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
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