psidev-ms-dev — Mass spectroscopy standard development

[Psidev-ms-dev] New CV needed

[Seymour, S. (ABSCIEX) <Sea...@ab...>]

Hi all,

I'm not sure if it's been done already but we need a new instrument added to the CV: "TripleTOF 5600" (no space in TripleTOF). The vendor or brand should be listed as "AB SCIEX". Any more info needed than that?

Thanks!

Sean

[Psidev-ms-dev] PSI-MSS WG call notes

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

Present: Richard, Jim, Matt, Eric



1) mzML 1.1.0

- Manuscript has been resubmitted.

- Matt will update the example files to reference mzML 1.1.0 but indexedmzML
1.1.1

- Eric will update the web site announcing the change and update hyperlink

- Eric will update the other files

- Post by Andreas Schoenegger on Jun 9

- Richard will address this by updating the schema

- How do we handle lock mass corrections?

- We should assemble list of calibrants and make them specific terms

- Bruker uses Lithium Formiate; others?

- Jim will find out what Thermo is using

- Jim will talk to someone later today and compile a list of calibrants
commonly used

+ Answer is perhaps that what the Thermo calibration compound is is not well
known

- Matt will contact David Anderson and Mike Ashton and ask about a date in
lieu of checksum

- Need to test FAIMS support in mzML

- According to folks at ISB, addition of “compensation voltage” is all
that’s needed

- Eric will try create a real example

- Have the questions from Steffen on Apr 7 and Apr 8 all been resolved?

- Sometime in the future spend some time on a dozen CV terms per call to
resolve them.

- Other items?

+ Eric should test a recent file with multiple fragmentation types to see if
they are properly labelled



----

2) MIAPE-MS revision

- We have the needed 3 examples to go along with a document submission

- Until we provide the examples, it is not officially in the document
process

- We can use the sample MIAPE-compliant mzML file

+ Pierre-Alain has received an example from Proteo-Red

- Richard will look into PRIDE to see if there may be a good example there

- Pierre-Alain is looking through PRIDE to find a good example.

- The last example would be a MIAPE compliant mzML document

- Keep working on our documents and when we’re ready, see if we should wait

- We also need to coordinate the creation of MIAPE-Quant

- When officially in the process, send out submitted document to journal
editors and everyone else to get the word out

- Pierre-Alain will contact Proteo-Red again about comments

- Hope that MIAPE-MS can be submitted to document process in July

- Might we start a draft of MIAPE-Quant in parallel with the start of
development of mzQuantML?

- MIAPE-Quant will probably have different sections for each major type of
quanitification



----

3) TraML development

- TraML is currently undergoing formal review in the document process

- Version 0.9.4 released and is available at
http://www.psidev.info/index.php?q=node/405

- Implementations? Please update to 0.9.4 and test

  - Matt has implemented in ProteoWizard complete to 0.9.4

  + Matt will sent out a sample file

  - Matt hopes to finish the C# bindings sometime

 + Matt has finished the C# bindings

  - Eric will try validating with his tools

  - ISB implementation in ATAQS nearly done

  - Jim has an implementation but just will need to update to 0.9.4

  + Jim will work to update this soon

  - Eric will also contact Amol to discuss TraML implementations

  - Dave Cox at Sciex will test implement?

  + Dave is  reviewer

  + Need to add two new terms

- Are we ready to update validator page?:
http://www.psidev.info/index.php?q=node/304



----

4) PSI session at World HUPO in Sydney

- PSI will have a session. Presenters will be Juan Pablo, Henning, and Eric

- Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS

+ Scheduled for Thursday after lunch

- Other reports?



----

5) Work on improving CV

- Review action items from last teleconference 2010-07-13

+ Need to update CV based on the discussion and then review

+ Whenever updates are made, it is automatically



Next meeting:

- In 3 weeks? Aug 31?

+ Yes







*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Tuesday, August 10, 2010 1:17 AM
*To:* Mass spectrometry standard development
*Cc:* Eric Deutsch
*Subject:* PSI-MSS WG call reminder



Hi everyone, the next PSI Mass Spectrometry Standards Working Group call
will be Tuesday 8am PDT:



08:00 San Francisco

11:00 New York

16:00 London

17:00 Geneva



+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ USA: 1-866-314-3683

Generic international: +44 2083222500 (UK number)



access code: 297427 #





Agenda:

1) mzML 1.1.0

- Manuscript has been resubmitted.

- Matt will update the example files to reference mzML 1.1.0 but indexedmzML
1.1.1

- New schema is posted on the web. The tiny file has been updated.

- Eric will update the web site announcing the change and update hyperlink

- Eric will update the other files

- Post by Andreas Schoenegger on Jun 9

- Richard will address this by updating the schema

- How do we handle lock mass corrections?

- We should assemble list of calibrants and make them specific terms

- Bruker uses Lithium Formiate; others?

- Jim will find out what Thermo is using

- Jim will talk to someone later today and compile a list of calibrants
commonly used

- Matt will contact David Anderson and Mike Ashton and ask about a date in
lieu of checksum

- Need to test FAIMS support in mzML

- According to folks at ISB, addition of “compensation voltage” is all
that’s needed

- Eric will try create a real example

- Have the questions from Steffen on Apr 7 and Apr 8 all been resolved?

- Sometime in the future spend some time on a dozen CV terms per call to
resolve them.

- Other items?



----

2) MIAPE-MS revision

- We have the needed 3 examples to go along with a document submission

- Until we provide the examples, it is not officially in the document
process

- We can use the sample MIAPE-compliant mzML file

+ Pierre-Alain has received an example from Proteo-Red

- Richard will look into PRIDE to see if there may be a good example there

- Pierre-Alain is looking through PRIDE to find a good example.

- The last example would be a MIAPE compliant mzML document

- Keep working on our documents and when we’re ready, see if we should wait

- We also need to coordinate the creation of MIAPE-Quant

- When officially in the process, send out submitted document to journal
editors and everyone else to get the word out

+ Pierre-Alain will contact Proteo-Red again about comments

+ Hope that MIAPE-MS can be submitted to document process in July

+ Might we start a draft of MIAPE-Quant in parallel with the start of
development of mzQuantML?

+ MIAPE-Quant will probably have different sections for each major type of
quanitification



----

3) TraML development

- TraML is currently undergoing formal review in the document process

- Version 0.9.4 released and is available at
http://www.psidev.info/index.php?q=node/405

- Implementations? Please update to 0.9.4 and test

  - Matt has implemented in ProteoWizard complete to 0.9.4

  - Matt will sent out a sample file

  - Matt hopes to finish the C# bindings sometime

  - Eric will try validating with his tools

  - ISB implementation in ATAQS nearly done

  - Jim has an implementation but just will need to update to 0.9.4

  - Jim will work to update this soon

  - Eric will also contact Amol to discuss TraML implementations

  - David Cox at Sciex will test implement?

  - Eric will follow up with David

- Are we ready to update validator page?:
http://www.psidev.info/index.php?q=node/304



----

4) PSI session at World HUPO in Sydney

- PSI will have a session. Presenters will be Juan Pablo, Henning, and Eric

- Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS

- Abstract is accepted

- Other reports?



----

5) Work on improving CV

- Review action items from last teleconference 2010-07-13



Next meeting:

- In 3 weeks? Aug 31?

[Psidev-ms-dev] TraML example files from ProteoWizard

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

  Here are two examples, one very plain and one MIAPE(-ish).
http://proteowizard.svn.sourceforge.net/viewvc/proteowizard/trunk/pwiz/example_data/tiny.pwiz.0.9.4.traML
http://proteowizard.svn.sourceforge.net/viewvc/proteowizard/trunk/pwiz/example_data/tiny_miape.pwiz.0.9.4.traML

-Matt

[Psidev-ms-dev] PSI-MSS WG call reminder

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

Hi everyone, the next PSI Mass Spectrometry Standards Working Group call
will be Tuesday 8am PDT:



08:00 San Francisco

11:00 New York

16:00 London

17:00 Geneva



+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ USA: 1-866-314-3683

Generic international: +44 2083222500 (UK number)



access code: 297427 #





Agenda:

1) mzML 1.1.0

- Manuscript has been resubmitted.

- Matt will update the example files to reference mzML 1.1.0 but indexedmzML
1.1.1

- New schema is posted on the web. The tiny file has been updated.

- Eric will update the web site announcing the change and update hyperlink

- Eric will update the other files

- Post by Andreas Schoenegger on Jun 9

- Richard will address this by updating the schema

- How do we handle lock mass corrections?

- We should assemble list of calibrants and make them specific terms

- Bruker uses Lithium Formiate; others?

- Jim will find out what Thermo is using

- Jim will talk to someone later today and compile a list of calibrants
commonly used

- Matt will contact David Anderson and Mike Ashton and ask about a date in
lieu of checksum

- Need to test FAIMS support in mzML

- According to folks at ISB, addition of “compensation voltage” is all
that’s needed

- Eric will try create a real example

- Have the questions from Steffen on Apr 7 and Apr 8 all been resolved?

- Sometime in the future spend some time on a dozen CV terms per call to
resolve them.

- Other items?



----

2) MIAPE-MS revision

- We have the needed 3 examples to go along with a document submission

- Until we provide the examples, it is not officially in the document
process

- We can use the sample MIAPE-compliant mzML file

+ Pierre-Alain has received an example from Proteo-Red

- Richard will look into PRIDE to see if there may be a good example there

- Pierre-Alain is looking through PRIDE to find a good example.

- The last example would be a MIAPE compliant mzML document

- Keep working on our documents and when we’re ready, see if we should wait

- We also need to coordinate the creation of MIAPE-Quant

- When officially in the process, send out submitted document to journal
editors and everyone else to get the word out

+ Pierre-Alain will contact Proteo-Red again about comments

+ Hope that MIAPE-MS can be submitted to document process in July

+ Might we start a draft of MIAPE-Quant in parallel with the start of
development of mzQuantML?

+ MIAPE-Quant will probably have different sections for each major type of
quanitification



----

3) TraML development

- TraML is currently undergoing formal review in the document process

- Version 0.9.4 released and is available at
http://www.psidev.info/index.php?q=node/405

- Implementations? Please update to 0.9.4 and test

  - Matt has implemented in ProteoWizard complete to 0.9.4

  - Matt will sent out a sample file

  - Matt hopes to finish the C# bindings sometime

  - Eric will try validating with his tools

  - ISB implementation in ATAQS nearly done

  - Jim has an implementation but just will need to update to 0.9.4

  - Jim will work to update this soon

  - Eric will also contact Amol to discuss TraML implementations

  - David Cox at Sciex will test implement?

  - Eric will follow up with David

- Are we ready to update validator page?:
http://www.psidev.info/index.php?q=node/304



----

4) PSI session at World HUPO in Sydney

- PSI will have a session. Presenters will be Juan Pablo, Henning, and Eric

- Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS

- Abstract is accepted

- Other reports?



----

5) Work on improving CV

- Review action items from last teleconference 2010-07-13



Next meeting:

- In 3 weeks? Aug 31?

[Psidev-ms-dev] PSI-MSS WG call postponed until Aug 10

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

Hi everyone, it will be difficult for me to make tomorrow’s planned call and
I haven’t had a chance to follow up on the actions items from last time.



The only announcement is that the TraML specification has passed the
internal PSI review and has now entered the external reviewer phase.



Let’s skip this call and meet again in two weeks on Aug 10 at 8am PDT.



Regards,

Eric

Re: [Psidev-ms-dev] [Psidev-pi-dev] Request new CV terms to the PSI-MS Controlled Vocabulary submission

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

Hi Martin,

Before you do anything with these, there has been some discussion from Matt Chambers on the PSI-MS list about them that perhaps you've missed. Re-copied below...

Cheers
Andy




  Hi all,

I'd like to move this to the psidev-ms-vocab list because 2/3 of these proposed terms would probably go in an mzML file, not mzIdentML. Before the CV merge between MS/PI, having the separate vocab list was kind of superfluous, but it's necessary now to avoid people missing posts due to not being subscribed to the right list...

Salvador, this is a nicely annotated proposal IMO, thanks! The definitions are properly verbose for the most part. There are some terms that won't be necessary because they are already modeled by combinations of existing terms and a few where the definition or mapping doesn't really fit the name (AFAIK).

Redundant terms:
Quadrupole Time Of Flight
Electrospray Quadrupole Time Of Flight
Electrospray Quadrupole Ion Mobility Time Of Flight

These terms are redundant because more than one mass analyzer is allowed in an instrumentConfiguration. A QTOF looks like:
<componentList count="6">
<source order="1">
<cvParam cvRef="MS" accession="MS:1000397" name="microelectrospray" value=""/> <cvParam cvRef="MS" accession="MS:1000057" name="electrospray inlet" value=""/> </source> <analyzer order="2"> <cvParam cvRef="MS" accession="MS:1000081" name="quadrupole" value=""/> </analyzer> <analyzer order="3"> <cvParam cvRef="MS" accession="MS:1000081" name="quadrupole" value=""/> </analyzer> <analyzer order="4"> <cvParam cvRef="MS" accession="MS:1000084" name="time-of-flight" value=""/> </analyzer> <detector order="5"> <cvParam cvRef="MS" accession="MS:1000114" name="microchannel plate detector" value=""/> </detector> <detector order="6"> <cvParam cvRef="MS" accession="MS:1000116" name="photomultiplier" value=""/> </detector> </componentList>

Centroid and Sum are redundant with:
id: MS:1000801
name: area peak picking
def: "Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The area defined by all raw data points that belong to the peak is reported."
synonym: "sum peak picking"

id: MS:1000802
name: height peak picking
def: "Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The maximum intensity of all raw data points that belong to the peak is reported."


Mismapped/named/defined terms:
Ion Mobility: is this a mass analyzer? I was under the impression it's a separate kind of analysis which can be used as a separating metric (i.e. ion mobility 
analyzer)
If ion mobility is not mass analysis, it certainly is still a kind of analyzer though, so our term <analyzer> actually still fits. We would just need a parent 
term for "mass analyzer."

Area normalization: this is a specific kind of intensity normalization (is_a MS:1001484)

Median: The name should be more specific and the definition should probably be expanded upon a bit.

//Chemical Noise: The name should refer to wavelet transformation if it's specific to that algorithm. How is "Wavelet transformation smoothing"? Reducing noise 
is the intended effect of the algorithm, not a description of the algorithm itself, correct? The description seems ok to me.

It looks like we need terms for both Synapt and Synapt HDMS. Not that it matters, because AFAIK Waters .raw doesn't usually store enough metadata to get the 
precise instrument model. :(

I think most of the sample preparation terms should go into http://code.google.com/p/gelml/source/browse/trunk/CV/sep.obo. Incidentally, has there been 
discussion about merging sep.obo with psi-ms.obo?

Again, nice work with the spreadsheet Salvador; having a table that complete saves a lot of back-and-forth!
-Matt









> -----Original Message-----
> From: Martin Eisenacher [mailto:mar...@ru...]
> Sent: 19 July 2010 10:04
> To: 'Salvador Martínez de Bartolomé Izquierdo'; Jones, Andy
> Cc: psi...@li...; jp...@pr...
> Subject: AW: [Psidev-pi-dev] Request new CV terms to the PSI-MS Controlled
> Vocabulary submission
> 
> Hi all!
> 
> I will edit the obo and insert/edit the few software terms
> and mark them as "Done"...
> 
> The other terms are from the "spectrum generation" part and - although it's seems
> sometimes straightforward - should be inserted by Luisa or someone from the
> mzML
> group.
> 
>   Bye
>    Martin
> 
> 
> 
> 
> > -----Ursprüngliche Nachricht-----
> > Von: Salvador Martínez de Bartolomé Izquierdo
> > [mailto:sma...@pr...]
> > Gesendet: Freitag, 16. Juli 2010 15:17
> > An: 'Jones, Andy'
> > Cc: psi...@li...; jp...@pr...
> > Betreff: Re: [Psidev-pi-dev] Request new CV terms to the PSI-MS
> > Controlled Vocabulary submission
> >
> > Hi Andy and others:
> > 	Attached you can find a Word file in which you will find a table
> > with the new terms, their definitions, and the possible position in the
> > hierarchy.
> > 	The list of terms is a compilation of terms from several Spanish
> > proteomics experts. So I hope, this will be useful.
> > 	Please, take a look to the list and comment whatever you want.
> > 	Best regards,
> >
> > Salvador Martínez de Bartolomé Izquierdo Bioinformatics Support -
> > ProteoRed
> > Lab- B1, National Center for Biotechnology C/ Darwin, 3 Universidad
> > Autónoma de Madrid Cantoblanco,
> > 28049 Madrid Spain
> > Phone: +34 91 585 4613
> > Fax: +34 91 585 4506
> >
> > -----Mensaje original-----
> > De: Jones, Andy [mailto:And...@li...]
> > Enviado el: Friday, July 16, 2010 3:02 PM
> > Para: 'Salvador Martínez de Bartolomé Izquierdo'
> > CC: 'psi...@li...'
> > Asunto: RE: [Psidev-pi-dev] Request new CV terms to the PSI-MS
> > Controlled Vocabulary submission
> >
> > Hi Salvador,
> >
> > We'd be happy to add the new terms into the CV. Do you have an idea yet
> > where the terms need to go into the hierarchy? Why don't you send a
> > list of terms round the mailing list and we'll work out how they will
> > all slot in?
> > Cheers
> > Andy
> >
> > > -----Original Message-----
> > > From: web...@ps... [mailto:web...@ps...]
> > > Sent: 15 July 2010 13:34
> > > To: psi...@li...
> > > Subject: [Psidev-pi-dev] Request new CV terms to the PSI-MS
> > Controlled
> > > Vocabulary submission
> > >
> > > Title : Mr.
> > >
> > > First name : Salvador
> > >
> > > Surname / Family name : Martínez-Bartolomé
> > >
> > > e-mail : sma...@pr...
> > >
> > > Institution : ProteoRed
> > >
> > > Country : Spain
> > >
> > > Requested term/s : A lot (see explanation)<br />
> > >
> > > Explanation : <p>Hi:</p><p>In ProteoRed we have compiled a lot of new
> > > terms to be  added to the MS ontology, but since they are more than
> > > forty, I would like to ask you to contact me by email in order to
> > send
> > > you a word document with all these documents.</p><p>Looking forward
> > to hearing from you.</p><p>Regards.
> > > <br /></p>
> > >
> > > -----
> > > Submitted by  (http://psidev.info/index.php?q=user/0) on Thu,
> > > 2010-07-15 12:34
> > >
> > >
> > > ---------------------------------------------------------------------
> > -
> > > -------- This SF.net email is sponsored by Sprint What will you do
> > > first with EVO, the first 4G phone?
> > > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> > > _______________________________________________
> > > Psidev-pi-dev mailing list
> > > Psi...@li...
> > > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev

[Psidev-ms-dev] PSI-MSS WG call notes

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

Present: Fredrik, Matt, Richard, Jim, Eric



Next meeting:

July 27 same time: confirmed



Today’s discussion centered around recent and needed changes to the CV



- PSI web site maintenance:

  - Update OBO-Edit hyperlinks

  - Add browse link to OLS, too



- OBO-Edit 2.1 complains: non-critical warning: nth generation product ion
spectrum (MS:1000339) generated 1 warning:

  The term nth generation product ion spectrum links to the obsolete term
product ion spectrum



- term “run attribute” has no parent and is floating at the top. Fix. Move
under “object attribute” for now.



- Change the term “standard” and its children to be a more generic
“reference” although add term “approved standard”

- reference

  RT norm reference

    H-PINS RT norm reference

- Add Krohkin peptides reference



- Regarding peptide and protein, okay to keep current structure but add in
Chebi relationship

- chemical compound = polyatomic entity

- peptide = polypeptide

- protein = protein



- But strangely, Chebi defines “polypeptide” as being at least 10 AA long.
There is no plain “peptide”. So what is a 9 AA peptide in Chebi? Seems like
just a “molecule” which is odd. Why 10?? Our current definition of “peptide”
is at least 2 AAs. How do we resolve this? Contact Marcus Ennis (mennis@ebi)









*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Tuesday, July 13, 2010 1:17 AM
*To:* 'Mass spectrometry standard development'
*Cc:* 'Eric Deutsch'
*Subject:* PSI-MSS WG call reminder



Hi everyone, the next PSI Mass Spectrometry Standards Working Group call
will be Tuesday 8am PDT:



08:00 San Francisco

11:00 New York

16:00 London

17:00 Geneva



+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ USA: 1-866-314-3683

Generic international: +44 2083222500 (UK number)



access code: 297427 #



Agenda:

1) Review of controlled vocabulary file terms

Have your OBO-Edit open to the latest psi-ms.obo



Next meeting:

- In 2 weeks? July 27?

[Psidev-ms-dev] PSI-MSS WG call reminder

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

Hi everyone, the next PSI Mass Spectrometry Standards Working Group call
will be Tuesday 8am PDT:

 

08:00 San Francisco

11:00 New York

16:00 London

17:00 Geneva

 

+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ USA: 1-866-314-3683

Generic international: +44 2083222500 (UK number)

 

access code: 297427 #

 

Agenda:

1) Review of controlled vocabulary file terms

Have your OBO-Edit open to the latest psi-ms.obo

 

Next meeting: 

- In 2 weeks? July 27?

 

 

 

Re: [Psidev-ms-dev] Next call date?

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

  Neither the notes or the reminder the previous day reached me. These hi-tech mailing lists are not infallible, it seems.

-Matt


On 7/12/2010 6:18 PM, Eric Deutsch wrote:
> Hi Matt, the notes for the last call went out at 2010-06-29 8:30am PDT,
> let me know if you didn't get it. We agreed to meet again tomorrow. Until
> we hear back on the TraML submission, there may not be much to discuss so
> we could defer. We've been meaning to tackle the CV. If you're available
> tomorrow, maybe we can kick off the CV cleanup discussion. Let me know
> what you think, and I'll send out the announcement in a little while.
>
> Thanks,
> Eric
>
>
>> -----Original Message-----
>> From: Matthew Chambers [mailto:mat...@gm...]
>> Sent: Monday, July 12, 2010 3:58 PM
>> To: Mass spectrometry standard development
>> Subject: [Psidev-ms-dev] Next call date?
>>
>>    Hi Eric,
>>
>> What's the schedule for the next WG call? I may have missed the
>> previous one but I didn't see notes for it.
>>
>> Thanks,
>> -Matt

Re: [Psidev-ms-dev] Next call date?

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

Hi Matt, the notes for the last call went out at 2010-06-29 8:30am PDT,
let me know if you didn't get it. We agreed to meet again tomorrow. Until
we hear back on the TraML submission, there may not be much to discuss so
we could defer. We've been meaning to tackle the CV. If you're available
tomorrow, maybe we can kick off the CV cleanup discussion. Let me know
what you think, and I'll send out the announcement in a little while.

Thanks,
Eric


> -----Original Message-----
> From: Matthew Chambers [mailto:mat...@gm...]
> Sent: Monday, July 12, 2010 3:58 PM
> To: Mass spectrometry standard development
> Subject: [Psidev-ms-dev] Next call date?
>
>   Hi Eric,
>
> What's the schedule for the next WG call? I may have missed the
> previous one but I didn't see notes for it.
>
> Thanks,
> -Matt
>
> -----------------------------------------------------------------------
> -------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

[Psidev-ms-dev] Next call date?

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

  Hi Eric,

What's the schedule for the next WG call? I may have missed the previous one but I didn't see notes for it.

Thanks,
-Matt

Re: [Psidev-ms-dev] PSI-MSS WG call notes [XCMS / TraML example]

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

On Wed, 2010-06-16 at 23:18 -0700, Eric Deutsch wrote:
> The only problem is that there is no CV term for XCMS. Would you suggest
> one? (with definition!) so you don't need to use the custom software term?
Done. The file 

   http://msbi.ipb-halle.de/~sneumann/xcmsTraML.xml

now has a proper Software cvParam. The OpenMS validator 
is currently not working (Permission denied in /nfs/.../TraML/index.php)
but it *should* validate.

Yours,
Steffen

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

[Psidev-ms-dev] PSI-MSS WG call notes

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

Present: Richard, Jim, Eric, Pierre-Alain





Agenda:

1) mzML 1.1.0

- Manuscript has been reviewed and the comments addressed and resubmitted.

- The editors have come back and asked for the inclusion of a “tangible
example of an application" and then it will be acceptable for publication.
Response in progress.

- Richard suggests a jzmzml as an application

- Matt suggests quantification, wiff files, spectrum annotation

- Eric will write this and send back in

- Matt has released and posted the updated 1.1.1 version of indexedmzML
schema: <indexList> name attribute will be enumerated to “spectrum” or
“chromatogram” to disallow other creative values

- Matt will update the example files to reference mzML 1.1.0 but indexedmzML
1.1.1

- New schema is posted on the web. The tiny file has been updated.

- Eric will update the web site announcing the change and update hyperlink

- Eric will update the other files

- Post by Andreas Schoenegger on Jun 9

- Richard will address this by updating the schema

- How do we handle lock mass corrections?

- We should assemble list of calibrants and make them specific terms

- Bruker uses Lithium Formiate; others?

- Jim will find out what Thermo is using

- Jim will talk to someone later today and compile a list of calibrants
commonly used

- Matt will contact David Anderson and Mike Ashton and ask about a date in
lieu of checksum

- Need to test FAIMS support in mzML

- According to folks at ISB, addition of “compensation voltage” is all
that’s needed

- Eric will try create a real example

- Have the questions from Steffen on Apr 7 and Apr 8 all been resolved?

- Sometime in the future spend some time on a dozen CV terms per call to
resolve them.

- Other items?



----

2) MIAPE-MS revision

- We have the needed 3 examples to go along with a document submission

- Until we provide the examples, it is not officially in the document
process

- We can use the sample MIAPE-compliant mzML file

+ Pierre-Alain has received an example from Proteo-Red

- Richard will look into PRIDE to see if there may be a good example there

- Pierre-Alain is looking through PRIDE to find a good example.

- The last example would be a MIAPE compliant mzML document

- Keep working on our documents and when we’re ready, see if we should wait

- We also need to coordinate the creation of MIAPE-Quant

- When officially in the process, send out submitted document to journal
editors and everyone else to get the word out

+ Pierre-Alain will contact Proteo-Red again about comments

+ Hope that MIAPE-MS can be submitted to document process in July

+ Might we start a draft of MIAPE-Quant in parallel with the start of
development of mzQuantML?

+ MIAPE-Quant will probably have different sections for each major type of
quanitification



----

3) TraML development

- Version 0.9.4 released and is available at
http://www.psidev.info/index.php?q=node/405

- Specification document is updated. Please examine. Is it ready for
submission?


http://www.peptideatlas.org/tmp/TraML/0.9.4/TraML_0.9.4.1_specificationDocument.doc

- Implementations? Please update to 0.9.4 and test

  - Matt has implemented in ProteoWizard complete to 0.9.4

  - Matt will sent out a sample file

  - Matt hopes to finish the C# bindings sometime

  - Eric will try validating with his tools

  - ISB implementation in ATAQS nearly done

  - Jim has an implementation but just will need to update to 0.9.4

  - Jim will work to update this soon

  - Eric will also contact Amol to discuss TraML implementations

  - David Cox at Sciex will test implement?

  - Eric will follow up with David

- Are we ready to update validator page?:
http://www.psidev.info/index.php?q=node/304

- Eric emailed submission materials to PSI editors

+ A few minor things to fix and then resubmit



----

4) PSI session at World HUPO in Sydney

- PSI will have a session. Presenters will be Juan Pablo, Henning, and Eric

- Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS

- Abstract is accepted

- Other reports?



----

5) Working with ASMS on controlled vocabulary

- no update



Next meeting:

- In 2 weeks? July 13?

+ Yes





*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Monday, June 28, 2010 4:34 PM
*To:* Mass spectrometry standard development
*Cc:* Eric Deutsch
*Subject:* PSI-MSS WG call reminder



Hi everyone, the next PSI Mass Spectrometry Standards Working Group call
will be Tuesday 8am PDT:



08:00 San Francisco

11:00 New York

16:00 London

17:00 Geneva



+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ USA: 1-866-314-3683

Generic international: +44 2083222500 (UK number)



access code: 297427 #



Agenda:

1) mzML 1.1.0

- Manuscript has been reviewed and the comments addressed and resubmitted.

- The editors have come back and asked for the inclusion of a “tangible
example of an application" and then it will be acceptable for publication.
Response in progress.

- Richard suggests a jzmzml as an application

- Matt suggests quantification, wiff files, spectrum annotation

- Eric will write this and send back in

- Matt has released and posted the updated 1.1.1 version of indexedmzML
schema: <indexList> name attribute will be enumerated to “spectrum” or
“chromatogram” to disallow other creative values

- Matt will update the example files to reference mzML 1.1.0 but indexedmzML
1.1.1

- New schema is posted on the web. The tiny file has been updated.

- Eric will update the web site announcing the change and update hyperlink

- Eric will update the other files

- Post by Andreas Schoenegger on Jun 9

- Richard will address this by updating the schema

- How do we handle lock mass corrections?

- We should assemble list of calibrants and make them specific terms

- Bruker uses Lithium Formiate; others?

- Jim will find out what Thermo is using

- Jim will talk to someone later today and compile a list of calibrants
commonly used

- Matt will contact David Anderson and Mike Ashton and ask about a date in
lieu of checksum

- Need to test FAIMS support in mzML

- According to folks at ISB, addition of “compensation voltage” is all
that’s needed

- Eric will try create a real example

- Have the questions from Steffen on Apr 7 and Apr 8 all been resolved?

- Sometime in the future spend some time on a dozen CV terms per call to
resolve them.

- Other items?



----

2) MIAPE-MS revision

- Document is ready to be submitted, but..

- We need to have 3 examples to go along with a document submission

- Until we provide the examples, it is not officially in the document
process

- We can use the sample MIAPE-compliant mzML file

- Pierre-Alain will contact Juan-Pablo to see if he has some suitable
examples in Proteo-Red

- Pierre-Alain has received an example from Proteo-Red

- Richard will look into PRIDE to see if there may be a good example there

- Pierre-Alain is looking through PRIDE to find a good example.

- The last example would be a MIAPE compliant mzML document

- Looking in Peptidome might be an alternative for finding a nicely
annotated dataset

- Waiting to sync with MIAPE-MSI as well

- Keep working on our documents and when we’re ready, see if we should wait

- We also need to coordinate the creation of MIAPE-Quant

- When officially in the process, send out submitted document to journal
editors and everyone else to get the word out



----

3) TraML development

- Version 0.9.4 released and is available at
http://www.psidev.info/index.php?q=node/405

- Specification document is updated. Please examine. Is it ready for
submission?


http://www.peptideatlas.org/tmp/TraML/0.9.4/TraML_0.9.4.1_specificationDocument.doc

- Implementations? Please update to 0.9.4 and test

  - Matt has implemented in ProteoWizard complete to 0.9.4

  - Matt will sent out a sample file

  - Matt hopes to finish the C# bindings sometime

  - Eric will try validating with his tools

  - ISB implementation in ATAQS nearly done

  - Jim has an implementation but just will need to update to 0.9.4

  - Jim will work to update this soon

  - Eric will also contact Amol to discuss TraML implementations

  - David Cox at Sciex will test implement?

  - Eric will follow up with David

- Are we ready to update validator page?:
http://www.psidev.info/index.php?q=node/304

- Eric emailed submission materials to PSI editors



----

4) PSI session at World HUPO in Sydney

- PSI will have a session. Presenters will be Juan Pablo, Henning, and Eric

- Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS

- Abstract is accepted

- Other reports?



----

5) Working with ASMS on controlled vocabulary

- no update



Next meeting:

- In 2 weeks? July 13?

[Psidev-ms-dev] PSI-MSS WG call reminder

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

Hi everyone, the next PSI Mass Spectrometry Standards Working Group call
will be Tuesday 8am PDT:



08:00 San Francisco

11:00 New York

16:00 London

17:00 Geneva



+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ USA: 1-866-314-3683

Generic international: +44 2083222500 (UK number)



access code: 297427 #



Agenda:

1) mzML 1.1.0

- Manuscript has been reviewed and the comments addressed and resubmitted.

- The editors have come back and asked for the inclusion of a “tangible
example of an application" and then it will be acceptable for publication.
Response in progress.

- Richard suggests a jzmzml as an application

- Matt suggests quantification, wiff files, spectrum annotation

- Eric will write this and send back in

- Matt has released and posted the updated 1.1.1 version of indexedmzML
schema: <indexList> name attribute will be enumerated to “spectrum” or
“chromatogram” to disallow other creative values

- Matt will update the example files to reference mzML 1.1.0 but indexedmzML
1.1.1

- New schema is posted on the web. The tiny file has been updated.

- Eric will update the web site announcing the change and update hyperlink

- Eric will update the other files

- Post by Andreas Schoenegger on Jun 9

- Richard will address this by updating the schema

- How do we handle lock mass corrections?

- We should assemble list of calibrants and make them specific terms

- Bruker uses Lithium Formiate; others?

- Jim will find out what Thermo is using

- Jim will talk to someone later today and compile a list of calibrants
commonly used

- Matt will contact David Anderson and Mike Ashton and ask about a date in
lieu of checksum

- Need to test FAIMS support in mzML

- According to folks at ISB, addition of “compensation voltage” is all
that’s needed

- Eric will try create a real example

- Have the questions from Steffen on Apr 7 and Apr 8 all been resolved?

- Sometime in the future spend some time on a dozen CV terms per call to
resolve them.

- Other items?



----

2) MIAPE-MS revision

- Document is ready to be submitted, but..

- We need to have 3 examples to go along with a document submission

- Until we provide the examples, it is not officially in the document
process

- We can use the sample MIAPE-compliant mzML file

- Pierre-Alain will contact Juan-Pablo to see if he has some suitable
examples in Proteo-Red

- Pierre-Alain has received an example from Proteo-Red

- Richard will look into PRIDE to see if there may be a good example there

- Pierre-Alain is looking through PRIDE to find a good example.

- The last example would be a MIAPE compliant mzML document

- Looking in Peptidome might be an alternative for finding a nicely
annotated dataset

- Waiting to sync with MIAPE-MSI as well

- Keep working on our documents and when we’re ready, see if we should wait

- We also need to coordinate the creation of MIAPE-Quant

- When officially in the process, send out submitted document to journal
editors and everyone else to get the word out



----

3) TraML development

- Version 0.9.4 released and is available at
http://www.psidev.info/index.php?q=node/405

- Specification document is updated. Please examine. Is it ready for
submission?


http://www.peptideatlas.org/tmp/TraML/0.9.4/TraML_0.9.4.1_specificationDocument.doc

- Implementations? Please update to 0.9.4 and test

  - Matt has implemented in ProteoWizard complete to 0.9.4

  - Matt will sent out a sample file

  - Matt hopes to finish the C# bindings sometime

  - Eric will try validating with his tools

  - ISB implementation in ATAQS nearly done

  - Jim has an implementation but just will need to update to 0.9.4

  - Jim will work to update this soon

  - Eric will also contact Amol to discuss TraML implementations

  - David Cox at Sciex will test implement?

  - Eric will follow up with David

- Are we ready to update validator page?:
http://www.psidev.info/index.php?q=node/304

- Eric emailed submission materials to PSI editors



----

4) PSI session at World HUPO in Sydney

- PSI will have a session. Presenters will be Juan Pablo, Henning, and Eric

- Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS

- Abstract is accepted

- Other reports?



----

5) Working with ASMS on controlled vocabulary

- no update



Next meeting:

- In 2 weeks? July 13?

[Psidev-ms-dev] mzQuantML

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

Hi all,

We are starting to plan for a mzQuantML (format for quantitative proteomic data) development meeting for September at the EBI in Cambridge. At present, we are provisionally looking at 1st-3rd Sept.

Can people send me a mail if you are:

-          Interested in contributing to this development

-          If these dates are possible for you or if you'd prefer another week

Best wishes
Andy

Re: [Psidev-ms-dev] PSI-MSS WG call notes

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

On Wed, 2010-06-16 at 23:18 -0700, Eric Deutsch wrote:
> The only problem is that there is no CV term for XCMS.

Then it is about high time:

[Term]
id: MS:100XXXX
name: XCMS software
def: "XCMS (A Bioconductor package to analyse high-throughput mass spectrometry data." [PSI:MS]
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

Yours,
Steffen


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

Re: [Psidev-ms-dev] PSI-MSS WG call notes

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

Hi Steffen, this looks great, many thanks!

The only problem is that there is no CV term for XCMS. Would you suggest
one? (with definition!) so you don't need to use the custom software term?

Thanks!
Eric


> -----Original Message-----
> From: Steffen Neumann [mailto:sne...@ip...]
> Sent: Wednesday, June 16, 2010 1:37 AM
> To: Mass spectrometry standard development
> Subject: Re: [Psidev-ms-dev] PSI-MSS WG call notes
> 
> On Tue, 2010-06-15 at 08:32 -0700, Eric Deutsch wrote:
> > 3) TraML development
> ...
> > - Implementations? Please update to 0.9.4 and test
> 
> There is now a preview of TraML export for xcms,
> for an example (validated by OpenMS for 0.9.4)
> 
> http://msbi.ipb-halle.de/~sneumann/xcmsTraML.xml
> 
> Yours,
> Steffen
> 
> --
> IPB Halle                    AG Massenspektrometrie & Bioinformatik
> Dr. Steffen Neumann          http://www.IPB-Halle.DE
> Weinberg 3                   http://msbi.bic-gh.de
> 06120 Halle                  Tel. +49 (0) 345 5582 - 1470
>                                   +49 (0) 345 5582 - 0
> sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409
> 
> 
> --------------------------------------------------------------------------
> ----
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] PSI-MSS WG call notes

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

On Tue, 2010-06-15 at 08:32 -0700, Eric Deutsch wrote:
> 3) TraML development
...
> - Implementations? Please update to 0.9.4 and test

There is now a preview of TraML export for xcms, 
for an example (validated by OpenMS for 0.9.4)

http://msbi.ipb-halle.de/~sneumann/xcmsTraML.xml

Yours,
Steffen

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

[Psidev-ms-dev] PSI-MSS WG call notes

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

Present: Matt, Richard, Jim, Eric



Agenda:

1) mzML 1.1.0

- Manuscript has been reviewed and the comments addressed and resubmitted.

- The editors have come back and asked for the inclusion of a “tangible
example of an application" and then it will be acceptable for publication.
Response in progress.

+ Richard suggests a jzmzml as an application

+ Matt suggests quantification, wiff files, spectrum annotation

+ Eric will write this and send back in

- Matt has released and posted the updated 1.1.1 version of indexedmzML
schema: <indexList> name attribute will be enumerated to “spectrum” or
“chromatogram” to disallow other creative values

- Matt will update the example files to reference mzML 1.1.0 but indexedmzML
1.1.1

- New schema is posted on the web. The tiny file has been updated.

- Eric will update the web site announcing the change and update hyperlink

+ Eric will update the other files

- Post by Andreas Schoenegger on Jun 9

+ Richard will address this by updating the schema

- How do we handle lock mass corrections?

- We should assemble list of calibrants and make them specific terms

- Bruker uses Lithium Formiate; others?

- Jim will find out what Thermo is using

- Jim will look at an old email and send out the information

+ Jim will talk to someone later today and compile a list of calibrants
commonly used

- Matt will contact David Anderson and Mike Ashton and ask about a date in
lieu of checksum

- Need to test FAIMS support in mzML

+ Eric will talk to Chris and Kristian at ISB

+ According to folks at ISB, addition of “compensation voltage” is all
that’s needed

+ Eric will try create a real example

- Other items?

+ Have the questions from Steffen on Apr 7 and Apr 8 all been resolved?

+ Sometime in the future spend some time on a dozen CV terms per call to
resolve them.



----

2) MIAPE-MS revision

- Document is ready to be submitted, but..

- We need to have 3 examples to go along with a document submission

- Until we provide the examples, it is not officially in the document
process

- We can use the sample MIAPE-compliant mzML file

- Pierre-Alain will contact Juan-Pablo to see if he has some suitable
examples in Proteo-Red

- Pierre-Alain has received an example from Proteo-Red

- Richard will look into PRIDE to see if there may be a good example there

- Pierre-Alain is looking through PRIDE to find a good example.

- The last example would be a MIAPE compliant mzML document

- Looking in Peptidome might be an alternative for finding a nicely
annotated dataset

- Waiting to sync with MIAPE-MSI as well

- Keep working on our documents and when we’re ready, see if we should wait

- We also need to coordinate the creation of MIAPE-Quant

- When officially in the process, send out submitted document to journal
editors and everyone else to get the word out



----

3) TraML development

- New version 0.9.4 released and is available at
http://www.psidev.info/index.php?q=node/405

- Specification document is updated. Please examine. Is it ready for
submission?


http://www.peptideatlas.org/tmp/TraML/0.9.4/TraML_0.9.4.1_specificationDocument.doc

- Implementations? Please update to 0.9.4 and test

  - Matt will implement in ProteoWizard

  + ProteoWizard implementation is complete to 0.9.4

  + Matt will sent out a sample file

  + Matt hopes to finish the C# bindings sometime

  + Eric will try validating with his tools

  - ISB implementation in ATAQS nearly done

  - Jim has an implementation but just will need to update to 0.9.4

  + Jim will work to update this soon

  + Eric will also contact Amol to discuss TraML implementations

  - David Cox at Sciex will test implement?

  + Eric will follow up with David

- Are we ready to update validator page?:
http://www.psidev.info/index.php?q=node/304

- Manuscript is in preparation and will be sent out shortly



----

4) PSI session at World HUPO in Sydney

- PSI will have a session. Presenters will be Eric, Sandra?, Henning.

- Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS

- Abstract is accepted

- Other reports?



----

5) Working with ASMS on controlled vocabulary

- no update

+ Matt suggested slowly working through purgatory at these calls. Eric will
prep.



Next meeting:

- In 2 weeks? June 29? Regular time

+ agreed







*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Tuesday, June 15, 2010 7:31 AM
*To:* 'Mass spectrometry standard development'
*Cc:* 'Eric Deutsch'
*Subject:* PSI-MSS WG call reminder



Hi everyone, sorry I forgot yesterday to send around the reminder for the
call. Let’s go ahead with the call 30 minutes from now as scheduled.



08:00 San Francisco

11:00 New York

16:00 London

17:00 Geneva



+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ USA: 1-866-314-3683

Generic international: +44 2083222500 (UK number)



access code: 297427 #



Agenda:

1) mzML 1.1.0

- Manuscript has been reviewed and the comments addressed and resubmitted.

- The editors have come back and asked for the inclusion of a “tangible
example of an application" and then it will be acceptable for publication.
Response in progress.

- Matt has released and posted the updated 1.1.1 version of indexedmzML
schema: <indexList> name attribute will be enumerated to “spectrum” or
“chromatogram” to disallow other creative values

- Matt will update the example files to reference mzML 1.1.0 but indexedmzML
1.1.1

- New schema is posted on the web. The tiny file has been updated.

- Eric will update the web site announcing the change and update hyperlink

- How do we handle lock mass corrections?

- We should assemble list of calibrants and make them specific terms

- Bruker uses Lithium Formiate; others?

- Jim will find out what Thermo is using

- Jim will look at an old email and send out the information

- Matt will contact David Anderson and Mike Ashton and ask about a date in
lieu of checksum

- Need to test FAIMS support in mzML

- Other items?



----

2) MIAPE-MS revision

- Document is ready to be submitted, but..

- We need to have 3 examples to go along with a document submission

- Until we provide the examples, it is not officially in the document
process

- We can use the sample MIAPE-compliant mzML file

- Pierre-Alain will contact Juan-Pablo to see if he has some suitable
examples in Proteo-Red

- Pierre-Alain has received an example from Proteo-Red

- Richard will look into PRIDE to see if there may be a good example there

- Pierre-Alain is looking through PRIDE to find a good example.

- The last example would be a MIAPE compliant mzML document

- Looking in Peptidome might be an alternative for finding a nicely
annotated dataset

- Waiting to sync with MIAPE-MSI as well

- Keep working on our documents and when we’re ready, see if we should wait

- We also need to coordinate the creation of MIAPE-Quant

- When officially in the process, send out submitted document to journal
editors and everyone else to get the word out



----

3) TraML development

- New version 0.9.4 released and is available at
http://www.psidev.info/index.php?q=node/405

- Specification document is updated. Please examine. Is it ready for
submission?


http://www.peptideatlas.org/tmp/TraML/0.9.4/TraML_0.9.4.1_specificationDocument.doc

- Implementations? Please update to 0.9.4 and test

  - Matt will implement in ProteoWizard

  - Andreas will implement in OpenMS and update on-line validator

  - ISB implementation in ATAQS nearly done

  - Jim has an implementation but just will need to update to 0.9.4

  - David Cox at Sciex will test implement?

- Are we ready to update validator page?:
http://www.psidev.info/index.php?q=node/304

- Manuscript is in preparation and will be sent out shortly



----

4) PSI session at World HUPO in Sydney

- PSI will have a session. Presenters will be Eric, Juan Antonio, Henning.

- JuanAn maybe can’t go?

- Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS

- Abstract is accepted

- Other reports?

- Perhaps some of us try to meet at ASMS briefly?

- Note that there will be a Computational Mass Spectrometry/Bioinformatics
for MS meeting at ASMS

  - Wednesday, May 26th, 2010, 05:45-07:00pm Hall 2, Salt Palace Convention
Center

  - Featuring Alexey Nesvizhskii and David L. Tabb



----

5) Working with ASMS on controlled vocabulary

- no update



Next meeting:

- In 3 weeks? June 8?

[Psidev-ms-dev] MzML schema - minor things

[Andreas S. <as...@eb...>]

Hi all,

I wanted to report the following minor inconsistencies I stumbled across 
in the current version of MzML.

1.)
ComponentType & ScanWindowListType:

count element is of type xs:int instead of xs:nonNegativeInteger
All other count elements in the schema are xs:nonNegativeInteger

2.)
SpectrumList:

The list of spectra is optional
All other lists in the list wrappers are required

3.)
InstrumentConfiguration:

The attribute scanSettingsRef has no usage definition
Also the HTML documentation is faulty:
http://www.peptideatlas.org/tmp/mzML1.1.0.html#instrumentConfiguration

4.)
The HTML doc for a scanWindow does not exist at all

Have a look at ScanWindowList:
http://www.peptideatlas.org/tmp/mzML1.1.0.html#scanWindowList

-- 
Andreas Schoenegger
Trainee - PRIDE Project Team
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom

Re: [Psidev-ms-dev] PSI-MSS WG call deferred 1 week

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

Do we have the call now?

-Matt


On 6/7/2010 12:33 PM, Eric Deutsch wrote:
>
> Hi everyone, due a schedule change, I am unable to make it to 
> tomorrow’s PSI-MSS WG call. Let’s meet a week later instead, Jun 15 
> 8am PDT, unless this causes some serious problem?
>
> Thanks,
>
> Eric
>
> *From:* Eric Deutsch [mailto:ede...@sy... 
> <mailto:ede...@sy...>]
> *Sent:* Tuesday, May 18, 2010 9:38 AM
> *To:* Mass spectrometry standard development
> *Cc:* Eric Deutsch
> *Subject:* PSI-MSS WG call notes
>
> Present: Matt, Richard, Jim, Eric
>
> Agenda:
>
> 1) mzML 1.1.0
>
> - Manuscript has been reviewed and the comments addressed and resubmitted.
>
> - The editors have come back and asked for the inclusion of a 
> “tangible example of an application" and then it will be acceptable 
> for publication. Response in progress.
>
> + Richard suggests a jzmzml as an application
>
> + Matt suggests quantification, wiff files, spectrum annotation
>
> - Matt has released and posted the updated 1.1.1 version of 
> indexedmzML schema: <indexList> name attribute will be enumerated to 
> “spectrum” or “chromatogram” to disallow other creative values
>
> - Matt will update the example files to reference mzML 1.1.0 but 
> indexedmzML 1.1.1
>
> - New schema is posted on the web. The tiny file has been updated.
>
> - Eric will update the web site announcing the change and update hyperlink
>
> + Eric will update the other files
>
> - How do we handle lock mass corrections?
>
> - We should assemble list of calibrants and make them specific terms
>
> - Bruker uses Lithium Formiate; others?
>
> - Jim will find out what Thermo is using
>
> - Jim will look at an old email and send out the information
>
> + Jim will ask around at ASMS and compile a list of calibrants 
> commonly used
>
> - Matt will contact David Anderson and Mike Ashton and ask about a 
> date in lieu of checksum
>
> - Need to test FAIMS support in mzML
>
> + Eric will talk to Chris at ISB
>
> - Other items?
>
> + Have the questions from Steffen on Apr 7 and Apr 8 all been resolved?
>
> + Sometime in the future spend some time on a dozen terms per call to 
> resolve them.
>
> ----
>
> 2) MIAPE-MS revision
>
> - Document is ready to be submitted, but..
>
> - We need to have 3 examples to go along with a document submission
>
> - Until we provide the examples, it is not officially in the document 
> process
>
> - We can use the sample MIAPE-compliant mzML file
>
> - Pierre-Alain will contact Juan-Pablo to see if he has some suitable 
> examples in Proteo-Red
>
> - Pierre-Alain has received an example from Proteo-Red
>
> - Richard will look into PRIDE to see if there may be a good example there
>
> - Pierre-Alain is looking through PRIDE to find a good example.
>
> - The last example would be a MIAPE compliant mzML document
>
> - Looking in Peptidome might be an alternative for finding a nicely 
> annotated dataset
>
> - Waiting to sync with MIAPE-MSI as well
>
> - Keep working on our documents and when we’re ready, see if we should 
> wait
>
> - We also need to coordinate the creation of MIAPE-Quant
>
> - When officially in the process, send out submitted document to 
> journal editors and everyone else to get the word out
>
> ----
>
> 3) TraML development
>
> - New version 0.9.4 released and is available at 
> http://www.psidev.info/index.php?q=node/405
>
> - Specification document is updated. Please examine. Is it ready for 
> submission?
>
> http://www.peptideatlas.org/tmp/TraML/0.9.4/TraML_0.9.4.1_specificationDocument.doc
>
> - Implementations? Please update to 0.9.4 and test
>
>   - Matt will implement in ProteoWizard
>
>   + ProteoWizard implementation is complete to 0.9.4
>
>   + Matt has sent out a sample file
>
>   + Matt hopes to finish the C# bindings this week
>
>   + Eric will try validating with his tools
>
>   - Andreas will implement in OpenMS and update on-line validator
>
>   + Sadly Andreas has perished in a car accident and is no longer with us
>
>   - ISB implementation in ATAQS nearly done
>
>   - Jim has an implementation but just will need to update to 0.9.4
>
>   - David Cox at Sciex will test implement?
>
>   + Eric will follow up with David
>
> - Are we ready to update validator page?: 
> http://www.psidev.info/index.php?q=node/304
>
> - Manuscript is in preparation and will be sent out shortly
>
> ----
>
> 4) PSI session at World HUPO in Sydney
>
> - PSI will have a session. Presenters will be Eric, Juan Antonio, Henning.
>
> - JuanAn maybe can’t go?
>
> - Eric will present on the work of the group: mzML 1.1, TraML x.x, 
> MIAPE-MS
>
> - Abstract is accepted
>
> - Other reports?
>
> - Perhaps some of us try to meet at ASMS briefly?
>
> - Note that there will be a Computational Mass 
> Spectrometry/Bioinformatics for MS meeting at ASMS
>
>   - Wednesday, May 26th, 2010, 05:45-07:00pm Hall 2, Salt Palace 
> Convention Center
>
>   - Featuring Alexey Nesvizhskii and David L. Tabb
>
> ----
>
> 5) Working with ASMS on controlled vocabulary
>
> - no update
>
> + Matt suggested slowly working through purgatory at these calls. Eric 
> will prep.
>
> Next meeting:
>
> - In 3 weeks? June 8? Regular time
>
> + agreed
>
> *From:* Eric Deutsch [mailto:ede...@sy... 
> <mailto:ede...@sy...>]
> *Sent:* Monday, May 17, 2010 9:59 AM
> *To:* Mass spectrometry standard development
> *Cc:* Eric Deutsch
> *Subject:* PSI-MSS WG call reminder <1 hr time shift!>
>
> Hi everyone, I now have a conflicting meeting at the usual 8am 
> timeslot, and next week is ASMS, so I’d like to try to squeeze in the 
> call one hour later. I hope most participants can be tolerant of this.
>
> So, the next PSI Mass Spectrometry Standards Working Group call will 
> be Tuesday 9am PDT:
>
> http://www.timeanddate.com/worldclock/fixedtime.html?day=18&month=5&year=2010&hour=17&min=0&sec=0&p1=136 
> <http://www.timeanddate.com/worldclock/fixedtime.html?day=18&month=5&year=2010&hour=17&min=0&sec=0&p1=136>
>
> 09:00 San Francisco
>
> 12:00 New York
>
> 17:00 London
>
> 18:00 Geneva
>
> + Germany: 08001012079
>
> + Switzerland: 0800000860
>
> + UK: 08081095644
>
> + USA: 1-866-314-3683
>
> Generic international: +44 2083222500 (UK number)
>
> access code: 297427 #
>
> Agenda:
>
> 1) mzML 1.1.0
>
> - Manuscript has been reviewed and the comments addressed and resubmitted.
>
> - The editors have come back and asked for the inclusion of a 
> “tangible example of an application" and then it will be acceptable 
> for publication. Response in progress.
>
> - Matt has released and posted the updated 1.1.1 version of 
> indexedmzML schema: <indexList> name attribute will be enumerated to 
> “spectrum” or “chromatogram” to disallow other creative values
>
> - Matt will update the example files to reference mzML 1.1.0 but 
> indexedmzML 1.1.1
>
> - New schema is posted on the web. The tiny file has been updated.
>
> - Eric will update the web site announcing the change and update hyperlink
>
> - How do we handle lock mass corrections?
>
> - We should assemble list of calibrants and make them specific terms
>
> - Bruker uses Lithium Formiate; others?
>
> - Jim will find out what Thermo is using
>
> - Jim will look at an old email and send out the information
>
> - Matt will contact David Anderson and Mike Ashton and ask about a 
> date in lieu of checksum
>
> - Need to test FAIMS support in mzML
>
> - Other items?
>
> ----
>
> 2) MIAPE-MS revision
>
> - Document is ready to be submitted, but..
>
> - We need to have 3 examples to go along with a document submission
>
> - Until we provide the examples, it is not officially in the document 
> process
>
> - We can use the sample MIAPE-compliant mzML file
>
> - Pierre-Alain will contact Juan-Pablo to see if he has some suitable 
> examples in Proteo-Red
>
> - Pierre-Alain has received an example from Proteo-Red
>
> - Richard will look into PRIDE to see if there may be a good example there
>
> - Pierre-Alain is looking through PRIDE to find a good example.
>
> - The last example would be a MIAPE compliant mzML document
>
> - Looking in Peptidome might be an alternative for finding a nicely 
> annotated dataset
>
> - Waiting to sync with MIAPE-MSI as well
>
> - Keep working on our documents and when we’re ready, see if we should 
> wait
>
> - We also need to coordinate the creation of MIAPE-Quant
>
> - When officially in the process, send out submitted document to 
> journal editors and everyone else to get the word out
>
> ----
>
> 3) TraML development
>
> - New version 0.9.4 released and is available at 
> http://www.psidev.info/index.php?q=node/405
>
> - Specification document is updated. Please examine. Is it ready for 
> submission?
>
> http://www.peptideatlas.org/tmp/TraML/0.9.4/TraML_0.9.4.1_specificationDocument.doc
>
> - Implementations? Please update to 0.9.4 and test
>
>   - Matt will implement in ProteoWizard
>
>   - Andreas will implement in OpenMS and update on-line validator
>
>   - ISB implementation in ATAQS nearly done
>
>   - Jim has an implementation but just will need to update to 0.9.4
>
>   - David Cox at Sciex will test implement?
>
> - Are we ready to update validator page?: 
> http://www.psidev.info/index.php?q=node/304
>
> - Manuscript is in preparation and will be sent out shortly
>
> ----
>
> 4) PSI session at World HUPO in Sydney
>
> - PSI will have a session. Presenters will be Eric, Juan Antonio, Henning.
>
> - JuanAn maybe can’t go?
>
> - Eric will present on the work of the group: mzML 1.1, TraML x.x, 
> MIAPE-MS
>
> - Abstract is accepted
>
> - Other reports?
>
> - Perhaps some of us try to meet at ASMS briefly?
>
> - Note that there will be a Computational Mass 
> Spectrometry/Bioinformatics for MS meeting at ASMS
>
>   - Wednesday, May 26th, 2010, 05:45-07:00pm Hall 2, Salt Palace 
> Convention Center
>
>   - Featuring Alexey Nesvizhskii and David L. Tabb
>
> ----
>
> 5) Working with ASMS on controlled vocabulary
>
> - no update
>
> Next meeting:
>
> - In 3 weeks? June 8?
>
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
>
>
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>    

[Psidev-ms-dev] PSI-MSS WG call reminder

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

Hi everyone, sorry I forgot yesterday to send around the reminder for the
call. Let's go ahead with the call 30 minutes from now as scheduled.

 

08:00 San Francisco

11:00 New York

16:00 London

17:00 Geneva

 

+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ USA: 1-866-314-3683

Generic international: +44 2083222500 (UK number)

 

access code: 297427 #

 

Agenda:

1) mzML 1.1.0

- Manuscript has been reviewed and the comments addressed and resubmitted.

- The editors have come back and asked for the inclusion of a "tangible
example of an application" and then it will be acceptable for publication.
Response in progress.

- Matt has released and posted the updated 1.1.1 version of indexedmzML
schema: <indexList> name attribute will be enumerated to "spectrum" or
"chromatogram" to disallow other creative values

- Matt will update the example files to reference mzML 1.1.0 but indexedmzML
1.1.1

- New schema is posted on the web. The tiny file has been updated.

- Eric will update the web site announcing the change and update hyperlink

- How do we handle lock mass corrections?

- We should assemble list of calibrants and make them specific terms

- Bruker uses Lithium Formiate; others?

- Jim will find out what Thermo is using

- Jim will look at an old email and send out the information

- Matt will contact David Anderson and Mike Ashton and ask about a date in
lieu of checksum

- Need to test FAIMS support in mzML

- Other items?

 

----

2) MIAPE-MS revision

- Document is ready to be submitted, but..

- We need to have 3 examples to go along with a document submission

- Until we provide the examples, it is not officially in the document
process

- We can use the sample MIAPE-compliant mzML file

- Pierre-Alain will contact Juan-Pablo to see if he has some suitable
examples in Proteo-Red

- Pierre-Alain has received an example from Proteo-Red

- Richard will look into PRIDE to see if there may be a good example there

- Pierre-Alain is looking through PRIDE to find a good example.

- The last example would be a MIAPE compliant mzML document

- Looking in Peptidome might be an alternative for finding a nicely
annotated dataset

- Waiting to sync with MIAPE-MSI as well

- Keep working on our documents and when we're ready, see if we should wait

- We also need to coordinate the creation of MIAPE-Quant

- When officially in the process, send out submitted document to journal
editors and everyone else to get the word out

 

----

3) TraML development

- New version 0.9.4 released and is available at
<http://www.psidev.info/index.php?q=node/405>
http://www.psidev.info/index.php?q=node/405

- Specification document is updated. Please examine. Is it ready for
submission?

 
<http://www.peptideatlas.org/tmp/TraML/0.9.4/TraML_0.9.4.1_specificationDocu
ment.doc>
http://www.peptideatlas.org/tmp/TraML/0.9.4/TraML_0.9.4.1_specificationDocum
ent.doc

- Implementations? Please update to 0.9.4 and test

  - Matt will implement in ProteoWizard

  - Andreas will implement in OpenMS and update on-line validator

  - ISB implementation in ATAQS nearly done

  - Jim has an implementation but just will need to update to 0.9.4

  - David Cox at Sciex will test implement?

- Are we ready to update validator page?:
<http://www.psidev.info/index.php?q=node/304>
http://www.psidev.info/index.php?q=node/304

- Manuscript is in preparation and will be sent out shortly

 

----

4) PSI session at World HUPO in Sydney

- PSI will have a session. Presenters will be Eric, Juan Antonio, Henning.

- JuanAn maybe can't go?

- Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS

- Abstract is accepted

- Other reports?

- Perhaps some of us try to meet at ASMS briefly?

- Note that there will be a Computational Mass Spectrometry/Bioinformatics
for MS meeting at ASMS

  - Wednesday, May 26th, 2010, 05:45-07:00pm Hall 2, Salt Palace Convention
Center

  - Featuring Alexey Nesvizhskii and David L. Tabb

 

----

5) Working with ASMS on controlled vocabulary

- no update

 

Next meeting: 

- In 3 weeks? June 8?

 

 

 

[Psidev-ms-dev] mzml schema location outdated

[Andreas S. <as...@eb...>]

Dear all,

I want to report that the schema at 
http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd is out of date. Since 
the example files use exactly this schema location, XML validation fails.

Let's have a look at tiny.pwiz.1.1.mzML:

Within the chromatogram element the precursor and product elements are 
not allowed by the referenced schema.
This does not happen with the latest schema version in the CVS 
repository 
(http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/schema/mzML1.1.0.xsd). 
This version is also linked from the psidev homepage.

Best regards,
Andreas Schoenegger

PS:
Oxygen validation output of tiny...:

Invalid content was found starting with element 'precursor'. One of 
'{"http://psi.hupo.org/ms/mzml":cvParam, 
"http://psi.hupo.org/ms/mzml":userParam, 
"http://psi.hupo.org/ms/mzml":binaryDataArrayList}' is expected.

Comparison of the two schema versions:

Schema (http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd)
<xs:complexType name="ChromatogramType">
     [...]
<xs:complexContent mixed="false">
<xs:extension base="dx:ParamGroupType">
<xs:sequence>
<xs:element minOccurs="1" maxOccurs="1" name="binaryDataArrayList" 
type="dx:BinaryDataArrayListType" />
</xs:sequence>
         [...]
</xs:extension>
</xs:complexContent>
</xs:complexType>

  Schema 
(http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/schema/mzML1.1.0.xsd)
<xs:complexType name="ChromatogramType">
     [...]
<xs:complexContent mixed="false">
<xs:extension base="dx:ParamGroupType">
<xs:sequence>
<xs:element minOccurs="0" name="precursor" type="dx:PrecursorType" />
<xs:element minOccurs="0" name="product" type="dx:ProductType" />
<xs:element minOccurs="1" maxOccurs="1" name="binaryDataArrayList" 
type="dx:BinaryDataArrayListType" />
</xs:sequence>
         [...]
</xs:extension>
</xs:complexContent>
</xs:complexType>

Notice the presence of the precursor and product elements in the latest 
schema version.

-- 
Andreas Schoenegger
Trainee - PRIDE Project Team
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom

[Psidev-ms-dev] PSI-MSS WG call deferred 1 week

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

Hi everyone, due a schedule change, I am unable to make it to tomorrow’s
PSI-MSS WG call. Let’s meet a week later instead, Jun 15 8am PDT, unless
this causes some serious problem?



Thanks,

Eric





*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Tuesday, May 18, 2010 9:38 AM
*To:* Mass spectrometry standard development
*Cc:* Eric Deutsch
*Subject:* PSI-MSS WG call notes



Present: Matt, Richard, Jim, Eric



Agenda:

1) mzML 1.1.0

- Manuscript has been reviewed and the comments addressed and resubmitted.

- The editors have come back and asked for the inclusion of a “tangible
example of an application" and then it will be acceptable for publication.
Response in progress.

+ Richard suggests a jzmzml as an application

+ Matt suggests quantification, wiff files, spectrum annotation

- Matt has released and posted the updated 1.1.1 version of indexedmzML
schema: <indexList> name attribute will be enumerated to “spectrum” or
“chromatogram” to disallow other creative values

- Matt will update the example files to reference mzML 1.1.0 but indexedmzML
1.1.1

- New schema is posted on the web. The tiny file has been updated.

- Eric will update the web site announcing the change and update hyperlink

+ Eric will update the other files

- How do we handle lock mass corrections?

- We should assemble list of calibrants and make them specific terms

- Bruker uses Lithium Formiate; others?

- Jim will find out what Thermo is using

- Jim will look at an old email and send out the information

+ Jim will ask around at ASMS and compile a list of calibrants commonly used

- Matt will contact David Anderson and Mike Ashton and ask about a date in
lieu of checksum

- Need to test FAIMS support in mzML

+ Eric will talk to Chris at ISB

- Other items?

+ Have the questions from Steffen on Apr 7 and Apr 8 all been resolved?

+ Sometime in the future spend some time on a dozen terms per call to
resolve them.



----

2) MIAPE-MS revision

- Document is ready to be submitted, but..

- We need to have 3 examples to go along with a document submission

- Until we provide the examples, it is not officially in the document
process

- We can use the sample MIAPE-compliant mzML file

- Pierre-Alain will contact Juan-Pablo to see if he has some suitable
examples in Proteo-Red

- Pierre-Alain has received an example from Proteo-Red

- Richard will look into PRIDE to see if there may be a good example there

- Pierre-Alain is looking through PRIDE to find a good example.

- The last example would be a MIAPE compliant mzML document

- Looking in Peptidome might be an alternative for finding a nicely
annotated dataset

- Waiting to sync with MIAPE-MSI as well

- Keep working on our documents and when we’re ready, see if we should wait

- We also need to coordinate the creation of MIAPE-Quant

- When officially in the process, send out submitted document to journal
editors and everyone else to get the word out



----

3) TraML development

- New version 0.9.4 released and is available at
http://www.psidev.info/index.php?q=node/405

- Specification document is updated. Please examine. Is it ready for
submission?


http://www.peptideatlas.org/tmp/TraML/0.9.4/TraML_0.9.4.1_specificationDocument.doc

- Implementations? Please update to 0.9.4 and test

  - Matt will implement in ProteoWizard

  + ProteoWizard implementation is complete to 0.9.4

  + Matt has sent out a sample file

  + Matt hopes to finish the C# bindings this week

  + Eric will try validating with his tools

  - Andreas will implement in OpenMS and update on-line validator

  + Sadly Andreas has perished in a car accident and is no longer with us

  - ISB implementation in ATAQS nearly done

  - Jim has an implementation but just will need to update to 0.9.4

  - David Cox at Sciex will test implement?

  + Eric will follow up with David

- Are we ready to update validator page?:
http://www.psidev.info/index.php?q=node/304

- Manuscript is in preparation and will be sent out shortly



----

4) PSI session at World HUPO in Sydney

- PSI will have a session. Presenters will be Eric, Juan Antonio, Henning.

- JuanAn maybe can’t go?

- Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS

- Abstract is accepted

- Other reports?

- Perhaps some of us try to meet at ASMS briefly?

- Note that there will be a Computational Mass Spectrometry/Bioinformatics
for MS meeting at ASMS

  - Wednesday, May 26th, 2010, 05:45-07:00pm Hall 2, Salt Palace Convention
Center

  - Featuring Alexey Nesvizhskii and David L. Tabb



----

5) Working with ASMS on controlled vocabulary

- no update

+ Matt suggested slowly working through purgatory at these calls. Eric will
prep.



Next meeting:

- In 3 weeks? June 8? Regular time

+ agreed





*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Monday, May 17, 2010 9:59 AM
*To:* Mass spectrometry standard development
*Cc:* Eric Deutsch
*Subject:* PSI-MSS WG call reminder <1 hr time shift!>



Hi everyone, I now have a conflicting meeting at the usual 8am timeslot, and
next week is ASMS, so I’d like to try to squeeze in the call one hour later.
I hope most participants can be tolerant of this.



So, the next PSI Mass Spectrometry Standards Working Group call will be
Tuesday 9am PDT:



http://www.timeanddate.com/worldclock/fixedtime.html?day=18&month=5&year=2010&hour=17&min=0&sec=0&p1=136



09:00 San Francisco

12:00 New York

17:00 London

18:00 Geneva



+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ USA: 1-866-314-3683

Generic international: +44 2083222500 (UK number)



access code: 297427 #



Agenda:

1) mzML 1.1.0

- Manuscript has been reviewed and the comments addressed and resubmitted.

- The editors have come back and asked for the inclusion of a “tangible
example of an application" and then it will be acceptable for publication.
Response in progress.

- Matt has released and posted the updated 1.1.1 version of indexedmzML
schema: <indexList> name attribute will be enumerated to “spectrum” or
“chromatogram” to disallow other creative values

- Matt will update the example files to reference mzML 1.1.0 but indexedmzML
1.1.1

- New schema is posted on the web. The tiny file has been updated.

- Eric will update the web site announcing the change and update hyperlink

- How do we handle lock mass corrections?

- We should assemble list of calibrants and make them specific terms

- Bruker uses Lithium Formiate; others?

- Jim will find out what Thermo is using

- Jim will look at an old email and send out the information

- Matt will contact David Anderson and Mike Ashton and ask about a date in
lieu of checksum

- Need to test FAIMS support in mzML

- Other items?



----

2) MIAPE-MS revision

- Document is ready to be submitted, but..

- We need to have 3 examples to go along with a document submission

- Until we provide the examples, it is not officially in the document
process

- We can use the sample MIAPE-compliant mzML file

- Pierre-Alain will contact Juan-Pablo to see if he has some suitable
examples in Proteo-Red

- Pierre-Alain has received an example from Proteo-Red

- Richard will look into PRIDE to see if there may be a good example there

- Pierre-Alain is looking through PRIDE to find a good example.

- The last example would be a MIAPE compliant mzML document

- Looking in Peptidome might be an alternative for finding a nicely
annotated dataset

- Waiting to sync with MIAPE-MSI as well

- Keep working on our documents and when we’re ready, see if we should wait

- We also need to coordinate the creation of MIAPE-Quant

- When officially in the process, send out submitted document to journal
editors and everyone else to get the word out



----

3) TraML development

- New version 0.9.4 released and is available at
http://www.psidev.info/index.php?q=node/405

- Specification document is updated. Please examine. Is it ready for
submission?


http://www.peptideatlas.org/tmp/TraML/0.9.4/TraML_0.9.4.1_specificationDocument.doc

- Implementations? Please update to 0.9.4 and test

  - Matt will implement in ProteoWizard

  - Andreas will implement in OpenMS and update on-line validator

  - ISB implementation in ATAQS nearly done

  - Jim has an implementation but just will need to update to 0.9.4

  - David Cox at Sciex will test implement?

- Are we ready to update validator page?:
http://www.psidev.info/index.php?q=node/304

- Manuscript is in preparation and will be sent out shortly



----

4) PSI session at World HUPO in Sydney

- PSI will have a session. Presenters will be Eric, Juan Antonio, Henning.

- JuanAn maybe can’t go?

- Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS

- Abstract is accepted

- Other reports?

- Perhaps some of us try to meet at ASMS briefly?

- Note that there will be a Computational Mass Spectrometry/Bioinformatics
for MS meeting at ASMS

  - Wednesday, May 26th, 2010, 05:45-07:00pm Hall 2, Salt Palace Convention
Center

  - Featuring Alexey Nesvizhskii and David L. Tabb



----

5) Working with ASMS on controlled vocabulary

- no update



Next meeting:

- In 3 weeks? June 8?

[Psidev-ms-dev] PSI-MSS WG call notes

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

Present: Matt, Richard, Jim, Eric



Agenda:

1) mzML 1.1.0

- Manuscript has been reviewed and the comments addressed and resubmitted.

- The editors have come back and asked for the inclusion of a “tangible
example of an application" and then it will be acceptable for publication.
Response in progress.

+ Richard suggests a jzmzml as an application

+ Matt suggests quantification, wiff files, spectrum annotation

- Matt has released and posted the updated 1.1.1 version of indexedmzML
schema: <indexList> name attribute will be enumerated to “spectrum” or
“chromatogram” to disallow other creative values

- Matt will update the example files to reference mzML 1.1.0 but indexedmzML
1.1.1

- New schema is posted on the web. The tiny file has been updated.

- Eric will update the web site announcing the change and update hyperlink

+ Eric will update the other files

- How do we handle lock mass corrections?

- We should assemble list of calibrants and make them specific terms

- Bruker uses Lithium Formiate; others?

- Jim will find out what Thermo is using

- Jim will look at an old email and send out the information

+ Jim will ask around at ASMS and compile a list of calibrants commonly used

- Matt will contact David Anderson and Mike Ashton and ask about a date in
lieu of checksum

- Need to test FAIMS support in mzML

+ Eric will talk to Chris at ISB

- Other items?

+ Have the questions from Steffen on Apr 7 and Apr 8 all been resolved?

+ Sometime in the future spend some time on a dozen terms per call to
resolve them.



----

2) MIAPE-MS revision

- Document is ready to be submitted, but..

- We need to have 3 examples to go along with a document submission

- Until we provide the examples, it is not officially in the document
process

- We can use the sample MIAPE-compliant mzML file

- Pierre-Alain will contact Juan-Pablo to see if he has some suitable
examples in Proteo-Red

- Pierre-Alain has received an example from Proteo-Red

- Richard will look into PRIDE to see if there may be a good example there

- Pierre-Alain is looking through PRIDE to find a good example.

- The last example would be a MIAPE compliant mzML document

- Looking in Peptidome might be an alternative for finding a nicely
annotated dataset

- Waiting to sync with MIAPE-MSI as well

- Keep working on our documents and when we’re ready, see if we should wait

- We also need to coordinate the creation of MIAPE-Quant

- When officially in the process, send out submitted document to journal
editors and everyone else to get the word out



----

3) TraML development

- New version 0.9.4 released and is available at
http://www.psidev.info/index.php?q=node/405

- Specification document is updated. Please examine. Is it ready for
submission?


http://www.peptideatlas.org/tmp/TraML/0.9.4/TraML_0.9.4.1_specificationDocument.doc

- Implementations? Please update to 0.9.4 and test

  - Matt will implement in ProteoWizard

  + ProteoWizard implementation is complete to 0.9.4

  + Matt has sent out a sample file

  + Matt hopes to finish the C# bindings this week

  + Eric will try validating with his tools

  - Andreas will implement in OpenMS and update on-line validator

  + Sadly Andreas has perished in a car accident and is no longer with us

  - ISB implementation in ATAQS nearly done

  - Jim has an implementation but just will need to update to 0.9.4

  - David Cox at Sciex will test implement?

  + Eric will follow up with David

- Are we ready to update validator page?:
http://www.psidev.info/index.php?q=node/304

- Manuscript is in preparation and will be sent out shortly



----

4) PSI session at World HUPO in Sydney

- PSI will have a session. Presenters will be Eric, Juan Antonio, Henning.

- JuanAn maybe can’t go?

- Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS

- Abstract is accepted

- Other reports?

- Perhaps some of us try to meet at ASMS briefly?

- Note that there will be a Computational Mass Spectrometry/Bioinformatics
for MS meeting at ASMS

  - Wednesday, May 26th, 2010, 05:45-07:00pm Hall 2, Salt Palace Convention
Center

  - Featuring Alexey Nesvizhskii and David L. Tabb



----

5) Working with ASMS on controlled vocabulary

- no update

+ Matt suggested slowly working through purgatory at these calls. Eric will
prep.



Next meeting:

- In 3 weeks? June 8? Regular time

+ agreed





*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Monday, May 17, 2010 9:59 AM
*To:* Mass spectrometry standard development
*Cc:* Eric Deutsch
*Subject:* PSI-MSS WG call reminder <1 hr time shift!>



Hi everyone, I now have a conflicting meeting at the usual 8am timeslot, and
next week is ASMS, so I’d like to try to squeeze in the call one hour later.
I hope most participants can be tolerant of this.



So, the next PSI Mass Spectrometry Standards Working Group call will be
Tuesday 9am PDT:



http://www.timeanddate.com/worldclock/fixedtime.html?day=18&month=5&year=2010&hour=17&min=0&sec=0&p1=136



09:00 San Francisco

12:00 New York

17:00 London

18:00 Geneva



+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ USA: 1-866-314-3683

Generic international: +44 2083222500 (UK number)



access code: 297427 #



Agenda:

1) mzML 1.1.0

- Manuscript has been reviewed and the comments addressed and resubmitted.

- The editors have come back and asked for the inclusion of a “tangible
example of an application" and then it will be acceptable for publication.
Response in progress.

- Matt has released and posted the updated 1.1.1 version of indexedmzML
schema: <indexList> name attribute will be enumerated to “spectrum” or
“chromatogram” to disallow other creative values

- Matt will update the example files to reference mzML 1.1.0 but indexedmzML
1.1.1

- New schema is posted on the web. The tiny file has been updated.

- Eric will update the web site announcing the change and update hyperlink

- How do we handle lock mass corrections?

- We should assemble list of calibrants and make them specific terms

- Bruker uses Lithium Formiate; others?

- Jim will find out what Thermo is using

- Jim will look at an old email and send out the information

- Matt will contact David Anderson and Mike Ashton and ask about a date in
lieu of checksum

- Need to test FAIMS support in mzML

- Other items?



----

2) MIAPE-MS revision

- Document is ready to be submitted, but..

- We need to have 3 examples to go along with a document submission

- Until we provide the examples, it is not officially in the document
process

- We can use the sample MIAPE-compliant mzML file

- Pierre-Alain will contact Juan-Pablo to see if he has some suitable
examples in Proteo-Red

- Pierre-Alain has received an example from Proteo-Red

- Richard will look into PRIDE to see if there may be a good example there

- Pierre-Alain is looking through PRIDE to find a good example.

- The last example would be a MIAPE compliant mzML document

- Looking in Peptidome might be an alternative for finding a nicely
annotated dataset

- Waiting to sync with MIAPE-MSI as well

- Keep working on our documents and when we’re ready, see if we should wait

- We also need to coordinate the creation of MIAPE-Quant

- When officially in the process, send out submitted document to journal
editors and everyone else to get the word out



----

3) TraML development

- New version 0.9.4 released and is available at
http://www.psidev.info/index.php?q=node/405

- Specification document is updated. Please examine. Is it ready for
submission?


http://www.peptideatlas.org/tmp/TraML/0.9.4/TraML_0.9.4.1_specificationDocument.doc

- Implementations? Please update to 0.9.4 and test

  - Matt will implement in ProteoWizard

  - Andreas will implement in OpenMS and update on-line validator

  - ISB implementation in ATAQS nearly done

  - Jim has an implementation but just will need to update to 0.9.4

  - David Cox at Sciex will test implement?

- Are we ready to update validator page?:
http://www.psidev.info/index.php?q=node/304

- Manuscript is in preparation and will be sent out shortly



----

4) PSI session at World HUPO in Sydney

- PSI will have a session. Presenters will be Eric, Juan Antonio, Henning.

- JuanAn maybe can’t go?

- Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS

- Abstract is accepted

- Other reports?

- Perhaps some of us try to meet at ASMS briefly?

- Note that there will be a Computational Mass Spectrometry/Bioinformatics
for MS meeting at ASMS

  - Wednesday, May 26th, 2010, 05:45-07:00pm Hall 2, Salt Palace Convention
Center

  - Featuring Alexey Nesvizhskii and David L. Tabb



----

5) Working with ASMS on controlled vocabulary

- no update



Next meeting:

- In 3 weeks? June 8?