Hello Bjorn, The difference in the 2nd way that you are running the tools is that the ProteinProphet analysis is done only based on PeptideProphet results, and not on iProphet. The only way to run iProphet results in ProteinProphet through Petunia is by checking the "Also run ProteinProphet on these results" box. An option will be added to the ProteinProphet page in the next release of the TPP, coming soon!
You can also run ProteinProphet on the command-line, with the IPROPHET option. Hope this helps, --Luis On Wed, Jul 27, 2011 at 3:04 AM, Bjorn <[email protected]> wrote: > Hello, > > First: I'm using TPP 4.4 rev 1 on Mac OS 10.6.8 > > Let me describe the situation: > - I merge my tandem.pep.xml files in the xinteract GUI. > - I select decoy option with decoy tag. > - I select the run iProphet box and just below I select the "run > ProteinProphet on these results" box. > - run. > The output is 3 files: a PeptideProphet pep.xml file, an iProphet > iproph.pep.xml file and a ProteinProphet iproph.prot.xml file. > > from ProteinProphet file: > min_peptide_probability="0.20" min_peptide_weight="0.50" > num_predicted_correct_prots="105.3" num_input_1_spectra="0" > num_input_2_spectra="32019" num_input_3_spectra="13729" > num_input_4_spectra="0" num_input_5_spectra="0" > initial_min_peptide_prob="0.05" total_no_spectrum_ids="37232.9" > sample_enzyme="trypsin"> > <program_details analysis="proteinprophet" > > > Now I try this: > - I merge my tandem.pep.xml files in the xinteract GUI. > - I select decoy option with decoy tag. > - I select run iProphet box. > - run. > The output is 2 files: a PeptideProphet pep.xml file and an iProphet > iproph.pep.xml file. > I take the iproph.pep.xml as input for a separate ProteinProphet run > and the output is again a prot.xml file, but this time it is much > bigger and has much more identifications than the all-in-one run > before. > > from ProteinProphet file: > min_peptide_probability="0.20" min_peptide_weight="0.50" > num_predicted_correct_prots="1105.5" num_input_1_spectra="0" > num_input_2_spectra="57155" num_input_3_spectra="22808" > num_input_4_spectra="0" num_input_5_spectra="0" > initial_min_peptide_prob="0.05" total_no_spectrum_ids="39629.9" > sample_enzyme="trypsin"> > <program_details analysis="proteinprophet" > > What causes this difference? I would assume that, if the input is the > same, the output should be the same as well. Does it matter if you run > this all-in-one or separate? > I'm not selecting any other option in the ProteinProphet GUI. > > Any ideas? > > Thanks, > Bjorn > > > > -- > 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. > > -- 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.
