Re: [Psidev-qc-dev] qcML format evolution

[Tabb, D. P. <dt...@su...>]

Hi, Stefan.

Yes, I would really appreciate it if you could put me in contact with either of both of these researchers.  I would like to frame some specific examples of metrics that would be appropriate to measurement in DIA/SWATH for the revision of Wout's manuscript introducing our group.  For example, the distribution of "cycle time" that is required for the instrument to repeat a set of SWATHs would seem an appropriate metric for evaluating one of these experiments.  I would imagine this to vary in response to the number of ions exiting from LC-ESI at a particular moment in time.  A blocked column might lead to suddenly longer cycle times, I would think.

If we can be more specific about the way QC metrics could inform us of SWATH quality, I think we'll have a good case to make in that space.  I will write with Karl Clauser about the case of iTRAQ next.

I will also take a look at some of the R libraries that have been produced in support of SRM QC.

Thanks,
Dave

From: Tenzer, Stefan [mailto:te...@un...]
Sent: Wednesday, 02 November 2016 10:17
To: Tabb, David, Prof <dt...@su...>
Cc: psi...@li...; Kuharev, Joerg
Subject: Re: [Psidev-qc-dev] qcML format evolution

Hi everybody,

it could be that you spoke with Pedro Navarro (he was in my group at this time, but now unfortunately has moved on and joined Thermo as a programmer).

For QC for SWATH-MS, in my opinion, it would be great to get in contact with George Rosenberger (ros...@im...<mailto:ros...@im...>) or Hannes Röst (hr...@st...<mailto:hr...@st...>), both are bioinfomaticians and experts in SWATH-MS.
If you agree, I could of course invite them to contribute.

Jörg Kuharev (Postdoc in my group) and I would be happy to contribute metrics for HDMSE/UDMSE (ion-mobility based DIA approaches).


Best wishes,

Stefan



Univ.-Prof. Dr. rer. nat. Stefan Tenzer
______________________________________________

UNIVERSITÄTSMEDIZIN
der Johannes Gutenberg-Universität
Institut für Immunologie
Core Facility für Massenspektrometrie
Gebäude 708
Langenbeckstr. 1, 55131 Mainz
www.immunologie-mainz.de<http://www.immunologie-mainz.de>

Telefon: +49 (0) 6131 17-6199
Telefax: +49 (0) 6131 17-6202
E-mail: te...@un...<mailto:te...@un...>

Am 01.11.2016 um 13:57 schrieb Tabb, David, Prof <dt...@su...<mailto:dt...@su...>> <dt...@su...<mailto:dt...@su...>>:


Hi, all!

We had such a lot of interesting topics that arose during our meeting in April.  Now that we are rapidly approaching the submission of our group announcement whitepaper (courtesy of consistent labors by Wout Bittremieux), I wanted to check in on various other questions that arose during Ghent:

1)      Mathias, you received a lot of feedback on the qcML format at our meeting.  Could you describe the nature of changes that you have already made to the format along with the set of topics that still need addressing in the months to come?
2)      Reza, we have talked about various partners in the metabolomics community who may be assisting us as we move forward with our work.  Could you identify the primary people who will be most closely connected with the quality control effort?
3)      All, I spoke with a researcher who was tightly associated with the development of SWATH technologies (a type of DIA).  He was interested in seeing QC tools for the SWATH platform.  Could someone help me remember his name?  I'd like to see if that group has already roughed out some metrics in the DIA space.
4)      Wout, thank you for your persistence in the announcement white paper (https://www.overleaf.com/5671898jfvtyd).  In the month and a half together at Cape Town that we have remaining, I hope to get a better grip on the iMonDB (https://bitbucket.org/proteinspector/imondb/wiki/Home) framework.

Thanks!
Dave Tabb
------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi_______________________________________________
Psidev-qc-dev mailing list
Psi...@li...<mailto:Psi...@li...>
https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev