This repository contains code for publication [DOI].
Input data is on Zenodo: 10.5281/zenodo.18023698
To reproduce the entrapment analysis: https://github.com/Labo-MAB/Ionbot_FDP/tree/tpp-fragpipe-ranks-groupwalk
TPP and FragPipe parameters (oui-discovery-vv): tpp_run/ & fragpipe_run/
Figures in .svg: publication-data/Final-figures/
Panels for figures 1-5 & 8-10: oui-discovery-vv-plot/
f1 oui-discovery-vv/: plot-0-fdp.ipynb
f2-3 oui-discovery-vv/: explore-1-tpp-1-preprocess.ipynb → do-0-protein-inference-tpp-fragpipe.ipynb & explore-1-tpp-2-stats.ipynb; explore-1-ionbot-1-preprocess.ipynb → explore-1-ionbot-closed-2-stats.ipynb; compare-2-tpp-ionbot-closed.ipynb
f4-5 oui-discovery-vv/: explore-1-fragpipe-1-preprocess.ipynb → do-0-protein-inference-tpp-fragpipe.ipynb & explore-1-fragpipe-2-stats.ipynb; explore-1-ionbot-1-preprocess.ipynb → explore-1-ionbot-open-2-stats.ipynb; compare-2-fragpipe-ionbot-open.ipynb
f6: Comparison-4-new-Sankey-global.ipynb & Comparison-5-ionbot-features-tr-combo-global.ipynb
f7: Comparison-6b-open-vs-closed-search-global.ipynb
f8 oui-discovery-vv/: explore-1-ionbot-1-preprocess.ipynb → explore-1-ionbot-open-2-stats.ipynb
f9 oui-discovery-vv/: explore-1-ionbot-1-preprocess.ipynb → explore-1-ionbot-open-2-stats.ipynb & explore-1-ionbot-closed-2-stats.ipynb → compare-2-ionbot-closed-open.ipynb
f10 oui-discovery-vv/: explore-1-ionbot-1-preprocess.ipynb → explore-1-ionbot-open-2-stats.ipynb → explore-3-ionbot-open-noncanon-hpp.ipynb & explore-3-ionbot-open-noncanon-spectra.ipynb
fs1-2 oui-discovery-vv/: plot-0-fdr-vs-ranks.ipynb
fs3: see f2-5
fs4: see f10