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

[Psidev-qc-dev] Upcoming teleconference 24/05

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

Dear colleagues,

We have our next teleconference tomorrow, Wednesday May 24, at 16h00 CEST (7h00 PDT, 14h00 GMT, 15h00 BST, 16h00 SAST).

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
(Password: 012575)

Agenda items:

  *   Working group chair election. Currently we have one candidate: Wout Bittremieux. You can vote electronically prior to the teleconference here<https://forms.gle/e9q6mxeRU8h2QL8N9>, or during the meeting.
  *   mzQC software tools manuscript<https://docs.google.com/document/d/1d-Il6MYJ5zQ-8UpabHe84L3Vau7bzuu5UZlTieGT2Js/edit>: Discuss updated analyses.
  *   mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: Task division and planning.

Best,
Wout

[Psidev-qc-dev] Candidacy QC working group chair

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

Dear colleagues,

As discussed during our previous meetings, Dave has indicated that he will step down as working group chair. First of all, I think I speak for all of us in extending our heartfelt thanks for expertly guiding the group over the past years.

This also means that we need to elect a new WG chair. As discussed last time, currently the nominations for WG chair are:

  *   Mathias Walzer has nominated Wout Bittremieux. Wout has accepted the nomination.
  *   Dave Tabb has nominated Mathias Walzer. Mathias has declined the nomination.

There is now an opportunity to submit your candidacy for WG chair or nominate alternative candidates. Please do so by Monday May 22, 2023 by replying to this email.

We will elect a new WG chair during our upcoming teleconference next week on Wednesday May 24, 2023 or via online ballot for people who are unable to join the meeting.

Thank you,
Wout

[Psidev-qc-dev] Upcoming teleconference 26/04

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

Dear colleagues,

We have our next teleconference tomorrow, Wednesday April 26, at 16h00 CEST (7h00 PDT, 14h00 GMT, 15h00 BST, 16h00 SAST).

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
(Password: 012575)

Agenda items:

  *   Revisit working group roles<https://psidev.info/groups/quality-control#QC_group_structure>: new (co-)chair?
  *   Update working group charter<https://psidev.info/quality-control-working-group-charter> with future goals.
  *   Discuss mzQC software tools<https://docs.google.com/document/d/1d-Il6MYJ5zQ-8UpabHe84L3Vau7bzuu5UZlTieGT2Js/edit> manuscript after Wout's recent editing pass.

Best,
Wout

[Psidev-qc-dev] PSI Spring Meeting April 17–19

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

Dear colleagues,

This is a last-minute reminder that this week the PSI Spring Meeting<https://psidev.info/hupo-psi-meeting-2023> is taking place from Monday April 17 to Wednesday April 19.

This is a hybrid meeting, so even if you will not be present in Leiden or haven't signed up yet, just reply to this email or send a message on Slack to receive the Zoom information.

This is the schedule for the QC working group:


Monday, April 17

  *   9:00–18:30: Joint MS / PI / QC / MOD session.

Tuesday, April 18

  *   9:00–12:30: Lipidomics Standards Initiative (Gerhard Liebisch & Nils Hoffmann).
  *   14:30–15:45: Polish GitHub repository (address open issues, check examples for completeness and consistency, update documentation).
  *   16:00–18:30: Software library round-up and finalize manuscript. (Invite David

Wednesday, April 19

  *   9:00–10:30: mzQC format manuscript & develop the use cases.
  *   11:00–12:30: Discuss the future of QC working group.
  *   14:30–18:30: Common session.

Best,
Wout

Re: [Psidev-qc-dev] Upcoming teleconference 29/03 (today!)

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

Dear colleagues,

A few important updates from our teleconference this week (meeting notes<https://github.com/HUPO-PSI/mzQC/blob/main/meeting_notes/2023/20230329_telco.md>):

1. This is the proposed schedule for the QC working group during the PSI Spring Meeting:


Monday, April 17

  *   9:00–18:30: Joint MS / PI / QC / MOD session.

Tuesday, April 18

  *   9:00–12:30: Lipidomics Standards Initiative (Gerhard Liebisch & Nils Hoffmann).
  *   14:30–15:45: Polish GitHub repository (address open issues, check examples for completeness and consistency, update documentation).
  *   16:00–18:30: Software library round-up and finalize manuscript. (Invite David J. to join.)

Dave has teaching engagements today and will only be available to a limited extent.


Wednesday, April 19

  *   9:00–10:30: mzQC format manuscript & develop the use cases.
  *   11:00–12:30: Discuss the future of QC working group.
  *   14:30–18:30: Common session.

2. This was the final teleconference before the PSI Spring Meeting! Due to the Easter break, we will skip our teleconference the next two weeks. See you all in Leiden/online in April! Preparation for the Spring Meeting will be conducted asynchronously via Slack and email.

Best,
Wout
________________________________
From: Wout Bittremieux <wou...@ua...>
Sent: Wednesday, March 29, 2023 11:48
To: psi...@li... <psi...@li...>
Subject: Upcoming teleconference 29/03 (today!)

Dear colleagues,

We have our next teleconference today, Wednesday March 29, at 16h00 CEST (7h00 PDT, 14h00 GMT, 15h00 BST, 16h00 SAST).

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
(Password: 012575)

Agenda items:

  *   PSI Spring Meeting<https://psidev.info/hupo-psi-meeting-2023>
     *   April 17-19 in Leiden, the Netherlands.
     *   Draft agenda<https://docs.google.com/spreadsheets/d/1J4ui2ILZvSMasix0xuZ5qUAOMDbgKsebnt6gqVHY1oA/edit#gid=1021763599>; compile QC schedule.
  *   CV: proposal for new CV terms (see Slack).
  *   Manuscripts: mzQC software tools<https://docs.google.com/document/d/1d-Il6MYJ5zQ-8UpabHe84L3Vau7bzuu5UZlTieGT2Js/edit> (and mzQC format manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit?usp=sharing>).

Best,
Wout

[Psidev-qc-dev] Upcoming teleconference 29/03 (today!)

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

Dear colleagues,

We have our next teleconference today, Wednesday March 29, at 16h00 CEST (7h00 PDT, 14h00 GMT, 15h00 BST, 16h00 SAST).

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
(Password: 012575)

Agenda items:

  *   PSI Spring Meeting<https://psidev.info/hupo-psi-meeting-2023>
     *   April 17-19 in Leiden, the Netherlands.
     *   Draft agenda<https://docs.google.com/spreadsheets/d/1J4ui2ILZvSMasix0xuZ5qUAOMDbgKsebnt6gqVHY1oA/edit#gid=1021763599>; compile QC schedule.
  *   CV: proposal for new CV terms (see Slack).
  *   Manuscripts: mzQC software tools<https://docs.google.com/document/d/1d-Il6MYJ5zQ-8UpabHe84L3Vau7bzuu5UZlTieGT2Js/edit> (and mzQC format manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit?usp=sharing>).

Best,
Wout

[Psidev-qc-dev] Upcoming teleconference 15/03

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

Dear colleagues,

We have our next teleconference tomorrow, Wednesday March 15, at 16h00 CET (8h00 PST, 15h00 GMT, 17h00 SAST). Note that this is one hour later than usual for the US due to differing DST switch.

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
(Password: 012575)

Agenda items:

  *   PSI Spring Meeting<https://psidev.info/hupo-psi-meeting-2023>: Updates?
     *   April 17-19 in Leiden, the Netherlands.
     *   Draft agenda<https://docs.google.com/spreadsheets/d/1J4ui2ILZvSMasix0xuZ5qUAOMDbgKsebnt6gqVHY1oA/edit#gid=1021763599>.
  *   mzQC repository: Please consult the open issues on GitHub<https://github.com/HUPO-PSI/mzQC/issues> prior to the meeting.
  *   Manuscripts: mzQC software tools<https://docs.google.com/document/d/1d-Il6MYJ5zQ-8UpabHe84L3Vau7bzuu5UZlTieGT2Js/edit> and mzQC format manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit?usp=sharing>.

Best,
Wout

[Psidev-qc-dev] HUPO-PSI Specification document mzPAF format - 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 Mass Spectrometry and Proteomics Informatics PSI working groups have 
submitted a new recommendation, the PSI Peak Annotation Format (mzPAF) 
consideration and review as a PSI standard. This document presents a 
specification for a fragment ion peak annotation format for mass 
spectra, focused on peptides. This provides a standardized format for 
describing the origin of fragment ions to be used in spectral libraries, 
other formats that aim to describe fragment ions, and software tools 
that annotate fragment ions.

After having passed a 14-day review of the PSI steering group and having 
been revised as requested by the internal reviewers, the proposed 
document, Draft 10 of Version 1.0, now goes through the 45-day public 
and external review until *April 18th, 2023*. The current draft 
specification (.docx) is attached to this e-mail. Further information, 
including any updates to this document, implementations, and examples is 
available in the GitHub repository: https://github.com/HUPO-PSI/mzPAF 
and at https://psidev.info/mzPAF.

This message is to encourage you to contribute to the standards 
development activity by commenting on the document. We invite both 
positive and negative comments on the relevance, correctness, clarity 
and appropriateness of the specification (e.g. is it presented in 
accordance with the templates and clearly written, is it sufficiently 
detailed and comprehensively described and are the examples in agreement 
with the specification?). Comments can be made on the specification as a 
whole or on specific parts.

If you do not feel experienced enough to comment on this document, but 
know colleagues who are, please feel free to forward this message to 
them. There is no requirement that people commenting should have had any 
prior contact with the PSI.

Please send comments by e-mail directly to 
syl...@un... before*April 18th, 2023*.

Thank you very much in advance for your valuable help.

Best regards.

Professor Sylvie RICARD-BLUM - PSI Editor
Pericellular and Extracellular Supramolecular Assemblies
UMR 5246 CNRS - University Lyon 1
Institute of Molecular and Supramolecular Chemistry and Biochemistry
University Claude Bernard Lyon 1, 43 Boulevard du 11 novembre 1918
69622 Villeurbanne Cedex, France
Phone: +33(0)4 72 44 82 32
E-mail: syl...@un...

[Psidev-qc-dev] Upcoming teleconference 01/03 (today!)

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

Dear colleagues,

We have our next teleconference today, Wednesday March 1, at 16h00 CET (7h00 PST, 15h00 GMT).

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
(Password: 012575)

Agenda items:

  *   PSI Spring Meeting<https://psidev.info/hupo-psi-meeting-2023>
     *   April 17-19 in Leiden, the Netherlands.
     *   Draft agenda<https://docs.google.com/spreadsheets/d/1J4ui2ILZvSMasix0xuZ5qUAOMDbgKsebnt6gqVHY1oA/edit#gid=1021763599>.
  *   Document process<https://drive.google.com/drive/folders/1IfXpzuiVPRjFVaRYfRgVLmH6Kkytu9Df>: status check if necessary.
  *   mzQC repository: GitHub issues<https://github.com/HUPO-PSI/mzQC/issues> status check.
  *   Manuscripts: mzQC software tools<https://docs.google.com/document/d/1d-Il6MYJ5zQ-8UpabHe84L3Vau7bzuu5UZlTieGT2Js/edit> and mzQC format manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit?usp=sharing>.

Best,
Wout

[Psidev-qc-dev] Upcoming teleconference 15/02

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

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

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09<https://urldefense.com/v3/__https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09__;!!LLK065n_VXAQ!jXFP1i7y3S3FbuKHw14120R20-aWpu7purYUpyppmPPk7RfsSRAxfX9heL5sxiZDHki-8zLIu2xuvk0n28m5Ixq2EUSrMb1V_M31zX8$>
(Password: 012575)

Agenda items:

  *
PSI Spring Meeting<https://psidev.info/hupo-psi-meeting-2023>
     *
April 17-19 in Leiden, the Netherlands.
     *   Draft agenda.<https://docs.google.com/spreadsheets/d/1J4ui2ILZvSMasix0xuZ5qUAOMDbgKsebnt6gqVHY1oA/edit#gid=1021763599>
  *   CV: #172<https://github.com/HUPO-PSI/psi-ms-CV/pull/172>, updates.
  *   Document process:<https://drive.google.com/drive/folders/1IfXpzuiVPRjFVaRYfRgVLmH6Kkytu9Df> updates.
  *   Manuscripts: mzQC software tools<https://docs.google.com/document/d/1d-Il6MYJ5zQ-8UpabHe84L3Vau7bzuu5UZlTieGT2Js/edit> and mzQC format manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit?usp=sharing>.

Best,
Wout

[Psidev-qc-dev] Upcoming teleconference 15/02

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

Dear colleagues,

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

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09<https://urldefense.com/v3/__https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09__;!!LLK065n_VXAQ!jXFP1i7y3S3FbuKHw14120R20-aWpu7purYUpyppmPPk7RfsSRAxfX9heL5sxiZDHki-8zLIu2xuvk0n28m5Ixq2EUSrMb1V_M31zX8$>
(Password: 012575)

Agenda items:

  *
PSI Spring Meeting<https://psidev.info/hupo-psi-meeting-2023>
     *
April 17-19 in Leiden, the Netherlands.
     *   Draft agenda.<https://docs.google.com/spreadsheets/d/1J4ui2ILZvSMasix0xuZ5qUAOMDbgKsebnt6gqVHY1oA/edit#gid=1021763599>
  *   CV: #172<https://github.com/HUPO-PSI/psi-ms-CV/pull/172>, updates.
  *   Document process:<https://drive.google.com/drive/folders/1IfXpzuiVPRjFVaRYfRgVLmH6Kkytu9Df> updates.
  *   Manuscripts: mzQC software tools<https://docs.google.com/document/d/1d-Il6MYJ5zQ-8UpabHe84L3Vau7bzuu5UZlTieGT2Js/edit> and mzQC format manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit?usp=sharing>.

Best,
Wout

Re: [Psidev-qc-dev] PSI-QC webpage

[Tenzer, S. <te...@un...>]

Hi Dave, Hi everyone,

I am very sorry for the long silence and deeply apologize for not being available as I had planned to be, as my workload here in Mainz exploded in a way that i had not foreseen.
I agree that under these circumstances, it does not make sense to have me listed as a co-chair, so I am very happy to pass that role to Wout.

Looking forward to see the future process of qcML!

Best wishes,

Stefan




Am 06.04.2021 um 08:54 schrieb David TABB <dav...@pa...<mailto:dav...@pa...>>:

Hi, folks.  I really enjoyed talking with you at the HUPO-PSI spring meeting!

The steering committee is trying to ensure that the websites for individual work groups are still up-to-date.  In looking at ours (https://www.psidev.info/groups/quality-control), I have the following comments and suggestions:

  1.  “View Documents” at the top points to the PSI file collection rather than our GitHub.
  2.  Under “Focus and Purpose” we specify that we have industry researchers, journal representatives, and instrument manufacturers represented in our team.  Has that ever been true?
  3.  The “Current Projects” section specifies our development of qcML (sic).  Similarly our second though sixth points in “Goals/Milestones” specify development of qcML.
  4.  Stefan Tenzer is listed as a co-chair, but I think it has been more than a year since our last contact, yes?
  5.  “Formats, Definitions and Metrics” highlights qcML again.


When the PSI-SC removed the “Secretary” column from “Roles and Responsibilities” (https://www.psidev.info/roles) it was to move Wout Bittremieux’s name to co-chair, replacing Stefan Tenzer’s name.  I see that “Secretary” vanished, but that removed Wout’s name entirely!

Mathias, the page lists you as our website maintainer.  Would you coordinate with Chuqiao Gong to update this information?

Thanks,
Dave
_______________________________________________
Psidev-qc-dev mailing list
Psi...@li...<mailto:Psi...@li...>
https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev

[Psidev-qc-dev] No teleconference today

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

Dear colleagues,

Due to conflicting meetings we will not have a call today. Asynchronous communication can proceed on Slack.

Best,
Wout

[Psidev-qc-dev] No teleconference today

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

Due to conflicting meetings we will not have a call today. Asynchronous communication can proceed on Slack.

Best,
Wout

Re: [Psidev-qc-dev] Retirement from mzQC development and best wishes

[walzer <wa...@eb...>]

Hej Julian,

basically just arrived back from holiday, so let me chime in here a 
little late.
Thank you, it has been a pleasure working with you, all the best with 
the new position and let's hope our paths cross again!

cheers,
   mths

On 2023-01-15 13:42, David  TABB wrote:
> Hi, Julian.
> 
> I entirely agree with Wout.  Your contributions over the last few
> years have been key to our success.  Thank you for all your work with
> the CV, and we will also miss your company on our calls!
> 
> Natasha and I have moved back home to Cape Town at the start of this
> year.  At the moment, we don’t even have reliable network
> connectivity at the house, so I am able to check my mail quite rarely.
>  We hope to get that link fixed in the coming week.
> 
> Thank you again!
> 
> Dave
> 
> From: Bittremieux, Wout via Psidev-qc-dev
> <psi...@li...>
> Sent: Wednesday, 11 January 2023 15:55
> To: Psidev-qc-dev <psi...@li...>; Julian
> Uszkoreit <jul...@ru...>
> Subject: Re: [Psidev-qc-dev] Retirement from mzQC development and best
> wishes
> 
> Hi Julian,
> 
> I think I speak for the entire group when I say that it was an
> absolute pleasure to work with you for all those years! Lots of
> problems to solve in medical bioinformatics as well, so I don't think
> you'll be bored. 😉
> 
> We'll continue to make progress on the mzQC manuscript. I'm hopeful
> we'll have a nice end result soon, so we'll reach out for that in the
> near future.
> 
> Best of luck in your future career, and hopefully we'll meet again
> some time!
> 
> Best,
> 
> Wout
> 
> -------------------------
> 
> From: Julian Uszkoreit via Psidev-qc-dev
> <psi...@li...>
> Sent: Wednesday, January 11, 2023 9:29
> To: Psidev-qc-dev <psi...@li...>
> Subject: [Psidev-qc-dev] Retirement from mzQC development and best
> wishes
> 
> Hej all,
> 
> As you know, I switched my position away from the proteomics context
> into the medical bioinformatics (I am the head of Research IT at
> University Hospital Duesseldorf now). As this, I unfortunately don't
> have the time to actively work on the development of mzQC anymore. But
> 
> if the paper gets to a state for final reading and commenting, I would
> 
> still like to help there and give my 2 cents :)
> 
> Obviously, I need to retire from my position as the ontology
> coordinator
> at the next convenient time point.
> 
> It was a pleasure working with you all in the very important topic of
> standardization! Looking forward to meet you again and all the best to
> you!
> 
> See you,
> Julian
> 
> _______________________________________________
> Psidev-qc-dev mailing list
> Psi...@li...
> https://urldefense.com/v3/__https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev__;!!LLK065n_VXAQ!ntKpot6c7D1zQ1KQBKlm50FAQ7BW5BEJVjhm-h-0JwBj8-sF9tTEiMqF11Y5TLSxDQo3VklGzJcpJtSDShPQJbeTGi-YqLkVZ-_TMLQ$
> [1]
> 
> Links:
> ------
> [1] 
> https://urldefense.com/v3/__https:/lists.sourceforge.net/lists/listinfo/psidev-qc-dev__;!!LLK065n_VXAQ!ntKpot6c7D1zQ1KQBKlm50FAQ7BW5BEJVjhm-h-0JwBj8-sF9tTEiMqF11Y5TLSxDQo3VklGzJcpJtSDShPQJbeTGi-YqLkVZ-_TMLQ$
> _______________________________________________
> Psidev-qc-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev

-- 
Mathias Walzer
European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome
Campus, Hinxton, Cambridge, UK
Office: +44 (0)1223 494 2610
E-mail: wa...@eb...

Re: [Psidev-qc-dev] Upcoming teleconference 18/01

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

Dear all,

currently on vacation. I will see you all in about two weeks at the next TC.

Cheers Chris

Am 17.01.2023 16:40 schrieb "Bittremieux, Wout via Psidev-qc-dev" <psi...@li...>:
Dear colleagues,

We have our next teleconference tomorrow, Wednesday January 18, at 16h00 CET (7h00 PST, 15h00 GMT).

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09<https://urldefense.com/v3/__https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09__;!!LLK065n_VXAQ!jXFP1i7y3S3FbuKHw14120R20-aWpu7purYUpyppmPPk7RfsSRAxfX9heL5sxiZDHki-8zLIu2xuvk0n28m5Ixq2EUSrMb1V_M31zX8$>
(Password: 012575)

Agenda items:

  *   PSI-QC working group member status in 2023.
  *
PSI Spring Meeting<https://psidev.info/hupo-psi-meeting-2023>
     *
April 17-19 in Leiden, the Netherlands.
     *   Draft agenda.<https://docs.google.com/spreadsheets/d/1J4ui2ILZvSMasix0xuZ5qUAOMDbgKsebnt6gqVHY1oA/edit#gid=1021763599>
  *   ASMS<https://www.asms.org/conferences/annual-conference/annual-conference-homepage>: abstract deadline is Feb 3. Do we want to submit an abstract on mzQC?
  *   CV: GitHub PRs: #165<https://github.com/HUPO-PSI/psi-ms-CV/pull/165>, #172<https://github.com/HUPO-PSI/psi-ms-CV/pull/172>.
  *   Document process:<https://drive.google.com/drive/folders/1IfXpzuiVPRjFVaRYfRgVLmH6Kkytu9Df> status update.
  *   Manuscripts: status update mzQC software tools<https://docs.google.com/document/d/1d-Il6MYJ5zQ-8UpabHe84L3Vau7bzuu5UZlTieGT2Js/edit> and mzQC format manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit?usp=sharing>.

Best,
Wout

[Psidev-qc-dev] Upcoming teleconference 18/01

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

We have our next teleconference tomorrow, Wednesday January 18, at 16h00 CET (7h00 PST, 15h00 GMT).

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09<https://urldefense.com/v3/__https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09__;!!LLK065n_VXAQ!jXFP1i7y3S3FbuKHw14120R20-aWpu7purYUpyppmPPk7RfsSRAxfX9heL5sxiZDHki-8zLIu2xuvk0n28m5Ixq2EUSrMb1V_M31zX8$>
(Password: 012575)

Agenda items:

  *   PSI-QC working group member status in 2023.
  *
PSI Spring Meeting<https://psidev.info/hupo-psi-meeting-2023>
     *
April 17-19 in Leiden, the Netherlands.
     *   Draft agenda.<https://docs.google.com/spreadsheets/d/1J4ui2ILZvSMasix0xuZ5qUAOMDbgKsebnt6gqVHY1oA/edit#gid=1021763599>
  *   ASMS<https://www.asms.org/conferences/annual-conference/annual-conference-homepage>: abstract deadline is Feb 3. Do we want to submit an abstract on mzQC?
  *   CV: GitHub PRs: #165<https://github.com/HUPO-PSI/psi-ms-CV/pull/165>, #172<https://github.com/HUPO-PSI/psi-ms-CV/pull/172>.
  *   Document process:<https://drive.google.com/drive/folders/1IfXpzuiVPRjFVaRYfRgVLmH6Kkytu9Df> status update.
  *   Manuscripts: status update mzQC software tools<https://docs.google.com/document/d/1d-Il6MYJ5zQ-8UpabHe84L3Vau7bzuu5UZlTieGT2Js/edit> and mzQC format manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit?usp=sharing>.

Best,
Wout

Re: [Psidev-qc-dev] Retirement from mzQC development and best wishes

[David T. <dav...@pa...>]

Hi, Julian.

I entirely agree with Wout.  Your contributions over the last few years have been key to our success.  Thank you for all your work with the CV, and we will also miss your company on our calls!

Natasha and I have moved back home to Cape Town at the start of this year.  At the moment, we don’t even have reliable network connectivity at the house, so I am able to check my mail quite rarely.  We hope to get that link fixed in the coming week.

Thank you again!
Dave

From: Bittremieux, Wout via Psidev-qc-dev <psi...@li...>
Sent: Wednesday, 11 January 2023 15:55
To: Psidev-qc-dev <psi...@li...>; Julian Uszkoreit <jul...@ru...>
Subject: Re: [Psidev-qc-dev] Retirement from mzQC development and best wishes

Hi Julian,

I think I speak for the entire group when I say that it was an absolute pleasure to work with you for all those years! Lots of problems to solve in medical bioinformatics as well, so I don't think you'll be bored. 😉

We'll continue to make progress on the mzQC manuscript. I'm hopeful we'll have a nice end result soon, so we'll reach out for that in the near future.

Best of luck in your future career, and hopefully we'll meet again some time!

Best,
Wout
________________________________
From: Julian Uszkoreit via Psidev-qc-dev <psi...@li...<mailto:psi...@li...>>
Sent: Wednesday, January 11, 2023 9:29
To: Psidev-qc-dev <psi...@li...<mailto:psi...@li...>>
Subject: [Psidev-qc-dev] Retirement from mzQC development and best wishes

Hej all,

As you know, I switched my position away from the proteomics context
into the medical bioinformatics (I am the head of Research IT at
University Hospital Duesseldorf now). As this, I unfortunately don't
have the time to actively work on the development of mzQC anymore. But
if the paper gets to a state for final reading and commenting, I would
still like to help there and give my 2 cents :)

Obviously, I need to retire from my position as the ontology coordinator
at the next convenient time point.

It was a pleasure working with you all in the very important topic of
standardization! Looking forward to meet you again and all the best to you!

See you,
Julian



_______________________________________________
Psidev-qc-dev mailing list
Psi...@li...<mailto:Psi...@li...>
https://urldefense.com/v3/__https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev__;!!LLK065n_VXAQ!ntKpot6c7D1zQ1KQBKlm50FAQ7BW5BEJVjhm-h-0JwBj8-sF9tTEiMqF11Y5TLSxDQo3VklGzJcpJtSDShPQJbeTGi-YqLkVZ-_TMLQ$<https://urldefense.com/v3/__https:/lists.sourceforge.net/lists/listinfo/psidev-qc-dev__;!!LLK065n_VXAQ!ntKpot6c7D1zQ1KQBKlm50FAQ7BW5BEJVjhm-h-0JwBj8-sF9tTEiMqF11Y5TLSxDQo3VklGzJcpJtSDShPQJbeTGi-YqLkVZ-_TMLQ$>

Re: [Psidev-qc-dev] Retirement from mzQC development and best wishes

[Bittremieux, W. <wbi...@he...>]

Hi Julian,

I think I speak for the entire group when I say that it was an absolute pleasure to work with you for all those years! Lots of problems to solve in medical bioinformatics as well, so I don't think you'll be bored. 😉

We'll continue to make progress on the mzQC manuscript. I'm hopeful we'll have a nice end result soon, so we'll reach out for that in the near future.

Best of luck in your future career, and hopefully we'll meet again some time!

Best,
Wout
________________________________
From: Julian Uszkoreit via Psidev-qc-dev <psi...@li...>
Sent: Wednesday, January 11, 2023 9:29
To: Psidev-qc-dev <psi...@li...>
Subject: [Psidev-qc-dev] Retirement from mzQC development and best wishes

Hej all,

As you know, I switched my position away from the proteomics context
into the medical bioinformatics (I am the head of Research IT at
University Hospital Duesseldorf now). As this, I unfortunately don't
have the time to actively work on the development of mzQC anymore. But
if the paper gets to a state for final reading and commenting, I would
still like to help there and give my 2 cents :)

Obviously, I need to retire from my position as the ontology coordinator
at the next convenient time point.

It was a pleasure working with you all in the very important topic of
standardization! Looking forward to meet you again and all the best to you!

See you,
Julian



_______________________________________________
Psidev-qc-dev mailing list
Psi...@li...
https://urldefense.com/v3/__https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev__;!!LLK065n_VXAQ!ntKpot6c7D1zQ1KQBKlm50FAQ7BW5BEJVjhm-h-0JwBj8-sF9tTEiMqF11Y5TLSxDQo3VklGzJcpJtSDShPQJbeTGi-YqLkVZ-_TMLQ$

[Psidev-qc-dev] Retirement from mzQC development and best wishes

[Julian U. <jul...@ru...>]

Hej all,

As you know, I switched my position away from the proteomics context 
into the medical bioinformatics (I am the head of Research IT at 
University Hospital Duesseldorf now). As this, I unfortunately don't 
have the time to actively work on the development of mzQC anymore. But 
if the paper gets to a state for final reading and commenting, I would 
still like to help there and give my 2 cents :)

Obviously, I need to retire from my position as the ontology coordinator 
at the next convenient time point.

It was a pleasure working with you all in the very important topic of 
standardization! Looking forward to meet you again and all the best to you!

See you,
Julian

[Psidev-qc-dev] 2-Minute highlight slide for mzQC?

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

Hi everyone and Happy New Year!

Apologies for the short heads-up, but I will be giving a presentation on 
my work on lipids, MS, data standards etc. in front of the EPILIPIDNET 
WG2 [1] tomorrow.

Does anyone have a slide deck or a single summary slide on mzQC that you 
maybe already presented and that you would be willing to share with me?

Best
Nils

[1] https://www.epilipid.net/wg2/

-- 

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

c/o Centrum für Biotechnologie (CeBiTec)
Universität Bielefeld
33594 Bielefeld

Room: Building X C4-233
Tel: +49(0)521-106-86780

E-Mail: nil...@ce...
E-Mail: co...@de...
www.denbi.de
elixir-europe.org

Re: [Psidev-qc-dev] Upcoming teleconference November 30

[walzer <wa...@eb...>]

Dear all,

due to travel- and illness-related absences, we will postpone today's 
teleconference.
In case you should have a time-sensitive issue that needs discussion, 
you can catch me (and others) on slack, certainly around the usual call 
time.

until next time, best,
   mths

On 2022-11-29 15:15, walzer wrote:
> Dear colleagues,
> 
> We have our next teleconference on Wednesday November 30, at 15h00 GMT
> (15h00 London, 16h00 Western Europe, 7h00 US West Coast).
> 
> You can connect to our teleconference on Zoom through the following
> link:
> https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
> (Password: 012575)
> 
> Let's make this a quick one, Agenda items:
> 
>     CV: Improvement discussion on current draft PRs
>     Manuscripts: Synchronise usecase progress
> 
> Best,
>   mths

-- 
Mathias Walzer
European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome
Campus, Hinxton, Cambridge, UK
Office: +44 (0)1223 494 2610
E-mail: wa...@eb...

[Psidev-qc-dev] Upcoming teleconference November 30

[walzer <wa...@eb...>]

Dear colleagues,

We have our next teleconference on Wednesday November 30, at 15h00 GMT 
(15h00 London, 16h00 Western Europe, 7h00 US West Coast).

You can connect to our teleconference on Zoom through the following 
link: 
https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
(Password: 012575)

Let's make this a quick one, Agenda items:

     CV: Improvement discussion on current draft PRs
     Manuscripts: Synchronise usecase progress

Best,
   mths
-- 
Mathias Walzer
European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome
Campus, Hinxton, Cambridge, UK
Office: +44 (0)1223 494 2610
E-mail: wa...@eb...

[Psidev-qc-dev] Upcoming teleconference November 16

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

We have our next teleconference on Wednesday November 16, at 15h00 GMT (15h00 London, 16h00 Western Europe, 7h00 US West Coast).

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
(Password: 012575)

Agenda items:

  *   Milestones and planning through the end of the year.
  *   CV: Further terms<https://github.com/HUPO-PSI/psi-ms-CV/pull/165> to be integrated in the PSI-MS CV.
  *   Manuscripts: Updates on the mzQC format manuscript<https://urldefense.com/v3/__https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit?usp=sharing__;!!LLK065n_VXAQ!jZoLIRjtmTBgpWZWgoI84DguPiIluiUgtrE8zISsg-lwncCgD5FqF5jcO-oYWeQ9cOEtImz_SBoBajsQN0U1WDoLOOuxEEvImsTlGg$> and mzQC software technical note<https://urldefense.com/v3/__https://docs.google.com/document/d/1d-Il6MYJ5zQ-8UpabHe84L3Vau7bzuu5UZlTieGT2Js/edit?usp=sharing__;!!LLK065n_VXAQ!hfXlGVuzOHt3F1O1ZUG9sgNnGp9VI720QJk4e4slXBQXduzMv6i7vj7kQe_joOXCMQjjJHdEee3wLniebRjEg_uj0OXL5ue6Iogghg$>.

Best,
Wout

Re: [Psidev-qc-dev] Upcoming teleconference November 2

[David T. <dav...@pa...>]

Hi, all.

I'm sorry for missing the call last week.  I was driving back from Bretagne (where we celebrated Natasha's birthday).

Thanks,
Dave

From: Bittremieux, Wout via Psidev-qc-dev <psi...@li...>
Sent: Wednesday, 2 November 2022 00:42
To: psi...@li...
Subject: [Psidev-qc-dev] Upcoming teleconference November 2

Dear colleagues,

We have our next teleconference on Wednesday November 2, at 15h00 GMT (15h00 London, 16h00 Western Europe, 8h00 US West Coast). Note that this is one hour difference compared to usual for US-based people (no daylight savings switch yet).

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09<https://urldefense.com/v3/__https:/uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09__;!!LLK065n_VXAQ!jXFP1i7y3S3FbuKHw14120R20-aWpu7purYUpyppmPPk7RfsSRAxfX9heL5sxiZDHki-8zLIu2xuvk0n28m5Ixq2EUSrMb1V_M31zX8$>
(Password: 012575)

I haven't been able to find meeting notes from the meeting I missed, so I propose the following agenda items. Please reply or message on Slack with changes/additions.

  *   Specification document<https://urldefense.com/v3/__https:/docs.google.com/document/d/132F3MBgDJgtFlXxDZhpJ1oHGbKL8pT6dk9fvL55L5_M/edit?usp=sharing__;!!JFdNOqOXpB6UZW0!t0gopHeBEqVJP7EAhxPwNjYaFCL0heosd-v095w9VMxAEa1JzMHehixvv2OCr1lgdRunTFR1ZUY8LyNJHzrhi1fZCp4Qg7T2$>: Address reviewer comments<https://urldefense.com/v3/__https:/drive.google.com/drive/folders/1IfXpzuiVPRjFVaRYfRgVLmH6Kkytu9Df__;!!JFdNOqOXpB6UZW0!t0gopHeBEqVJP7EAhxPwNjYaFCL0heosd-v095w9VMxAEa1JzMHehixvv2OCr1lgdRunTFR1ZUY8LyNJHzrhi1fZCjesaRVt$>.
  *   Manuscripts: Use case updates for the mzQC format manuscript<https://urldefense.com/v3/__https:/docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit?usp=sharing__;!!LLK065n_VXAQ!jZoLIRjtmTBgpWZWgoI84DguPiIluiUgtrE8zISsg-lwncCgD5FqF5jcO-oYWeQ9cOEtImz_SBoBajsQN0U1WDoLOOuxEEvImsTlGg$> and mzQC software technical note<https://urldefense.com/v3/__https:/docs.google.com/document/d/1d-Il6MYJ5zQ-8UpabHe84L3Vau7bzuu5UZlTieGT2Js/edit?usp=sharing__;!!JFdNOqOXpB6UZW0!t0gopHeBEqVJP7EAhxPwNjYaFCL0heosd-v095w9VMxAEa1JzMHehixvv2OCr1lgdRunTFR1ZUY8LyNJHzrhi1fZCjcO1xk1$>.
  *   CV: Progress on PSI-MS CV integration (see PR 155<https://urldefense.com/v3/__https:/github.com/HUPO-PSI/psi-ms-CV/pull/155__;!!LLK065n_VXAQ!jZoLIRjtmTBgpWZWgoI84DguPiIluiUgtrE8zISsg-lwncCgD5FqF5jcO-oYWeQ9cOEtImz_SBoBajsQN0U1WDoLOOuxEEuuz-v-pQ$>) and discussion on newly proposed terms (see Slack messages since Sept 7).
Best,
Wout