psidev-ms-dev — Mass spectroscopy standard development

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

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

Hi Steffen, hi list!

Am 15.03.11 16:19, schrieb Steffen Neumann:
> Hi,
> 
> Nils, do you have some (small!!) example data for GCxGC ?
In which format? What would be the file size limit?
Where should I upload it?
> 
> We're wondering whether mzML could encode that with the current schema,
> or if it has to be extended somehow. 
Well, basically, all you need is the second column modulation time (time
interval between releases from the cryo-modulator onto the second
column, for Leco Pegasus GCxGC-MS that is). This allows you, along with
the scan rate, to calculate the
number of scans for the second dimension (e.g. t_mod = 5s,
scans_per_second:=spm =500 => 2500 scans per modulation (mass spectra)).
Then, with the number of scans per modulation, you can simply index
every scan in the two-dimensional coordinate system. Basically, this
should also work for LCxLC-(MS).
> 
> How is netCDF handling 2D retention time ?
Not at all, netCDF 2D from LECO ChromATof looks identical to 1D output,
just with a very large number of scans (>1000000). We have to know the
modulation time (duration on the second column) in advance or infer it
from the baseline modulations.
> 
> Yours,
> Steffen
> 
Yours,
Nils

-- 
#####################################################################
# Please note: since March 1st, 2010, my phone and room numbers have
# changed!
# New room: U10-144
# New phone number: +49-521-106-4342
#####################################################################
Nils Hoffmann                            phone:    +49-521-106-4342
Universitaet Bielefeld                    room:             U10-144
Techn. Fakultaet, AG Genominformatik
Nil...@Ce...
33594 Bielefeld, Germany    http://www.cebitec.uni-bielefeld.de/~hoffmann/

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

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

Hi,

Nils, do you have some (small!!) example data for GCxGC ?

We're wondering whether mzML could encode that with the current schema,
or if it has to be extended somehow. 

How is netCDF handling 2D retention time ?

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] traML: Multiplicity of <Configuration>

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

Hi Steffen, thanks for catching this. I'm pretty sure this is just a
multiplicity schema error. <Configuration> should be (1,N). For example if
you had optimization information for a transitions for both a TSQ and a
QTRAP 5500 (i.e. different optimal collision energies, etc.), then you would
have two <Configuration>s in the <ConfigurationList>.

I propose we change <Configuration> to (1..N) unless there are objections?

Thanks,
Eric


> -----Original Message-----
> From: Steffen Neumann [mailto:sne...@ip...]
> Sent: Tuesday, March 15, 2011 12:27 AM
> To: Mass spectrometry standard development
> Subject: [Psidev-ms-dev] traML: Multiplicity of <Configuration>
> 
> Hi,
> 
> independently from the other mail I am just writing,
> I found that <ConfigurationList> is (0,1) and <Configuration> is (1,1),
> so the question arises whether we couldn't simply drop
> the <ConfigurationList> and change multiplicity
> of <Configuration> to (0,1).
> 
> Or was that already mentioned somewhere ?
> 
> 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
> 
> 
> --------------------------------------------------------------------------
> ----
> Colocation vs. Managed Hosting
> A question and answer guide to determining the best fit
> for your organization - today and in the future.
> http://p.sf.net/sfu/internap-sfd2d
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

[Psidev-ms-dev] TraML change of <Validation> element

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

Hi everyone, upon recommendation of one of the reviewers, we plan on
changing the <Validation> element to <VerificationStatus>. For example:

 

<Validation>

  <cvParam cvRef="MS" accession="MS:1000910" name="transition optimized on
specified instrument"/>

  <cvParam cvRef="MS" accession="MS:1000139" name="4000 Q TRAP"/>

  <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity"
value="4072" unitCvRef="MS" unitAccession="MS:1000905" unitName="percent of
base peak times 100"/>

  <cvParam cvRef="MS" accession="MS:1000906" name="peak intensity rank"
value="2"/>

  <cvParam cvRef="MS" accession="MS:1000907" name="peak targeting
suitability rank" value="1"/>

</Validation>

 

The main reason is just that the word validation just doesn't cover the
intended meaning. The element name would ideally be the parent term for:

 

MS:1000910 (transition optimized on specified instrument)

MS:1000911 (transition validated with an MS/MS spectrum on specified
instrument)

MS:1000912 (transition purported from an MS/MS spectrum on a different,
specified instrument)

MS:1000913 (transition predicted by informatic analysis)

 

VerificationStatus is the best we have. Other suggestions? So the result
would be:

 

<VerificationStatus>

  <cvParam cvRef="MS" accession="MS:1000910" name="transition optimized on
specified instrument"/>

  <cvParam cvRef="MS" accession="MS:1000139" name="4000 Q TRAP"/>

  <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity"
value="4072" unitCvRef="MS" unitAccession="MS:1000905" unitName="percent of
base peak times 100"/>

  <cvParam cvRef="MS" accession="MS:1000906" name="peak intensity rank"
value="2"/>

  <cvParam cvRef="MS" accession="MS:1000907" name="peak targeting
suitability rank" value="1"/>

</VerificationStatus>

 

What do you think?

 

Thanks,

Eric

 

 

 

 

 

[Psidev-ms-dev] traML: Multiplicity of <Configuration>

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

Hi,

independently from the other mail I am just writing, 
I found that <ConfigurationList> is (0,1) and <Configuration> is (1,1),
so the question arises whether we couldn't simply drop 
the <ConfigurationList> and change multiplicity 
of <Configuration> to (0,1). 

Or was that already mentioned somewhere ?

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] How to encode MS3 in TraML?

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

On Mon, 2011-03-14 at 11:55 -0700, Eric Deutsch wrote:
> QTRAP 5500. The group discussed this on a call some time ago, and it
> seemed like the simplest way to implement this would be via multiple
> <Product> elements. 

Why not multiple <Precursor> ? Or, even more adventurous, 
nested <Precursor> ?  

> A) Rely on tag order to denote the various levels of fragmentation:
Probably the weakest option, since you can't rely 
on the ordering in XML through various transformations,
such as database persisting etc.

> B) Explicity provide an ordering via order attribute:
Semantically vague, the additional information should 
more closely resemble the MS experiment.

> C) Explicitly state an MS level, which accomplishes the same thing,
> but also provides more information:
Makes sense. 

Now that we're including MSn, we should make sure it is treated 
as a first-class citizen, and that the current MS2 handling 
is just a subset of MSn:

* Can we encode different collision energies in MS2/MS3 ?
  Currently, CE is encoded in <Configuration> of which 
  there can be only one per <Target>. 

  - Include MSn settings in the <Configuration> ?

  - Should we allow multiple <Configuration>, 
    and require referencing from the <Precursor> ?

  - Allow additional <cvParam> which carry a subset of what 
    is otherwise kept in <Configuration> ? Better not.
  
* Other points ?

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] How to encode MS3 in TraML?

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

Hi everyone, one of the problems with TraML that was pointed out by the
reviewers was the lack of support for MSn where n>=3. Some instruments are
able to do MS3 at least, and while this still seems to be rare, I’ve seen at
last one poster of someone doing MS3 SRM on a QTRAP 5500. The group
discussed this on a call some time ago, and it seemed like the simplest way
to implement this would be via multiple <Product> elements. One question we
were unable to resolve is whether there should be come explicit ordering or
whether just relying on the order was sufficient. Here are some
possibilities. What do you all think?



A) Rely on tag order to denote the various levels of fragmentation:



<Transition id="ADTHFLLNIYDQLR-M1-T1" peptideRef="ADTHFLLNIYDQLR-M1">

  <Precursor>

    <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target
m/z" value="862.9467" unitCvRef="MS" unitAccession="MS:1000040"
unitName="m/z"/>

   <cvParam cvRef="MS" accession="MS:1000041" name="charge state"
value="2"/>

  </Precursor>

  <Product>

    <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target
m/z" value="1040.57" unitCvRef="MS" unitAccession="MS:1000040"
unitName="m/z"/>

    <cvParam cvRef="MS" accession="MS:1000041" name="charge state"
value="1"/>

  </Product>

  <Product>

    <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target
m/z" value="534.28" unitCvRef="MS" unitAccession="MS:1000040"
unitName="m/z"/>

    <cvParam cvRef="MS" accession="MS:1000041" name="charge state"
value="1"/>

  </Product>

</Transition>



B) Explicity provide an ordering via order attribute:



<Transition id="ADTHFLLNIYDQLR-M1-T1" peptideRef="ADTHFLLNIYDQLR-M1">

  <Precursor>

    <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target
m/z" value="862.9467" unitCvRef="MS" unitAccession="MS:1000040"
unitName="m/z"/>

   <cvParam cvRef="MS" accession="MS:1000041" name="charge state"
value="2"/>

  </Precursor>

  <Product order=”1”>

    <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target
m/z" value="1040.57" unitCvRef="MS" unitAccession="MS:1000040"
unitName="m/z"/>

    <cvParam cvRef="MS" accession="MS:1000041" name="charge state"
value="1"/>

  </Product>

  <Product order=”2”>

    <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target
m/z" value="534.28" unitCvRef="MS" unitAccession="MS:1000040"
unitName="m/z"/>

    <cvParam cvRef="MS" accession="MS:1000041" name="charge state"
value="1"/>

  </Product>

</Transition>



C) Explicitly state an MS level, which accomplishes the same thing, but also
provides more information:



<Transition id="ADTHFLLNIYDQLR-M1-T1" peptideRef="ADTHFLLNIYDQLR-M1">

  <Precursor>

    <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target
m/z" value="862.9467" unitCvRef="MS" unitAccession="MS:1000040"
unitName="m/z"/>

   <cvParam cvRef="MS" accession="MS:1000041" name="charge state"
value="2"/>

  </Precursor>

  <Product msLevel=”2”>

    <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target
m/z" value="1040.57" unitCvRef="MS" unitAccession="MS:1000040"
unitName="m/z"/>

    <cvParam cvRef="MS" accession="MS:1000041" name="charge state"
value="1"/>

  </Product>

  <Product msLevel=”3”>

    <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target
m/z" value="534.28" unitCvRef="MS" unitAccession="MS:1000040"
unitName="m/z"/>

    <cvParam cvRef="MS" accession="MS:1000041" name="charge state"
value="1"/>

  </Product>

</Transition>



Maybe with option A, we could include the “MS Level” CV param instead to
describe which MS level.



Presumably these additional items would only be required if there was more
than one <Product> element. I’m not if the current validator can check that?
Anyone know?



What do you think?



Thanks,

Eric

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

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

Hi everyone, this is a reminder for the PSI MSS WG teleconference call
tomorrow, Tuesday. Please note the times below. Since USA and Europe are out
of sync on daylight savings time, the times are a little different than
usual.



08:00 San Francisco

11:00 New York

15:00 London         ß   !!

16:00 Geneva        ß    !!



+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ USA: 1-866-314-3683

Generic international: +44 2083222500 (UK number)



access code: 297427 #



Agenda:

1) PSI Spring Workshop April 11-13

- Collaborative efforts with the PI WG on mzIdentML, mzQuantML, CV

- Finishing TraML

- Drafting SRM experiment guidelines

- Drafting a format for SRM experimental results

- MIAPE-MS finalization

- MIAPE-Quant work?

- Adjacent to the ProteomeXchange workshop

- Please attend and encourage attendance



----

2) mzML 1.1.0

- We have been contacted by Vladimir Likic, who has said that he is
representing some portions of the metabolomics community and they are
interested in seeing if mzML would be a good fit for them as a
next-generation format. See:
http://bioinformatics.bio21.unimelb.edu.au/mzml.html

- Other outstanding todo items:

  - Eric should test FAIMS support in mzML

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

- Other items?



----

3) TraML development

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

- TraML was submitted to PSI document process

- Reviews are back and partially addressed.Still outstanding todo items

- Implementations? Please update to 0.9.4 and test

  - Matt has implemented in ProteoWizard complete to 0.9.4

  - Matt has finished the C# bindings which will enable Skyline support

  - Matt will sent out a sample file

  - 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

  - Eric will also contact Amol to discuss TraML implementations

  - Dave Cox at Sciex will test implement?

  - Need to add two new terms

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



----

4) 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

- 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



----

5) Improving the controlled vocabulary

- There is a todo list based on a previous discussion

- Need someone with some time to work on it

- Some folks from PRIDE have expressed the desired to clean up the CV. Work
with them.



----

6) SRM analysis guidelines and format

- At a “Data Quality Metrics” workshop in Sydney before World HUPO (hosted
by NCI), there was strong support to try to develop a set of guidelines for
reporting of SRM experiments as there currently are none. A working group
was identified at the meeting. Eric will organize some discussions on this.

- It was also proposed that PSI work on a standard format for the reporting
of SRM experiment analysis. There was some support for this. This is
distinct from mzML, which holds the chromatograms. It is distinct from TraML
which holds the input transitions. It might have some overlap with
mzQuantML. This should be discussed and a subgroup identified.





Next meeting:

- In 2 weeks Mar 29?

Re: [Psidev-ms-dev] Proposed telecon schedule for next month

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

Yes, sorry the calendar wasn't so clear. Only two calls before the PSI
meeting as marked. The other days with no call label means no call unless
we later decide otherwise.

So, next in one week. I'll send out some material prior to that.

Thanks,
Eric


> -----Original Message-----
> From: Shofstahl, Jim [mailto:jim...@th...]
> Sent: Tuesday, March 08, 2011 8:41 AM
> To: Mass spectrometry standard development
> Subject: Re: [Psidev-ms-dev] Proposed telecon schedule for next month
>
> Matt,
>
> I think the next call is on the 15th.
>
> Jim Shofstahl
>
> -----Original Message-----
> From: Matthew Chambers [mailto:mat...@gm...]
> Sent: Tuesday, March 08, 2011 8:38 AM
> To: psi...@li...
> Subject: Re: [Psidev-ms-dev] Proposed telecon schedule for next month
>
> So is there supposed to be a call today or did I already miss it? I'm
> afraid I've gotten used to the PSI-PI time of 10:30 instead of 10:00.
>
> -Matt
>
>
> On 3/7/2011 2:48 PM, Eric Deutsch wrote:
> > Hi everyone, in preparation for the upcoming PSI workshop, I'd like
> to
> > get hold a few phone conferences to prime us for work in Heidelberg.
> This is what I propose:
> >
> > Tue Mar  8
> >
> > Tue Mar 15 PSI call 8am PDT / 3pm London
> >
> > Tue Mar 22
> >
> > Tue Mar 29 PSI call 8am PDT / 4pm London
> >
> > Tue Apr  5
> >
> > Tue Apr 12 HEIDELBERG
> >
> > Does this present any major conflicts I should know about? We could
> > squeeze in one more if it seems warranted.
> >
> > Thanks,
> >
> > Eric
>
> -----------------------------------------------------------------------
> -------
> What You Don't Know About Data Connectivity CAN Hurt You This paper
> provides an overview of data connectivity, details its effect on
> application quality, and explores various alternative solutions.
> http://p.sf.net/sfu/progress-d2d
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>
> -----------------------------------------------------------------------
> -------
> What You Don't Know About Data Connectivity CAN Hurt You
> This paper provides an overview of data connectivity, details
> its effect on application quality, and explores various alternative
> solutions. http://p.sf.net/sfu/progress-d2d
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] Proposed telecon schedule for next month

[Shofstahl, J. <jim...@th...>]

Matt,

I think the next call is on the 15th.

Jim Shofstahl

-----Original Message-----
From: Matthew Chambers [mailto:mat...@gm...] 
Sent: Tuesday, March 08, 2011 8:38 AM
To: psi...@li...
Subject: Re: [Psidev-ms-dev] Proposed telecon schedule for next month

So is there supposed to be a call today or did I already miss it? I'm afraid I've gotten used to the PSI-PI time of 10:30 instead of 10:00.

-Matt


On 3/7/2011 2:48 PM, Eric Deutsch wrote:
> Hi everyone, in preparation for the upcoming PSI workshop, I'd like to 
> get hold a few phone conferences to prime us for work in Heidelberg. This is what I propose:
>
> Tue Mar  8
>
> Tue Mar 15 PSI call 8am PDT / 3pm London
>
> Tue Mar 22
>
> Tue Mar 29 PSI call 8am PDT / 4pm London
>
> Tue Apr  5
>
> Tue Apr 12 HEIDELBERG
>
> Does this present any major conflicts I should know about? We could 
> squeeze in one more if it seems warranted.
>
> Thanks,
>
> Eric

------------------------------------------------------------------------------
What You Don't Know About Data Connectivity CAN Hurt You This paper provides an overview of data connectivity, details its effect on application quality, and explores various alternative solutions. http://p.sf.net/sfu/progress-d2d _______________________________________________
Psidev-ms-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] Proposed telecon schedule for next month

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

So is there supposed to be a call today or did I already miss it? I'm afraid I've gotten used to the 
PSI-PI time of 10:30 instead of 10:00.

-Matt


On 3/7/2011 2:48 PM, Eric Deutsch wrote:
> Hi everyone, in preparation for the upcoming PSI workshop, I’d like to get hold a few phone
> conferences to prime us for work in Heidelberg. This is what I propose:
>
> Tue Mar  8
>
> Tue Mar 15 PSI call 8am PDT / 3pm London
>
> Tue Mar 22
>
> Tue Mar 29 PSI call 8am PDT / 4pm London
>
> Tue Apr  5
>
> Tue Apr 12 HEIDELBERG
>
> Does this present any major conflicts I should know about? We could squeeze in one more if it seems
> warranted.
>
> Thanks,
>
> Eric

[Psidev-ms-dev] Proposed telecon schedule for next month

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

Hi everyone, in preparation for the upcoming PSI workshop, I’d like to get
hold a few phone conferences to prime us for work in Heidelberg. This is
what I propose:



Tue Mar  8

Tue Mar 15 PSI call 8am PDT / 3pm London

Tue Mar 22

Tue Mar 29 PSI call 8am PDT / 4pm London

Tue Apr  5

Tue Apr 12 HEIDELBERG



Does this present any major conflicts I should know about? We could squeeze
in one more if it seems warranted.



Thanks,

Eric

[Psidev-ms-dev] PSI MSSWG plans for PSI Workshop Apr 11-13

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

Hi everyone, as you may be aware, the next PSI workshop is April 11-13 in
Heidelberg, please see:

http://www.psidev.info/index.php?q=node/452



The topics for discussion/collaboration/progress for the Mass Spectrometry
Standards Working Group are:

- Finishing TraML format

- Holding joint discussions with PSI PI WG on mzIdentML, mzQuantML,
MIAPE-Quant, SRM

- Drafting SRM experiment guidelines

- Drafting SRM analysis results format



I would encourage as many attendees as possible to help with the development
of these resources. Please register (free) and come if you are able!



Please let me know if you have any questions.



Thanks,

Eric







Eric Deutsch, Ph.D.

Institute for Systems Biology

1441 North 34th Street

Seattle WA 98103

Tel: 206-732-1397

Fax: 206-732-1260

Email: ede...@sy...

WWW: http://www.systemsbiology.org/Senior_Research_Scientists/Eric_Deutsch

[Psidev-ms-dev] MZ mine software

[Virginia B. <be...@em...>]

Dear Mr/Ms

I would like have some information on the MZ mine import data. I'm 
working with carotenoids run with HPLC and photodiode array, that will 
give me dat file with chromatogram,  and Retention time and Area in 
table for each peaks detected.
I find MZ mine software really useful in the view to compare different 
chromatogam obtained from different samples by alignment and profiling. 
We have also manually read each chromatogram creating an excel data set 
with a raw for each sample and columns for each peak detected (blank 
where the peak have been not detected in the chromatogram.

I would like import the dat file, or the excel table similar to the 
MAster peak list matrix obtained by the alignment process but I don't 
know how.

More  I read in the manual that is possible obtain parameters like 
weight for RT or M/Z that in my case could be amplitude or intensity or 
area, and a distance between a peak in the sample and a master peak raw.

I will really apreciate any advice or suggestion on the possible way to 
proceed to obtain a reliable analysis of diffrence between my samples, 
that, I care to mention,  are in the samples in same case not 
independent as precursor and metabolite.

Thanks for your availability

Best regards
Virginia Belloni

-- 
Dr Virginia Belloni
Ecology and Evolutionary Biology
University of Arizona
Tucson, AZ 85721-0088,US
be...@em...

Re: [Psidev-ms-dev] [Psidev-ms-vocab] CV terms for MS ontology

[Martin E. <mar...@ru...>]

Hi!

 

I could add them technically, but I'm not familiar with the structure and
previous design logic of the PSI-MS part

of the ontology.

Thus I would be grateful if Luisa could do it...

 

  bye

   Martin

 

 

Von: Salvador Martínez de Bartolomé [mailto:sma...@pr...] 
Gesendet: Donnerstag, 24. Februar 2011 14:47
An: psi...@li...;
psi...@li...; psi...@li...
Betreff: [Psidev-ms-vocab] CV terms for MS ontology

 

Hi all:

Maybe you remember some months ago, I sent to the mailing list a document
with some candidate CV terms for the HUPO-PSI ontologies.

                Matt Chambers sent some comments and Martin Eisenacher also
checked the CV list and added some terms, related to the PI group (CVs for
use in mzIdentML) to the PSI Mass Spectrometry ontology.

                However, Martin asked if Luisa or someone else could check
the rest of CV terms in the list, related with MS group (CVs for use in
mzML), but, as far as I know, nobody answered to that in the mailing list.

                The list with the MS-related CV terms is attached here.

                I hope some people could check them and add them (or not) to
the ontology obo file.

                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

 

[Psidev-ms-dev] CV terms for MS ontology regarding modifications

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

Hello,

I have some further candidates for CV terms in psi-ms.obo:

Proteome Discoverer for instance has two parameters regarding the number 
of modifications:
1) Max. Modifications Per Peptide
2) Max. identical Modifications Per Peptide
which seem to be missing until now in the CV.

In addition under
AnalysisProtocolCollection\SpectrumIdentificationProtocol\ModificationParams\SearchModification\ModParam
there are only CvParams allowed.

Would it make sense to allow here also UserParams?

Best Regards,

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

Phone:	+49(0)234/32-29262
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

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

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

Hi everyone, we had tentatively agreed to meet again November 9, but due to
vacation and other conflicts, it probably doesn't make sense to have a call
today. Instead, I'll follow up with emails.

 

Thanks,

Eric

 

 

  _____  

From: Eric Deutsch [mailto:ede...@sy...] 
Sent: Tuesday, October 19, 2010 10:42 AM
To: Mass spectrometry standard development
Cc: Eric Deutsch
Subject: PSI MSS WG call notes

 

Present: Matt, Steffen, Florian, Jim, Eric

 

The current response to the review comments was gone through and discussed.

 

Action items:

 

- Do we want to show a little figure showing an out-of-sync transition?

 

- <VerficationStatus> [This is not settled. Eric will grok the situation and
email out a question to the list for further discussion].

 

- The question is do we rely order alone, or do we add a "n" attribute or
"order" attribute. OR better yet use MS Level CV term? Come up with an
example and email the list.

 

- Add isolation width  to mapping file

 

- Talk to Brendan again about Skyline and TraML

 

- add the protein terms

 

- add link to spML file and msrun data URL probably as new CV terms

 

- Matt suggests for last point to just use transitions relative intensity

 

- Steffen asks about adducts?

 

Next meeting:

Next in 3 weeks. Nov 9

 

 

 

 

 

 

 

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

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

Hi all,

One things we forgot to add. We're going to move all the development work for mzQuantML back onto the PSI-PI list so we don't parallel post everything. Could anyone from the MS group who is interested sign up for that list: https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev

I am also looking for volunteers for someone to take charge of the MIAPE quantification section, which will likely become a module in its own right. If anyone would like to volunteer to take a lead on this, let me know,
Cheers
Andy



> -----Original Message-----
> From: Florian [mailto:fl...@eb...]
> Sent: 28 October 2010 17:45
> To: psi...@li...; Mass spectrometry standard
> development
> Subject: [Psidev-ms-dev] PSI PI WG call notes
> 
> Attendees:
> 
> Andy Jones (U. Liv)
> Ritesh Krishna (U. Liv)
> Frederik Levander (Lund)
> Oliver Kohlbacher (Tuebingen)
> Mathias Walzer (Tuebingen)
> Julian Selley (U. Manchester)
> Pieter Neerincx (Utrecht University)
> Henk van den Toorn (Utrecht University)
> Alberto Medina (ProteoRed) + anyone else?
> Florian Reisinger (EBI)
> Laurent Gatto (CCP/EBI)
> Martin Eisenacher (Bochum) +1 I didn't get
> Eric Deutsch (ISB)
> 
> 
> Discussion items on scope of mzQuantML
> --------------------------------------
> 
> - possible delay of schema development/publication.
> 
> - need schema not just for reporting protein/peptide abundance levels,
> but also as data exchange/interoperability standard for tools where
> features/matches are necessary.
> 
> - features also basis of quality/confidence, need to trace back to the
> data giving rise to the quantitation data.
> 
> - schema prototypes already existing (developed by OpenMS/APML).
> possible replacement for former schemas (analysisXML)?
> 
> - possible issues with nesting/cyclic structure of features? Define
> conventions for different use cases?
> 
> 
> Organisation of work
> --------------------
> 
> - Agree to decouple/parallelise work for level 1 (protein/peptide
> abundance) and level 2 (features/matches).
> 
> - need to organize regrouping and later merging of work. strategies and
> time lines should be set up.
> 
> - define early on how level 2 would be integrated into level 1.
> 
> - data on level 1 should be possible without need for level 2 data and
> possibly vice versa
> 
> 
> Other topics
> ------------
> 
> - MRM/SRM data: possible overlap with features in MzQuantML? Possibility
> to join efforts.
> 
> - bring MS and PI groups closer together to benefit from each others
> work and expertise.
> 
> - Oliver to take lead in mzQuantML level 2 development using PSI
> mechanisms i.e. googlecode and conference calls.
> 
> - Telephone conferences Thursdays every two weeks, possibly with focus
> on one or the other level (as required).
> 
> - mzIdentML implementations: openMS, ProteoWizard and jmzIdentML some
> way done, but not quite there.
> 
> - ProteoRed: MIAPE check tool for mzIdentML
> 
> - MIAPE document update for quantitation. Remove of quantitation section
> from MIAPE MS and prepare separately (to be done).
> 
> 
> Main ACTION points:
> -------------------
> 
> - Oliver and Mathias to work integrating current schema in googlecode
> with the feature part of their schema
> - Andy to arrange next call for same slot in two weeks time
> - Oliver to send round example of MRM encoded in their quant schema
> 
> 
> 
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
> http://p.sf.net/sfu/nokia-dev2dev
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

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

[Florian <fl...@eb...>]

Attendees:

Andy Jones (U. Liv)
Ritesh Krishna (U. Liv)
Frederik Levander (Lund)
Oliver Kohlbacher (Tuebingen)
Mathias Walzer (Tuebingen)
Julian Selley (U. Manchester)
Pieter Neerincx (Utrecht University)
Henk van den Toorn (Utrecht University)
Alberto Medina (ProteoRed) + anyone else?
Florian Reisinger (EBI)
Laurent Gatto (CCP/EBI)
Martin Eisenacher (Bochum) +1 I didn't get
Eric Deutsch (ISB)


Discussion items on scope of mzQuantML
--------------------------------------

- possible delay of schema development/publication.

- need schema not just for reporting protein/peptide abundance levels, 
but also as data exchange/interoperability standard for tools where 
features/matches are necessary.

- features also basis of quality/confidence, need to trace back to the 
data giving rise to the quantitation data.

- schema prototypes already existing (developed by OpenMS/APML). 
possible replacement for former schemas (analysisXML)?

- possible issues with nesting/cyclic structure of features? Define 
conventions for different use cases?


Organisation of work
--------------------

- Agree to decouple/parallelise work for level 1 (protein/peptide 
abundance) and level 2 (features/matches).

- need to organize regrouping and later merging of work. strategies and 
time lines should be set up.

- define early on how level 2 would be integrated into level 1.

- data on level 1 should be possible without need for level 2 data and 
possibly vice versa


Other topics
------------

- MRM/SRM data: possible overlap with features in MzQuantML? Possibility 
to join efforts.

- bring MS and PI groups closer together to benefit from each others 
work and expertise.

- Oliver to take lead in mzQuantML level 2 development using PSI 
mechanisms i.e. googlecode and conference calls.

- Telephone conferences Thursdays every two weeks, possibly with focus 
on one or the other level (as required).

- mzIdentML implementations: openMS, ProteoWizard and jmzIdentML some 
way done, but not quite there.

- ProteoRed: MIAPE check tool for mzIdentML

- MIAPE document update for quantitation. Remove of quantitation section
from MIAPE MS and prepare separately (to be done).


Main ACTION points:
-------------------

- Oliver and Mathias to work integrating current schema in googlecode 
with the feature part of their schema
- Andy to arrange next call for same slot in two weeks time
- Oliver to send round example of MRM encoded in their quant schema

Re: [Psidev-ms-dev] mzQuantML update

[Oliver K. <oli...@un...>]

Dear all,

in preparation for the mzQuantML discussion a simplifed version of the feature 
part that we would like to bring into the discussion.

Cheers,
  Oliver + Mathias

Re: [Psidev-ms-dev] mzQuantML update

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

Hi all,

Prior to the call today, I’m re-sending my mail that followed our last development workshop as a point for discussion. Some example files have since been updated in the googlecode repository, and there has been further discussion of scope since I realise we are not all 100% agreed on this yet, but this is gives us something to start the discussions.

Cheers
Andy



From: Jones, Andy [mailto:And...@li...]
Sent: 03 September 2010 11:12
To: 'psi...@li...'
Cc: 'psi...@li...'
Subject: [Psidev-ms-dev] mzQuantML update

Hi all,

Just a quick update for those who were unable to attend the recent mzQuantML meeting, Juan Antonio is going to circulate the full minutes later on. Hopefully we can arrange the next meeting at a time and place where others can attend, especially those from US, since we’re of course very keen to take on board input from all interested parties!

At the meeting we reached a tentative agreements on development approach:


-          We plan for development in stages, where we aim first for a mzQuantML level 1 that captures Protein and Peptide abundance values, but no models of underlying MS features or matches. MS features and feature matches will be added in Level 2. The rational is that the community needs a working data exchange model in the short term, most importantly to support database submission and data reporting.

-          Plan for monthly development conference calls starting from September, open to any interested parties. Date of first meeting to be set, but 4pm UK time on a Thursday seemed to be a good slot for meeting participants. If you would like to join these and would prefer another slot, let me know.

Most time at the meeting was spent working on data models for reporting protein and peptide relative/absolute abundance, grouping across replicates and protocols for specifying how these measures were generated. All artefacts have been (or will be soon) loaded into the SVN on googlecode: http://code.google.com/p/mzquantml/. We have uploaded a version 0.1 schema and some example files, although the repository and example files need tidying up over the coming weeks. Older example files are still archived there, so look at the dates files were uploaded to see which are recent.

It should be stressed that there are of course many open issues and nothing is seen as being close to a final modelling decision, so those who were not able to attend the meeting should get involved and push alternative ideas.

In summary, the model has the following structure at present:


ProteinList
     ProteinAmbiguityGroup

-          Optional quant values
 ProteinDetectionHypothesis

o   Optional quant values

o   peptideRefs

PeptideList
     Peptide

-          Optional quant values

AssayList (summarises collections of raw files)

-          QuantUnit (looking for a better name – encapsulates concept of one “run” on a label-free or one “channel” of a SILAC or iTRAQ, to be referenced elsewhere)

StudyVariablesList (groupings of QuantUnits – for purposes of grouping replicate values at PAG, PDH or PeptideLevel; this model has some recognised flaws that need to be fixed)

ProtocolList (definitions of how measures or ratios are calculated, for example with references to QuantUnits)

The optional quant values at PAG, PDH or PeptideLevel can be given for single QuantUnits or for StudyVariables (i.e. groups of replicates), and these can be single measures of abundance (plus associated stats) or ratios of abundance (plus associated stats).

Hopefully, this should spark some discussion on the list and then let’s aim for a first conference call towards the end of the month,
Best wishes
Andy

[Psidev-ms-dev] PSI-PI conference call

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

Hi all,

Just to confirm, we will have a conference call this Thurs at 4pm UK time: http://www.timeanddate.com/worldclock/fixedtime.html?day=25&month=10&year=2010&hour=16&min=0&sec=0&p1=136

Agenda:


1.       Scope and remit for mzQuantML (i.e. for first release features in or out)

2.       Review current examples in the googlecode: http://code.google.com/p/mzquantml/

3.       Short discussion about status of mzIdentML (paper and implementations)

4.       Plan for future development and calls

5.       AOB

Let me know if you’d like to add anything to the agenda.


Dial in details:

+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ USA: 1-866-314-3683

+ Generic international: +44 2083222500 (UK number)

access code: 297427

Florian / Juan, I hope the call details are still correct, let me know if anything has changed.
Cheers
Andy


From: Jones, Andy [mailto:And...@li...]
Sent: 19 October 2010 14:00
To: 'Mass spectrometry standard development'; 'psi...@li...'
Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on mzQuantML consideration

Hi all,

It looks like 28th Oct at 4pm UK time (http://www.timeanddate.com/worldclock/fixedtime.html?day=25&month=10&year=2010&hour=16&min=0&sec=0&p1=136) is the best slot for most people, so let’s go with that.

Juan, would you be able to find someone else to start the call for us, using the EBI line? I’ll send round an agenda for discussion early next week,
Best wishes
Andy


From: Jones, Andy [mailto:And...@li...]
Sent: 14 October 2010 11:54
To: 'Mass spectrometry standard development'; 'psi...@li...'
Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on mzQuantML consideration

Hi all,

Seems difficult to find a slot :) Doodle poll created, can you complete with availability: http://www.doodle.com/nqe59tnb7bmzce7q

Cheers
Andy

From: David Creasy [mailto:dc...@ma...]
Sent: 14 October 2010 10:11
To: psi...@li...
Cc: Mass spectrometry standard development
Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on mzQuantML consideration

I'll be away then, so it's unlikely that I'll be able to make it. But please go ahead without me - I think that my views and Andy's views are pretty similar.

David

Eric Deutsch wrote:
Not as convenient for me, but it will be fine, yes.

From: Jones, Andy [mailto:And...@li...<mailto:And...@li...>]
Sent: Wednesday, October 13, 2010 7:43 AM
To: Mass spectrometry standard development; psi...@li...<mailto:psi...@li...>
Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on mzQuantML consideration

28/10 would also be okay with me, anyone else?
cheers
Andy
________________________________
From: Henk van den Toorn [h.w...@uu...<mailto:h.w...@uu...>]
Sent: 13 October 2010 15:28
To: Mass spectrometry standard development
Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on mzQuantML consideration
Fine by us, Henk & Pieter

On 12-10-2010 19:08, Oliver Kohlbacher wrote:

Dear all,



not good for me -- I will be on a plane during that time.

How about one week later, 10/28 same time?



Cheers,

 Oliver



On 12.10.2010, at 15:33, Jones, Andy wrote:



Hi all,



There has been some interesting discussions on the scope of mzQuantML and some work been done on use cases fulfilling the first draft we built after the Sept development meeting. I’d like to arrange a conference call to discuss the main issues. It appears that the most convenient time for people in different locations is usually 4pm UK time. I would like to take on board as many opinions as possible so let’s try find a time that is suitable for most people.



How would Thurs 21st Oct at 4pm UK (8am West coast, 11am East Coast) suit people? If not please suggest some alternatives,

Cheers

Andy













From: Henk van den Toorn [mailto:h.w...@uu...]

Sent: 01 October 2010 16:44

To: psi...@li...<mailto:psi...@li...>; mbr...@sy...<mailto:mbr...@sy...>

Subject: [Psidev-pi-dev] Fwd: [Psidev-ms-dev] Essential element on mzQuantML consideration



Hello all,



Sorry for cross-forwarding (is that a word?), but I noticed this message was sent to the ms-dev mailinglist while I guess it should have gone to the mzQuantML (psidev-pi) mailing list.



-----------





Dear PSI mzQuantML discussion participants,



Background of APML

Corra (http://www.biomedcentral.com/1471-2105/9/542) is published in 2008 with APML (Annotated Putative peptide Markup Language) that enables using several different ms1 peak extraction and alignment modules. After publication, Damon May, who is a lead developer on MSInspect from Fred Hutchinson Cancer Research Center, initiated to use APML for broader use for MsInspect and LabKey as well as Parag Mallick group in Los Angeles. After review and merging all institutions’ needs for capturing MS1 dataset, we introduced APML v2.0 schema and java written parsers (http://sourceforge.net/projects/corra/files/ ) . Then Eric Deutsch introduced APML v2.0 to PSI in 2008.



mzQuantML that Oliver is leading.

Recent my visit to Oliver Kohlbacher group in University of Tubingen and meeting with Peter Horvatovich from University of Groningen in HUPO Sydney, The mzQuantML schema and availability of its parser and validator can be an important contribution to bioinformatician and computational biologists, who develop or process MS1 based dataset for biological system studies.



Essential elements in the schema

To the best of my knowledge, we (ISB, FHCRC, Labkey, Peter’s group) are using APML v2.0, it would be nice (or rather essential) to have some of elements that can capture essential dataset to reproduce or reprocessing (e.g., statistical analysis on quantification etc). Thus, without further explanation, I have absolute agreement on Dr. Kohlbacher comments on “complexity is expected”  posted on Sep 13 to this mailing list.  The “feature” element is an absolute “must” for MS1 based pipeline. In my experience and perspective of continuous usage of Corra for several biomarker discovery projects, we need the feature element for mzQuantML  and  it will help for broad future mzQuantML schema in proteomics community.



Thank you for reading.



Warm Regards,

Mi-Youn



Mi-Youn Brusniak, Ph.D.

Computational Biology

Seattle Proteome Center

mbr...@sy...<mailto:mbr...@sy...>

Tel: (206)732-1327





Mi-Youn Brusniak, Ph.D.

Computational Biology

Seattle Proteome Center

mbr...@sy...<mailto:mbr...@sy...>

Tel: (206)732-1327

------------------------------------------------------------------------------

Beautiful is writing same markup. Internet Explorer 9 supports

standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.

Spend less time writing and  rewriting code and more time creating great

experiences on the web. Be a part of the beta today.

http://p.sf.net/sfu/beautyoftheweb_______________________________________________

Psidev-ms-dev mailing list

Psi...@li...<mailto:Psi...@li...>

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

---

Oliver Kohlbacher (oli...@un...<mailto:oli...@un...>)

Professor, Center for Bioinformatics Tuebingen, Eberhard Karls University Tuebingen

phone: +49-7071-29-70457   http://www-bs.informatik.uni-tuebingen.de



vCard at: http://www-bs.informatik.uni-tuebingen.de/People/kohlbach/vCard















------------------------------------------------------------------------------

Beautiful is writing same markup. Internet Explorer 9 supports

standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.

Spend less time writing and  rewriting code and more time creating great

experiences on the web. Be a part of the beta today.

http://p.sf.net/sfu/beautyoftheweb

_______________________________________________

Psidev-ms-dev mailing list

Psi...@li...<mailto:Psi...@li...>

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

--
-------------------------------------------------------------------------------------------------------
Henk van den Toorn, bioinformatician
Biomolecular Mass Spectrometry and Proteomics Group
Bijvoet Center for Biomolecular Research and
Utrecht Institute for Pharmaceutical Sciences
Utrecht University
Padualaan, 8
3584 CH Utrecht
The Netherlands

E-mail: h.w...@uu...<mailto:h.w...@uu...>
Tel: +31 30 253 6758
Fax: +31 30 253 6919
--------------------------------------------------------------------------------------------------














________________________________














------------------------------------------------------------------------------

Beautiful is writing same markup. Internet Explorer 9 supports

standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.

Spend less time writing and  rewriting code and more time creating great

experiences on the web. Be a part of the beta today.

http://p.sf.net/sfu/beautyoftheweb














________________________________














_______________________________________________

Psidev-pi-dev mailing list

Psi...@li...<mailto:Psi...@li...>

https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev




--

David Creasy

Matrix Science

64 Baker Street

London W1U 7GB, UK

Tel: +44 (0)20 7486 1050

Fax: +44 (0)20 7224 1344



dc...@ma...<mailto:dc...@ma...>

http://www.matrixscience.com



Matrix Science Ltd. is registered in England and Wales

Company number 3533898

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

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

Present: Matt, Steffen, Florian, Jim, Eric



The current response to the review comments was gone through and discussed.



Action items:



- Do we want to show a little figure showing an out-of-sync transition?



- <VerficationStatus> [This is not settled. Eric will grok the situation and
email out a question to the list for further discussion].



- The question is do we rely order alone, or do we add a “n” attribute or
“order” attribute. OR better yet use MS Level CV term? Come up with an
example and email the list.



- Add isolation width  to mapping file



- Talk to Brendan again about Skyline and TraML



- add the protein terms



- add link to spML file and msrun data URL probably as new CV terms



- Matt suggests for last point to just use transitions relative intensity



- Steffen asks about adducts?



Next meeting:

Next in 3 weeks. Nov 9

Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on mzQuantML consideration

[Florian <fl...@eb...>]

Hi Andy,
I am sure we will find someone here at the EBI to start the phone conf. 
Either Richard or myself should be around to do this.

Cheers,
Florian


On 19/10/2010 14:00, Jones, Andy wrote:
> Hi all,
>
> It looks like 28^th Oct at 4pm UK time
> (http://www.timeanddate.com/worldclock/fixedtime.html?day=25&month=10&year=2010&hour=16&min=0&sec=0&p1=136
> <http://www.timeanddate.com/worldclock/fixedtime.html?day=25&month=10&year=2010&hour=16&min=0&sec=0&p1=136>)
> is the best slot for most people, so let’s go with that.
>
> Juan, would you be able to find someone else to start the call for us,
> using the EBI line? I’ll send round an agenda for discussion early next
> week,
>
> Best wishes
>
> Andy
>
> *From:* Jones, Andy [mailto:And...@li...]
> *Sent:* 14 October 2010 11:54
> *To:* 'Mass spectrometry standard development';
> 'psi...@li...'
> *Subject:* Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on
> mzQuantML consideration
>
> Hi all,
>
> Seems difficult to find a slot J Doodle poll created, can you complete
> with availability: http://www.doodle.com/nqe59tnb7bmzce7q
>
> Cheers
>
> Andy
>
> *From:* David Creasy [mailto:dc...@ma...]
> *Sent:* 14 October 2010 10:11
> *To:* psi...@li...
> *Cc:* Mass spectrometry standard development
> *Subject:* Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on
> mzQuantML consideration
>
> I'll be away then, so it's unlikely that I'll be able to make it. But
> please go ahead without me - I think that my views and Andy's views are
> pretty similar.
>
> David
>
> Eric Deutsch wrote:
>
> Not as convenient for me, but it will be fine, yes.
>
> *From:* Jones, Andy [mailto:And...@li...
> <mailto:And...@li...>]
> *Sent:* Wednesday, October 13, 2010 7:43 AM
> *To:* Mass spectrometry standard development;
> psi...@li...
> <mailto:psi...@li...>
> *Subject:* Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on
> mzQuantML consideration
>
> 28/10 would also be okay with me, anyone else?
>
> cheers
>
> Andy
>
> ------------------------------------------------------------------------
>
> *From:* Henk van den Toorn [h.w...@uu...
> <mailto:h.w...@uu...>]
> *Sent:* 13 October 2010 15:28
> *To:* Mass spectrometry standard development
> *Subject:* Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on
> mzQuantML consideration
>
> Fine by us, Henk & Pieter
>
> On 12-10-2010 19:08, Oliver Kohlbacher wrote:
>
> Dear all,
>
>
>
> not good for me -- I will be on a plane during that time.
>
> How about one week later, 10/28 same time?
>
>
>
> Cheers,
>
>   Oliver
>
>
>
> On 12.10.2010, at 15:33, Jones, Andy wrote:
>
>
>
>     Hi all,
>
>
>
>     There has been some interesting discussions on the scope of mzQuantML and some work been done on use cases fulfilling the first draft we built after the Sept development meeting. I’d like to arrange a conference call to discuss the main issues. It appears that the most convenient time for people in different locations is usually 4pm UK time. I would like to take on board as many opinions as possible so let’s try find a time that is suitable for most people.
>
>
>
>     How would Thurs 21st Oct at 4pm UK (8am West coast, 11am East Coast) suit people? If not please suggest some alternatives,
>
>     Cheers
>
>     Andy
>
>
>
>
>
>
>
>
>
>
>
>
>
>     From: Henk van den Toorn [mailto:h.w...@uu...]
>
>     Sent: 01 October 2010 16:44
>
>     To:psi...@li...  <mailto:psi...@li...>;mbr...@sy...  <mailto:mbr...@sy...>
>
>     Subject: [Psidev-pi-dev] Fwd: [Psidev-ms-dev] Essential element on mzQuantML consideration
>
>
>
>     Hello all,
>
>
>
>     Sorry for cross-forwarding (is that a word?), but I noticed this message was sent to the ms-dev mailinglist while I guess it should have gone to the mzQuantML (psidev-pi) mailing list.
>
>
>
>     -----------
>
>
>
>
>
>     Dear PSI mzQuantML discussion participants,
>
>
>
>     Background of APML
>
>     Corra (http://www.biomedcentral.com/1471-2105/9/542) is published in 2008 with APML (Annotated Putative peptide Markup Language) that enables using several different ms1 peak extraction and alignment modules. After publication, Damon May, who is a lead developer on MSInspect from Fred Hutchinson Cancer Research Center, initiated to use APML for broader use for MsInspect and LabKey as well as Parag Mallick group in Los Angeles. After review and merging all institutions’ needs for capturing MS1 dataset, we introduced APML v2.0 schema and java written parsers (http://sourceforge.net/projects/corra/files/  ) . Then Eric Deutsch introduced APML v2.0 to PSI in 2008.
>
>
>
>     mzQuantML that Oliver is leading.
>
>     Recent my visit to Oliver Kohlbacher group in University of Tubingen and meeting with Peter Horvatovich from University of Groningen in HUPO Sydney, The mzQuantML schema and availability of its parser and validator can be an important contribution to bioinformatician and computational biologists, who develop or process MS1 based dataset for biological system studies.
>
>
>
>     Essential elements in the schema
>
>     To the best of my knowledge, we (ISB, FHCRC, Labkey, Peter’s group) are using APML v2.0, it would be nice (or rather essential) to have some of elements that can capture essential dataset to reproduce or reprocessing (e.g., statistical analysis on quantification etc). Thus, without further explanation, I have absolute agreement on Dr. Kohlbacher comments on “complexity is expected”    posted on Sep 13 to this mailing list.    The “feature” element is an absolute “must” for MS1 based pipeline. In my experience and perspective of continuous usage of Corra for several biomarker discovery projects, we need the feature element for mzQuantML    and    it will help for broad future mzQuantML schema in proteomics community.
>
>
>
>     Thank you for reading.
>
>
>
>     Warm Regards,
>
>     Mi-Youn
>
>
>
>     Mi-Youn Brusniak, Ph.D.
>
>     Computational Biology
>
>     Seattle Proteome Center
>
>     mbr...@sy...  <mailto:mbr...@sy...>
>
>     Tel: (206)732-1327
>
>
>
>
>
>     Mi-Youn Brusniak, Ph.D.
>
>     Computational Biology
>
>     Seattle Proteome Center
>
>     mbr...@sy...  <mailto:mbr...@sy...>
>
>     Tel: (206)732-1327
>
>     ------------------------------------------------------------------------------
>
>     Beautiful is writing same markup. Internet Explorer 9 supports
>
>     standards for HTML5, CSS3, SVG 1.1,    ECMAScript5, and DOM L2&  L3.
>
>     Spend less time writing and    rewriting code and more time creating great
>
>     experiences on the web. Be a part of the beta today.
>
>     http://p.sf.net/sfu/beautyoftheweb_______________________________________________
>
>     Psidev-ms-dev mailing list
>
>     Psi...@li...  <mailto:Psi...@li...>
>
>     https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>
> ---
>
> Oliver Kohlbacher (oli...@un...  <mailto:oli...@un...>)
>
> Professor, Center for Bioinformatics Tuebingen, Eberhard Karls University Tuebingen
>
> phone: +49-7071-29-70457      http://www-bs.informatik.uni-tuebingen.de
>
>
>
> vCard at:http://www-bs.informatik.uni-tuebingen.de/People/kohlbach/vCard
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
>
> Beautiful is writing same markup. Internet Explorer 9 supports
>
> standards for HTML5, CSS3, SVG 1.1,    ECMAScript5, and DOM L2&  L3.
>
> Spend less time writing and    rewriting code and more time creating great
>
> experiences on the web. Be a part of the beta today.
>
> http://p.sf.net/sfu/beautyoftheweb
>
> _______________________________________________
>
> Psidev-ms-dev mailing list
>
> Psi...@li...  <mailto:Psi...@li...>
>
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>
> --
>
> -------------------------------------------------------------------------------------------------------
> *Henk van den Toorn, bioinformatician*
> Biomolecular Mass Spectrometry and Proteomics Group
> Bijvoet Center for Biomolecular Research and
> Utrecht Institute for Pharmaceutical Sciences
> Utrecht University
> Padualaan, 8
> 3584 CH Utrecht
> The Netherlands
>
> E-mail: h.w...@uu... <mailto:h.w...@uu...>
> Tel: +31 30 253 6758
> Fax: +31 30 253 6919
> --------------------------------------------------------------------------------------------------
>
>
>
>
>
>
>
>
> ------------------------------------------------------------------------
>
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
>
> Beautiful is writing same markup. Internet Explorer 9 supports
>
> standards for HTML5, CSS3, SVG 1.1,    ECMAScript5, and DOM L2&  L3.
>
> Spend less time writing and    rewriting code and more time creating great
>
> experiences on the web. Be a part of the beta today.
>
> http://p.sf.net/sfu/beautyoftheweb
>
>
>
>
>
>
>
>
> ------------------------------------------------------------------------
>
>
>
>
>
>
>
>
> _______________________________________________
>
> Psidev-pi-dev mailing list
>
> Psi...@li...  <mailto:Psi...@li...>
>
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
>
>
>
> --
>
> David Creasy
>
> Matrix Science
>
> 64 Baker Street
>
> London W1U 7GB, UK
>
> Tel: +44 (0)20 7486 1050
>
> Fax: +44 (0)20 7224 1344
>
>
>
> dc...@ma...  <mailto:dc...@ma...>
>
> http://www.matrixscience.com
>
>
>
> Matrix Science Ltd. is registered in England and Wales
>
> Company number 3533898
>
>
>
> ------------------------------------------------------------------------------
> Download new Adobe(R) Flash(R) Builder(TM) 4
> The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly
> Flex(R) Builder(TM)) enable the development of rich applications that run
> across multiple browsers and platforms. Download your free trials today!
> http://p.sf.net/sfu/adobe-dev2dev
>
>
>
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on mzQuantML consideration

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

Hi all,

It looks like 28th Oct at 4pm UK time (http://www.timeanddate.com/worldclock/fixedtime.html?day=25&month=10&year=2010&hour=16&min=0&sec=0&p1=136) is the best slot for most people, so let’s go with that.

Juan, would you be able to find someone else to start the call for us, using the EBI line? I’ll send round an agenda for discussion early next week,
Best wishes
Andy


From: Jones, Andy [mailto:And...@li...]
Sent: 14 October 2010 11:54
To: 'Mass spectrometry standard development'; 'psi...@li...'
Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on mzQuantML consideration

Hi all,

Seems difficult to find a slot :) Doodle poll created, can you complete with availability: http://www.doodle.com/nqe59tnb7bmzce7q

Cheers
Andy

From: David Creasy [mailto:dc...@ma...]
Sent: 14 October 2010 10:11
To: psi...@li...
Cc: Mass spectrometry standard development
Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on mzQuantML consideration

I'll be away then, so it's unlikely that I'll be able to make it. But please go ahead without me - I think that my views and Andy's views are pretty similar.

David

Eric Deutsch wrote:
Not as convenient for me, but it will be fine, yes.

From: Jones, Andy [mailto:And...@li...<mailto:And...@li...>]
Sent: Wednesday, October 13, 2010 7:43 AM
To: Mass spectrometry standard development; psi...@li...<mailto:psi...@li...>
Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on mzQuantML consideration

28/10 would also be okay with me, anyone else?
cheers
Andy
________________________________
From: Henk van den Toorn [h.w...@uu...<mailto:h.w...@uu...>]
Sent: 13 October 2010 15:28
To: Mass spectrometry standard development
Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on mzQuantML consideration
Fine by us, Henk & Pieter

On 12-10-2010 19:08, Oliver Kohlbacher wrote:

Dear all,



not good for me -- I will be on a plane during that time.

How about one week later, 10/28 same time?



Cheers,

 Oliver



On 12.10.2010, at 15:33, Jones, Andy wrote:



Hi all,



There has been some interesting discussions on the scope of mzQuantML and some work been done on use cases fulfilling the first draft we built after the Sept development meeting. I’d like to arrange a conference call to discuss the main issues. It appears that the most convenient time for people in different locations is usually 4pm UK time. I would like to take on board as many opinions as possible so let’s try find a time that is suitable for most people.



How would Thurs 21st Oct at 4pm UK (8am West coast, 11am East Coast) suit people? If not please suggest some alternatives,

Cheers

Andy













From: Henk van den Toorn [mailto:h.w...@uu...]

Sent: 01 October 2010 16:44

To: psi...@li...<mailto:psi...@li...>; mbr...@sy...<mailto:mbr...@sy...>

Subject: [Psidev-pi-dev] Fwd: [Psidev-ms-dev] Essential element on mzQuantML consideration



Hello all,



Sorry for cross-forwarding (is that a word?), but I noticed this message was sent to the ms-dev mailinglist while I guess it should have gone to the mzQuantML (psidev-pi) mailing list.



-----------





Dear PSI mzQuantML discussion participants,



Background of APML

Corra (http://www.biomedcentral.com/1471-2105/9/542) is published in 2008 with APML (Annotated Putative peptide Markup Language) that enables using several different ms1 peak extraction and alignment modules. After publication, Damon May, who is a lead developer on MSInspect from Fred Hutchinson Cancer Research Center, initiated to use APML for broader use for MsInspect and LabKey as well as Parag Mallick group in Los Angeles. After review and merging all institutions’ needs for capturing MS1 dataset, we introduced APML v2.0 schema and java written parsers (http://sourceforge.net/projects/corra/files/ ) . Then Eric Deutsch introduced APML v2.0 to PSI in 2008.



mzQuantML that Oliver is leading.

Recent my visit to Oliver Kohlbacher group in University of Tubingen and meeting with Peter Horvatovich from University of Groningen in HUPO Sydney, The mzQuantML schema and availability of its parser and validator can be an important contribution to bioinformatician and computational biologists, who develop or process MS1 based dataset for biological system studies.



Essential elements in the schema

To the best of my knowledge, we (ISB, FHCRC, Labkey, Peter’s group) are using APML v2.0, it would be nice (or rather essential) to have some of elements that can capture essential dataset to reproduce or reprocessing (e.g., statistical analysis on quantification etc). Thus, without further explanation, I have absolute agreement on Dr. Kohlbacher comments on “complexity is expected”  posted on Sep 13 to this mailing list.  The “feature” element is an absolute “must” for MS1 based pipeline. In my experience and perspective of continuous usage of Corra for several biomarker discovery projects, we need the feature element for mzQuantML  and  it will help for broad future mzQuantML schema in proteomics community.



Thank you for reading.



Warm Regards,

Mi-Youn



Mi-Youn Brusniak, Ph.D.

Computational Biology

Seattle Proteome Center

mbr...@sy...<mailto:mbr...@sy...>

Tel: (206)732-1327





Mi-Youn Brusniak, Ph.D.

Computational Biology

Seattle Proteome Center

mbr...@sy...<mailto:mbr...@sy...>

Tel: (206)732-1327

------------------------------------------------------------------------------

Beautiful is writing same markup. Internet Explorer 9 supports

standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.

Spend less time writing and  rewriting code and more time creating great

experiences on the web. Be a part of the beta today.

http://p.sf.net/sfu/beautyoftheweb_______________________________________________

Psidev-ms-dev mailing list

Psi...@li...<mailto:Psi...@li...>

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

---

Oliver Kohlbacher (oli...@un...<mailto:oli...@un...>)

Professor, Center for Bioinformatics Tuebingen, Eberhard Karls University Tuebingen

phone: +49-7071-29-70457   http://www-bs.informatik.uni-tuebingen.de



vCard at: http://www-bs.informatik.uni-tuebingen.de/People/kohlbach/vCard















------------------------------------------------------------------------------

Beautiful is writing same markup. Internet Explorer 9 supports

standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.

Spend less time writing and  rewriting code and more time creating great

experiences on the web. Be a part of the beta today.

http://p.sf.net/sfu/beautyoftheweb

_______________________________________________

Psidev-ms-dev mailing list

Psi...@li...<mailto:Psi...@li...>

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

--
-------------------------------------------------------------------------------------------------------
Henk van den Toorn, bioinformatician
Biomolecular Mass Spectrometry and Proteomics Group
Bijvoet Center for Biomolecular Research and
Utrecht Institute for Pharmaceutical Sciences
Utrecht University
Padualaan, 8
3584 CH Utrecht
The Netherlands

E-mail: h.w...@uu...<mailto:h.w...@uu...>
Tel: +31 30 253 6758
Fax: +31 30 253 6919
--------------------------------------------------------------------------------------------------










________________________________










------------------------------------------------------------------------------

Beautiful is writing same markup. Internet Explorer 9 supports

standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.

Spend less time writing and  rewriting code and more time creating great

experiences on the web. Be a part of the beta today.

http://p.sf.net/sfu/beautyoftheweb










________________________________










_______________________________________________

Psidev-pi-dev mailing list

Psi...@li...<mailto:Psi...@li...>

https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev




--

David Creasy

Matrix Science

64 Baker Street

London W1U 7GB, UK

Tel: +44 (0)20 7486 1050

Fax: +44 (0)20 7224 1344



dc...@ma...<mailto:dc...@ma...>

http://www.matrixscience.com



Matrix Science Ltd. is registered in England and Wales

Company number 3533898