Peptide Prophet ERROR

[user1]

Hi,

I am trying to run the mzXML files with TPP. The X! Tandem search is correct and as an output we get the pep.xml file. The problems starts, when I want to run the peptide prophet. I start the run and it cannont be compleated. I have run several samples so far and I have not faced this problem. I was trying even run the samples which I had run previosly, but again with the same results. Please find attached below the dialog window. Any ideas what can be wrong? Thank you in advance! 

c:\Inetpub\tpp-bin\xinteract (TPP v4.6 OCCUPY rev 3, Build 201307241109 (MinGW))

running: "C:/Inetpub/tpp-bin/InteractParser "100214-Agn-Er-Golgi-E10-100ul-01.interact.pep.xml" "100214-Agn-Er-Golgi-E10-100ul-01.tandem.pep.xml" -I -L"6""
 file 1: 100214-Agn-Er-Golgi-E10-100ul-01.tandem.pep.xml
SUCCESS: CORRECTED data file c:/Inetpub/wwwroot/ISB/data/ER-GOLGI-experiment/E10/100214-Agn-Er-Golgi-E10-100ul-01.mzXML in msms_run_summary tag ...
Unknown file type. No file loaded.
Failed to open input file 'c:/Inetpub/wwwroot/ISB/data/ER-GOLGI-experiment/E10/100214-Agn-Er-Golgi-E10-100ul-01.mzML'.
 processed altogether 51735 results
INFO: Results written to file: c:/Inetpub/wwwroot/ISB/data/ER-GOLGI-experiment/E10/100214-Agn-Er-Golgi-E10-100ul-01.interact.pep.xml
command completed in 98 sec 

running: "C:/Inetpub/tpp-bin/DatabaseParser "100214-Agn-Er-Golgi-E10-100ul-01.interact.pep.xml""
command completed in 0 sec 

running: "C:/Inetpub/tpp-bin/RefreshParser "100214-Agn-Er-Golgi-E10-100ul-01.interact.pep.xml" "c:/Inetpub/wwwroot/ISB/data/dbase/BCaRun_301013/CONCAT_Uniprot_reviewed_human_301013.fasta""
  - Searching the tree...
  - Linking duplicate entries...  - Printing results...

  - Building Commentz-Walter keyword tree...command completed in 25 sec 

running: "C:/Inetpub/tpp-bin/PeptideProphetParser "100214-Agn-Er-Golgi-E10-100ul-01.interact.pep.xml" MINPROB=0.05 ACCMASS DECOY=DECOY_"
using Accurate Mass Bins
Using Decoy Label "DECOY_".
 (X! Tandem (k-score))
adding Accurate Mass mixture distr
init with X! Tandem (k-score) trypsin 
MS Instrument info: Manufacturer: Thermo Scientific, Model: LTQ Orbitrap Velos, Ionization: nanoelectrospray, Analyzer: radial ejection linear ion trap, Detector: electron multiplier

 PeptideProphet  (TPP v4.6 OCCUPY rev 3, Build 201307241109 (MinGW)) AKeller@ISB
 read in 0 1+, 27515 2+, 20201 3+, 3650 4+, 364 5+, 0 6+, and 0 7+ spectra.
Initialising statistical models ...
Found 10795 Decoys, and 40935 Non-Decoys
Iterations: .........10.........20........
model complete after 29 iterations
command completed in 127 sec 

running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i 100214-Agn-Er-Golgi-E10-100ul-01.interact.pep.xml -d "DECOY_""
Analyzing 100214-Agn-Er-Golgi-E10-100ul-01.interact.pep.xml ...
Reading Accurate Mass Model model +1 ...
Reading Accurate Mass Model model +2 ...
Reading Accurate Mass Model model +3 ...
Reading Accurate Mass Model model +4 ...
Reading Accurate Mass Model model +5 ...
Reading Accurate Mass Model model +6 ...
Reading Accurate Mass Model model +7 ...
Parsing search results "c:/Inetpub/wwwroot/ISB/data/ER-GOLGI-experiment/E10/100214-Agn-Er-Golgi-E10-100ul-01 (X! Tandem (k-score))"...
  => Found 33382 hits. (0 decoys, 0 excluded)
  => Total so far: 33382 hits. (0 decoys, 0 excluded)
The system cannot find the path specified.
command completed in 13 sec 

running: "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/wwwroot/ISB/data/ER-GOLGI-experiment/E10/100214-Agn-Er-Golgi-E10-100ul-01.interact.pep.xml"

[David Shteynberg]

I think the results are probably there as PeptideProphet finished ok and the failing step is the step that plots the models and some performance metrics.  It might be complaining about not being able to find gnuplot on your system for generating the images.  I would suggest trying to reinstall the TPP and perhaps try the latest 4.7.0 version.  You should be able to view the results by going to Utilites->BrowseFiles and finding the file 100214-Agn-Er-Golgi-E10-100ul-01.interact.pep.xml in your directory.  Are there corresponding png files that have AccMass in their names present in that directory?

-David

--
You received this message because you are subscribed to the Google Groups "spctools-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discu...@googlegroups.com.
To post to this group, send email to spctools...@googlegroups.com.
Visit this group at http://groups.google.com/group/spctools-discuss.
For more options, visit https://groups.google.com/groups/opt_out.

[user1]

Hi David!

You are absolutelly right! The file exist (pep.xml), but I cannot open it, even via 'browse files'. I have the AccMass images in the proper directory. The protein file is not created at all.  Below you wiil find the further comunicat after the peptide and protein prophet had finshed work  (overnight, failed with code 256). Usually, I am using the option run the protein prophet directly after peptide prophet. But I have checked even the peptide prophet and again run takes too long (until it is finished by the server, due to time limit). 

Thanks a lot!

Best regards,

Agnieszka

running: "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/wwwroot/ISB/data/ER-GOLGI-experiment/E10/100214-Agn-Er-Golgi-E10-100ul-01.interact.pep.xml"

command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/wwwroot/ISB/data/ER-GOLGI-experiment/E10/100214-Agn-Er-Golgi-E10-100ul-01.interact.pep.xml" failed: Operation not permitted

command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/wwwroot/ISB/data/ER-GOLGI-experiment/E10/100214-Agn-Er-Golgi-E10-100ul-01.interact.pep.xml" exited with non-zero exit code: 1
QUIT - the job is incomplete

command "c:\Inetpub\tpp-bin\xinteract -N100214-Agn-Er-Golgi-E10-100ul-01.interact.pep.xml -p0.05 -l6 -PREC -OApu -dDECOY_ 100214-Agn-Er-Golgi-E10-100ul-01.tandem.pep.xml" failed: Operation not permitted

[user1]

How can I download 4.7. version? There are still links to the 4.6.3 as the latest at wiki webpage. Thanks!

[Jesse]

Hi all,

I am trying to use xpress to quantify peptides that have SILAC labeled
lysine and variable diglycine on lysine. When I run Xpress with the
following command:

C:\Inetpub\tpp-bin\XPressPeptideParser c:[path
removed]\UV0.all.ptmtest1.interact.ptm.pep.xml -m0.05 -nK,8.014199 -c5 -p1

Xpress incorrectly chooses whether the calculated peptide mass is
heavy/light when diglycyl-lysine or heavy lysine are present in the
peptide. (1) If the peptide only has heavy lysines and no
diglycyl-lysine, then xpress sets the calculated mass to the light. (2)
If the peptide has only light lysine and a diglycyl-lysine modification,
xpress sets the calculated mass as heavy. (3) If the peptide has both
heavy lysine and at least one diglycyl-lysine, xpress assigns the
calculated mass as the light value. (4) If the peptide contains no
diglycine and no heavy lysine.

Any help would be appreciated.

Best regards,
Jesse

--
Jesse Meyer
Graduate Student
Department of Chemistry and Biochemistry
University of California, San Diego
La Jolla, CA 92092


---
This email has been checked for viruses by Avast antivirus software.
http://www.avast.com