Add meeting notes April

meeting_notes/2024/20240403_telco.md

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+# QC working group teleconference 3 April 2024
+
+- Chris Bielow
+- Wout Bittremieux
+- Tim Van Den Bossche
+- Mathias Walzer
+
+---
+
+## mzQC software libraries manuscript
+
+Rather than synchronizing publication of the manuscript with the main manuscript describing the mzQC format itself, we decided to submit it to the [JASMS special issue on computational mass spectrometry](https://axial.acs.org/analytical-chemistry/jasms-call-for-papers-special-issue-on-computational-mass-spectrometry) (submission deadline April 30, 2024).
+
+Technical aspects related to finalizing the manuscript:
+- Move away from the Nextflow analysis workflow because it just added complexity and compatibility issue. It is also overkill for this limited example.
+- Discussion on the necessity of proper FDR control, including lowering the FDR threshold to 1% to account for E. coli's small proteome, and the need for protein-level FDR control, as we report protein results.
+- All software libraries and the analysis repository on GitHub need to be brought up to date matching the results in the manuscript. Repository cleanup can still happen after the manuscript submission as well.
+- Discussion on how to represent the results of the QC analysis in the manuscript. Tim had some suggestions and will try to clarify the figure, after Mathias shares the latest updated version.
+- Requests for missing CV terms were submitted to the PSI-MS-CV repository.
+
+Related discussions:
+- mzQC file merging is a relevant task that should be easily supported by the software libraries. For the current manuscript a somewhat hacked-together solution initially suffices.

meeting_notes/2024/20240417_telco.md

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+# QC working group teleconference 17 April 2024
+
+- Chris Bielow
+- Wout Bittremieux
+- Nils Hoffmann
+- Dave Tabb
+- Tim Van Den Bossche
+- Mathias Walzer
+
+---
+
+## Working group charter
+
+We went over the [working group charter](https://www.psidev.info/quality-control-working-group-charter) with an eye on its annual update. Some minor updates (affiliation update), but other than that, no major changes are needed.
+
+Our key effort during the next year will be to demonstrate the benefits and applications of mzQC in practice, through the development of use cases and support of QC software.
+
+Wout will update the charter and send it for consultation to Slack.
+
+## CV
+
+- Precursor mass deviation ([#254](https://github.com/HUPO-PSI/psi-ms-CV/pull/254)): Good to be merged. Note that FragPipe reports the absolute mass deviation (although not explicitly as a QC metric).
+- Number of missed cleavages ([#255](https://github.com/HUPO-PSI/psi-ms-CV/pull/255)): Discussion on how to represent this metric and its definition. Mathias will apply some refinements.
+- identified MS2 vs RT ([#255](https://github.com/HUPO-PSI/psi-ms-CV/pull/255)): Some confusion around what this metric precisely represents, indicating that its definition should be clarified. Mathias will update it in analogy to some existing related terms.
+
+## mzQC software libraries manuscript
+
+- Mathias reported on the updated data analysis workflow (including protein-level FDR control, which necessitated switching search engines).
+- Mathias will share the updated data analysis figure with Tim for some visual edits.
+- The [JASMS special issue on computational mass spectrometry](https://axial.acs.org/analytical-chemistry/jasms-call-for-papers-special-issue-on-computational-mass-spectrometry) submission deadline is April 30, 2024. We will have an additional meeting next week to finalize the manuscript by this deadline.