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

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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
>
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> ---
>
> 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
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> --
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> -------------------------------------------------------------------------------------------------------
> *Henk van den Toorn, bioinformatician*
> Biomolecular Mass Spectrometry and Proteomics Group
> Bijvoet Center for Biomolecular Research and
> Utrecht Institute for Pharmaceutical Sciences
> Utrecht University
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> David Creasy
>
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