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

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Hi Dave, Weimin and all,

I had added my information together with Weimin's affiliation to the manuscript (I am not sure what's the sorting method of our name, so I just put mine next to Weimin). 
The text is good and I completely agree with Martin's point that 'it will be interesting discussion, what should be minimally reported regarding QC'.
up to date, I have collected a set of LC-MS/MS QC metadata based on the existing works of QC metrics, qcML and QC ontology, as well as additional metrics collected from experimentalists in National Center for Protein Science, Beijing. 54 QC metrics together with 5 general features are collected and classified as a first draft. You can see it in the attachment file. 
I will added some more inforamation to it based on my on going work, and I am considering if we it is necessary to add a few more sentences about MIAPE-like document of QC to the manuscript.  
Document of MIAPE-QC draft attatched. Any suggestion and discussion will be appreciated!

Sincerely,
Jinmeng

At 2016-08-26 12:15:49, "weimin zhu" <wmz...@gm...> wrote:

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!
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>
>
>
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