Julian Uszkoreit

Yes, this is what I meant, that you can use PIA for the merging of search engine results and calculating the FDR. After an mzIdentML export, you might be able...

You obviously need any protein inference, if you want to go from the identified/quantified peptides of your DIA experiment to the corresponding proteins. But as said before, I don't know...

Apologies for the late reply, but could you elaborate, how you called PIA from the CLI? Could you maybe also post the param file here, so I can double check...

You should use the json file to run a CLI analysis by now.

Hej @algalcms , Could you provide the version of KNIME and the PIA plugin you are using?

Could you please try to upgrade to the newest version of the PIA plugin? There was a major internal change for KNIME 4.4 which took place some versions later than...

Hm, this looks weird. The error rather indicates, that there is the old version still used, which breaks with KNIME >4.3 though. Could you try to cleanly uninstall the current...

I would expect this error, if for some reason a wrong Java version was used. But this should not be possible with KNIME. Last week, new versions of PIA were...

(closed due to inactivity and KNIME updates)

An implementation which passes the compilation directly to the modeller, instead of writing it to a file, should fix this and is a very good thing to have.