Hi Adina,

Here's the relevant section from your log file:

09 Feb 2009 15:55:52,919 INFO : PeptideProphet v3.0 April 1, 2004 (TPP v3.4 SQUALL rev.1, Build 200803020850(Win32)) AKeller@ISB
09 Feb 2009 15:55:52,919 INFO : read in 2 1+, 5536 2+, 5576 3+, 0 4+, and 0 5+ spectra
09 Feb 2009 15:55:52,919 INFO : Initialising statistical models ...
09 Feb 2009 15:55:52,919 INFO : negmean = -0.335708
09 Feb 2009 15:55:52,919 INFO : negmean = 0.299213
09 Feb 2009 15:55:52,919 INFO : negmean = 0.074056
09 Feb 2009 15:55:52,934 INFO : negmean = -0.2
09 Feb 2009 15:55:52,934 INFO : negmean = -0.2
09 Feb 2009 15:55:52,981 INFO : iteration 1 2 3 Too much overlap detected at high f-vals: negSlice = 219.322 > posSlice = 239.084
09 Feb 2009 15:55:53,012 INFO : 4 5 Too much overlap detected at high f-vals: negSlice = 321.67 > posSlice = 327.017
09 Feb 2009 15:55:53,012 INFO : 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Too much overlap detected at high f-vals: negSlice = 270.103 > posSlice = 228.71
09 Feb 2009 15:55:53,012 INFO : Too much overlap detected at high f-vals: negSlice = 321.67 > posSlice = 327.017
09 Feb 2009 15:55:53,012 INFO : model complete after 26 iterations
09 Feb 2009 15:55:53,574 INFO : command completed in 1 sec
09 Feb 2009 15:55:53,574 INFO :
09 Feb 2009 15:55:53,589 INFO : running: "ProteinProphet "080207-1.pep.xml" "080207-1.pep-prot.xml" XML NOPLOT"
09 Feb 2009 15:55:53,605 INFO : ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v3.4 SQUALL rev.1, Build 200803020850(Win32))
09 Feb 2009 15:55:53,621 INFO : . . . reading in C:/CPAS_TEST/xtandem/new/080207-1.work/080207-1.pep.xml. . .
09 Feb 2009 15:55:53,621 INFO : . . . read in 0 1+, 0 2+, 0 3+, 0 4+ spectra with min prob 0.05
09 Feb 2009 15:55:53,621 INFO : (xml input) (using degen pep info)
09 Feb 2009 15:55:53,636 INFO : no data - quitting
09 Feb 2009 15:55:53,636 INFO : command "ProteinProphet "080207-1.pep.xml" "080207-1.pep-prot.xml" XML NOPLOT" exited with non-zero exit code: 1
09 Feb 2009 15:55:53,636 INFO : QUIT - the job is incomplete


PeptideProphet is failing to model the run, so it's not outputting any peptide probabilities that ProteinProphet can use as input. Therefore, ProteinProphet is failing when it tries to run.

You will probably need to change your search parameters so that XTandem and the TPP can produce better results for your inputs, but I don't know enough about your particular case to make specific recommendations.

Thanks,
Josh

Sorry your having trouble. The example data you chose is a little more complex than most. It worked on the TPP because they prepared the sequest.params file in advance to show off the advanced features. Here's params that should work with Xtandem. I would highly recommend getting a basic data set just to get started. I'm attaching a small mzXML with database.

<bioml>
  <note label="residue, potential modification mass" type="input">15.994915@M,8.0@C</note>
  <note label="residue, modification mass" type="input">442.5728@C</note>
  <note label="protein, cleavage site" type="input">[KR]|{P}</note>
  <note label="pipeline quantitation, algorithm" type="input">xpress</note>
  <note label="pipeline quantitation, residue label mass" type="input">8.0@C</note>
  <note label="scoring, algorithm" type="input">k-score</note>
  <note label="spectrum, use conditioning" type="input">no</note>
  <note label="pipeline, data type" type="input">Fractions</note>
</bioml>

I have gotten Xtandem working with the CPAS demo file. I'm getting a new error with my file. Wonder if anyone has seen this before? The original file I was searching was part of a fraction protocol. I applied it to a sample set as a fraction and it seems like XTandem liked it better. I think I'm getting hung up on TPP now.

...
10 Feb 2009 17:02:22,892 INFO : command "PeptideProphetParser "all.pep.xml" EXTRAITRS=20" exited with non-zero exit code: -1073741819
10 Feb 2009 17:02:22,892 INFO : QUIT - the job is incomplete
10 Feb 2009 17:02:22,892 INFO :
10 Feb 2009 17:02:22,892 INFO : command "PeptideProphetParser "all.pep.xml" EXTRAITRS=20" failed: Unknown error
10 Feb 2009 17:02:22,892 ERROR: Failed to clean up work directory after error condition, see full error information below.
java.io.IOException: Failed to remove work directory ...

Hi Adina,

I haven't seen that particular failure before, but it's certainly coming from a failure running PeptideProphet. There's only one reference to it in the TPP mailing list archives, and it doesn't indicate if the user tracked it down.

http://www.mail-archive.com/spctools-discuss@googlegroups.com/msg00293.html

Thanks,
Josh