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Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on mzQuantML consideration
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From: Eric D. <ede...@sy...> - 2010-10-13 16:53:57
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Not as convenient for me, but it will be fine, yes. *From:* Jones, Andy [mailto:And...@li...] *Sent:* Wednesday, October 13, 2010 7:43 AM *To:* Mass spectrometry standard development; 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...] *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... <h.w...@uu...>] Sent: 01 October 2010 16:44 To: psi...@li...; 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... Tel: (206)732-1327 Mi-Youn Brusniak, Ph.D. Computational Biology Seattle Proteome Center 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... https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev --- Oliver Kohlbacher (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... 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... Tel: +31 30 253 6758 Fax: +31 30 253 6919 -------------------------------------------------------------------------------------------------- |
