I have been experimenting with a new dataset analyzed by OMSSA (v2.1.8), taking the pepXML output into the TPP. Currently I am analyzing the dataset by successive commands, (1) InteractParser, (2) PeptideProphetParser, and (3) RefreshParser. In particular the InteractParser includes the -C -P and -Et flags, which seem to be the most important for successful import of the OMSSA identifications. I would like to analyze the dataset using the xinteract wrapper, but wasn't able to invoke these previous commands with much success. In particular the -P command does not seem to be recognized by xinteract under general options. Is there a way to do this? Thanks!
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