Hi David, Thanks for the reply. Unfortunately, this does not help as the PeptideProphet probability score does not translate to xcorr and deltacn cutoffs I am using, i.e. (Xcorr +1=1.9, +2=2.2, +3=3.5, and deltacn scores of > or = to 0.08. That is, probability scores as low as 0 appear in my post-xcorr and deltacn filtered list. I am concerned that I will end up with false protein groups assignments in ProteinProphet if I do not use the actual list of peptides which pass the above xcorr and deltacn criteria. There must be another way to this end. Such as,
1) Is there a way to write filtered results from the PeptdieProphet viewer to a .xml file for input into ProteinProphet? 2) Is there a way to convert the .xls output from PeptidePropher viewer to an .xml file for input into ProteinProphet? 3) Does ProteinProphet tolerate any other input file format aside from a PeptideProphet formatted .xml file? 4) Are there any ProteinProhet commands which will direct ProteinProphet to utilize the xcorr and deltacn cutoffs I desire that I can use at the command line? Thanks much for whatever insights you can provide!!! Nick On Oct 19, 1:36 pm, David Shteynberg <[email protected]> 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]> 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 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 -~----------~----~----~----~------~----~------~--~---
