This is not ready to be merged yet, but a pull request may facilitate discussion.
The debug_calibration.ipynb notebook is currently set to run on the HeLa data and library from the alphadia performance tests (as in the debug_lvl1.ipynb file). I attach a plot made with some mixed-species data (also from Orbitrap Astral) run with a fully-predicted library, which is similar. It seems likely that some alternative to simply taking the number of precursors will be needed to calibrate the MS1 tolerance and possibly the RT tolerance, but it works reasonably well for the MS2 tolerance. The mobility data is shown as part of the automatic plot at the moment but this is not relevant to data analysed; this will be changed soon.
This is not ready to be merged yet, but a pull request may facilitate discussion.
The debug_calibration.ipynb notebook is currently set to run on the HeLa data and library from the alphadia performance tests (as in the debug_lvl1.ipynb file). I attach a plot made with some mixed-species data (also from Orbitrap Astral) run with a fully-predicted library, which is similar. It seems likely that some alternative to simply taking the number of precursors will be needed to calibrate the MS1 tolerance and possibly the RT tolerance, but it works reasonably well for the MS2 tolerance. The mobility data is shown as part of the automatic plot at the moment but this is not relevant to data analysed; this will be changed soon.