Hi Arti,

We pass that option to xinteract when we run the TPP, but we don't do anything else with it ourselves. The value inside the <note> element should be the prefix that's added to the decoy proteins in the FASTA. For example, if the decoys look like "DECOY_ProteinA", "DECOY_ProteinB", "DECOY_IPI5432895", you'd want to use the parameter:

<note label="pipeline prophet, decoy tag" type="input">DECOY_</note>

White space is not allowed.

My understanding is that PeptideProphet and ProteinProphet will use it internally when calculating their distributions and scores. We'll load any decoy matches that happen to make it through the pipeline just like any other result.

Thanks,
Josh