit many
applications. Will this format be solely intended for ion mobility
experiments, or do you also aim to target "regular" experiment data?
>>
>> The HDF5 library was utilized once already for a MS data format: mz5
(http://www.mcponline.org/content/11/1/O111.011379.full.pdf+html), maybe
something can be reused from there. Depending on how data will be stored
locally, numerical compression through Numpress might be interesting?
Further I would recommend to walk the extra mile and benchmark the file
format using data-files from different vendors and on different samples.
Your result will vary depending on data density.
>>
>> A last mention is that I've had great experience with Google protobuf
based binary file format, if the HDF5 does not work out for you. Protobuf
does NOT have any support for random access though, so that would require
a custom solution.
>>
>> Just my few cents, good luck with the implementation!
>>
>> /J
>>
>> Johan Teleman
>> Ph.D. student
>> Dept. of Immunotechnology
>> Lund University
>>
>> ________________________________________
>> Från: jeleclai [jel...@un...]
>> Skickat: den 25 januari 2016 13:34
>> Till:psi...@li...
>> Kopia: Navarro, Pedro
>> Ämne: [Psidev-ms-dev] HDF5-based mass spectrometry formats
>>
>> Hi all,
>>
>> I am a Phd student in Stefan Tenzer's lab. We are currently working on
a
>> new format for mass spectrometric data, based on HDF5.
>>
>> We started to develop this format because we struggled with ion
mobility
>> data: random access data to vendor's raw files is, as everyone knows,
>> suboptimal, and especially in the case of including ion mobility, we
>> foresee better ways to organize MS data in order to improve random
access.
>>
>> In this regard, the HDF5 library is of great advantage as it combines a
>> simple and flexible way to structure the data with several efficient
>> methods for I/O access.
>>
>> Additionally, HDF5 library offers a good support for developers. It is
>> already successfully implemented in many other scientific fields like
>> Astronomy, Climatology, Genetics... All of this makes it a good
>> candidate for future developing of standard formats of large data,
which
>> are interrogated in a random access way.
>>
>> We would be very happy to bring this topic to discussion for the next
>> PSI meeting!
>>
>> Best wishes,
>>
>> Jenny
>>
>> --
>>
>> Jennifer Leclaire
>> M.Sc. Angewandte Bioinformatik
>>
>> --------------------------------------------------
>> Institut für Immunologie
>> Universitätsmedizin der
>> Johannes Gutenberg-Universität
>> Langenbeckstr.1
>> 55131 Mainz
>> www.immunologie.uni-mainz.de
>>
>>
>>
--------------------------------------------------------------------------
----
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>
>>
--------------------------------------------------------------------------
----
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> --
>
> Jennifer Leclaire
> M.Sc. Angewandte Bioinformatik
>
> --------------------------------------------------
> Institut für Immunologie
> Universitätsmedizin der
> Johannes Gutenberg-Universität
> Langenbeckstr.1
> 55131 Mainz
> www.immunologie.uni-mainz.de
>
>
>
--------------------------------------------------------------------------
----
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>
>
--------------------------------------------------------------------------
----
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

--

Jennifer Leclaire
M.Sc. Angewandte Bioinformatik

--------------------------------------------------
Institut für Immunologie
Universitätsmedizin der
Johannes Gutenberg-Universität
Langenbeckstr.1
55131 Mainz
www.immunologie.uni-mainz.de


--------------------------------------------------------------------------
----
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Psidev-ms-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] HDF5-based mass spectrometry formats

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

Hi,
I am cc'ing this to the msdk-devel List (Mass Spectrometry Development
Kit for Java: https://msdk.github.io/) since it may be of interest to us
as well.

HDF5 is mostly readable (with some minor limitations) via netcdf-java:

http://www.unidata.ucar.edu/software/thredds/v4.6/netcdf-java/CDM/

I have successfully used that to read MZ5 data into a common data model
in Maltcms.

I could not really find out whether HDF5 files could be written by
netcdf-java, but there is another library which seems to provide more
user friendly access to reading and writing HDF5 directly:

https://wiki-bsse.ethz.ch/display/JHDF5/Documentation+page

If you consider using HDF5 it would make sense to identify the common
subset of the features that are supported by the Java bindings and
libraries before fixing a data format.

Best regards,
Nils

Am 26.01.16 um 16:41 schrieb jeleclai:
> Hi Andy,
> 
> I am using the c++ libraries but lately, we tried  HDF5's dotnet 
> framework with c# successfully to read and write HDF5 files. In case of 
> Java and Python, I currently have little experience, but as far as I 
> know most functionalities of HDF5 are supported in these languages, and 
> some datatypes (such as compound and variable length datatypes), which 
> were problematic some time ago are now supported by translation to 
> alternative datatypes. Concerning the Java interface, there are some 
> functions that are not supported, most of them connected to pointers. 
> See 
> (https://www.hdfgroup.org/products/java/JNI/jhi5/jhi5_unsupported_functions.html) 
> for a complete list.
> 
> So far, we converted Waters HDMS data to our format without storing 
> empty scans. I will attend the PSI, so it would be great to discuss with 
> you about it.
> Best,
> 
> Jenny
> 
> 
> Am 26.01.2016 um 15:36 schrieb Jones, Andy:
>> Hi Jenny,
>>
>> When we last evaluated mz5, one of the issues appeared to be lack of good libraries beyond C++ for HDF5, so I would be interested to see if Java and Python libraries have improved in the last few years - do you know if much has changed? My recollection was that the Java methods only worked by bridging into C++, and did not provide native support for all reading and writing tasks that would be needed. As such, unless we took on the job of building true HDF5 support into Java and other languages, it seemed that other developers would be locked out. In the PSI we need to be quite conservative about the technologies we build upon, and this was certainly a concern at that time.
>>
>> All that said, I think there is still interest in the PSI for exploring how data representations might evolve in the future. It is ultimately up to Eric Deutsch who leads the PSI-MS part, but I would be keen to hear about what you've been doing at the upcoming PSI meeting in Ghent (18-20th April) if you can come along?
>>
>> Eric - what do you think, is there room on the agenda for this?
>>
>> I also have a few projects going with Waters, and I'm far from convinced that mzML is the right solution for representing their HDMS (ion mobility) data sets, at least without very specialised compression for all the empty scans that result. Independently of progress within the PSI, I would be interested to see what you've been developing.
>> best wishes
>> Andy
>>
>>
>>
>>
>>
>> ________________________________________
>> From: jeleclai [jel...@un...]
>> Sent: 26 January 2016 14:14
>> To: psi...@li...
>> Subject: Re: [Psidev-ms-dev] HDF5-based mass spectrometry formats
>>
>> Hi,
>>
>> thanks for your email.
>>
>> So far, the file format is implemented for ion mobility data but the
>> design is applicable to non-IMS data as well. So the support for
>> "regular" experiments is planned as well.
>>
>> We are aware of the mz5 implementation as it is a good example how mass
>> spectrometry data can be transferred to a binary format in combination
>> with the benefits from the mzML ontology. Nevertheless, it seems that
>> mz5, although being available now for quite some time (2012),  it has
>> not been extensively used. mz5 is more efficient in terms of file size
>> and I/O compared to mzML. But this gain in performance alone didn't seem
>> to convince the broad mass spectrometry community to change to a new
>> file format.  I can see two reasons for that: First, never change a
>> running system. Second, data was not "large enough" to push a change in
>> using a different file format. But especially with the addition of ion
>> mobility as an extra dimension of separation, data complexity is
>> increasing and will continue to increase in the future with evolving
>> techniques. Therefore, although it requires  the use of an additional
>> library (HDF5) a binary format will become essential when working with
>> large data. HDF5 is portable and has C, C++,  Java and python
>> interfaces, so it should not be an obstacle.  In addition, it is
>> well-established as scientific file format with many different tools
>> including tools to inspect the file (HDF5View) and the hdf group offers
>> good service ( detailed documentation, free email support, new release
>> twice a year...).
>>
>> Numpress definitely sounds interesting and I will take a look at it. ;-)
>>
>> Best wishes,
>>
>> Jenny
>>
>>
>>
>> Am 25.01.2016 um 16:43 schrieb Johan Teleman:
>>> Hi Jenny,
>>>
>>> Having access to a binary format could clearly benefit many applications. Will this format be solely intended for ion mobility experiments, or do you also aim to target "regular" experiment data?
>>>
>>> The HDF5 library was utilized once already for a MS data format: mz5 (http://www.mcponline.org/content/11/1/O111.011379.full.pdf+html), maybe something can be reused from there. Depending on how data will be stored locally, numerical compression through Numpress might be interesting? Further I would recommend to walk the extra mile and benchmark the file format using data-files from different vendors and on different samples. Your result will vary depending on data density.
>>>
>>> A last mention is that I've had great experience with Google protobuf based binary file format, if the HDF5 does not work out for you. Protobuf does NOT have any support for random access though, so that would require a custom solution.
>>>
>>> Just my few cents, good luck with the implementation!
>>>
>>> /J
>>>
>>> Johan Teleman
>>> Ph.D. student
>>> Dept. of Immunotechnology
>>> Lund University
>>>
>>> ________________________________________
>>> Från: jeleclai [jel...@un...]
>>> Skickat: den 25 januari 2016 13:34
>>> Till:psi...@li...
>>> Kopia: Navarro, Pedro
>>> Ämne: [Psidev-ms-dev] HDF5-based mass spectrometry formats
>>>
>>> Hi all,
>>>
>>> I am a Phd student in Stefan Tenzer's lab. We are currently working on a
>>> new format for mass spectrometric data, based on HDF5.
>>>
>>> We started to develop this format because we struggled with ion mobility
>>> data: random access data to vendor's raw files is, as everyone knows,
>>> suboptimal, and especially in the case of including ion mobility, we
>>> foresee better ways to organize MS data in order to improve random access.
>>>
>>> In this regard, the HDF5 library is of great advantage as it combines a
>>> simple and flexible way to structure the data with several efficient
>>> methods for I/O access.
>>>
>>> Additionally, HDF5 library offers a good support for developers. It is
>>> already successfully implemented in many other scientific fields like
>>> Astronomy, Climatology, Genetics... All of this makes it a good
>>> candidate for future developing of standard formats of large data, which
>>> are interrogated in a random access way.
>>>
>>> We would be very happy to bring this topic to discussion for the next
>>> PSI meeting!
>>>
>>> Best wishes,
>>>
>>> Jenny
>>>
>>> --
>>>
>>> Jennifer Leclaire
>>> M.Sc. Angewandte Bioinformatik
>>>
>>> --------------------------------------------------
>>> Institut für Immunologie
>>> Universitätsmedizin der
>>> Johannes Gutenberg-Universität
>>> Langenbeckstr.1
>>> 55131 Mainz
>>> www.immunologie.uni-mainz.de
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>> Monitor end-to-end web transactions and take corrective actions now
>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>> _______________________________________________
>>> Psidev-ms-dev mailing list
>>> Psi...@li...
>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>>
>>> ------------------------------------------------------------------------------
>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>> Monitor end-to-end web transactions and take corrective actions now
>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>> _______________________________________________
>>> Psidev-ms-dev mailing list
>>> Psi...@li...
>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>> --
>>
>> Jennifer Leclaire
>> M.Sc. Angewandte Bioinformatik
>>
>> --------------------------------------------------
>> Institut für Immunologie
>> Universitätsmedizin der
>> Johannes Gutenberg-Universität
>> Langenbeckstr.1
>> 55131 Mainz
>> www.immunologie.uni-mainz.de
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>