Hi Nick, I did something like that once with msInspect. As far as I can remember the msInspect command for this task is '--filter' (do not use the --filterpepxml command, it is not meant for what you want to do). I believe you can only search scores or peptide prophet prob to filter your files. Another way to do it with msInspect is to convert msInspect.tsv files to pep.xml. Since the msInspect.tsv is very similar to the .xls output from peptide prophet, you could use it to convert your .xls files to .pep.xml. All you have to do is to change the column positions on your .xls file in order to mock the msInspect.tsv format. The advantage here is that you can use TPP (which has more filter options) to filter your interact.pep.xml and then export to .xls.
alex On Oct 21, 5:34 pm, NB <[email protected]> wrote: > 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 -~----------~----~----~----~------~----~------~--~---
