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From: Eric D. <ede...@sy...> - 2010-10-18 23:47:50
|
Hi everyone, this is a reminder for the PSI MSS WG teleconference call tomorrow, Tuesday, at the usual time. The primary agenda item will be to finish discussion of the TraML reviews and set action items to address them. 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 accepted to MCP: http://www.mcponline.org/content/early/2010/08/17/mcp.R110.000133.full.pdf+html - 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? - 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? ---- 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 - 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, see attached. Discuss how to address these concerns - 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) PSI session at World HUPO in Sydney - Eric presented on the work of the group: mzML 1.1, TraML 0.9.4, MIAPE-MS ---- 5) Improving the controlled vocabulary - There is a todo list based on a previous discussion - Need someone with some time to work on it 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 1 week? Oct 19? |
|
From: Jones, A. <And...@li...> - 2010-10-14 10:53:55
|
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 |
|
From: David C. <dc...@ma...> - 2010-10-14 09:11:05
|
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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.<br>
<br>
David<br>
<br>
Eric Deutsch wrote:
<blockquote cite="mid:42c...@ma..."
type="cite">
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<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Not
as convenient for me, but it will be fine, yes.</span></p>
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style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span></p>
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<p class="MsoNormal"><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";"> Jones,
Andy
[mailto:<a moz-do-not-send="true"
href="mailto:And...@li...">And...@li...</a>]
<br>
<b>Sent:</b> Wednesday, October 13, 2010 7:43 AM<br>
<b>To:</b> Mass spectrometry standard development;
<a moz-do-not-send="true"
href="mailto:psi...@li...">psi...@li...</a><br>
<b>Subject:</b> Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential
element on
mzQuantML consideration</span></p>
</div>
</div>
<p class="MsoNormal"> </p>
<div>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: black;">28/10
would also be okay with me, anyone else?</span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";">cheers</span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";">Andy
</span></p>
</div>
<div id="divRpF963125">
<div class="MsoNormal" style="text-align: center;" align="center">
<hr align="center" size="2" width="100%"></div>
<p class="MsoNormal" style="margin-bottom: 12pt;"><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";"> Henk van
den Toorn
[<a moz-do-not-send="true" href="mailto:h.w...@uu...">h.w...@uu...</a>]<br>
<b>Sent:</b> 13 October 2010 15:28<br>
<b>To:</b> Mass spectrometry standard development<br>
<b>Subject:</b> Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential
element on
mzQuantML consideration</span></p>
</div>
<div>
<p class="MsoNormal">Fine by us, Henk & Pieter <br>
<br>
On 12-10-2010 19:08, Oliver Kohlbacher wrote: </p>
<pre>Dear all,</pre>
<pre> </pre>
<pre>not good for me -- I will be on a plane during that time.</pre>
<pre>How about one week later, 10/28 same time?</pre>
<pre> </pre>
<pre>Cheers,</pre>
<pre> Oliver</pre>
<pre> </pre>
<pre>On 12.10.2010, at 15:33, Jones, Andy wrote:</pre>
<pre> </pre>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<pre>Hi all,</pre>
<pre> </pre>
<pre>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.</pre>
<pre> </pre>
<pre>How would Thurs 21st Oct at 4pm UK (8am West coast, 11am East Coast) suit people? If not please suggest some alternatives,</pre>
<pre>Cheers</pre>
<pre>Andy</pre>
<pre> </pre>
<pre> </pre>
<pre> </pre>
<pre> </pre>
<pre> </pre>
<pre> </pre>
<pre>From: Henk van den Toorn [<a moz-do-not-send="true"
href="mailto:h.w...@uu...">mailto:h.w...@uu...</a>] </pre>
<pre>Sent: 01 October 2010 16:44</pre>
<pre>To: <a moz-do-not-send="true"
href="mailto:psi...@li...">psi...@li...</a>; <a
moz-do-not-send="true" href="mailto:mbr...@sy...">mbr...@sy...</a></pre>
<pre>Subject: [Psidev-pi-dev] Fwd: [Psidev-ms-dev] Essential element on mzQuantML consideration</pre>
<pre> </pre>
<pre>Hello all,</pre>
<pre> </pre>
<pre>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.</pre>
<pre> </pre>
<pre>-----------</pre>
<pre> </pre>
<pre> </pre>
<pre>Dear PSI mzQuantML discussion participants,</pre>
<pre> </pre>
<pre>Background of APML</pre>
<pre>Corra (<a moz-do-not-send="true"
href="http://www.biomedcentral.com/1471-2105/9/542" target="_blank">http://www.biomedcentral.com/1471-2105/9/542</a>) 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 (<a
moz-do-not-send="true"
href="http://sourceforge.net/projects/corra/files/" target="_blank">http://sourceforge.net/projects/corra/files/</a> ) . Then Eric Deutsch introduced APML v2.0 to PSI in 2008.</pre>
<pre> </pre>
<pre>mzQuantML that Oliver is leading.</pre>
<pre>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.</pre>
<pre> </pre>
<pre>Essential elements in the schema</pre>
<pre>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.</pre>
<pre> </pre>
<pre>Thank you for reading.</pre>
<pre> </pre>
<pre>Warm Regards,</pre>
<pre>Mi-Youn</pre>
<pre> </pre>
<pre>Mi-Youn Brusniak, Ph.D.</pre>
<pre>Computational Biology</pre>
<pre>Seattle Proteome Center</pre>
<pre><a moz-do-not-send="true"
href="mailto:mbr...@sy...">mbr...@sy...</a></pre>
<pre>Tel: (206)732-1327</pre>
<pre> </pre>
<pre> </pre>
<pre>Mi-Youn Brusniak, Ph.D.</pre>
<pre>Computational Biology</pre>
<pre>Seattle Proteome Center</pre>
<pre><a moz-do-not-send="true"
href="mailto:mbr...@sy...">mbr...@sy...</a></pre>
<pre>Tel: (206)732-1327</pre>
<pre>------------------------------------------------------------------------------</pre>
<pre>Beautiful is writing same markup. Internet Explorer 9 supports</pre>
<pre>standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3.</pre>
<pre>Spend less time writing and rewriting code and more time creating great</pre>
<pre>experiences on the web. Be a part of the beta today.</pre>
<pre><a moz-do-not-send="true"
href="http://p.sf.net/sfu/beautyoftheweb_______________________________________________"
target="_blank">http://p.sf.net/sfu/beautyoftheweb_______________________________________________</a></pre>
<pre>Psidev-ms-dev mailing list</pre>
<pre><a moz-do-not-send="true"
href="mailto:Psi...@li...">Psi...@li...</a></pre>
<pre><a moz-do-not-send="true"
href="https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev"
target="_blank">https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev</a></pre>
</blockquote>
<pre>---</pre>
<pre>Oliver Kohlbacher (<a moz-do-not-send="true"
href="mailto:oli...@un...">oli...@un...</a>)</pre>
<pre>Professor, Center for Bioinformatics Tuebingen, Eberhard Karls University Tuebingen</pre>
<pre>phone: +49-7071-29-70457 <a moz-do-not-send="true"
href="http://www-bs.informatik.uni-tuebingen.de" target="_blank">http://www-bs.informatik.uni-tuebingen.de</a> </pre>
<pre> </pre>
<pre>vCard at: <a moz-do-not-send="true"
href="http://www-bs.informatik.uni-tuebingen.de/People/kohlbach/vCard"
target="_blank">http://www-bs.informatik.uni-tuebingen.de/People/kohlbach/vCard</a></pre>
<pre> </pre>
<pre> </pre>
<pre> </pre>
<pre> </pre>
<pre> </pre>
<pre> </pre>
<pre> </pre>
<pre>------------------------------------------------------------------------------</pre>
<pre>Beautiful is writing same markup. Internet Explorer 9 supports</pre>
<pre>standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3.</pre>
<pre>Spend less time writing and rewriting code and more time creating great</pre>
<pre>experiences on the web. Be a part of the beta today.</pre>
<pre><a moz-do-not-send="true"
href="http://p.sf.net/sfu/beautyoftheweb" target="_blank">http://p.sf.net/sfu/beautyoftheweb</a></pre>
<pre>_______________________________________________</pre>
<pre>Psidev-ms-dev mailing list</pre>
<pre><a moz-do-not-send="true"
href="mailto:Psi...@li...">Psi...@li...</a></pre>
<pre><a moz-do-not-send="true"
href="https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev"
target="_blank">https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev</a></pre>
<p class="MsoNormal" style="margin-bottom: 12pt;"> </p>
<div>
<p class="MsoNormal">-- </p>
<p class="MsoNormal" style="text-align: center;" align="center">-------------------------------------------------------------------------------------------------------<br>
<b>Henk van den Toorn, bioinformatician</b><br>
<span style="font-size: 11pt; color: rgb(16, 16, 221);">Biomolecular
Mass Spectrometry and
Proteomics Group</span><br>
Bijvoet Center for Biomolecular Research and<br>
Utrecht Institute for Pharmaceutical Sciences<br>
Utrecht University<br>
Padualaan, 8<br>
3584 CH Utrecht<br>
The Netherlands<br>
<br>
E-mail: <a moz-do-not-send="true" href="mailto:h.w...@uu...">h.w...@uu...</a><br>
Tel: +31 30 253 6758<br>
Fax: +31 30 253 6919<br>
--------------------------------------------------------------------------------------------------</p>
</div>
</div>
</div>
</div>
<pre wrap="">
<hr size="4" width="90%">
------------------------------------------------------------------------------
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.
<a class="moz-txt-link-freetext" href="http://p.sf.net/sfu/beautyoftheweb">http://p.sf.net/sfu/beautyoftheweb</a></pre>
<pre wrap="">
<hr size="4" width="90%">
_______________________________________________
Psidev-pi-dev mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Psi...@li...">Psi...@li...</a>
<a class="moz-txt-link-freetext" href="https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev">https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev</a>
</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344
<a class="moz-txt-link-abbreviated" href="mailto:dc...@ma...">dc...@ma...</a>
<a class="moz-txt-link-freetext" href="http://www.matrixscience.com">http://www.matrixscience.com</a>
Matrix Science Ltd. is registered in England and Wales
Company number 3533898</pre>
</body>
</html>
|
|
From: Eric D. <ede...@sy...> - 2010-10-13 16:53:57
|
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 -------------------------------------------------------------------------------------------------- |
|
From: Laurent G. <lg...@ca...> - 2010-10-13 14:50:02
|
Fine for me. Laurent 2010/10/13 Jones, Andy <And...@li...>: > 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...] > 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 > -------------------------------------------------------------------------------------------------- > ------------------------------------------------------------------------------ > 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... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > -- Laurent Gatto Cambridge Centre For Proteomics http://www.bio.cam.ac.uk/proteomics |
|
From: Jones, A. <And...@li...> - 2010-10-13 14:43:50
|
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...] 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 -------------------------------------------------------------------------------------------------- |
|
From: Henk v. d. T. <h.w...@uu...> - 2010-10-13 14:28:49
|
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...; 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 -------------------------------------------------------------------------------------------------- |
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From: Eric D. <ede...@sy...> - 2010-10-12 22:28:47
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Present: Florian, Steffen, Pierre-Alain, Eric Agenda: 1) mzML 1.1.0 - Manuscript has been accepted to MCP: http://www.mcponline.org/content/early/2010/08/17/mcp.R110.000133.full.pdf+html - 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? - 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? + Work on these action items + No 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 + Ask Pierre-Alain to send Juan Antonio the latest documents ---- 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, see attached. Discuss how to address these concerns + Comments from reviewers 3 and 4 were discussed, and response/action outlined. + Eric will start officially addressing these and send around result and open questions + Ran out of time. - 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) PSI session at World HUPO in Sydney - Eric presented on the work of the group: mzML 1.1, TraML 0.9.4, MIAPE-MS ---- 5) Improving the controlled vocabulary - There is a todo list based on a previous discussion - Need someone with some time to work on it 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? Oct 26? + Unclear on what best date is. Create doodle poll. |
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From: Oliver K. <oli...@un...> - 2010-10-12 17:09:05
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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...; 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 |
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From: Henk v. d. T. <h.w...@uu...> - 2010-10-12 14:42:06
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Hi Andy, That's a good idea, and the time is fine for us! Pieter and Henk On 12-10-2010 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 21^st 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...; 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... > 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 -------------------------------------------------------------------------------------------------- |
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From: Jones, A. <And...@li...> - 2010-10-12 13:58:38
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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...; 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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From: Mi-Youn B. <mbr...@sy...> - 2010-09-30 20:48:50
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Dear PSI mzQuantML discussion participants, 1. 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. 2. 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. 3. 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 |
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From: Mi-Youn B. <mbr...@sy...> - 2010-09-30 20:46:31
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Dear PSI mzQuantML discussion participants, 1. 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. 2. 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. 3. 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 |
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From: Eric D. <ede...@sy...> - 2010-09-28 16:09:39
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Present: Matt, Richard, Steffen, Jim, Eric Agenda: 1) mzML 1.1.0 - Manuscript has been accepted to MCP: http://www.mcponline.org/content/early/2010/08/17/mcp.R110.000133.full.pdf+html - 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? - 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? + Work on these action items + No 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 + Ask Pierre-Alain to send Juan Antonio the latest documents ---- 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, see attached. Discuss how to address these concerns + Comments from reviewers 1 and 2 were discussed, and response/action outlined. + Eric will start officially addressing these and send around result and open questions + Ran out of time. + Comments from reviewers 3 and 4 next time - 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) PSI session at World HUPO in Sydney - Eric presented on the work of the group: mzML 1.1, TraML 0.9.4, MIAPE-MS ---- 5) Improving the controlled vocabulary - There is a todo list based on a previous discussion - Need someone with some time to work on it 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? Oct 12? + Yes |
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From: Steffen N. <sne...@ip...> - 2010-09-28 15:05:58
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Hi, here's my 2c: > Reviewer 1: ... > Section 1.3.1: The importance of retention time seems to be > underplayed here, as a transition is defined as a precursor and Right, I remember discussions here on normalized/predicted/local retention times, and their roles should be mentioned in 1.3 > Section 1.3.2: The meaning and relevance of the last sentence in this ... > good to have a clear explanation of why Targeted MS/MS is explicitly > supported in TraML because to me it seems like an unnecessary > bolt-on. I am/was one of the supporters of Targeted MS/MS, because we use QqTOF machines where you can't do the "classic" MRM experiments. Nevertheless, as the reviewer mentioned, the format could be adopted by "Control software for mass spectrometry based instruments", and why shouldn't that also include targeted MS/MS, and expand beyond "instruments capable of carrying out SRM". > Sections 1.3.5 and 1.3.6: Neutral loss scans and n>=3 experiments are > not supported, with good reason. However, it would be good to have > some reassurance that it would be technically possible to add these > through a minor version change should the need arise. This would give > developers additional confidence in adopting the standard. Actually, this supports my opinion on the inclusion of Targeted MS/MS above! > Section 2.2: Reuse of existing PSI work is great to see. It clearly > decreased the time needed to design TraML and should similarly > decrease the time needed to implement it. Bullet point 3, about the > relationship between TraML and mzIdentML contains some speculation > about the future. If such speculation is to be included would it not > be wise to consider that linkage between TraML and a future > quantitation data standard would be a natural progression? Maybe that is too much speculation, the document is a *specification*, rather than speculation ... OTOH, the interplay of the formats could be placed in the 1.3 use cases section ? > Section 2.3.2: I can’t conceive of the special case described where a > transition would consist solely of two masses and a retention time, What if there is no identification yet, but somehow a prior experiment has shown something to be differential and hence of interest for an MRM run ? Actually, why is this section limited to "retention times in <Transition>" ? I think it holds true for <Target>s as well. > Reviewer 2: > M/Z window width ... > m/z’ (MS:1000827) and ‘isolation width’ (MS:1000023) are very ion > trap specific Nope. The corresponding element in a Bruker micrOTOFq method file is "MSMSManual_ListIsolationWidth" for a targeted MSMS run. > Pure schema versus pure controlled vocabulary ... > The TraML format relies too heavily on controlled vocabulary. I can > not think of any practical scenario where the precursor or product of > a transition would not contain an m/z. Including this one element > would vastly simplify implementing reading and writing from TraML > files, and remove dependency on 3rd party tools. The PSI cvTerm is much more than "just a CV", it's an ontology. To use it to its full power will require the use of a 3rd party tool anyway. > I’m very pleased to see that a Windows dll from ProteoWizard is > available to simplify working with TraML files. I would prefer to have > this dll available directly from the group responsible for TraML, so > that updates to the TraML format or controlled vocabulary will be > supported. At a minimum, I would like to see stronger assurances that > ProteoWizard will be the reference implementation for TraML, and how > this will be synchronized with TraML updates. That's beyond the scope of a specification document. But the website could do a better job of marketing the TraML ecosystem. Do we have any Java Implementations for TraML ? > Simple format I guess that format could only handle a limited subset of the TraML spec. Section 1.2 mentions that existing CSV stuff is very diverse, so why add another flavor ? Maybe pwiz could promote one or two flavors to de-facto standards by adding converters, but I doubt it makes sense within TraML. > Reviewer 3: ... > A few points: > 1. I was surprised by the decision to exclude neutral loss ions. For > modified peptides these seem to be key, and need to be considered > almost always. Does that mean neutral loss scans ? Or how could those be consideren in an MRM experiment ? > 2. The decision to keep retention time linked with transition seems is This was raised by Reviewr #1 as well, see comments above > allows for possible errors, e.g., allowing for different retention > time for each peptide. That could be caught by a validator ? > Reviewer 4: > 1) Unless the TraML format is supported by the various vendors and ... > We didn't see any converters or conversion examples for TraML format > documented at the site: http://www.psidev.info/index.php?q=node/405. Again, marketing the ecosystem on the web site. 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 |
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From: Mi-Youn B. <mbr...@sy...> - 2010-09-15 05:02:26
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Dear Oliver, I flew in to Sydney already for proteomics course. I agree with you regarding the feature elements. Quality of feature (istope pattern etc) can be an important information to capture. If there is big concern on including this, we can make "optional" elements but in my opinion, it is an essential element. I hope to see you during HUPO. Mi-Youn On Mon, Sep 13, 2010 at 3:01 AM, Oliver Kohlbacher < oli...@un...> wrote: > Dear all, > > unfortunately, I could not attend the mzQuantML meeting as I am > constantly traveling this month, so I have to add my comments > from the off. > > The draft looks quite reasonable to me, except for two - rather > important - points: Feature information and Data Processing information. > Let me address them individually. > > Features: > > From my discussions with Mathias, who was there, I got the impression > that dropping the features from the draft was mostly due to two points: > it was seen as rather complex and not essential for storing the (final) > results of analyses in public databases. > > Complexity is to be expected and we should not be afraid of it. The draft > we provided prior to the meeting included feature information. While one > can always simplify the schema (as a matter of fact, we worked on that > on the OpenMS retreat last week), I would argue that this part of the > schema is rather mature. For this draft we merged the schemas of three > quantification formats form TPP and OpenMS (APML, featureXML, > consensusXML) and both the OpenMS team and the ISB people are happy with > this draft. I cannot perceive any undue complexity. > > As to whether one should store this information, I believe that not > storing it is absolutely detrimental and would disqualify mzQuantML > as a format for archiving published quantitative proteomics data. The > reason for that (and more on it below) is that we can no longer trace > back where the information for a specific peptide/protein comes from. > Apart from some particularly stupid quantification methods (i.e. spectral > counting), feature information allows to really go back and check the > original data for each peptide/protein and validate that the quantification > algorithms really did what they were supposed to do. By storing the > original data as mzML and then the final results only, we are back > to the current state: believe the table of differentially expressed > proteins or don't. Checking every piece of evidence as the data is being > processed is made impossible by this. > > Another - and to us equally important point - is the fact that most > quantification packages do not process the data in a single step. > It is not just 'mzML in and mzQuantML out'. Even for more monolithic > applications, the quantification involves multiple stages (feature > identification, peptide ID, protein inference, filtering for fold > changes, various statistical analyses). > For most of these steps, Features are essential and required information, > so basically mzQuantML would be useless in data processing pipelines. > AL we had gained would be yet another format because we would have to > keep the old ones. Doesn't convince me. > > Data Processing: > > Arguing along the same lnes as above, I would like to see the > DataProcessing portion of the mzML schema included in mzQuantML. > In order to provide complete and traceable information on anything > that was done to the data. In principle, the 'Materials & Methods' > section on data processing should be reconstructible from this > portion of the mzQuantML file. The advantages are obvious: if you > process your mzML file with various software packages, you can > transfer that information to the myQuantML file that contains the > results based on these files. In my opinion, an elegant solution > that would enable us to document the whole workflow. It could > enable us to make also the data processing reproducible, transparent, > and more consistent with common scientific standards. > Perhaps the protocolList part of mzQuantML could be simply an > extension of the dataProcessing part of mzML. > > Alright, just my thoughts on this. I am sorry I couldn't attend the > meeting, but perhaps a few of you will be attending HUPO 2010 in > Sydney. Just in case you are and are and interested in discussing > this over a beer, please don't hesitate to send me an email. > > Cheers from Sydney, > Oliver -- Mi-Youn Brusniak, Ph.D. Computational Biology Seattle Proteome Center mbr...@sy... Tel: (206) 732-1327 |
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From: Oliver K. <oli...@un...> - 2010-09-13 10:01:56
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Dear all, unfortunately, I could not attend the mzQuantML meeting as I am constantly traveling this month, so I have to add my comments from the off. The draft looks quite reasonable to me, except for two - rather important - points: Feature information and Data Processing information. Let me address them individually. Features: From my discussions with Mathias, who was there, I got the impression that dropping the features from the draft was mostly due to two points: it was seen as rather complex and not essential for storing the (final) results of analyses in public databases. Complexity is to be expected and we should not be afraid of it. The draft we provided prior to the meeting included feature information. While one can always simplify the schema (as a matter of fact, we worked on that on the OpenMS retreat last week), I would argue that this part of the schema is rather mature. For this draft we merged the schemas of three quantification formats form TPP and OpenMS (APML, featureXML, consensusXML) and both the OpenMS team and the ISB people are happy with this draft. I cannot perceive any undue complexity. As to whether one should store this information, I believe that not storing it is absolutely detrimental and would disqualify mzQuantML as a format for archiving published quantitative proteomics data. The reason for that (and more on it below) is that we can no longer trace back where the information for a specific peptide/protein comes from. Apart from some particularly stupid quantification methods (i.e. spectral counting), feature information allows to really go back and check the original data for each peptide/protein and validate that the quantification algorithms really did what they were supposed to do. By storing the original data as mzML and then the final results only, we are back to the current state: believe the table of differentially expressed proteins or don't. Checking every piece of evidence as the data is being processed is made impossible by this. Another - and to us equally important point - is the fact that most quantification packages do not process the data in a single step. It is not just 'mzML in and mzQuantML out'. Even for more monolithic applications, the quantification involves multiple stages (feature identification, peptide ID, protein inference, filtering for fold changes, various statistical analyses). For most of these steps, Features are essential and required information, so basically mzQuantML would be useless in data processing pipelines. AL we had gained would be yet another format because we would have to keep the old ones. Doesn't convince me. Data Processing: Arguing along the same lnes as above, I would like to see the DataProcessing portion of the mzML schema included in mzQuantML. In order to provide complete and traceable information on anything that was done to the data. In principle, the 'Materials & Methods' section on data processing should be reconstructible from this portion of the mzQuantML file. The advantages are obvious: if you process your mzML file with various software packages, you can transfer that information to the myQuantML file that contains the results based on these files. In my opinion, an elegant solution that would enable us to document the whole workflow. It could enable us to make also the data processing reproducible, transparent, and more consistent with common scientific standards. Perhaps the protocolList part of mzQuantML could be simply an extension of the dataProcessing part of mzML. Alright, just my thoughts on this. I am sorry I couldn't attend the meeting, but perhaps a few of you will be attending HUPO 2010 in Sydney. Just in case you are and are and interested in discussing this over a beer, please don't hesitate to send me an email. Cheers from Sydney, Oliver |
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From: Juan A. V. <ju...@eb...> - 2010-09-03 13:16:35
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Hi all, The minutes of the mzQuantML meeting are available at: http://www.psidev.info/index.php?q=node/451 Three presentations from the meeting are also available there for download. Since the text formatting is not the best possible one in the PSI website, I am also attaching the minutes in a .doc file. Please, feel free to edit them or make additions since I am sure I must have missed something important. It would be ideal if anyone who attended the meeting could be subscribe to psi...@li.... Best regards, Juan Antonio |
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From: Jones, A. <And...@li...> - 2010-09-03 10:11:59
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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 |
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From: Eric D. <ede...@sy...> - 2010-08-31 07:32:02
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Hi everyone, sorry for the late notice. I can't make the teleconference, and I don't think we need to meet anyway, so let's cancel. As Lennart announced, the MCP paper is accepted. Final materials have been uploaded. TraML is still under review. No information back from the TraML reviewers. I will present working group activities at HUPO on the 23rd. Most action items from the previous call still need to be done. Unless pressing issues come up, let's plan on meeting again soon after HUPO. Regards, Eric _____ From: Eric Deutsch [mailto:ede...@sy...] Sent: Tuesday, August 10, 2010 10:20 AM To: Mass spectrometry standard development Cc: Eric Deutsch Subject: PSI-MSS WG call notes 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? |
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From: Steffen N. <sne...@ip...> - 2010-08-24 06:27:48
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Hi, I just cam across the fact that the MS1, MSn et al in the filecontent_must rule appear twice in the explicit list in: http://www-bs2.informatik.uni-tuebingen.de/services/OpenMS/mzML/mapping_and_cv.html That's because the MS1 or MSn spectra are both is_a: MS:1000294 ! mass spectrum is_a: MS:1000524 ! data file content and [MS:1000294] itself is already is_a: MS:1000524 ! data file content therefore the MS1 and MSn are a "data file content" by transitivity. Cleaning this up will not have and semantic side effects, since [MS:1000579 ! MS1 spectrum] is_a [MS:1000294 ! mass spectrum] is_a [MS:1000524 ! data file content] *unless* there is some (broken, IMHO) software which does not check transitivity. I don't have experience with OBO edit, but the "Reasoner Plugin" will readily report "Found 39 redundant links". This could be considered if someone does the next round of maintenance on psi-ms.obo. 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 |
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From: Steffen N. <sne...@ip...> - 2010-08-23 16:47:13
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On Mon, 2010-08-23 at 18:19 +0200, Lennart Martens wrote: > Dear PSI-MS Enthusiasts, > At the risk of kicking in an open door, Not at all, thanks for making that happen! 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 |
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From: Lennart M. <len...@UG...> - 2010-08-23 16:19:34
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Dear PSI-MS Enthusiasts, At the risk of kicking in an open door, the mzmL manuscript is now accepted for publication in MCP, and an unformatted version is already available as freely accessible ePub. Link below. http://www.mcponline.org/content/early/2010/08/17/mcp.R110.000133.long Cheers, lnnrt. |
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From: Matthew C. <mat...@gm...> - 2010-08-18 15:00:55
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Hi Sara, That's some very neat work you've done. I can see why you'd propose it for quantitation, but it seems like a good general purpose format for any profile-centric analysis. It seems especially suited for creating pseudo 2d gel images to summarize an MS experiment. I'm interested in seeing it read and written with ProteoWizard (native C++). The main advantage of being able to build these from pwiz would be to convert directly from any of our supported open or RAW formats, but you might also see considerable speed boost from using native C++. I'll follow up off-list. -Matt On 8/18/2010 3:55 AM, Sara Nasso wrote: > Hi, > > since the mzQuant meeting is fast approaching I would like to let you know something about a work we did, in our Department, to solve some computational > issues related to LC-MS (or mass spectrometry) data storage and access arised during my work on a quantification software I am developing. I think it could be > worth to make use of such a data structure for data handling (i.e. handling of the data currently stored as Base64 encoded data in the mzML standard), > especially when an analysis pipeline needs to be developed. > It is just an idea and we actually did so, but I think it would be good to have an XML standard for all metadata and an efficient data structure, coupled to > the XML, only for data handling. We customized a well known data structure suitable for the handling of huge sparse data to implement mzRTree, a data > structure optimized for proteomics data (DOI:10.1016/j.jprot.2010.02.006 <http://dx.doi.org/10.1016/j.jprot.2010.02.006>), all information can be found here: > http://www.dei.unipd.it/wdyn/?sez_alias=mzrtree > We also developed a toolbox, to be released, which, using the JRAP library to gather the needed information, builds an mzRTree with all right parameters > settings. > Have a look and if you also think it would be worth to work on it, please write to us at /mzrtree AT dei.unipd.it/ > /I hope it could help,/ > / > / > cheers, > Sara > > // > > // > > / > ---------------------------------------------------------------------------------------------------------------------------------------------------------------- > //Sara Nasso, Ph.D. student > Department of Information Engineering (DEI) > University of Padova > Via Ognissanti 72 35129 PADOVA, ITALY > Voice: +39-049-8277834 > Fax: +39-049-8277826/ |
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From: Eric D. <ede...@sy...> - 2010-08-11 17:43:12
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Hi Sean, I have made the follow additions to the MS CV: [Term] id: MS:1000931 name: AB SCIEX QTRAP 5500 def: "Applied Biosystems|MDS SCIEX QTRAP 5500." [PSI:MS] is_a: MS:1000121 ! AB SCIEX instrument model [Term] id: MS:1000932 name: AB SCIEX TripleTOF 5600 def: "Applied Biosystems|MDS SCIEX TripleTOF 5500, a quadrupole - quadrupole - time-of-flight mass spectrometer." [PSI:MS] is_a: MS:1000121 ! AB SCIEX instrument model Does this seem good? Please suggest changes. While looking at the AB SCIEX tree, I noticed some additional issues. 1) We have two top-level entries: ---------------------------- [Term] id: MS:1000495 name: Applied Biosystems instrument model def: "Applied Biosystems instrument model." [PSI:MS] synonym: "ABI" EXACT [] is_a: MS:1000031 ! instrument model Has children: - 4700 Proteomics Analyzer - Voyager-DE PRO - Voyager-DE STR - 4800 Proteomics Analyzer ---------------------------- [Term] id: MS:1000121 name: AB SCIEX instrument model def: "The brand of instruments from the joint venture between Applied Biosystems and MDS Analytical Technologies (formerly MDS SCIEX). Previously branded as \"Applied Biosystems|MDS SCIEX\"." [PSI:MS] synonym: "Applied Biosystems|MDS SCIEX" RELATED [] is_a: MS:1000031 ! instrument model Has children: - everything else ---------------------------- Are we still happy with this. Can you suggest a definition change to help understand the distinction between these two? 2) We have currently the following terms (not a complete list) [Term] id: MS:1000140 name: 4700 Proteomics Analyzer def: "Applied Biosystems/MDS SCIEX 4700 Proteomics Analyzer MS." [PSI:MS] is_a: MS:1000495 ! Applied Biosystems instrument model [Term] id: MS:1000658 name: 4800 Proteomics Analyzer def: "Applied Biosystems|MDS SCIEX 4800 Proteomics Analyzer." [PSI:MS] is_a: MS:1000495 ! Applied Biosystems instrument model [Term] id: MS:1000139 name: 4000 Q TRAP def: "Applied Biosystems/MDS SCIEX Q 4000 TRAP MS." [PSI:MS] is_a: MS:1000121 ! AB SCIEX instrument model [Term] id: MS:1000187 name: Q TRAP def: "Applied Biosystems/MDS SCIEX Q TRAP MS." [PSI:MS] is_a: MS:1000121 ! AB SCIEX instrument model [Term] id: MS:1000870 name: 4000 QTRAP def: "AB SCIEX or Applied Biosystems|MDS SCIEX QTRAP 4000." [PSI:MS] is_a: MS:1000121 ! AB SCIEX instrument model [Term] id: MS:1000652 name: 4800 Plus MALDI TOF-TOF Analyzer def: "AB SCIEX or Applied Biosystems|MDS SCIEX 4800 Plus MALDI TOF-TOF Analyzer." [PSI:MS] is_a: MS:1000121 ! AB SCIEX instrument model [Term] id: MS:1001482 name: AB SCIEX TOF/TOF 5800 def: "AB SCIEX or Applied Biosystems|MDS Analytical Technologies AB SCIEX TOF/TOF 5800 Analyzer." [PSI:MS] is_a: MS:1000121 ! AB SCIEX instrument model ------------------------------------ I have the following questions: A) Is MS:1000658 (4800 Proteomics Analyzer) the same as MS:1000652 (4800 Plus MALDI TOF-TOF Analyzer) ? B) We appear to have a duplicate for the 4000 Q TRAP: MS:1000139 (4000 Q TRAP) and MS:1000870 (4000 QTRAP) According to marketing materials, there should be a space in Q TRAP, so the oroginal MS:1000139 appears to be correct. I propose obsoleting MS:1000870. Okay? C) Is MS:1000139 (4000 Q TRAP) different from MS:1000187 (Q TRAP) ? Thank you for helping to tidy up! Eric *From:* Seymour, Sean (ABSCIEX) [mailto:Sea...@ab...] *Sent:* Tuesday, August 10, 2010 12:07 PM *To:* psi...@li... *Subject:* [Psidev-ms-dev] New CV needed 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 |
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