Menu
▾
▴
psidev-qc-dev — PSI-QC working group mailinglist
You can subscribe to this list here.
| 2016 |
Jan
|
Feb
|
Mar
|
Apr
|
May
(11) |
Jun
(14) |
Jul
|
Aug
(11) |
Sep
|
Oct
(4) |
Nov
(15) |
Dec
(1) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2017 |
Jan
(1) |
Feb
(9) |
Mar
(2) |
Apr
(2) |
May
(6) |
Jun
(7) |
Jul
(10) |
Aug
(4) |
Sep
(15) |
Oct
(9) |
Nov
(5) |
Dec
(7) |
| 2018 |
Jan
(5) |
Feb
(7) |
Mar
(3) |
Apr
(15) |
May
(5) |
Jun
(4) |
Jul
(4) |
Aug
(2) |
Sep
(4) |
Oct
(8) |
Nov
(6) |
Dec
(7) |
| 2019 |
Jan
(7) |
Feb
(2) |
Mar
(4) |
Apr
(7) |
May
(5) |
Jun
(6) |
Jul
(11) |
Aug
(5) |
Sep
(4) |
Oct
(7) |
Nov
(3) |
Dec
(4) |
| 2020 |
Jan
(5) |
Feb
(5) |
Mar
(8) |
Apr
(3) |
May
(5) |
Jun
(3) |
Jul
(9) |
Aug
(2) |
Sep
(2) |
Oct
(3) |
Nov
(5) |
Dec
(4) |
| 2021 |
Jan
(3) |
Feb
(4) |
Mar
(2) |
Apr
(4) |
May
(5) |
Jun
(9) |
Jul
(4) |
Aug
(8) |
Sep
(5) |
Oct
(3) |
Nov
(2) |
Dec
(2) |
| 2022 |
Jan
(2) |
Feb
(2) |
Mar
(3) |
Apr
(3) |
May
(4) |
Jun
(5) |
Jul
(5) |
Aug
(4) |
Sep
(6) |
Oct
(2) |
Nov
(5) |
Dec
|
| 2023 |
Jan
(7) |
Feb
(5) |
Mar
(5) |
Apr
(2) |
May
(11) |
Jun
(3) |
Jul
(1) |
Aug
(2) |
Sep
(1) |
Oct
(1) |
Nov
(2) |
Dec
(2) |
| 2024 |
Jan
(2) |
Feb
(3) |
Mar
|
Apr
(2) |
May
(2) |
Jun
(5) |
Jul
(6) |
Aug
(2) |
Sep
(1) |
Oct
(7) |
Nov
(3) |
Dec
(1) |
| 2025 |
Jan
(3) |
Feb
(2) |
Mar
(1) |
Apr
(2) |
May
(2) |
Jun
(1) |
Jul
(3) |
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
|
From: Tabb, D. P. <dt...@su...> - 2016-11-30 13:05:24
|
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 |
|
From: Tabb, D. P. <dt...@su...> - 2016-11-30 12:19:16
|
Hi, Sue and Robert. I am writing in connection with my work in the HUPO-PSI Quality Control Working Group. We were founded in April as a way to facilitate the use of quality control workflows with proteomics and metabolomics data sets. Several groups have now produced tools to generate proteomics quality metrics from raw data or raw data plus identifications. Our working group hopes to put forward standard ways to communicate these metrics (particularly a file in an updated "qcML" format), making it possible to make downstream decision-support tools that are able to work with a variety of front-end metric generators. We believe one of the important ways we can leverage these metrics is by ensuring that data sets that reach publication have some basic quality information accompanying them (for some tools, this would mean spending just a few minutes of CPU time to generate the qcML document). The qcML document could, for example, inform potential users of the numbers of MS/MS scans acquired, the proportion of precursors that were +2, or the distribution of TIC throughout the MS scans. We submitted a manuscript to Analytical Chemistry that introduced the goals of the working group to solicit input from the broader community. A reviewer has suggested that we need to show greater clarity on how we will interact with journals to nudge publication guidelines to recommend the inclusion of qcML once the format is finalized and the tools to produce them are easily acquired. The two of you came to my mind as great resources on how this evolution could take place. Do you have some insights on how receptive ACS and ASBMB journals would be to including this recommendation for proteomics and metabolomics manuscripts? Thank you, Dave |
|
From: Lennart M. <len...@gm...> - 2016-11-23 15:34:46
|
Hello, Could the poll on QC that Bas Van Breukelen and I conducted a while back be of any use to appease reviewer 3? It clearly highlighted the need for QC and QC tools, and was answered by (off the top of my head) 80-odd participants. Cheers, lnnrt. On 23/11/2016 09:31, Bittremieux Wout wrote: > Hello everyone, > > In the meantime we have received the reviewer's comments for our manuscript. > > Two reviewers suggested a few clarifications, and these changes should be relatively straightforward. > > A third reviewer expected more tangible results though, resulting in a major revision. > The main goal of the manuscript is to solicit community interest to ensure that our work on QC has broad public support, which is somewhat at odds with presenting concrete results at this stage already. However, we should try to highlight some concrete use cases to show the value of our working group. Specifically, as mentioned by the reviewer, giving an overview of which types of QC metrics are relevant for various different experiments and detailing how a concrete pipeline of QC tools can improve experimental workflows would be beneficial. Additionally, the interplay between depositing QC data in public repositories and publication guidelines was suggested as a point of attention. > > We will mull over potential improvements for the manuscript in the next few days. There are multiple people involved with expert knowledge on some of the mentioned topics, so as always any suggestions are more than welcome. > > Regards, > Wout > >> On 13 Oct 2016, at 08:29, Bittremieux Wout <wou...@ua...> wrote: >> >> Hello everyone, >> >> It took some time, but we managed to finish the QC working group manuscript. I would like to ask (at least) the co-authors to go through it once more in detail and let me know any final comments. >> We aim to submit the manuscript by the end of October, so I would like to request your comments within the next two weeks, by 27 October at the latest. >> >> As a reminder, the manuscript can be accessed here. >> >> We are planning to submit the manuscript to Anal. Chem., to reach a wide audience of both proteomics and metabolomics people. Some suggestions for potential reviewers would come in handy, so if you have suitable reviewers in mind, please let me know. >> >> Thank you all for your contributions. >> >> Regards, >> Wout >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, SlashDot.org! http://sdm.link/slashdot_______________________________________________ >> 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 |
|
From: Reza S. <rez...@eb...> - 2016-11-23 15:13:51
|
Hi Wout, If you share reviewers comment as a gDoc, can help with that if needed. We are also working on capturing various types of QC within Metabolights and metabolomics, a guid on how to report it. We have now several use cases, but it is a work in progress. So it could help with the comment. > depositing QC data in public repositories Best Wishes, Reza > On 23 Nov 2016, at 08:31, Bittremieux Wout <wou...@ua...> wrote: > > Hello everyone, > > In the meantime we have received the reviewer's comments for our manuscript. > > Two reviewers suggested a few clarifications, and these changes should be relatively straightforward. > > A third reviewer expected more tangible results though, resulting in a major revision. > The main goal of the manuscript is to solicit community interest to ensure that our work on QC has broad public support, which is somewhat at odds with presenting concrete results at this stage already. However, we should try to highlight some concrete use cases to show the value of our working group. Specifically, as mentioned by the reviewer, giving an overview of which types of QC metrics are relevant for various different experiments and detailing how a concrete pipeline of QC tools can improve experimental workflows would be beneficial. Additionally, the interplay between depositing QC data in public repositories and publication guidelines was suggested as a point of attention. > > We will mull over potential improvements for the manuscript in the next few days. There are multiple people involved with expert knowledge on some of the mentioned topics, so as always any suggestions are more than welcome. > > Regards, > Wout > >> On 13 Oct 2016, at 08:29, Bittremieux Wout <wou...@ua...> wrote: >> >> Hello everyone, >> >> It took some time, but we managed to finish the QC working group manuscript. I would like to ask (at least) the co-authors to go through it once more in detail and let me know any final comments. >> We aim to submit the manuscript by the end of October, so I would like to request your comments within the next two weeks, by 27 October at the latest. >> >> As a reminder, the manuscript can be accessed here. >> >> We are planning to submit the manuscript to Anal. Chem., to reach a wide audience of both proteomics and metabolomics people. Some suggestions for potential reviewers would come in handy, so if you have suitable reviewers in mind, please let me know. >> >> Thank you all for your contributions. >> >> Regards, >> Wout >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, SlashDot.org! http://sdm.link/slashdot_______________________________________________ >> 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 |
|
From: Bittremieux W. <wou...@ua...> - 2016-11-23 08:31:14
|
Hello everyone, In the meantime we have received the reviewer's comments for our manuscript. Two reviewers suggested a few clarifications, and these changes should be relatively straightforward. A third reviewer expected more tangible results though, resulting in a major revision. The main goal of the manuscript is to solicit community interest to ensure that our work on QC has broad public support, which is somewhat at odds with presenting concrete results at this stage already. However, we should try to highlight some concrete use cases to show the value of our working group. Specifically, as mentioned by the reviewer, giving an overview of which types of QC metrics are relevant for various different experiments and detailing how a concrete pipeline of QC tools can improve experimental workflows would be beneficial. Additionally, the interplay between depositing QC data in public repositories and publication guidelines was suggested as a point of attention. We will mull over potential improvements for the manuscript in the next few days. There are multiple people involved with expert knowledge on some of the mentioned topics, so as always any suggestions are more than welcome. Regards, Wout > On 13 Oct 2016, at 08:29, Bittremieux Wout <wou...@ua...> wrote: > > Hello everyone, > > It took some time, but we managed to finish the QC working group manuscript. I would like to ask (at least) the co-authors to go through it once more in detail and let me know any final comments. > We aim to submit the manuscript by the end of October, so I would like to request your comments within the next two weeks, by 27 October at the latest. > > As a reminder, the manuscript can be accessed here. > > We are planning to submit the manuscript to Anal. Chem., to reach a wide audience of both proteomics and metabolomics people. Some suggestions for potential reviewers would come in handy, so if you have suitable reviewers in mind, please let me know. > > Thank you all for your contributions. > > Regards, > Wout > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot_______________________________________________ > Psidev-qc-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
|
From: Martin E. <mar...@ru...> - 2016-11-22 16:56:44
|
Dear colleague, dear member of the Proteomics community, this is a short reminder about the ongoing public review of the newly suggested PSI format proBed. PLEASE ADD COMMENTS to the submission page ( <http://www.psidev.info/proBed-in-docproc> http://www.psidev.info/proBed-in-docproc) (or send them directly to martin.eisenacher: at : rub.de). For further details see below. Many thanks for your valuable time and participation Martin Eisenacher (PSI Editor) -- 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 <mailto:mar...@ru...> mar...@ru... <http://www.medizinisches-proteom-center.de/> www.medizinisches-proteom-center.de Von: psi...@eb... [mailto:psi...@eb...] Im Auftrag von Martin Eisenacher Gesendet: Donnerstag, 20. Oktober 2016 11:11 An: psi...@li...; psi...@li...; psi...@li...; ps...@eb...; psi...@eb... Betreff: [Psi-announce] PSI recommendation document (file format proBed), 60-days public review Dear colleague, dear member of the Proteomics community, please forward this message to potentially interested colleagues! The HUPO Proteomics Standards Initiative (PSI) develops standards for documentation and storage of Proteomics data (see <http://www.psidev.info> http://www.psidev.info for an overview of activities). A recommendation document specifying the proBed file format has been submitted to the PSI document process. The submission can be found here: http://www.psidev.info/proBed-in-docproc After having passed a 30-day review of the PSI steering group with minor changes, the proposed document version 1.0.0 DRAFT now goes through 60-days public comments and external review phase (end: 19th December 2016). "The format represents systematically the output of proteogenomics analyses, by mapping peptide identification data retrieved from mass spectrometry (MS)-based experiments to the genome." (see also Cover Letter attached to the submission page) The format is based on the BED format (Browser Extensive Data, <https://genome.ucsc.edu/FAQ/FAQformat.html#format1> https://genome.ucsc.edu/FAQ/FAQformat.html#format1), developed by the UCSC (University of California, Santa Cruz) team. The public comment period enables the wider community to provide feedback on a proposed standard before it is formally accepted, and thus is an important step in the standardisation process. PLEASE ADD COMMENTS to the submission page (http://www.psidev.info/proBed-in-docproc) (or send them directly to martin.eisenacher: at : rub.de) for example regarding the following criteria: - That it is well formed that is, it is presented in accordance with the templates and is clearly written. - That it is sufficiently detailed and clearly contains and comprehensively describes the necessary and sufficient explanation of the format. - That the examples are in accordance with the specification.> > This message is to encourage you to contribute to the standards development activity by commenting on the material that is available online. We invite both positive and negative comments. If negative comments are being made, these could be on the relevance, clarity, correctness, appropriateness, etc, of the proposal as a whole or of specific parts of the proposal. If you do not feel well placed to comment on this document, but know someone who may be, please consider forwarding this request. There is no requirement that people commenting should have had any prior contact with the PSI. Many thanks for your valuable time and participation Martin Eisenacher (PSI Editor) -- 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 <mailto:mar...@ru...> mar...@ru... <http://www.medizinisches-proteom-center.de/> www.medizinisches-proteom-center.de |
|
From: Bittremieux W. <wou...@ua...> - 2016-11-17 06:49:27
|
Hi Mathias, Thank you for the detailed state of affairs. Concerning your iMonDB question, I don't have any notion of a 'set' in there, I only store data on the level of individual runs. There is however the possibility for the user to specify custom metadata through the GUI, which is stored as key-value pairs. Based on the metadata and combinations thereof the data can be filtered for the visualization. Also, currently I represent all metrics as summary statistics over the entire run, consisting of mean, median, standard deviation, quartiles, ... Therefore the discussion on how to represent single and multiple values is very relevant, but I'm not sure what would be the ideal solution. Also, it could be interesting not to discard the full data in favor of only summary statistics to for example investigate and optimize the performance of individual scans. But this is only interesting idea at the moment, not something I'm actively working on. You can find the current iMonDB database schema here <https://bitbucket.org/proteinspector/imondb/wiki/Database>, although this will be transformed to match the new qcML format once it has been specified. Regards, Wout > On 08 Nov 2016, at 18:14, Mathias Walzer <wa...@in...> wrote: > > Dear all, > > as promised here how I'd propose a schema working plan and first discussion points. > > But maybe first the current design main points from the top: > Right now, we compile calculated metrics results as QualityParameters, structured under either a particular run or a set of runs. Also given can be the software that calculated the metrics or other metadata, all cv controlled. Each parameter is under cv control as well, describing the metric. The results are stored in a subelement of the parameter. > > Now what I'd consider lead questions for our schema development (in suggested order of discussion and also from schema core outwards): > > How do our metrics look like? ('XML-any' seems like a hard task to maintain tool-compatibility) Is our list on GitHub complete enough to start with? Would it be beneficial to also add examples to each metric? > > How do we want our metrics to be represented? All defined by one cv term (hence creating an elaborate hierarchy of cv terms) or a combination of several (can we design cv terms that atomic to allow building block like features or does this hamper understanding the implications of a metric)? > > Do we need to change the nomenclature for intelligibility? > > Where to put additional data? A plot for instance. Or a distribution. For visualization, we probably do not want it to be necessary to re-read the whole source data again. > > Do we ditch the possibility to flag results in a report? (The schema right now gives the qcML producing software the possibility to reflect in the file if a flag was raised - on whichever thresholds the user has set) > > Should we change (flatten) the hierarchy? (i.e. the way metrics are categorized in per run or per set) > > How to link source data? Leave it as a quality parameter of a run/set or build in dedicated elements. > > What do we need to concisely present the metric (for visualization or further automated processing)? This circles back to the first question, 2nd iteration :) > > These questions should take up on the feedback points from Ghent and guide us in improving the schema to a version to start building software around. But did I miss any particulars only common in metabolomics? And shall we have a regular telco/hangouts/... (bi- or tri-weekly)? > > best, > mths > > ----- Original Message ----- > From: "Mathias Walzer" <wa...@in...> > To: psi...@li... > Sent: Tuesday, 8 November, 2016 1:41:04 PM > Subject: Re: [Psidev-qc-dev] qcML format evolution > > Dear all, > > Yes, as Dave pointed out there was quite some discussion and I agree this would be a good point to start with planning for the next parts of development. Though one thing I'd like to point out is that these were on-the-fly changes to explore the feasibility. > > In the following, I will summarize the feedback including changes, without taking sides (hopefully). > I guess to keep length in reasonable measures, in a follow-up mail, I will sketch up a proposed schema working plan and further discussion points. > As a side note, I've been in contact with George and Hannes about QC for openSWATH previously. Let me see if I can dig up our correspondence and give you a summary. > > A major point of feedback was going towards the attachment construct. > Having a quality parameter calculated, which result in more than a single value would have worked the way that the XML element of the parameter would have contained only the cv term to classify the parameter and one or more attachment elements, like a table or a plot, referring to the quality parameter element. > From the feedback, preferred was to just leave it all with the parameter. This is now reflected in the development draft as nested content element, which can contain any. > This leads to the second part of feedback about attachment element, that having base64 or lists of values (i.e. tables) would be insufficient. That is why there is now 'any'. > > A similar point of feedback was concerning the structure, over whether a separate structure for quality parameters of sets of files would be necessary. Here, no development draft changes were made, yet. Which brings me to an interesting side question @Wout, how do you handle such input in iMonDB like the type of run or any experiment structure that might influence how to calculate the statistics for quality assessment over the course of measurement acquisitions? > > Another point of the feedback was the reluctance accepting that the information of how to display the qcML may be contained in the file. (I.e. a stylesheet, removing the implicit necessity for a dedicated viewer program.) This however, remained in the development draft, as non-mandatory element tucked away in the outermost end of the schema. > > Next point and the last point of discussion in Ghent was to explore the different types of quality parameters or rather their result types to get a better grasp on how to adequately model the schema. Which resulted in the collection on GitHub (https://github.com/HUPO-PSI/qcML-development/blob/master/cv/qc-metric-collection.md). > > There was no time to discuss, but I wish we had, was regarding the source file(s) denomination of a calculated metric. Right now, there is no explicit element denominating the source of the data. > > And a very last point would be the naming of the elements, which was not addressed in particular, but I had a feeling this was a source of confusion at some points in time. Maybe we should put this under scrutiny as well. The overall structure of the schema is simple enough, maybe there is a better nomenclature to follow. > > > best, > mths > > ----- Original Message ----- > From: "Stefan Tenzer" <te...@un...> > To: "David Tabb, Prof <dt...@su...>" <dt...@su...> > Cc: "Joerg Kuharev" <ku...@un...>, psi...@li... > Sent: Wednesday, 2 November, 2016 9:17:22 AM > 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... ) or Hannes Röst ( 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 > > Telefon: +49 (0) 6131 17-6199 > Telefax: +49 (0) 6131 17-6202 > E-mail: te...@un... > > > Am 01.11.2016 um 13:57 schrieb Tabb, David, Prof < dt...@su... > < 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... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev > > ------------------------------------------------------------------------------ > 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... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev > > ------------------------------------------------------------------------------ > 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... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
|
From: Mathias W. <wa...@in...> - 2016-11-08 16:14:24
|
Dear all,
as promised here how I'd propose a schema working plan and first discussion points.
But maybe first the current design main points from the top:
Right now, we compile calculated metrics results as QualityParameters, structured under either a particular run or a set of runs. Also given can be the software that calculated the metrics or other metadata, all cv controlled. Each parameter is under cv control as well, describing the metric. The results are stored in a subelement of the parameter.
Now what I'd consider lead questions for our schema development (in suggested order of discussion and also from schema core outwards):
How do our metrics look like? ('XML-any' seems like a hard task to maintain tool-compatibility) Is our list on GitHub complete enough to start with? Would it be beneficial to also add examples to each metric?
How do we want our metrics to be represented? All defined by one cv term (hence creating an elaborate hierarchy of cv terms) or a combination of several (can we design cv terms that atomic to allow building block like features or does this hamper understanding the implications of a metric)?
Do we need to change the nomenclature for intelligibility?
Where to put additional data? A plot for instance. Or a distribution. For visualization, we probably do not want it to be necessary to re-read the whole source data again.
Do we ditch the possibility to flag results in a report? (The schema right now gives the qcML producing software the possibility to reflect in the file if a flag was raised - on whichever thresholds the user has set)
Should we change (flatten) the hierarchy? (i.e. the way metrics are categorized in per run or per set)
How to link source data? Leave it as a quality parameter of a run/set or build in dedicated elements.
What do we need to concisely present the metric (for visualization or further automated processing)? This circles back to the first question, 2nd iteration :)
These questions should take up on the feedback points from Ghent and guide us in improving the schema to a version to start building software around. But did I miss any particulars only common in metabolomics? And shall we have a regular telco/hangouts/... (bi- or tri-weekly)?
best,
mths
----- Original Message -----
From: "Mathias Walzer" <wa...@in...>
To: psi...@li...
Sent: Tuesday, 8 November, 2016 1:41:04 PM
Subject: Re: [Psidev-qc-dev] qcML format evolution
Dear all,
Yes, as Dave pointed out there was quite some discussion and I agree this would be a good point to start with planning for the next parts of development. Though one thing I'd like to point out is that these were on-the-fly changes to explore the feasibility.
In the following, I will summarize the feedback including changes, without taking sides (hopefully).
I guess to keep length in reasonable measures, in a follow-up mail, I will sketch up a proposed schema working plan and further discussion points.
As a side note, I've been in contact with George and Hannes about QC for openSWATH previously. Let me see if I can dig up our correspondence and give you a summary.
A major point of feedback was going towards the attachment construct.
Having a quality parameter calculated, which result in more than a single value would have worked the way that the XML element of the parameter would have contained only the cv term to classify the parameter and one or more attachment elements, like a table or a plot, referring to the quality parameter element.
>From the feedback, preferred was to just leave it all with the parameter. This is now reflected in the development draft as nested content element, which can contain any.
This leads to the second part of feedback about attachment element, that having base64 or lists of values (i.e. tables) would be insufficient. That is why there is now 'any'.
A similar point of feedback was concerning the structure, over whether a separate structure for quality parameters of sets of files would be necessary. Here, no development draft changes were made, yet. Which brings me to an interesting side question @Wout, how do you handle such input in iMonDB like the type of run or any experiment structure that might influence how to calculate the statistics for quality assessment over the course of measurement acquisitions?
Another point of the feedback was the reluctance accepting that the information of how to display the qcML may be contained in the file. (I.e. a stylesheet, removing the implicit necessity for a dedicated viewer program.) This however, remained in the development draft, as non-mandatory element tucked away in the outermost end of the schema.
Next point and the last point of discussion in Ghent was to explore the different types of quality parameters or rather their result types to get a better grasp on how to adequately model the schema. Which resulted in the collection on GitHub (https://github.com/HUPO-PSI/qcML-development/blob/master/cv/qc-metric-collection.md).
There was no time to discuss, but I wish we had, was regarding the source file(s) denomination of a calculated metric. Right now, there is no explicit element denominating the source of the data.
And a very last point would be the naming of the elements, which was not addressed in particular, but I had a feeling this was a source of confusion at some points in time. Maybe we should put this under scrutiny as well. The overall structure of the schema is simple enough, maybe there is a better nomenclature to follow.
best,
mths
----- Original Message -----
From: "Stefan Tenzer" <te...@un...>
To: "David Tabb, Prof <dt...@su...>" <dt...@su...>
Cc: "Joerg Kuharev" <ku...@un...>, psi...@li...
Sent: Wednesday, 2 November, 2016 9:17:22 AM
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... ) or Hannes Röst ( 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
Telefon: +49 (0) 6131 17-6199
Telefax: +49 (0) 6131 17-6202
E-mail: te...@un...
Am 01.11.2016 um 13:57 schrieb Tabb, David, Prof < dt...@su... > < 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...
https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev
------------------------------------------------------------------------------
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...
https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev
|
|
From: Mathias W. <wa...@in...> - 2016-11-08 12:41:19
|
Dear all, Yes, as Dave pointed out there was quite some discussion and I agree this would be a good point to start with planning for the next parts of development. Though one thing I'd like to point out is that these were on-the-fly changes to explore the feasibility. In the following, I will summarize the feedback including changes, without taking sides (hopefully). I guess to keep length in reasonable measures, in a follow-up mail, I will sketch up a proposed schema working plan and further discussion points. As a side note, I've been in contact with George and Hannes about QC for openSWATH previously. Let me see if I can dig up our correspondence and give you a summary. A major point of feedback was going towards the attachment construct. Having a quality parameter calculated, which result in more than a single value would have worked the way that the XML element of the parameter would have contained only the cv term to classify the parameter and one or more attachment elements, like a table or a plot, referring to the quality parameter element. >From the feedback, preferred was to just leave it all with the parameter. This is now reflected in the development draft as nested content element, which can contain any. This leads to the second part of feedback about attachment element, that having base64 or lists of values (i.e. tables) would be insufficient. That is why there is now 'any'. A similar point of feedback was concerning the structure, over whether a separate structure for quality parameters of sets of files would be necessary. Here, no development draft changes were made, yet. Which brings me to an interesting side question @Wout, how do you handle such input in iMonDB like the type of run or any experiment structure that might influence how to calculate the statistics for quality assessment over the course of measurement acquisitions? Another point of the feedback was the reluctance accepting that the information of how to display the qcML may be contained in the file. (I.e. a stylesheet, removing the implicit necessity for a dedicated viewer program.) This however, remained in the development draft, as non-mandatory element tucked away in the outermost end of the schema. Next point and the last point of discussion in Ghent was to explore the different types of quality parameters or rather their result types to get a better grasp on how to adequately model the schema. Which resulted in the collection on GitHub (https://github.com/HUPO-PSI/qcML-development/blob/master/cv/qc-metric-collection.md). There was no time to discuss, but I wish we had, was regarding the source file(s) denomination of a calculated metric. Right now, there is no explicit element denominating the source of the data. And a very last point would be the naming of the elements, which was not addressed in particular, but I had a feeling this was a source of confusion at some points in time. Maybe we should put this under scrutiny as well. The overall structure of the schema is simple enough, maybe there is a better nomenclature to follow. best, mths ----- Original Message ----- From: "Stefan Tenzer" <te...@un...> To: "David Tabb, Prof <dt...@su...>" <dt...@su...> Cc: "Joerg Kuharev" <ku...@un...>, psi...@li... Sent: Wednesday, 2 November, 2016 9:17:22 AM 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... ) or Hannes Röst ( 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 Telefon: +49 (0) 6131 17-6199 Telefax: +49 (0) 6131 17-6202 E-mail: te...@un... Am 01.11.2016 um 13:57 schrieb Tabb, David, Prof < dt...@su... > < 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... https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev ------------------------------------------------------------------------------ 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... https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
|
From: Bittremieux W. <wou...@ua...> - 2016-11-03 06:59:07
|
Dear colleagues, Thank you for your contributions. I would like to let you know that we submitted the manuscript to Analytical Chemistry just now. I will keep you informed of any updates. Regards, Wout > On 13 Oct 2016, at 08:29, Bittremieux Wout <wou...@ua...> wrote: > > Hello everyone, > > It took some time, but we managed to finish the QC working group manuscript. I would like to ask (at least) the co-authors to go through it once more in detail and let me know any final comments. > We aim to submit the manuscript by the end of October, so I would like to request your comments within the next two weeks, by 27 October at the latest. > > As a reminder, the manuscript can be accessed here. > > We are planning to submit the manuscript to Anal. Chem., to reach a wide audience of both proteomics and metabolomics people. Some suggestions for potential reviewers would come in handy, so if you have suitable reviewers in mind, please let me know. > > Thank you all for your contributions. > > Regards, > Wout > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot_______________________________________________ > Psidev-qc-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
|
From: Tenzer, S. <te...@un...> - 2016-11-02 08:17:32
|
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... 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 |
|
From: Reza S. <rez...@eb...> - 2016-11-01 16:58:58
|
Hi Dave, > On 1 Nov 2016, at 12:57, Tabb, David, Prof <dt...@su...> <dt...@su...> wrote: > > 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? I can bring this up in the next MSI Data Standards TG telecon, and ask who would be interested in assisting. Separately, I can suggest names that are working on QC related routines. How about industry? They are usually interest in QC so can try approach them too? or do we need to coordinate it. Best Wishes, Reza > 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 <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 <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_______________________________________________ <http://sdm.link/xeonphi_______________________________________________> > Psidev-qc-dev mailing list > Psi...@li... <mailto:Psi...@li...> > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev <https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev> |
|
From: Tabb, D. P. <dt...@su...> - 2016-11-01 16:34:09
|
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 |
|
From: Martin E. <mar...@ru...> - 2016-10-20 09:11:25
|
Dear colleague, dear member of the Proteomics community, please forward this message to potentially interested colleagues! The HUPO Proteomics Standards Initiative (PSI) develops standards for documentation and storage of Proteomics data (see <http://www.psidev.info> http://www.psidev.info for an overview of activities). A recommendation document specifying the proBed file format has been submitted to the PSI document process. The submission can be found here: http://www.psidev.info/proBed-in-docproc After having passed a 30-day review of the PSI steering group with minor changes, the proposed document version 1.0.0 DRAFT now goes through 60-days public comments and external review phase (end: 19th December 2016). "The format represents systematically the output of proteogenomics analyses, by mapping peptide identification data retrieved from mass spectrometry (MS)-based experiments to the genome." (see also Cover Letter attached to the submission page) The format is based on the BED format (Browser Extensive Data, <https://genome.ucsc.edu/FAQ/FAQformat.html#format1> https://genome.ucsc.edu/FAQ/FAQformat.html#format1), developed by the UCSC (University of California, Santa Cruz) team. The public comment period enables the wider community to provide feedback on a proposed standard before it is formally accepted, and thus is an important step in the standardisation process. PLEASE ADD COMMENTS to the submission page (http://www.psidev.info/proBed-in-docproc) (or send them directly to martin.eisenacher: at : rub.de) for example regarding the following criteria: - That it is well formed that is, it is presented in accordance with the templates and is clearly written. - That it is sufficiently detailed and clearly contains and comprehensively describes the necessary and sufficient explanation of the format. - That the examples are in accordance with the specification.> > This message is to encourage you to contribute to the standards development activity by commenting on the material that is available online. We invite both positive and negative comments. If negative comments are being made, these could be on the relevance, clarity, correctness, appropriateness, etc, of the proposal as a whole or of specific parts of the proposal. If you do not feel well placed to comment on this document, but know someone who may be, please consider forwarding this request. There is no requirement that people commenting should have had any prior contact with the PSI. Many thanks for your valuable time and participation Martin Eisenacher (PSI Editor) -- 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 <mailto:mar...@ru...> mar...@ru... <http://www.medizinisches-proteom-center.de/> www.medizinisches-proteom-center.de |
|
From: weimin z. <wmz...@gm...> - 2016-10-17 08:06:47
|
Dear Wout, many thanks for the effort. the manuscript reads well for me. regards, weimin On Thu, Oct 13, 2016 at 2:29 PM, Bittremieux Wout < wou...@ua...> wrote: > Hello everyone, > > It took some time, but we managed to finish the QC working group > manuscript. I would like to ask (at least) the co-authors to go through it > once more in detail and let me know any final comments. > We aim to submit the manuscript by the end of October, so I would like to > request your comments within the next two weeks, by 27 October at the > latest. > > As a reminder, the manuscript can be accessed here > <https://www.overleaf.com/5671898jfvtyd>. > > We are planning to submit the manuscript to Anal. Chem., to reach a wide > audience of both proteomics and metabolomics people. Some suggestions for > potential reviewers would come in handy, so if you have suitable reviewers > in mind, please let me know. > > Thank you all for your contributions. > > Regards, > Wout > |
|
From: Tenzer, S. <te...@un...> - 2016-10-17 07:57:03
|
Hi everyone, great to see the progress - reads really well! Thanks to everyone for the great work! I added a few minor changes and one reference( Navarro et al, 2016, PMID: 27701404) - could you update the bibliography? My suggestions for reviewers would be: Lennart Martens (https://compomics.com/people/lennart-martens/) Rob Beynon (https://www.liverpool.ac.uk/integrative-biology/staff/robert-beynon/) Don Jones (http://www2.le.ac.uk/departments/csmm/people/dr-don-jl-jones) Best regards, 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... Am 13.10.2016 um 08:29 schrieb Bittremieux Wout <wou...@ua...<mailto:wou...@ua...>>: Hello everyone, It took some time, but we managed to finish the QC working group manuscript. I would like to ask (at least) the co-authors to go through it once more in detail and let me know any final comments. We aim to submit the manuscript by the end of October, so I would like to request your comments within the next two weeks, by 27 October at the latest. As a reminder, the manuscript can be accessed here<https://www.overleaf.com/5671898jfvtyd>. We are planning to submit the manuscript to Anal. Chem., to reach a wide audience of both proteomics and metabolomics people. Some suggestions for potential reviewers would come in handy, so if you have suitable reviewers in mind, please let me know. Thank you all for your contributions. Regards, Wout |
|
From: Bittremieux W. <wou...@ua...> - 2016-10-13 06:42:19
|
Hello everyone, It took some time, but we managed to finish the QC working group manuscript. I would like to ask (at least) the co-authors to go through it once more in detail and let me know any final comments. We aim to submit the manuscript by the end of October, so I would like to request your comments within the next two weeks, by 27 October at the latest. As a reminder, the manuscript can be accessed here <https://www.overleaf.com/5671898jfvtyd>. We are planning to submit the manuscript to Anal. Chem., to reach a wide audience of both proteomics and metabolomics people. Some suggestions for potential reviewers would come in handy, so if you have suitable reviewers in mind, please let me know. Thank you all for your contributions. Regards, Wout |
|
From: Jinmeng J. <jia...@16...> - 2016-08-31 01:14:19
|
Hi Wont,Martin and all, Sorry for the late reply. I am being on a vocation this week. I am totally agree with your opinions about both the MIAPE-like document and the author list. My mistake that I made you have some little misunderstanding about the MIAPE-like document results. We didn't mean to present the results in this manuscript, and planned to submit the final version of the MIAPE-QC draft to the 2017 PSI spring workshop for discussion. Now we only finished the first draft so we want to get some advice from QC group members first. This manuscript is a preview. It is an introduction about what is QC group and what are QC group members going to do. I think maybe Weimin thought I am a new member added to QC group so he suggested me to add my name to it. Thank all your kind suggestions. Kind regards, Jinmeng At 2016-08-30 00:08:53, "Bittremieux Wout" <wou...@ua...> wrote: >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 > |
|
From: Jinmeng J. <jia...@16...> - 2016-08-31 01:02:58
|
Hi Wont,Martin and all, Sorry for the late reply. I am being on a vocation this week. I am totally agree with your opinions about both the MIAPE-like document and the author list. My mistake that I made you have some little misunderstanding about the MIAPE-like document results. We didn't mean to present the results in this manuscript, and planned to submit the final version of the MIAPE-QC draft to the 2017 PSI spring workshop for discussion. Now we only finished the first draft so we want to get some advice from QC group members first. This manuscript is a preview. It is an introduction about what is QC group and what are QC group members going to do. I think maybe Weimin thought I am a new member added to QC gourp so he suggested me to add my name to it. Thank all your kind suggestions. Kind regards, Jinmeng At 2016-08-30 00:08:53, "Bittremieux Wout" <wou...@ua...> wrote: >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 > |
|
From: Martin E. <mar...@ru...> - 2016-08-30 13:22:31
|
Hi all,
I strongly support Wout's thoughts about not presenting
results in this manuscript and about the author list.
Moreover: A MIAPE-QC document should be extensively discussed
in a PSI meeting before publication; especially as QC is a sensitive topic
and - presumably - there will be no easy consensus about "minimal QC".
Once such a MIAPE-like doc. is discussed and has passed the
PSI DocProc, an article it that may be authored by Jinmeng Jia.
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: Bittremieux Wout [mailto:wou...@ua...]
Gesendet: Montag, 29. August 2016 18:09
An: Martin Eisenacher <mar...@ru...>
Cc: psi...@li...
Betreff: Re: [Psidev-qc-dev] PSI QC Announcement Draft
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
|
|
From: Bittremieux W. <wou...@ua...> - 2016-08-29 16:09:05
|
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 |
|
From: Jinmeng J. <jia...@16...> - 2016-08-27 05:56:36
|
Here is the MIAPE-QC draft.
在 2016-08-27 13:52:53，"Jinmeng Jia" <jia...@16...> 写道：
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!
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> 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
|
|
From: Jinmeng J. <jia...@16...> - 2016-08-27 05:53:04
|
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!
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> 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
|
|
From: weimin z. <wmz...@gm...> - 2016-08-26 04:15:59
|
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 > |
|
From: Martin E. <mar...@ru...> - 2016-08-24 15:55:17
|
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
|
1 message has been excluded from this view by a project administrator.
