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From: Wout B. <wou...@ua...> - 2025-07-17 09:56:02
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Dear colleagues, We have our next teleconference tomorrow, Friday July 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: * GitHub: broken links [Mathias to integrate fix in validator PR] * pymzqc & rmzqc updates * Semantic validation: see discussion on Slack<https://hupo-psi.slack.com/archives/CJJHF8EBX/p1750946912901659?thread_ts=1750229425.643959&cid=CJJHF8EBX>, semantic checks severity logging level<https://github.com/MS-Quality-Hub/pymzqc/issues/60> [Wout to review wording of messages] * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: CV term requests for McQuaC<https://github.com/HUPO-PSI/psi-ms-CV/issues/380>, TDAuditor, and DIAMetric<https://github.com/HUPO-PSI/psi-ms-CV/pull/391> * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: continuation of use cases * Outlier detection * Lipidomics * DIAMetric * Repository-scale QC (metabolomics) * Other use cases * BioHackathon<https://biohackathon-europe.org/>: project description<https://github.com/elixir-europe/biohackathon-projects-2025/blob/main/29.md>, planning * AOB Best, Wout |
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From: Sylvie R. <syl...@un...> - 2025-07-16 16:37:09
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Dear colleagues, dear members of the HUPO-PSI community, The HUPO Proteomics Standards Initiative (PSI) develops standards for documentation and storage of proteomics, glycomics and interaction data (see http://www.psidev.info for an overview of activities). Members of the Molecular Interactions Working Group have submitted a new recommendation for a PSI standard, *PSI-MI FeatureTab*, *an exchange format for molecular interaction features*. The PSI-MI FeatureTab format is part of the PSI-MI 2.5 standard. It is related to the tabular format provided by PSI MITAB 2.5 and subsequent updates. However, while the PSI MITAB 2.5 describes binary interactions, one pair of interactors per row, in the PSI-MI FeatureTab each row is feature centric and describes in detail a specific feature at the participant level and the effect of a feature, if any, on the second participant. After having passed a 14-day review by two members of the PSI steering committee, who suggested minor changes, the proposed specification now goes through the 30-day public and external review, which should end on August 16th, 2025 but is *extended to August 31st, 2025 *due to summer holidays. The draft of the specification (version 1.0, draft 02) is attached to this e-mail. 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 August 31st, 2025.* I thank you very much in advance for your contribution and time. Kind regards. Professor Sylvie RICARD-BLUM, HUPO-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)6 82 02 44 22 E-mail: syl...@un... |
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From: Wout B. <wou...@ua...> - 2025-07-03 13:08:56
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Dear colleagues, We have our next teleconference tomorrow, Friday July 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: * mzQC specification: JSON schema out of data (label in metadata<https://github.com/HUPO-PSI/mzQC/pull/312>, URI for analysisSoftware<https://github.com/HUPO-PSI/mzQC/pull/316>) * pymzqc: various updates and bugfixes * Semantic validation: see discussion on Slack<https://hupo-psi.slack.com/archives/CJJHF8EBX/p1750946912901659?thread_ts=1750229425.643959&cid=CJJHF8EBX>, semantic checks severity logging level<https://github.com/MS-Quality-Hub/pymzqc/issues/60> * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: CV term requests for McQuaC<https://github.com/HUPO-PSI/psi-ms-CV/issues/380>, TDAuditor, and DIAMetric<https://github.com/HUPO-PSI/psi-ms-CV/pull/391> * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: continuation of use cases * Outlier detection * Lipidomics * DIAMetric * Repository-scale QC (metabolomics) * Other use cases * BioHackathon<https://biohackathon-europe.org/>: project description<https://github.com/elixir-europe/biohackathon-projects-2025/blob/main/29.md>, planning * AOB Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-06-12 18:42:31
|
Dear colleagues, We have our next teleconference tomorrow, Friday June 13, 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 specification: JSON schema out of data (label in metadata) * pymzqc: cvParameters in metadata * rmzqc: table export * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: CV term requests for McQuaC, TDAuditor, and DIAMetric * pymzqc validator: semantic checks severity logging level<https://github.com/MS-Quality-Hub/pymzqc/issues/60> * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: continuation of use cases * Outlier detection * Lipidomics * DIAMetric * Repository-scale QC (metabolomics) * Other use cases * BioHackathon * AOB Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-05-22 13:32:10
|
Dear colleagues, We have our next teleconference on Friday May 23, 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/>: metabo-batches example (#233<https://github.com/HUPO-PSI/mzQC/pull/233>) * @Mathias: Validation fails with message "No mzQC structure detectable." * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: CV term requests for McQuaC, TDAuditor, and DIAMetric * pymzqc validator: semantic checks severity logging level<https://github.com/MS-Quality-Hub/pymzqc/issues/60> * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: continuation of use cases * Outlier detection * Lipidomics * DIAmetric: QC for DIA * Repository-scale QC (metabolomics) * Other use cases * AOB Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-05-15 10:21:07
|
Dear colleagues, We have our next teleconference on Friday May 16, 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/>: metabo-batches example (#233<https://github.com/HUPO-PSI/mzQC/pull/233>) * @Mathias: Validation fails with message "No mzQC structure detectable." * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: CV term requests for McQuaC, TDAuditor, and DIAMetric * pymzqc validator: semantic checks severity logging level<https://github.com/MS-Quality-Hub/pymzqc/issues/60> * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: continuation of use cases * Outlier detection * Lipidomics * DIAmetric: QC for DIA * Repository-scale QC (metabolomics) * Other use cases * AOB Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-04-16 14:56:42
|
Dear colleagues, We have our next teleconference on Friday April 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: * Spring Meeting: recap<https://github.com/HUPO-PSI/mzQC/blob/main/meeting_notes/2025/20250402_psi2025.md> * mzQC website<https://hupo-psi.github.io/mzQC/>: metabo-batches example (#233<https://github.com/HUPO-PSI/mzQC/pull/233>) * @Mathias: Validation fails with message "No mzQC structure detectable." * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: CV term requests for McQuaC and TDAuditor * pymzqc validator: semantic checks severity logging level * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: continuation of use cases * DIAmetric: QC for DIA * Repository-scale QC (metabolomics) * Other use cases * AOB Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-04-03 11:07:37
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Dear colleagues, Thank you for the fruitful discussion on the mzQC manuscript and related use cases. You can find the draft manuscript here<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit?usp=sharing>. Feel free to add comments and text. Best, Wout ________________________________ From: Wout Bittremieux <wou...@ua...> Sent: Wednesday, April 2, 2025 14:09 To: d.l...@ru... <d.l...@ru...>; jul...@ru... <jul...@ru...>; pa...@eb... <pa...@eb...>; yel...@uc... <yel...@uc...>; sw...@ko... <sw...@ko...>; n.h...@fz... <n.h...@fz...>; bo....@nu... <bo....@nu...>; ser...@br... <ser...@br...> Subject: HUPO-PSI QC working group links Dear colleagues, Thank you for your participation in the PSI QC Working Group. Here are some relevant links: * Meeting notes: https://docs.google.com/document/d/1zFye2rlhoHs7zVIorftIizPeqAuGT0w-vHYRlF6S5E8/edit?usp=sharing * Feel free to take notes liberally and add any other thoughts. * mzQC GitHub repository: https://github.com/HUPO-PSI/mzQC * mzQC documentation website: https://hupo-psi.github.io/mzQC/ Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-03-06 14:38:24
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Dear colleagues, We have our next teleconference on Friday March 7, 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: * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: CV term requests * mzQC website<https://hupo-psi.github.io/mzQC/>: metabo-batches example (#233<https://github.com/HUPO-PSI/mzQC/pull/233>) * pymzqc validator: semantic checks severity logging level * TDAuditor<https://docs.google.com/document/d/10idAq_WiL8rhWNSYdLnnxV03u7amh28qMW-nd3FeXJ8/edit>: CV terms for top-down proteomics * DIAmetric: QC for DIA * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: continuation of use cases * AOB. Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-02-26 12:40:21
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Dear colleagues, We have our next teleconference on Friday February 28, 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: * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: CV term requests * TDAuditor<https://docs.google.com/document/d/10idAq_WiL8rhWNSYdLnnxV03u7amh28qMW-nd3FeXJ8/edit>: CV terms for top-down proteomics * mzQC website<https://hupo-psi.github.io/mzQC/>: metabo-batches example (#233<https://github.com/HUPO-PSI/mzQC/pull/233>) * pymzqc validator: semantic checks severity logging level * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: continuation of use cases * AOB. Best, Wout |
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From: Martin E. <mar...@ru...> - 2025-02-03 13:17:46
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UNSUBSCRIBE -----Ursprüngliche Nachricht----- Von: Wout Bittremieux <wou...@ua...> Gesendet: Mittwoch, 29. Januar 2025 09:03 An: psi...@li... Betreff: [Psidev-qc-dev] Upcoming teleconference January 31 Dear colleagues, We have our next teleconference on Friday January 31, 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_MzNhNGFmODEtY2QxZi00M TAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb -2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217 e647f61b0%22%7d <https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00 MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08f b-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-21 7e647f61b0%22%7d> * Meeting ID: 311 403 481 845 * Passcode: Jm4d4s Agenda items: * GitHub <https://github.com/HUPO-PSI/mzQC/issues> : CV term requests * mzQC website <https://hupo-psi.github.io/mzQC/> : metabo-batches example (#233 <https://github.com/HUPO-PSI/mzQC/pull/233> ) * pymzqc validator: semantic checks severity logging level * mzQC specification manuscript <https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfq cjqs/edit> : continuation of use cases * AOB. Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-01-29 08:37:35
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Dear colleagues, We have our next teleconference on Friday January 31, 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: * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: CV term requests * mzQC website<https://hupo-psi.github.io/mzQC/>: metabo-batches example (#233<https://github.com/HUPO-PSI/mzQC/pull/233>) * pymzqc validator: semantic checks severity logging level * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: continuation of use cases * AOB. Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-01-23 19:16:11
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Dear colleagues, We have our next teleconference tomorrow, Friday January 24, 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: * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: CV term requests * mzQC website<https://hupo-psi.github.io/mzQC/>: metabo-batches example (#233<https://github.com/HUPO-PSI/mzQC/pull/233>) * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: continuation of use cases * AOB. Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-01-10 09:40:16
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Dear colleagues, We have our next teleconference today, Friday January 10, 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: * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: CV term requests * mzQC website<https://hupo-psi.github.io/mzQC/>: metabo-batches example (#233<https://github.com/HUPO-PSI/mzQC/pull/233>) * mzQC meeting Antwerp (January 15–17, 2025): planning and preparation. I will also send an email later today to all participants with some additional information. * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: progress update * AOB. Best, Wout |
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From: Wout B. <wou...@ua...> - 2024-12-13 09:54:39
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Dear colleagues, We have our next teleconference today, Friday December 13, 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 meeting Antwerp (January 15–17, 2025): planning and preparation * pymzqc<https://github.com/MS-Quality-hub/pymzqc>: completed issues recap * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: CV term requests * mzQC website<https://hupo-psi.github.io/mzQC/>: metabo-batches example (#233<https://github.com/HUPO-PSI/mzQC/pull/233>) * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: progress update * AOB. Best, Wout |
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From: Wout B. <wou...@ua...> - 2024-11-28 19:11:52
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Dear colleagues, We have our next teleconference Friday November 29, 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 meeting Antwerp (January 15–17, 2025) * PSI Spring Meeting 2025<https://www.psidev.info/spring-meeting-2025>: schedule * GitHub & pymzqc: open issues<https://github.com/HUPO-PSI/mzQC/issues> * mzQC website<https://hupo-psi.github.io/mzQC/>: metabo-batches example (#233<https://github.com/HUPO-PSI/mzQC/pull/233>) * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: progress update * AOB. Best, Wout |
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From: Wout B. <wou...@ua...> - 2024-11-18 10:29:17
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Dear colleagues,
Based on availability, the mzQC in-person meeting will take place on January 15–17, 2025 in Antwerp, Belgium. Additional details will be shared shortly.
[cid:e9025994-0779-4857-9820-8ec01338b99e]
Please let me know:
1.
If you are planning to join in-person.
*
If you need support for travel and lodging. Some funding is available from my budgets.
2.
If you are planning to join remotely.
I'm looking forward to welcoming you in Antwerp and having a productive mzQC meeting.
Best,
Wout
________________________________
From: Wout Bittremieux <wou...@ua...>
Sent: Friday, October 25, 2024 15:37
To: psi...@li... <psi...@li...>; Tim Van Den Bossche <tim...@ug...>; d.l...@ru... <d.l...@ru...>; n.h...@fz... <n.h...@fz...>; jul...@ru... <jul...@ru...>; chr...@fu... <chr...@fu...>; wa...@eb... <wa...@eb...>; edu...@cr... <edu...@cr...>
Subject: Planning for mzQC manuscript meeting – January 2025
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
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From: Wout B. <wou...@ua...> - 2024-11-14 11:44:57
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Dear colleagues, We have our next teleconference Friday November 15, 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: * January 2025 mzQC meeting * PSI Spring Meeting 2025<https://www.psidev.info/spring-meeting-2025>: March 31–April 3, 2025 in Tübingen, Germany * mzQC website<https://hupo-psi.github.io/mzQC/>: metabo-batches example (#233<https://github.com/HUPO-PSI/mzQC/pull/233>) * pymzqc: validator improvements * Use cases: MS imaging<https://github.com/HUPO-PSI/mzQC/blob/main/meeting_notes/2024/20241112_msi_meeting.md> [Wout], clinical lipidomics [Nils] * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: progress update * AOB. Best, Wout |
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From: Wout B. <wou...@ua...> - 2024-10-25 17:14:43
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Hi Theo, Great to hear that there are robust QC initiatives for MS imaging ongoing. We'd be more than happy to include Chris and Kumar as co-authors on the manuscript as well, based on the use case to be developed. This is already going to be a paper with a decent number of authors because many people contributed to mzQC over the years. 🙂 Sounds good to have a meeting to discuss this in some more detail, where I can then highlight mzQC. Do you mind making the initial connection with Chris and Kumar? Thanks, Wout ________________________________ From: Alexandrov, Theodore <tal...@he...> Sent: Friday, October 25, 2024 16:22 To: Wout Bittremieux <wou...@ua...> Cc: psi...@li... <psi...@li...> Subject: Re: Input on QC in MS Imaging for mzQC use case CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe. 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 |
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From: Alexandrov, T. <tal...@he...> - 2024-10-25 15:22:58
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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 |
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From: Alexandrov, T. <tal...@he...> - 2024-10-25 14:37:56
|
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 |
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From: Wout B. <wou...@ua...> - 2024-10-25 14:35:10
|
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 |
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From: Wout B. <wou...@ua...> - 2024-10-25 13:37:48
|
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 |
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From: Wout B. <wou...@ua...> - 2024-10-17 14:11:09
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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. |
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From: Wout B. <wou...@ua...> - 2024-10-03 16:57:24
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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 |
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