It currently is very challenging to retrieve the matched spectrum from MS2Query. The result table has all information and metadata can easily be added, however peaks and intensities are not stored in the sqlite file. This is done to save some memory, since the peaks are not needed for MS2Query, since embeddings have been precomputed.
However, this makes it very hard to retrieve the match made and makes it nearly impossible to for instance create mirror plots.
Potential solutions:
- Quick hacky fix. Add the original MGF file when uploading to zenodo. This should not be downloaded by default, but we could add some tutorial on how the mapping could be done.
- Actually fix this well. Include the spectrum info in SQLite again and add some functionality that allows to easily create mirror plots, e.g. in a jupyter notebook.
It currently is very challenging to retrieve the matched spectrum from MS2Query. The result table has all information and metadata can easily be added, however peaks and intensities are not stored in the sqlite file. This is done to save some memory, since the peaks are not needed for MS2Query, since embeddings have been precomputed.
However, this makes it very hard to retrieve the match made and makes it nearly impossible to for instance create mirror plots.
Potential solutions: