Dear Luis, Thank you for the reply! In the first way, I run PeptideProphet, iProphet and ProteinProphet through petunia in one run.
In the second way, I'm running the PeptideProphet and iProphet first (1st run) and then ProteinProphet on the iProphet pep xml file (2nd run). When looking at the top of both ProteinProphet files, the source file is the same: the iProphet.pep.xml file. Sorry if this sounds stupid, but if the input file is the same, shouldn't the output be the same as well? Basically, even if I run ProteinProphet on the iProphet.pep.xml, it doesn't matter unless I specifically tell it to use the iProphet on the command line? Bjorn -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
