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From: Wout B. <wou...@ua...> - 2026-04-17 06:47:40
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Dear colleagues, We have our next teleconference on Friday April 17, at 13h00 CET (12h00 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 manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: finalization of use cases * Outlier detection * Lipidomics * DIAuditor * Repository-scale metabolomics QC * QC metrics categorization [#323<https://github.com/HUPO-PSI/mzQC/pull/323>] * CV term review sheet<http://docs.google.com/spreadsheets/d/1E3fGvzMEmrYU5wlQdGIKznA_XvLRHEWN0LfNKFrLTmA/edit> * GitHub<https://github.com/HUPO-PSI/mzQC/issues> * CV term requests: TDAuditor [#324<https://github.com/HUPO-PSI/mzQC/issues/324>] & DIAuditor [#318–#320] * QC tools overview [#326<https://github.com/HUPO-PSI/mzQC/pull/326>] * PSI Spring Meeting<https://www.psidev.info/hupo-psi-meeting-2026>: May 5–8, 2026 * AOB Best, Wout |
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From: Bielow, C. <chr...@fu...> - 2026-04-10 10:52:41
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Hey all, I'm still in exams. Will be 15min late to the call. Cheers Chris Am 09.04.2026 21:21 schrieb Wout Bittremieux <wou...@ua...>: Dear colleagues, We have our next teleconference on Friday April 10, at 13h00 CET (12h00 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 manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: finalization of use cases * Outlier detection * Lipidomics * DIAuditor * Repository-scale metabolomics QC * QC metrics categorization [#323<https://github.com/HUPO-PSI/mzQC/pull/323>] * CV term review sheet<http://docs.google.com/spreadsheets/d/1E3fGvzMEmrYU5wlQdGIKznA_XvLRHEWN0LfNKFrLTmA/edit> * GitHub<https://github.com/HUPO-PSI/mzQC/issues> * CV term requests: TDAuditor [#324<https://github.com/HUPO-PSI/mzQC/issues/324>] & DIAuditor [#318–#320] * QC tools overview [#326<https://github.com/HUPO-PSI/mzQC/pull/326>] * PSI Spring Meeting<https://www.psidev.info/hupo-psi-meeting-2026>: May 5–8, 2026 * AOB Best, Wout |
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From: Wout B. <wou...@ua...> - 2026-04-09 19:21:01
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Dear colleagues, We have our next teleconference on Friday April 10, at 13h00 CET (12h00 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 manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: finalization of use cases * Outlier detection * Lipidomics * DIAuditor * Repository-scale metabolomics QC * QC metrics categorization [#323<https://github.com/HUPO-PSI/mzQC/pull/323>] * CV term review sheet<http://docs.google.com/spreadsheets/d/1E3fGvzMEmrYU5wlQdGIKznA_XvLRHEWN0LfNKFrLTmA/edit> * GitHub<https://github.com/HUPO-PSI/mzQC/issues> * CV term requests: TDAuditor [#324<https://github.com/HUPO-PSI/mzQC/issues/324>] & DIAuditor [#318–#320] * QC tools overview [#326<https://github.com/HUPO-PSI/mzQC/pull/326>] * PSI Spring Meeting<https://www.psidev.info/hupo-psi-meeting-2026>: May 5–8, 2026 * AOB Best, Wout |
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From: ricard-blum s. <syl...@un...> - 2026-03-27 21:38:31
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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). The Mass Spectrometry and Proteomics Informatics Working Groups have submitted a corrected version of the mzPAF (Peak Annotation Format) specification which was released on September 22nd, 2025. They updated the x-ion formula, fixed some reference ion formulas/masses and added one contributor and precision about spectra acquired in the negative ion mode. This amended document has been reviewed by two members of the Steering Group. Given that it has been submitted within 12 months after the acceptance and that very minor changes were made, the document now goes through a 14-day public review, which should end on April 10th, 2026 in agreement with the PSI Document Process. The version 1, draft 04 of the specification is attached to this e-mail and is also available at https://www.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. 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 to syl...@un... before*April 10th, 2026*. 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: Bielow, C. <chr...@fu...> - 2026-03-20 12:38:23
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I'm still busy elsewhere. Sorry. Wont make it today Am 19.03.2026 10:26 schrieb Wout Bittremieux <wou...@ua...>: Dear colleagues, We have our next teleconference on Friday March 20, at 13h00 CET (12h00 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 manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: finalization of use cases ⚠️ * Outlier detection * Lipidomics * DIAuditor * Repository-scale metabolomics QC * QC metrics categorization [#323<https://github.com/HUPO-PSI/mzQC/pull/323>] ⚠️ * CV term review sheet<http://docs.google.com/spreadsheets/d/1E3fGvzMEmrYU5wlQdGIKznA_XvLRHEWN0LfNKFrLTmA/edit> * GitHub<https://github.com/HUPO-PSI/mzQC/issues> * CV term requests: TDAuditor [#324<https://github.com/HUPO-PSI/mzQC/issues/324>] & DIAuditor [#318–#320] * QC tools overview [#326<https://github.com/HUPO-PSI/mzQC/pull/326>] * PSI Spring Meeting<https://www.psidev.info/hupo-psi-meeting-2026>: May 5–8, 2026 * AOB Best, Wout |
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From: Wout B. <wou...@ua...> - 2026-03-19 09:26:23
|
Dear colleagues, We have our next teleconference on Friday March 20, at 13h00 CET (12h00 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 manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: finalization of use cases ⚠️ * Outlier detection * Lipidomics * DIAuditor * Repository-scale metabolomics QC * QC metrics categorization [#323<https://github.com/HUPO-PSI/mzQC/pull/323>] ⚠️ * CV term review sheet<http://docs.google.com/spreadsheets/d/1E3fGvzMEmrYU5wlQdGIKznA_XvLRHEWN0LfNKFrLTmA/edit> * GitHub<https://github.com/HUPO-PSI/mzQC/issues> * CV term requests: TDAuditor [#324<https://github.com/HUPO-PSI/mzQC/issues/324>] & DIAuditor [#318–#320] * QC tools overview [#326<https://github.com/HUPO-PSI/mzQC/pull/326>] * PSI Spring Meeting<https://www.psidev.info/hupo-psi-meeting-2026>: May 5–8, 2026 * AOB Best, Wout |
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From: ricard-blum s. <syl...@un...> - 2026-03-18 18:27:20
|
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 HUPO-PSI activities). A Minimum Information document, the *Minimum Information Describing a Proteoform (MIDAP) document*, has been submitted to the Document Process by two members of the PSI steering committee. It has been reviewed by two other members of the PSI steering committee and revised to address their concerns. *The revised document now goes through 30-day public and external reviewing until April 19th, 2026. * *The document and two example files are 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 document (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 document?). Comments can be made on the document 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 19th, 2026.* I thank you very much in advance for your contribution and time. Kind regards. Professor Sylvie RICARD-BLUM, HUPO-PSI Editor 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...> - 2026-03-05 11:52:37
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Dear colleagues, We have our next teleconference on Friday March 6, at 13h00 CET (12h00 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 manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: finalization of use cases ⚠️ * Outlier detection * Lipidomics * DIAuditor * Repository-scale metabolomics QC * QC metrics categorization [#323<https://github.com/HUPO-PSI/mzQC/pull/323>] ⚠️ * CV term review sheet<http://docs.google.com/spreadsheets/d/1E3fGvzMEmrYU5wlQdGIKznA_XvLRHEWN0LfNKFrLTmA/edit> * GitHub<https://github.com/HUPO-PSI/mzQC/issues> * CV term requests: TDAuditor [#324<https://github.com/HUPO-PSI/mzQC/issues/324>] & DIAuditor [#318–#320] * QC tools overview [#326<https://github.com/HUPO-PSI/mzQC/pull/326>] * PSI Spring Meeting<https://www.psidev.info/hupo-psi-meeting-2026>: May 5–8, 2026 * AOB Best, Wout |
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From: Wout B. <wou...@ua...> - 2026-02-19 08:24:00
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Dear colleagues, We have our next teleconference on Friday February 20, at 13h00 CET (12h00 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 manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: finalization of use cases * Outlier detection * Lipidomics * DIAuditor * Repository-scale metabolomics QC * QC metrics categorization [#323<https://github.com/HUPO-PSI/mzQC/pull/323>] * CV term review sheet<http://docs.google.com/spreadsheets/d/1E3fGvzMEmrYU5wlQdGIKznA_XvLRHEWN0LfNKFrLTmA/edit> * GitHub<https://github.com/HUPO-PSI/mzQC/issues> * CV term requests: TDAuditor [#324<https://github.com/HUPO-PSI/mzQC/issues/324>] & DIAuditor [#318–#320] * QC tools overview [#326<https://github.com/HUPO-PSI/mzQC/pull/326>] * PSI Spring Meeting<https://www.psidev.info/hupo-psi-meeting-2026>: May 5–8, 2026 * AOB Best, Wout PS: I will need to depend on good internet while at the airport waiting to board a flight, so there is a small chance I might not make it myself. |
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From: Wout B. <wou...@ua...> - 2026-01-28 22:02:30
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Dear colleagues, We have our next teleconference on Friday January 30, at 13h00 CET (12h00 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 manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: finalization of use cases * Outlier detection * Lipidomics * DIAuditor * Repository-scale metabolomics QC * QC metrics categorization [#323<https://github.com/HUPO-PSI/mzQC/pull/323>] * CV term review sheet<http://docs.google.com/spreadsheets/d/1E3fGvzMEmrYU5wlQdGIKznA_XvLRHEWN0LfNKFrLTmA/edit> * GitHub<https://github.com/HUPO-PSI/mzQC/issues> * CV term requests: TDAuditor [#324<https://github.com/HUPO-PSI/mzQC/issues/324>] & DIAuditor [#318–#320] * QC tools overview [#326<https://github.com/HUPO-PSI/mzQC/pull/326>] * PSI Spring Meeting<https://www.psidev.info/hupo-psi-meeting-2026>: May 5–8, 2026 * AOB Best, Wout |
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From: Wout B. <wou...@ua...> - 2026-01-08 18:25:07
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Dear colleagues, We have our next teleconference tomorrow, Friday January 9, at 13h00 CET (12h00 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 manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: finalization of use cases * Outlier detection * Lipidomics * DIAuditor * Repository-scale metabolomics QC * QC metrics categorization [#323<https://github.com/HUPO-PSI/mzQC/pull/323>] * CV term review sheet<http://docs.google.com/spreadsheets/d/1E3fGvzMEmrYU5wlQdGIKznA_XvLRHEWN0LfNKFrLTmA/edit> * GitHub<https://github.com/HUPO-PSI/mzQC/issues> * CV term requests: TDAuditor [#324<https://github.com/HUPO-PSI/mzQC/issues/324>] & DIAuditor [#318–#320] * QC tools overview [#326<https://github.com/HUPO-PSI/mzQC/pull/326>] * PSI Spring Meeting<https://www.psidev.info/hupo-psi-meeting-2026>: May 5–8, 2026 * AOB Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-12-11 17:00:53
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Dear colleagues, We have our next teleconference tomorrow, Friday December 12, at 13h00 CET (12h00 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 manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: finalization of use cases * Outlier detection * Lipidomics * DIAuditor * Repository-scale metabolomics QC * QC metrics categorization [#323<https://github.com/HUPO-PSI/mzQC/pull/323>] * CV term review sheet<http://docs.google.com/spreadsheets/d/1E3fGvzMEmrYU5wlQdGIKznA_XvLRHEWN0LfNKFrLTmA/edit> * GitHub<https://github.com/HUPO-PSI/mzQC/issues> * CV term requests: TDAuditor [#324<https://github.com/HUPO-PSI/mzQC/issues/324>] & DIAuditor [#318–#320] * QC tools overview [#326<https://github.com/HUPO-PSI/mzQC/pull/326>] * PSI Spring Meeting<https://www.psidev.info/hupo-psi-meeting-2026>: May 5–8, 2026 * AOB Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-11-27 17:40:32
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Dear colleagues, We have our next teleconference tomorrow, Friday November 28, at 11h00 CET (10h00 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: * Biohackathon<https://github.com/MS-Quality-Hub/biohackathon2025>: recap * QC metrics categorization [#323<https://github.com/HUPO-PSI/mzQC/pull/323>] * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: finalization of use cases * Outlier detection * Lipidomics * DIAMetric * Repository-scale QC (metabolomics) * GitHub<https://github.com/HUPO-PSI/mzQC/issues> * CV term requests: TDAuditor [#324<https://github.com/HUPO-PSI/mzQC/issues/324>] & DIAMetric [#318–#320] * QC tools overview [#326<https://github.com/HUPO-PSI/mzQC/pull/326>] * pymzQC<https://github.com/MS-Quality-hub/pymzqc> v1.0.1 updates [Matthias]: semantic validation * AOB Best, Wout |
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From: ricard-blum s. <syl...@un...> - 2025-11-10 13:30:41
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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). The Mass Spectrometry and Proteomics Informatics Working Groups have submitted a new recommendation for a PSI standard, the ProForma (Proteoform and Peptidoform Notation) version 2.1 specification. This version is an update of ProForma version 2.0 which was ratified in February 2022. This update adds some options to describe more complex peptidoforms and is heavily rewritten te remove ambiguities and provide a better overview for implementors. 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 December 10th, 2025.* The version 2.1, draft 02 of the specification 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 December 10th, 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...> - 2025-10-30 17:50:30
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Dear colleagues, We have our next teleconference tomorrow, Friday October 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: * Biohackathon preparation: participant instructions<https://github.com/MS-Quality-Hub/biohackathon2025> [everyone: review in advance] * pymzQC<https://github.com/MS-Quality-hub/pymzqc> v1.0.1 updates [Matthias]: semantic validation * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: TDAuditor CV term requests * 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 * AOB Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-10-28 16:46:38
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Awesome, thanks Yasset. Yes, I don't expect that we will fully finish all tasks. The different options are more so that people can pick a project that most appeals to them. I agree that mzQC export is definitely a priority. Best, Wout ________________________________ From: Yasset Perez-Riverol <ypr...@gm...> Sent: Tuesday, October 28, 2025 17:03 To: Wout Bittremieux <wou...@ua...> Cc: psi...@li... <psi...@li...> Subject: Re: Please review ELIXIR BioHackathon instructions & tasks 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. I have given a quick view. My only question is that the amount of tasks looks heavy for a hackathon of five days, but I also have to say that I don’t know the specs of BioHackathon2025. If you have enough people, you can try to achieve this. >From my point of view, having support for mzQC in MultiQC and an IDFree scalable workflow and MultiQC+mzQC report that we can try to deploy in prod will be a dream that PRIDE has tried for years. Regards, Yasset Yasset Perez-Riverol Team Coordinator PRIDE resources Proteomics Services, EMBL-EBI ypr...@gm... On 28 Oct 2025, at 15:27, Wout Bittremieux <wou...@ua...> wrote: Hi all, I've prepared the hackathon materials here: https://github.com/MS-Quality-Hub/biohackathon2025 Could you please give everything a careful pass to ensure: 1. Completeness: all info participants need is present (setup, tasks, links, examples). 2. Clarity: instructions and task scopes make sense for newcomers. 3. Technical accuracy: commands, repositories/branches, CV terms, and validation steps are correct. Feel free to edit directly, open a PR with proposed changes, or send comments to me if that's easier. Thanks, Wout |
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From: Yasset Perez-R. <ypr...@gm...> - 2025-10-28 16:04:11
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I have given a quick view. My only question is that the amount of tasks looks heavy for a hackathon of five days, but I also have to say that I don’t know the specs of BioHackathon2025. If you have enough people, you can try to achieve this. From my point of view, having support for mzQC in MultiQC and an IDFree scalable workflow and MultiQC+mzQC report that we can try to deploy in prod will be a dream that PRIDE has tried for years. Regards, Yasset Yasset Perez-Riverol Team Coordinator PRIDE resources Proteomics Services, EMBL-EBI ypr...@gm... > On 28 Oct 2025, at 15:27, Wout Bittremieux <wou...@ua...> wrote: > > Hi all, > > I've prepared the hackathon materials here: https://github.com/MS-Quality-Hub/biohackathon2025 > > Could you please give everything a careful pass to ensure: > Completeness: all info participants need is present (setup, tasks, links, examples). > Clarity: instructions and task scopes make sense for newcomers. > Technical accuracy: commands, repositories/branches, CV terms, and validation steps are correct. > > Feel free to edit directly, open a PR with proposed changes, or send comments to me if that's easier. > > Thanks, > Wout |
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From: Wout B. <wou...@ua...> - 2025-10-28 16:00:27
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Hi all, I've prepared the hackathon materials here: https://github.com/MS-Quality-Hub/biohackathon2025 Could you please give everything a careful pass to ensure: 1. Completeness: all info participants need is present (setup, tasks, links, examples). 2. Clarity: instructions and task scopes make sense for newcomers. 3. Technical accuracy: commands, repositories/branches, CV terms, and validation steps are correct. Feel free to edit directly, open a PR with proposed changes, or send comments to me if that's easier. Thanks, Wout |
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From: Wout B. <wou...@ua...> - 2025-10-23 09:40:40
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Dear colleagues, We have our next teleconference tomorrow, Friday October 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: * Biohackathon preparation: internal TODO list<https://docs.google.com/document/d/1PEsWowuvagZSw7m4ohimwtOGr-_qXiO2hF0KPV4LojU/edit>, organization document<https://docs.google.com/document/d/1x9aDGEUVWcThQZV9Lp9viBmC9ASw0GGCeZK-02lQBgM/edit?usp=sharing> * pymzQC<https://github.com/MS-Quality-hub/pymzqc> v1.0.1 updates [Matthias]: semantic validation * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: TDAuditor CV term requests * 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 * AOB Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-10-09 19:34:37
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Dear colleagues, We have our next teleconference tomorrow, Friday October 10, at 15h00 CET (12h00 BST, 11h00 GMT). ⚠️ Please note the deviation from our usual time slot. 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 We have one key agenda item: * Biohackathon preparation: internal TODO list<https://docs.google.com/document/d/1PEsWowuvagZSw7m4ohimwtOGr-_qXiO2hF0KPV4LojU/edit> If time and desires permit, we might tackle some of our regular topics afterwards. Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-09-18 15:18:13
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Dear colleagues, We have our next teleconference tomorrow, Friday September 19, 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<https://github.com/HUPO-PSI/mzQC/pull/314>] * 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 has reviewed wording of messages] * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: CV term requests for McQuaC<https://github.com/HUPO-PSI/psi-ms-CV/pull/400> and TDAuditor * 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...> - 2025-09-11 15:43:36
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Dear colleagues, We have our next teleconference tomorrow, Friday September 12, 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: * BioHackathon<https://biohackathon-europe.org/>: project description<https://github.com/elixir-europe/biohackathon-projects-2025/blob/main/29.md>, planning * Introduction to pMultiQC<https://docs.quantms.org/latest/pmultiqc.html> [Yasset] * GitHub: broken links [Mathias to integrate fix in validator PR<https://github.com/HUPO-PSI/mzQC/pull/314>] * 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 has reviewed 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> and TDAuditor * 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 * AOB Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-08-21 14:32:50
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Dear colleagues, We have our next teleconference tomorrow, Friday August 22, 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<https://github.com/HUPO-PSI/mzQC/pull/314>] * 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: Wout B. <wou...@ua...> - 2025-08-07 14:15:53
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Dear colleagues, We have our next teleconference tomorrow, Friday August 8, 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<https://github.com/HUPO-PSI/mzQC/pull/314>] * 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: Wout B. <wou...@ua...> - 2025-07-31 19:14:55
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Dear colleagues, We have our next teleconference tomorrow, Friday August 1, 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] * 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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