This folder contains the experimental data and analysis scripts that accompany the paper: 
Rapid Development of Improved Data-Dependent Acquisition Strategies
https://pubs.acs.org/doi/10.1021/acs.analchem.0c03895

Folder and file explanations:
- 01_ROIvTopN_Rerun.ipynb is the Jupyter notebook that was used to run the controllers in the paper (TopN, SmartROI and WeightedDEW).
- Analysis.ipynb and OptimalAnalysis.ipynb are the two analysis notebooks used to analyse results.
- results/seed contain the files (.raw and .mzml) on which peak picking was done. This was used when computing coverage (Table 1) and efficiency (Table 2) in the paper.
- results/iter_0 contain the first iteration injection results (.raw and .mzml) from running the controllers in the paper (TopN, SmartROI and WeightedDEW).
- results/iter_1 contain the second iteration injection results (.raw and .mzml) from running the controllers in the paper (TopN, SmartROI and WeightedDEW).