📝 add quantms output files for modules to table and highlight some parameter#782
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enryH wants to merge 3 commits into
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📝 add quantms output files for modules to table and highlight some parameter#782enryH wants to merge 3 commits into
enryH wants to merge 3 commits into
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- change test to reflect the default for the dda quant module
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Jun 17, 2025
User comments: In [PR782](Proteobench/ProteoBench#782) I added parsing of Match-Between-Runs (parameter: `targeted_only`), so that this will be correctly parsed. The search engine parsing with the correct version is still missing (see other submission PR: #571) ### Parameter changes detected: - **ident_fdr_peptide**: `None` → `nan` - **enable_match_between_runs**: `False` → `True` - **search_engine_version**: `None` → `2023.01 rev. 2 (7c9150d)` - **abundance_normalization_ions**: `None` → `nan` - **search_engine**: `None` → `comet` Dataset URL: https://proteobench.cubimed.rub.de/datasets/88dd7f984f7580c7d082dd98969fb5a49a15f009/
* 📝 document latest changes in quantms pipeline * 🔧 enable admonition directives enabeling colon_fence see docs in comment and a list of admonitions here: https://myst-parser.readthedocs.io/en/latest/syntax/admonitions.html --------- Co-authored-by: RobbinBouwmeester <Robbin.bouwmeester@ugent.be>
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