Hi David, Just following up on this question as I am wondering whether it is possible with the current TPP version to perform filtering and save it before moving on to the next step in the pipeline (for example to filter PSMs at 0.01 FDR using PeptideProphet/iProphet and feeding this file to ProteinProphet) or would I have to perform trial runs like you suggest and then implement the cutoffs when running the the entire pipeline with ProteinProphet enabled?
Best, Adam On Monday, October 19, 2009 at 12:36:00 PM UTC-5, David Shteynberg wrote: > > Hello Nick, > > You can run PeptideProphet once to find the probability threshold that > satisfies your criteria. You can then rerun the pipeline, this time > including ProteinProphet with the probability cutoff you decided on in > the first pass. Hope that helps. > > -David > > On Mon, Oct 19, 2009 at 8:05 AM, NB <[email protected] <javascript:>> > wrote: > > > > Hi, > > > > Hopefuly this is a pedestrian question. I am interested in analyzing > > post-filtered peptideprophet results using proteinprophet. Outside of > > exporting filtered pepprophet data (interact.pep.xml) as an excel > > file, I have not discovered a way to save the post-filtered pepprophet > > data as a new interact.pep.xml file for input into proteinprohet. Any > > ideas? Thanks much!!! > > > > Nick > > > > > > > > -- 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.
