Joshua Charkow

Feature: Read .TSV Spectral Library In Batches

3

## Description When working with large libraries (such as in-silico libraries), formatting the libraries using `OpenSwathAssayGenerator` and `OpenSwathDecoyGenerator` can be very memory intensive requiring over 100Gb of memory. This PR...

Apply changes outlined in https://github.com/MannLabs/alphapeptdeep/issues/254 to fix issue with zero intensity MS2 predictions.

--apply_weights requires --ss_main_score to be specified as in the original command

1

I get unexpected results when using `--apply_weights` with XGBoost if a `--ss_main_score` was set manually. E.g. `pyprophet score --in in.oswpq --level=ms1ms2 --classifier=XGBoost --ss_main_score=var_dotprod_score` - Trains the model as expected However...

New Workflow: LDA then XGBoost

1

New workflow which first runs LDA and then runs XGBoost using the LDA results as the main score. This helps prevent pi0 errors that run into with XGBoost. Overall, the...

Create a new results file parser for the .oswpq file. The .oswpq is a directory containing a `precursors_features.parquet` and a `transition_features.parquet` file The specifications are as follows: precursor_features.parquet Schema([ ('PROTEIN_ID',...

It seems that the binder links in the documentation are broken.

Simplifying MultiPlot Interface

5

Currently, plotting across several axes in pyopenms_viz can be cumbersome. Some examples include: https://github.com/OpenMS/pyopenms_viz/blob/main/docs/gallery_scripts_template/plot_spyogenes_subplots_ms_matplotlib.py https://github.com/OpenMS/pyopenms_viz/blob/main/docs/gallery_scripts_template/plot_investigate_spectrum_binning_ms_matplotlib.py In both of these scripts, the `.plot` function must be called multiple times in a...

Plot peptide sequence with matched fragments.

3

https://github.com/OpenMS/pyopenms_viz/pull/29 shows an implementation of how to add a sequence plot into the matplotlib plots. Unfortunately with the new updates to pyopenms_viz although this feature is highly useful for mass...

Update Parameters in documentation

4

With new refactoring, the parameters in the documentation might be out of date. Double check this by comparing the parameters in the _config.py class with those outlined in the documentation....

Seems that in this example of an extracted spectrum, when binning is turned on there is a big shift in the m/z (by 2 Da). Code: https://pyopenms-viz.readthedocs.io/en/latest/gallery/ms_bokeh/plot_spectrum_dia_ms_bokeh.html Add bin_peaks =...