Re: [Psidev-qc-dev] PSI QC Announcement Draft

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 422-6466

Hi Dave,
Jinmeng has also contributed some content about MIAPE-like document. Could
you add her to the author list of manuscript?

thanks,

weimin

On Wed, Aug 24, 2016 at 11:36 PM, Martin Eisenacher <
mar...@ru...> wrote:

> Hi!
>
> Many thanks for preparing this manuscript!
>
> I added my affiliation to the overleaf doc., one more
> reason for using CVs (no necessity to update the format
> version) and half a sentence in the "MIAPE-like QC doc."
> section with an article reference (Wout, if you
> think that this really makes sense in that section, that ref
> may be deleted then from the conclusion section).
>
> Some remarks (no changes in text yet):
> 1) At the end of the introduction (after last sentence with the
> definition of  the main goal) we may stress, that the aim is NOT
> to define thresholds for the quality metrics, as their interpretation
> depends on the design and the individual data set (sometimes not
> the actual values but only outliers of a bunch of runs are
> quality-relevant).
> I suggest this as for some MS experimentators QC is a sensitive subject.
>
> 2) (in my version on page 3) When content the first times switches
> from Proteomics to Metabolomics, that switch is a bit rough for me, as
> the discussion is directly about different types of QC samples. Maybe
> that section may be introduced by examples of specific Metabolomics QC
> metrics? Or it may be stated that "In principle many of the Proteomics
> metrics
> can also be acquired for Metabolomics" and then discussing the QC samples?
> The other way round, "blanks", "internal standards", and
> "calibration curve samples" may also be used in Proteomics.
> The last sentence (about 30-40% of runs consisting of QC samples)  seems
> somewhat off-topic (may be deleted or moved to the introduction to stress
> the importance or the efforts necessary).
>
> 3) (in my version on page 4) At the beginning of the qcML section it is
> stated
> that we will create a software library to "extract information from these
> [qcML]
> files". For the mentioned quality metric generators it may be more
> attractive to
> also write / create the format, i.e. "to export and import information to
> / from
> these files." Or is this not possible with jqcML?
>
> 4) The sentences about the "MIAPE-like QC document" separates two
> sections about jqcML, and may be moved the end of the second.
> BTW: It will be interesting discussion, what should be minimally reported
> regarding QC.
>
>   Bye from Bochum
>       Martin
>
> --
> PD DR. MARTIN EISENACHER
> Department Leader
> DEPARTMENT Medical Bioinformatics
> Medizinisches Proteom-Center
> Ruhr-University Bochum
> Building ZKF E.141 | Universitätsstraße 150 | D-44801 Bochum
> Fon +49 (0)234 32-29288 | Fax +49 (0)234 32-14554
> E-mail mar...@ru...
> www.medizinisches-proteom-center.de
>
>
> -----Ursprüngliche Nachricht-----
> Von: Lennart Martens [mailto:len...@vi...]
> Gesendet: Montag, 22. August 2016 15:03
> An: Reza Salek <rez...@eb...>; Prof <dt...@su...> Tabb David <
> dt...@su...>
> Cc: psi...@li...
> Betreff: Re: [Psidev-qc-dev] PSI QC Announcement Draft
>
> Hello,
>
>
> I took the liberty of going through the text (which is great!), and made a
> few additions, adding three references in the process.
>
> I also put a comment at line 257-260, where i suggest a change in a
> sentence that probably needs a look from whoever wrote the original.
>
>
> Cheers,
>
> lnnrt.
>
> On 19/08/2016 20:00, Reza Salek wrote:
> > Hello Daivd, all.
> >
> >
> >> On 1 Aug 2016, at 17:16, Tabb, David, Prof <dt...@su...
> >> <mailto:dt...@su...>> <dt...@su... <mailto:dt...@su...>>
> >> wrote:
> >>
> >> Hi, all.
> >>
> >> I hope that our full team is now on the QC Dev mailing list.  I should
> >> probably figure out how to get the roster from SourceForge.
> >>
> >> I hope by now everyone has had a look at the draft of the QC
> >> Announcement draft at Overleaf
> >> (https://www.overleaf.com/5671898jfvtyd).  *Wout* did some key work
> >> getting us off the ground with an initial draft, and I think a few of
> >> us have made contributions to that draft, as well.
> >>
> >> *Reza*, I would like to request that you help us with some
> >> concreteness in metabolomics experimental methods.
> >
> > I have added several paragraphs to the manuscript,  covering role and
> > types of QC and QA samples in metabolomics. Also added tools, that I
> > hope would support qcML, as well added the initiative within the
> > Metabolomics Society that can support or we are coordinating with (Task
> > groups). Please have a looking and let me know if more details are
> > needed. I will be on holiday next week but back in September.
> >
> >
> >> We already mention a variety of techniques in proteomics into which we
> >> hope to expand QC (SRM, iTRAQ, DIA, MALDI).
> >
> > specially target and un-target methods but not much different from
> > proteomics
> >> We haven’t done the same for metabolomics.  Presumably data-dependent
> >> acquisition is not the dominant paradigm for metabolomics experiments;
> >
> > A work in progress ….
> >
> > Best Wishes
> > Reza
> >
> >> we would like to sketch out methods in metabolomic mass spectrometry
> >> that we hope to keep in mind as QC moves forward.
> >>
> >> I wanted to single out *Dave* for failing to navigate the HUPO 2016
> >> abstract submission site.  We learned two weeks after abstracts were
> >> due that the abstract I thought had been submitted had not, in fact,
> >> been sent (one must hit the submission button once, wait for the
> >> refresh, and then a second time).  Thankfully, *Eric* *Deutsch* caught
> >> the mistake when searching for our abstract for inclusion in his
> >> panel!  We were able to do a late submission courtesy of folks in the
> >> HUPO office.  I’m sorry for the foul-up, folks.
> >>
> >> Thank you for all your good work!
> >> Dave
> >>
> >> P.S. I ran QuaMeter today on a pile of RAW files to untangle a mystery
> >> about the origin of some files collected before the uniform naming
> >> strategy went into effect.  How useful!
> >> ------------------------------------------------------------
> ------------------
> >> _______________________________________________
> >> Psidev-qc-dev mailing list
> >> Psi...@li...
> >> <mailto:Psi...@li...>
> >> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev
> >
> >
> >
> > ------------------------------------------------------------
> ------------------
> >
> >
> >
> > _______________________________________________
> > Psidev-qc-dev mailing list
> > Psi...@li...
> > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev
>
> ------------------------------------------------------------
> ------------------
> _______________________________________________
> Psidev-qc-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev
>
>
> ------------------------------------------------------------
> ------------------
> _______________________________________________
> Psidev-qc-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev
>