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Re: [Psidev-qc-dev] PSI QC Announcement Draft
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From: Bittremieux W. <wou...@ua...> - 2016-08-29 16:09:05
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Hi Martin, Thank you for the valuable feedback. I agree with the issues you raised and accordingly made a few changes to the manuscript. The proteomics-metabolomics section (p. 3) could use some further refinements though. I'll try to make some more changes this week to make that part more coherent. I'm not really sure whether or not to add additional authors at this point though. I thought of this manuscript mostly to announce that we established a new working group, and hence included the people that have committed to taking up a leading role as the authors. However, multiple other people have of course already contributed as well, both during the PSI meeting in Ghent and locally in the various research groups. Therefore correct attribution of individual efforts should definitely be taken care of. However, at the moment we're not really presenting any new work yet, more our view on the importance and future aspects of QC in proteomics and metabolomics and how our working group will contribute to this. That's why I think it would be more logical to stick with those few people as authors on this manuscript at the moment, and compile a more elaborate author list for our subsequent work. Kind regards, Wout > On 24 Aug 2016, at 17:36, 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 |
