Limitations

Despite our best efforts pyXLMS still comes with some limitations that are a direct result of the differences in the output formats of crosslink search engines. Many crosslink search engines do not report any kind of decoy matches which makes validation in pyXLMS or export to xiFDR impossible which is why we recommend using validated results for pyXLMS. Validation within pyXLMS is currently only supported for MaxLynx, MS Annika, and xiSearch.

Furthermore, the different down-stream analysis tools require varying input information which might not be consistently available from all crosslink search engines. Some of this can be mitigated by functionality in pyXLMS such as annotation or by additional information that needs to be passed to pyXLMS for a successful export. Generally, the export to all downstream analysis tools should work for all crosslink search engines and input formats, with the exception of the export to xiFDR which is limited to MaxLynx, MS Annika, and xiSearch for above reasons. For safety pyXLMS makes sure before the export that all the required information is available and will otherwise throw an error. For more information please check the specific export pages in this user guide and the documentation .

The web app supports most of the features of the python package, features that are not supported in the web app are listed in here.

Interacting with STRING  requires an active internet connection and depends on the service availability of STRING.