Dear TPP community, I'm using both Mascot and X!tandem to process a batch of iTRAQ 8plex data, I use the TPP to combine search results from both engines. I started from the same mzXML file, and then went through the searches, pepXML conversion, and peptideProphet analysis for both engine's results, all works smoothly. However, I got stuck with the Libra. One way I tried to do the mix analysis along with Libra is to add all search results (in pepXML format from both Mascot and Tandem) in the Analyze Peptides Page, check 'RUN PeptideProphet', check 'RUN InterProphet', check 'Also run ProteinProphet on these results', check 'RUN Libra', and then hit 'RUN XInteract' button. It did'n work out. The other way I tired is to combined the search results first without running Libra, create the .iproph.pep.xml, then go back to the Analyze Peptides Page, run Libra on that result, and it worked nicely, that give me a pep.xml file with mixed results from both engine and Libra quantitation results. However, I don't know how to import that into ProteinProphet. When I go to the Analyze Protein page, I see options including 'Import XPRESS protein ratios', 'Import ASAPRatio protein ratios and pvalues', but no where to find option to import Libra results!
Any idea how to do this last step? thank you! sunsun -- 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.
