Is it possible to run the entire TPP pipeline from the "Analyze Peptides" section and set the MINPROB function to a user defined value for ProteinProphet when using the Petunia interface?
This feature is available when using the ProteinProphet tab in Petunia but the models tab is not visible (and hence the models aren't generated?) when viewing the prot.xml in Petunia. The models tab is available to me when I run the entire pipeline from the "Analyze Peptides" tab but doing this restricts the MINPROB to the default 0.05 as the same options are not listed in the Petunia interface as they are for the ProteinProphet tab. I ask this because I am interested in running the TPP and seeing the effect on changing the MINPROB (the iProphet probability of a peptide) on the number of proteins and I would also like to see how this changes the error rates for proteins within the models tab. Is this possible using command line? Thanks! Adam -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
