Feature Support

The webapp supports almost all functionality of the pyXLMS python package. However, the following features are exclusively available via the python package:

Some parser parameters are only available in the python package.
Processing of search results from more than one search engine and crosslinker at the same time.
Creating intersections of search results from more than one search engine or crosslinker. You can read more about how to do that with the python package here. We also used that for the pyXLMS manuscript to create intersections of different replicates and search engines, you can find the code for that here .
Creating Venn diagrams. You can read more about how to do that with the python package here. We also used that for the pyXLMS manuscript, you can find the code for that here .
Annotating estimated false-discovery-rate (FDR), more about that here.
[Re-]Annotating decoy labels is only available in the python package, see more here.
Some filters are only available in the python package, e.g. filtering by peptide or residue pair. You can read more here.
Export to ProForma is only available in the python package as described here.

Tip

The file size limit is 200 MB in the web app. For self-hosted instances this can be increased via the config using the maxUploadSize option. For more info see here .

However, we generally recommend to run anything with more than 50 000 crosslink-spectrum-matches/crosslinks via the python package. The python package shows progress bars for every operation and is therefore favorable for longer operations like validation or re-annotation.