psidev-qc-dev — PSI-QC working group mailinglist

Re: [Psidev-qc-dev] Input on QC in MS Imaging for mzQC use case

[Alexandrov, T. <tal...@he...>]

Hi Wout,

Thanks for the invitation! As we quickly discussed off this thread, I’m introducing Chris Anderton and Kumar Sharma with whom we worked on developing QC criteria for MALDI-imaging in KPMP.


Chris and Kumar,

I think this can help multiply the impact of our QC work in KPMP.


All,

Shall we have a joint meeting in the week of Nov 4th (I’m traveling till then) to discuss it? Maybe we can meet at 5pm CET to cover CET, Central, and Pacific time zones?

Cheers,
Theo


From: Wout Bittremieux <wou...@ua...>
Date: Friday, October 25, 2024 at 4:01 PM
To: Alexandrov, Theodore <tal...@he...>
Cc: psi...@li... <psi...@li...>
Subject: Input on QC in MS Imaging for mzQC use case
Hi Theodore,

I hope the transition to UCSD is going well, though I understand from Bishoy at the NCEMS meeting a few weeks back that it's been a process. Navigating visa and administrative hurdles during an international move can be stressful—I'm all too familiar with that myself unfortunately.

I'm reaching out regarding a project within the Proteomics Standards Initiative (PSI) that we've been working on for some time now: developing the mzQC file format<https://urldefense.com/v3/__https:/hupo-psi.github.io/mzQC/__;!!LLK065n_VXAQ!i679mes717kblm6Ji4uTvOmPJysMJoIf78CWj_FsZZqu1HhnSdr20fycqqxMBLBiTis3BcF06CMEsIAsMxc3EW-b6sZbtfwIMoEzMQ$> to store QC data specifically for biological mass spectrometry. The mzQC format has successfully passed the formal PSI approval process, and we've recently published a technical note<https://urldefense.com/v3/__https:/doi.org/10.1021/jasms.4c00174__;!!LLK065n_VXAQ!i679mes717kblm6Ji4uTvOmPJysMJoIf78CWj_FsZZqu1HhnSdr20fycqqxMBLBiTis3BcF06CMEsIAsMxc3EW-b6sZbtfzCnHrv6A$> detailing software libraries for operating on mzQC data.

As the next step, we're working on a more comprehensive manuscript to formally introduce the mzQC format to the community. We plan to show its utility with a variety of use cases, including outlier detection and longitudinal QC applications. To further demonstrate mzQC's broad relevance across diverse MS applications, we think that including MS imaging as a use case would be very interesting. However, our team lacks experience in that area.

I wanted to see if you might share your insights on QC practices currently used in MS imaging, including commonly used methods and tools. Additionally, if you have or know of any datasets we could use, that would be extremely helpful. Naturally, we would be happy to include you and relevant team members as co-authors on the manuscript.

Thanks very much in advance, and I look forward to any input you can offer.

Best regards,
Wout

Re: [Psidev-qc-dev] Input on QC in MS Imaging for mzQC use case

[Alexandrov, T. <tal...@he...>]

Hi Wout,

Yes, lab transition is never simple and we hit more roadblocks than I imagined, but we are blessed with a large part of our EMBL moving to UCSD. And great that you connected with Bishoy and thanks for the kind words.

Great to hear about the mzQC initiative – it’s great and very forward-looking.

I suggest to include into this discussion Chris Anderton from PNNL and Kumar Sharma from UT San Antonio. Together with Chris and Kumar, we participate for 5+ years in the NIH-funded Kidney Precision Medicine Project (KPMP), by performing MALDI-imaging-based spatial metabolomics and lipidomics on clinically-relevant samples from kidney, and a big part of our work was to develop QC criteria. Those criteria were reviewed by the KPMP project and NIH.

So, we can consider the QC criteria developed in KPMP as an example of QC criteria for MALDI-imaging for both metabolites and lipids.

If that’s OK, maybe we all can have a meeting to better understand what specifically you have in mind, what you call “QC criteria”, how our work and criteria can be formulated as an example.

I have not Cc’ed Chris and Kumar, because if we go down this route, this would include the number of authors in your manuscript (from our team it would be only me, but Chris and Kumar would need to be included and maybe +2 people from their team, up to you and them to decide), and I’d like to make sure that you are ok with this for an example section.

Cheers,
Theo







From: Wout Bittremieux <wou...@ua...>
Date: Friday, October 25, 2024 at 4:01 PM
To: Alexandrov, Theodore <tal...@he...>
Cc: psi...@li... <psi...@li...>
Subject: Input on QC in MS Imaging for mzQC use case
Hi Theodore,

I hope the transition to UCSD is going well, though I understand from Bishoy at the NCEMS meeting a few weeks back that it's been a process. Navigating visa and administrative hurdles during an international move can be stressful—I'm all too familiar with that myself unfortunately.

I'm reaching out regarding a project within the Proteomics Standards Initiative (PSI) that we've been working on for some time now: developing the mzQC file format<https://urldefense.com/v3/__https:/hupo-psi.github.io/mzQC/__;!!LLK065n_VXAQ!i679mes717kblm6Ji4uTvOmPJysMJoIf78CWj_FsZZqu1HhnSdr20fycqqxMBLBiTis3BcF06CMEsIAsMxc3EW-b6sZbtfwIMoEzMQ$> to store QC data specifically for biological mass spectrometry. The mzQC format has successfully passed the formal PSI approval process, and we've recently published a technical note<https://urldefense.com/v3/__https:/doi.org/10.1021/jasms.4c00174__;!!LLK065n_VXAQ!i679mes717kblm6Ji4uTvOmPJysMJoIf78CWj_FsZZqu1HhnSdr20fycqqxMBLBiTis3BcF06CMEsIAsMxc3EW-b6sZbtfzCnHrv6A$> detailing software libraries for operating on mzQC data.

As the next step, we're working on a more comprehensive manuscript to formally introduce the mzQC format to the community. We plan to show its utility with a variety of use cases, including outlier detection and longitudinal QC applications. To further demonstrate mzQC's broad relevance across diverse MS applications, we think that including MS imaging as a use case would be very interesting. However, our team lacks experience in that area.

I wanted to see if you might share your insights on QC practices currently used in MS imaging, including commonly used methods and tools. Additionally, if you have or know of any datasets we could use, that would be extremely helpful. Naturally, we would be happy to include you and relevant team members as co-authors on the manuscript.

Thanks very much in advance, and I look forward to any input you can offer.

Best regards,
Wout

[Psidev-qc-dev] Input on QC in MS Imaging for mzQC use case

[Wout B. <wou...@ua...>]

Hi Theodore,

I hope the transition to UCSD is going well, though I understand from Bishoy at the NCEMS meeting a few weeks back that it's been a process. Navigating visa and administrative hurdles during an international move can be stressful—I'm all too familiar with that myself unfortunately.

I'm reaching out regarding a project within the Proteomics Standards Initiative (PSI) that we've been working on for some time now: developing the mzQC file format<https://hupo-psi.github.io/mzQC/> to store QC data specifically for biological mass spectrometry. The mzQC format has successfully passed the formal PSI approval process, and we've recently published a technical note<https://doi.org/10.1021/jasms.4c00174> detailing software libraries for operating on mzQC data.

As the next step, we're working on a more comprehensive manuscript to formally introduce the mzQC format to the community. We plan to show its utility with a variety of use cases, including outlier detection and longitudinal QC applications. To further demonstrate mzQC's broad relevance across diverse MS applications, we think that including MS imaging as a use case would be very interesting. However, our team lacks experience in that area.

I wanted to see if you might share your insights on QC practices currently used in MS imaging, including commonly used methods and tools. Additionally, if you have or know of any datasets we could use, that would be extremely helpful. Naturally, we would be happy to include you and relevant team members as co-authors on the manuscript.

Thanks very much in advance, and I look forward to any input you can offer.

Best regards,
Wout

[Psidev-qc-dev] Planning for mzQC manuscript meeting – January 2025

[Wout B. <wou...@ua...>]

Dear colleagues,

Following our recent discussions, we are moving forward with plans to organize an in-person meeting to complete the mzQC manuscript. With just a few remaining steps—finalizing data analysis for the use cases and completing the manuscript writing—a dedicated session should allow us to bring this project across the finish line.

Meeting details:

  *
Proposed period: January 2025
  *
Location: Antwerp, Belgium
  *
Duration: 2 to 3 days, with options spanning Wednesday to Friday

To identify the best dates, please indicate your availability by filling out the Doodle poll here<https://doodle.com/meeting/participate/id/aQvMMN0b>. The link provides options for each week in January.

Participation and logistics

In-person attendance is encouraged to maximize productivity, but dedicated remote participation is possible for those unable to attend physically. Wout has some budget available for travel to/from Belgium and lodging in Antwerp (note: due to university regulations, any travel that can be completed by train within an 8-hour timeframe cannot be done by plane).

Please complete the Doodle poll by November 15 so we can finalize details during our call that day.

Best,
Wout

[Psidev-qc-dev] Upcoming teleconference October 18

[Wout B. <wou...@ua...>]

Dear colleagues,

We have our next teleconference Friday October 18, at 13h00 CET (12h00 BST, 11h00 GMT).

You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d

  *
Meeting ID: 311 403 481 845
  *
Passcode: Jm4d4s

Agenda items:

  *
mzQC website<https://hupo-psi.github.io/mzQC/>: review of previous and upcoming updates
  *
pymzqc: validator improvements
  *
mzQC support in tools: progress update
  *
mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: progress update
  *
mzQC in-person meeting: see below
  *
AOB.

Best,
Wout

---

There was an interesting proposal during the previous call (thank you Tim) to organize an mzQC writing session where we block a few days, meet in-person, and have dedicated time to work on the mzQC manuscript to get this over the finish line. Wout has funding available to cover travel and hotel costs to do this in Antwerp. Please consult your agendas to discuss whether you'd be interested in doing this in January 2025.

[Psidev-qc-dev] Upcoming teleconference October 4

[Wout B. <wou...@ua...>]

Dear colleagues,

We have our next teleconference Friday October 4, at 13h00 CET (12h00 BST, 11h00 GMT).

You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d
Meeting ID: 311 403 481 845
Passcode: Jm4d4s

Agenda items:

  *
CV: new term requests (#333<https://github.com/HUPO-PSI/psi-ms-CV/pull/333>)
  *
mzQC website<https://hupo-psi.github.io/mzQC/>: review of previous and upcoming updates
  *
pymzqc: validator improvements
  *
mzQC support in tools: progress update
  *
mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: progress update
  *
AOB.

Best,
Wout

[Psidev-qc-dev] Upcoming teleconference September 4

[Wout B. <wou...@ua...>]

Dear colleagues,

We have our next teleconference Wednesday September 4, at 16h00 CET (7h00 PST, 15h00 BST, 14h00 GMT).

You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d

  *
Meeting ID: 311 403 481 845
  *
Passcode: Jm4d4s

Agenda items:

  *
mzQC website<https://hupo-psi.github.io/mzQC/>: review of previous and upcoming updates
  *
pymzqc: validator improvements
  *
mzQC support in tools: progress update
  *
mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: progress update
  *
AOB.

Best,
Wout

[Psidev-qc-dev] Upcoming teleconference August 21

[Wout B. <wou...@ua...>]

Dear colleagues,

We have our next teleconference tomorrow, Wednesday August 21, at 16h00 CET (7h00 PST, 15h00 BST, 14h00 GMT).

You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d

  *
Meeting ID: 311 403 481 845
  *
Passcode: Jm4d4s

Agenda items:

  *
mzQC website<https://hupo-psi.github.io/mzQC/>: @everyone review the updated website content prior to the meeting (#234<https://github.com/HUPO-PSI/mzQC/pull/234>)
  *
pymzqc: validator improvements
  *
mzQC support in tools: progress update
  *
mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: progress update
  *
AOB.

Best,
Wout

[Psidev-qc-dev] Upcoming teleconference August 7

[Wout B. <wou...@ua...>]

Dear colleagues,

We have our next teleconference tomorrow, Wednesday August 7, at 16h00 CET (7h00 PST, 15h00 BST, 14h00 GMT).

You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d
Meeting ID: 311 403 481 845
Passcode: Jm4d4s

Agenda items:

  *
CV: fraction as a unit or value-concept (#316<https://github.com/HUPO-PSI/psi-ms-CV/pull/316>)
  *
mzQC website<https://hupo-psi.github.io/mzQC/>: update documentation (#234<https://github.com/HUPO-PSI/mzQC/pull/234>) and examples (#225<https://github.com/HUPO-PSI/mzQC/issues/225> and corresponding PRs)
  *
pymzqc: validator improvements (#42<https://github.com/MS-Quality-Hub/pymzqc/issues/42>, #43<https://github.com/MS-Quality-Hub/pymzqc/issues/43>, #46<https://github.com/MS-Quality-Hub/pymzqc/issues/46>)
  *
mzQC support in tools: progress update
  *
mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: progress update
  *
AOB.

Best,
Wout

Re: [Psidev-qc-dev] Upcoming teleconference July 24

[Eralp D. <era...@gm...>]

Hi all,

I won't be able to join you today due to a conflicting meeting.

@Mathias i will send a reply today. I wanted to have Olga's opinion about
the implementation. I will see her today and will let you know.

Thanks,
Eralp

On Tue, Jul 23, 2024, 10:06 Wout Bittremieux <wou...@ua...>
wrote:

> Dear colleagues,
>
> We have our next teleconference tomorrow, Wednesday July 24, at 16h00 CET
> (7h00 PST, 15h00 BST, 14h00 GMT).
>
> You can connect to our teleconference on Microsoft Teams through the
> following link:
> https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d
> Meeting ID: 311 403 481 845
> Passcode: Jm4d4s
>
> Agenda items:
>
>    - CV: STATO incompatibility (#296
>    <https://github.com/HUPO-PSI/psi-ms-CV/pull/296>, #299
>    <https://github.com/HUPO-PSI/psi-ms-CV/pull/299>)
>    - pymzqc: validator improvements (#42
>    <https://github.com/MS-Quality-Hub/pymzqc/issues/42>, #43
>    <https://github.com/MS-Quality-Hub/pymzqc/issues/43>)
>    - mzQC website <https://hupo-psi.github.io/mzQC/>: update
>    documentation and examples (#225
>    <https://github.com/HUPO-PSI/mzQC/issues/225> and corresponding PRs)
>    - GitHub: Review active and stale PRs
>    - mzQC support in tools: progress update
>    - mzQC specification manuscript
>    <https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>:
>    progress update
>    - AOB.
>
>
> Best,
> Wout
> _______________________________________________
> Psidev-qc-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev
>

[Psidev-qc-dev] Upcoming teleconference July 24

[Wout B. <wou...@ua...>]

Dear colleagues,

We have our next teleconference tomorrow, Wednesday July 24, at 16h00 CET (7h00 PST, 15h00 BST, 14h00 GMT).

You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d
Meeting ID: 311 403 481 845
Passcode: Jm4d4s

Agenda items:

  *
CV: STATO incompatibility (#296<https://github.com/HUPO-PSI/psi-ms-CV/pull/296>, #299<https://github.com/HUPO-PSI/psi-ms-CV/pull/299>)
  *
pymzqc: validator improvements (#42<https://github.com/MS-Quality-Hub/pymzqc/issues/42>, #43<https://github.com/MS-Quality-Hub/pymzqc/issues/43>)
  *
mzQC website<https://hupo-psi.github.io/mzQC/>: update documentation and examples (#225<https://github.com/HUPO-PSI/mzQC/issues/225> and corresponding PRs)
  *
GitHub: Review active and stale PRs
  *
mzQC support in tools: progress update
  *
mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: progress update
  *
AOB.

Best,
Wout

Re: [Psidev-qc-dev] Upcoming teleconference July 10

[Eralp D. <era...@gm...>]

Hi all,

I am planning to join to see how I can contribute to the longitudinal QC
part.

Thanks,
Eralp

On Tue, Jul 9, 2024 at 12:16 PM Wout Bittremieux <
wou...@ua...> wrote:

> Dear colleagues,
>
> We have our next teleconference tomorrow, Wednesday July 10, at 16h00 CET
> (7h00 PST, 15h00 BST, 14h00 GMT).
>
> You can connect to our teleconference on Microsoft Teams through the
> following link:
> https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d
> Meeting ID: 311 403 481 845
> Passcode: Jm4d4s
>
> Agenda items:
>
>    - mzQC website <https://hupo-psi.github.io/mzQC/>: update
>    documentation and examples (#225
>    <https://github.com/HUPO-PSI/mzQC/issues/225> and corresponding PRs)
>    - mzQC support in tools: progress
>    - mzQC specification manuscript
>    <https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>:
>    use cases
>    - AOB.
>
>
> Best,
> Wout
> _______________________________________________
> Psidev-qc-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev
>


-- 
Eralp DOGU, PhD
Assoc. Prof., Department of Statistics
<http://www.linkedin.com/in/eralpdogu>Mugla Sitki Kocman University,
Phone: +902522115446
era...@mu..., era...@gm...
https://sites.google.com/site/eralpdogu/

Re: [Psidev-qc-dev] Upcoming teleconference July 10

[Nils H. <nil...@ce...>]

Hi,


same here,


Best wishes
Nils


Am 09.07.24 um 19:49 schrieb Tim Van Den Bossche via Psidev-qc-dev:
> Hi everyone,
>
> I cannot make it tomorrow due to an overlapping RdA meeting.
>
> All the best,
> Tim
>
> ---
> Tim Van Den Bossche, FWO Postdoctoral Scientist
> Member Board of Governors, Ghent University
>
> Computational Omics and Systems Biology Group (CompOmics)
> Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
> VIB - UGent Center for Medical Biotechnology
> ------------------------------------------------------------------------
> *Van:* Wout Bittremieux <wou...@ua...>
> *Verzonden:* dinsdag 9 juli 2024 16:42
> *Aan:* psi...@li... 
> <psi...@li...>
> *Onderwerp:* [Psidev-qc-dev] Upcoming teleconference July 10
> Dear colleagues,
>
> We have our next teleconference tomorrow, Wednesday July 10, at 16h00 
> CET (7h00 PST, 15h00 BST, 14h00 GMT).
>
> You can connect to our teleconference on Microsoft Teams through the 
> following link: 
> https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d 
> <https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d>
> Meeting ID: 311 403 481 845
> Passcode: Jm4d4s
>
> Agenda items:
>
>  *
>     mzQC website <https://hupo-psi.github.io/mzQC/>: update
>     documentation and examples (#225
>     <https://github.com/HUPO-PSI/mzQC/issues/225> and corresponding PRs)
>  *
>     mzQC support in tools: progress
>  *
>     mzQC specification manuscript
>     <https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>:
>     use cases
>  *
>     AOB.
>
>
> Best,
> Wout
>
>
> _______________________________________________
> Psidev-qc-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev

-- 
Dr. Nils Hoffmann
Cloud and Interoperability Platform Coordinator - ELIXIR-DE
de.NBI - Deutsches Netzwerk für Bioinformatik-Infrastruktur
Institut für Bio- und Geowissenschaften
Computergestützte Metagenomik (IBG-5)
Forschungszentrum Jülich GmbH

c/o Centrum für Biotechnologie (CeBiTec)
Universität Bielefeld
Universitätsstraße 27
D-33615 Bielefeld

Room: Main Building M3-125
Tel: +49(0)521-106-86780

E-Mail:n.h...@fz...
E-Mail:co...@de...
www.denbi.de
elixir-europe.org

---------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------
Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Ir. Pieter Jansens
---------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------

Re: [Psidev-qc-dev] Upcoming teleconference July 10

[Tim V. D. B. <Tim...@UG...>]

Hi everyone,

I cannot make it tomorrow due to an overlapping RdA meeting.

All the best,
Tim

---
Tim Van Den Bossche, FWO Postdoctoral Scientist
Member Board of Governors, Ghent University

Computational Omics and Systems Biology Group (CompOmics)
Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
VIB - UGent Center for Medical Biotechnology
________________________________
Van: Wout Bittremieux <wou...@ua...>
Verzonden: dinsdag 9 juli 2024 16:42
Aan: psi...@li... <psi...@li...>
Onderwerp: [Psidev-qc-dev] Upcoming teleconference July 10

Dear colleagues,

We have our next teleconference tomorrow, Wednesday July 10, at 16h00 CET (7h00 PST, 15h00 BST, 14h00 GMT).

You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d
Meeting ID: 311 403 481 845
Passcode: Jm4d4s

Agenda items:

  *
mzQC website<https://hupo-psi.github.io/mzQC/>: update documentation and examples (#225<https://github.com/HUPO-PSI/mzQC/issues/225> and corresponding PRs)
  *
mzQC support in tools: progress
  *
mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: use cases
  *
AOB.

Best,
Wout

[Psidev-qc-dev] Upcoming teleconference July 10

[Wout B. <wou...@ua...>]

Dear colleagues,

We have our next teleconference tomorrow, Wednesday July 10, at 16h00 CET (7h00 PST, 15h00 BST, 14h00 GMT).

You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d
Meeting ID: 311 403 481 845
Passcode: Jm4d4s

Agenda items:

  *
mzQC website<https://hupo-psi.github.io/mzQC/>: update documentation and examples (#225<https://github.com/HUPO-PSI/mzQC/issues/225> and corresponding PRs)
  *
mzQC support in tools: progress
  *
mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: use cases
  *
AOB.

Best,
Wout

[Psidev-qc-dev] Upcoming teleconference June 26

[Wout B. <wou...@ua...>]

Dear colleagues,

We have our next teleconference today, Wednesday June 26, at 16h00 CET (7h00 PST, 15h00 BST, 14h00 GMT).

You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d
Meeting ID: 311 403 481 845
Passcode: Jm4d4s

Agenda items:

  *
mzQC website<https://hupo-psi.github.io/mzQC/>: update documentation and examples (#225<https://github.com/HUPO-PSI/mzQC/issues/225>)
  *
mzQC support in tools: overview and planning
  *
mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: planning
  *
AOB.

Best,
Wout

Re: [Psidev-qc-dev] Upcoming teleconference June 12

[Tim V. D. B. <Tim...@UG...>]

Hi everyone,

I have an overlapping meeting, so cannot attend today.

Congratulations on the manuscript!

Best,
Tim

Sent from my mobile phone, please excuse brevity.
________________________________
From: Nils Hoffmann <nil...@ce...>
Sent: Tuesday, June 11, 2024 10:58:03 PM
To: Bielow, Chris <Chr...@fu...>
Cc: psi...@li... <psi...@li...>
Subject: Re: [Psidev-qc-dev] Upcoming teleconference June 12

Congratulations!

I will also be absent tomorrow.
Greetings from Magnus, Veit and Samuel from the ELIXIR AllHands Meeting in Uppsala in Sweden.

Cheers
Nils

Am 11.06.2024 um 21:45 schrieb Bielow, Chris <Chr...@fu...>:


Dear all,
Im currently on vacation and will abstain tomorrow.

On another note: good news. Our paper got accepted today!

Cheers Chris

Am 11.06.2024 21:53 schrieb Wout Bittremieux <wou...@ua...>:
Dear colleagues,

We have our next teleconference tomorrow, Wednesday June 12th, at 16h00 CET (7h00 PST, 15h00 BST, 14h00 GMT).

You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d
Meeting ID: 311 403 481 845
Passcode: Jm4d4s

Agenda items:

  *
mzQC website<https://hupo-psi.github.io/mzQC/>: update documentation and examples
  *
mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: planning
  *
AOB.

Best,
Wout
_______________________________________________
Psidev-qc-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev

Re: [Psidev-qc-dev] Upcoming teleconference June 12

[Nils H. <nil...@ce...>]

<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div dir="ltr"></div><div dir="ltr">Congratulations!</div><div dir="ltr"><br></div><div dir="ltr">I will also be absent tomorrow.</div><div dir="ltr">Greetings from Magnus, Veit and Samuel from the ELIXIR AllHands Meeting in Uppsala in Sweden.</div><div dir="ltr"><br></div><div dir="ltr">Cheers</div><div dir="ltr">Nils</div><div dir="ltr"><br><blockquote type="cite">Am 11.06.2024 um 21:45 schrieb Bielow, Chris &lt;Chr...@fu...&gt;:<br><br></blockquote></div><blockquote type="cite"><div dir="ltr">

<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<meta content="text/html; charset=iso-8859-1">



<div dir="auto">Dear all,
<div dir="auto">Im currently on vacation and will abstain tomorrow.&nbsp;</div>
<div dir="auto"><br>
</div>
<div dir="auto">On another note: good news. Our paper got accepted today!&nbsp;</div>
<div dir="auto"><br>
</div>
<div dir="auto">Cheers Chris&nbsp;</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">Am 11.06.2024 21:53 schrieb Wout Bittremieux &lt;wou...@ua...&gt;:<br type="attribution">
</div>
</div>
<div>
<div class="elementToProof" style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
Dear colleagues,</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<div class="elementToProof" style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
We have our next teleconference tomorrow, Wednesday June 12th, at 16h00 CET (7h00 PST, 15h00 BST, 14h00 GMT).</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<div class="elementToProof" style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
You can connect to our teleconference on Microsoft Teams through the following link:
<a href="https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d" id="OWA750d9e35-7ed7-a626-74a2-1979a4335ecc" class="OWAAutoLink">
https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d</a></div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
Meeting ID: 311 403 481 845</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
Passcode: Jm4d4s</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<div class="elementToProof" style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
Agenda items:</div>
<ul>
<li style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<div class="elementToProof" style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<a href="https://hupo-psi.github.io/mzQC/" id="OWA53c7984a-3d49-4702-91e5-48534828096e" class="OWAAutoLink" title="https://hupo-psi.github.io/mzQC/">mzQC website</a>: update documentation and examples</div>
</li><li style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<div class="elementToProof" style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<a href="https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit" id="OWA3d10afb5-0c2e-7d2e-ccff-f6ed4bdd20e7" class="OWAAutoLink" title="https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit">mzQC
 specification manuscript</a>: planning</div>
</li><li style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<div class="elementToProof" style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
AOB.</div>
</li></ul>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
Best,</div>
<div class="elementToProof" style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
Wout</div>
</div>


<span>_______________________________________________</span><br><span>Psidev-qc-dev mailing list</span><br><span>Psi...@li...</span><br><span>https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev</span><br></div></blockquote></body></html>

Re: [Psidev-qc-dev] Upcoming teleconference June 12

[Bielow, C. <Chr...@fu...>]

Dear all,
Im currently on vacation and will abstain tomorrow.

On another note: good news. Our paper got accepted today!

Cheers Chris

Am 11.06.2024 21:53 schrieb Wout Bittremieux <wou...@ua...>:
Dear colleagues,

We have our next teleconference tomorrow, Wednesday June 12th, at 16h00 CET (7h00 PST, 15h00 BST, 14h00 GMT).

You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d
Meeting ID: 311 403 481 845
Passcode: Jm4d4s

Agenda items:

  *
mzQC website<https://hupo-psi.github.io/mzQC/>: update documentation and examples
  *
mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: planning
  *
AOB.

Best,
Wout

[Psidev-qc-dev] Upcoming teleconference June 12

[Wout B. <wou...@ua...>]

Dear colleagues,

We have our next teleconference tomorrow, Wednesday June 12th, at 16h00 CET (7h00 PST, 15h00 BST, 14h00 GMT).

You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d
Meeting ID: 311 403 481 845
Passcode: Jm4d4s

Agenda items:

  *
mzQC website<https://hupo-psi.github.io/mzQC/>: update documentation and examples
  *
mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: planning
  *
AOB.

Best,
Wout

Re: [Psidev-qc-dev] Upcoming teleconference May 15

[Bielow, C. <Chr...@fu...>]

Dear colleagues,

 

We have our next teleconference tomorrow, Wednesday May 29th, at 16h00 CET
(7h00 PST, 15h00 BST, 14h00 GMT).

 

Please use the following link to join: (Attention: Webex may require some
time to start up)

https://fu-berlin.webex.com/fu-berlin-en/j.php?MTID=m47d282d50d2e8e82630032e
746e2df27

 

 

Agenda items:

*	mzQC software libraries manuscript: revision (
<https://docs.google.com/document/d/1d-Il6MYJ5zQ-8UpabHe84L3Vau7bzuu5UZlTieG
T2Js/edit> manuscript &
<https://docs.google.com/document/d/1XDByyTl_ftbuPQ9lxlW_7PAGqrsHGf-G8esbaiR
7vLw/edit?usp=sharing> response to reviewers)

 

 

cheers

Chris

 

 

--

Dr. Chris Bielow

 

Bioinformatics Solution Center (BSC)

www.bsc.fu-berlin.de

Freie Universität Berlin, Institut für Informatik, Takustr. 9, room K21,
14195 Berlin

Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de

 

[Psidev-qc-dev] Upcoming teleconference May 15

[Wout B. <wou...@ua...>]

Dear colleagues,

We have our next teleconference tomorrow, Wednesday May 15th, at 16h00 CET (7h00 PST, 15h00 BST, 14h00 GMT).

You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d
Meeting ID: 311 403 481 845
Passcode: Jm4d4s

Agenda items:

  *
mzQC software libraries manuscript: revision (manuscript<https://docs.google.com/document/d/1d-Il6MYJ5zQ-8UpabHe84L3Vau7bzuu5UZlTieGT2Js/edit> & response to reviewers<https://docs.google.com/document/d/1XDByyTl_ftbuPQ9lxlW_7PAGqrsHGf-G8esbaiR7vLw/edit?usp=sharing>)
  *
mzQC website<https://hupo-psi.github.io/mzQC/>: update documentation and examples
  *
mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit#heading=h.om262uy0elzx>: planning
  *
AOB.

Best,
Wout

[Psidev-qc-dev] Upcoming teleconference April 17

[Wout B. <wou...@ua...>]

Dear colleagues,

We have our next teleconference today, Wednesday April 17th, at 15h00 CET (6h00 PST, 14h00 BST, 13h00 GMT). Note that this is one hour earlier than our usual meeting time!

You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d
Meeting ID: 311 403 481 845
Passcode: Jm4d4s

Agenda items:

  *
Working group charter<https://www.psidev.info/quality-control-working-group-charter>: revise for the upcoming year
  *
CV requests: precursor ppm (#254<https://github.com/HUPO-PSI/psi-ms-CV/pull/254>), missed cleavages & identified RT quarters (#255<https://github.com/HUPO-PSI/psi-ms-CV/pull/255>)
  *
mzQC software libraries manuscript<https://docs.google.com/document/d/1d-Il6MYJ5zQ-8UpabHe84L3Vau7bzuu5UZlTieGT2Js/edit#heading=h.2vumqqn1kasd>: finalize
  *
mzQC documentation and examples<https://hupo-psi.github.io/mzQC/>: updates
  *
mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit#heading=h.om262uy0elzx>: planning
  *
AOB.

Best,
Wout

[Psidev-qc-dev] Upcoming teleconference April 3

[Wout B. <wou...@ua...>]

Dear colleagues,

We have our next teleconference today, Wednesday April 3rd, at 16h00 CET (7h00 PST, 15h00 BST, 14h00 GMT).

You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d
Meeting ID: 311 403 481 845
Passcode: Jm4d4s

Agenda items:

  *
PSI Meeting 2024<https://www.psidev.info/hupo-psi-meeting-2024>: recap
  *
mzQC software libraries manuscript<https://docs.google.com/document/d/1d-Il6MYJ5zQ-8UpabHe84L3Vau7bzuu5UZlTieGT2Js/edit#heading=h.2vumqqn1kasd>: finalize
  *
mzQC documentation and examples<https://hupo-psi.github.io/mzQC/>: updates
  *
mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit#heading=h.om262uy0elzx>: planning
  *
AOB.

Best,
Wout

[Psidev-qc-dev] HUPO-PSI Specification mzIdentML version 1.3.0 + crosslinking extension 45-day public review

[Sylvie R. <syl...@un...>]

Dear colleagues, dear members of the HUPO-PSI community,

The HUPO Proteomics Standards Initiative (PSI) develops standards  for 
documentation and storage of Proteomics data (see http://www.psidev.info 
for an overview of activities).

The PSI Proteomics Informatics Working Group has submitted a new 
recommendation for consideration and review as a PSI standard. The 
mzIdentML document, draft of version 1.3.0, defines an XML schema that 
can be used to describe the outputs of proteomics search engines or 
similar software for peptide/protein identification from mass 
spectrometry(MS) data with an extension document for the identification 
of crosslinked peptides.

After having been reviewed by the PSI steering group and revised as 
requested by an internal reviewer, the proposed documents, mzIdentML 
draft of version 1.3.0 and the crosslinking extension document, now go 
through the 45-day public and external review until*April 8^th , 2024*.

The mzIdentML document (draft of version 1.3.0), a word document 
tracking changes from version 1.2.0, the crosslinking extension 
document, and the example files are available on GitHub as detailed below.

*The mzIdentML document version 1.3.0, draft *
https://github.com/HUPO-PSI/mzIdentML/blob/master/specification_document/specdoc1_3-draft/mzIdentML1.3.0-draft_vJuly2023.pdf

*A word document tracking changes from version 1.2.0*
https://github.com/HUPO-PSI/mzIdentML/blob/master/specification_document/specdoc1_3-draft/mzIdentML1.3.0-draft_vJuly2023_CC3%20JAV.docx

*The crosslinking extension document*
https://github.com/HUPO-PSI/mzIdentML/blob/master/specification_document/specdoc1_3-draft/mzIdentML%201.3.0%20Crosslinking%20Extension.pdf

*The example files*
https://github.com/HUPO-PSI/mzIdentML/tree/master/examples/1_3examples/crosslinking

*The pre-print*is available at 
https://www.authorea.com/users/672647/articles/671627-mzidentml 
-1-3-0-essential-progress-on-the-support-of-crosslinking-and-other-identifications-based-on-multiple-spectra

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Pericellular and Extracellular Supramolecular Assemblies
UMR 5246 CNRS - University Lyon 1
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