Dear All,
I have generated mgf file from the mzXML file
(OR20080317_S_SILAC-LH_1-1_01.mzXML) which is one of the input file used by
TPP team while presenting TPP tutorials during HUPO 2010 conference.
I run omssa search against it.
Then I have used following parameters in running PeptideProphet and
ProteinProphet with ASAPRatio
In the “PeptideProphet Options” pane select to “Use accurate mass binning”
In the “ASAPRatio Options” section .
1. “Labeled Residues” to K and R,
2. Then I set “m/z range to include in summation of peak:” to 0.05.
3. “Specified masses:” to M 147.035, K 136.10916 and R 166.10941.
4. Check box option “Use fixed scan range”.
*I was able to run PeptideProphet and ProteinProphet without any error
message on the screen,
*
------------------------------------------------------------------------------------------------------------------------------------------------------------
xinteract Command Line*/home/APCF/tpp/bin/xinteract
-Njagan-J1772.pepprophet.xml -eT -d'sp|decoy' -p0.05 -l7 -x20 -R -OAP
-A-s-lRK-F-r0.05-mM147.035K136.10916R166.10941---- jagan-J1772.pep.xml
*ProteinProphet
Command Line*/home/APCF/tpp/bin/ProteinProphet jagan-J1772.pepprophet.xml
jagan-J1772.prot.xml ASAP_PROPHET ;
-------------------------------------------------------------
*
*I am here with enclosing STDOUT and STDERR messages ...*
------------------------------------------------------------------------------------------------------------------------------------------------------
Stdout of TPP for jagan-J1772
Archive: /home/APCF/results/omssa/2011-01-31/jagan-J1771.zip
inflating: ./jagan-J1771/jagan-J1771.omx
Reading jagan-J1772.omx as XML
/home/APCF/tpp/bin/xinteract (TPP v4.4 JETSTREAM (unstable development
prerelease) rev 0, Build 201007011135 (linux))
running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/InteractParser
'jagan-J1772.pepprophet.xml' 'jagan-J1772.pep.xml' -P -L'7' -E'trypsin'"
file 1: jagan-J1772.pep.xml
processed altogether 8138 results
results written to file
/mnt/sanfs/APCF-PROD/results/tpp/2011-01-31/jagan-J1772.pepprophet.shtml
command completed in 6 sec
running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/PeptideProphetParser
'jagan-J1772.pepprophet.xml' DECOY='sp|decoy' MINPROB=0.05 EXTRAITRS=20
ACCMASS NONPARAM"
using Accurate Mass Bins
Using Decoy Label "sp|decoy".
Using non-parametric distributions
(OMSSA)
WARNING!! The discriminant function for OMSSA is not yet complete. It is
presented here to help facilitate trial and discussion. Reliance on this
code for publishable scientific results is not recommended.
adding Accurate Mass mixture distr
init with OMSSA trypsin
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization:
UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN
Initialising statistical models ...
Iterations: .........10.........20......
model complete after 27 iterations
command completed in 12 sec
running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/ProphetModels.pl -i
jagan-J1772.pepprophet.xml -d 'sp|decoy'"
Analyzing jagan-J1772.pepprophet.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
"/mnt/sanfs/APCF-PROD/results/tpp/2011-01-31/jagan-J1772 (OMSSA)"...
=> Total of 1485 hits.
command completed in 1 sec
running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/ASAPRatioPeptideParser
'jagan-J1772.pepprophet.xml' -s -lRK -F -r0.05
-mM147.035K136.10916R166.10941 - - - -"
command completed in 63 sec
running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/DatabaseParser
'jagan-J1772.pepprophet.xml'"
command completed in 0 sec
running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/RefreshParser
'jagan-J1772.pepprophet.xml'
'/mnt/sanfs/APCF/databases/SwissProt/decoy_uniprot_sprot_generic.fasta'"
- Searching the tree...
- Linking duplicate entries... - Printing results...
command completed in 19 sec
running: "/mnt/sanfs/APCF/APCF_WEB/tpp/cgi-bin/PepXMLViewer.cgi -I
/mnt/sanfs/APCF-PROD/results/tpp/2011-01-31/jagan-J1772.pepprophet.xml"
command completed in 1 sec
/mnt/sanfs/APCF/APCF_WEB/tpp/bin/InteractParser 'jagan-J1772.pepprophet.xml'
'jagan-J1772.pep.xml' -P -L'7' -E'trypsin' 6 sec
/mnt/sanfs/APCF/APCF_WEB/tpp/bin/PeptideProphetParser
'jagan-J1772.pepprophet.xml' DECOY='sp|decoy' MINPROB=0.05 EXTRAITRS=20
ACCMASS NONPARAM 12 sec
/mnt/sanfs/APCF/APCF_WEB/tpp/bin/ProphetModels.pl -i
jagan-J1772.pepprophet.xml -d 'sp|decoy' 1 sec
/mnt/sanfs/APCF/APCF_WEB/tpp/bin/ASAPRatioPeptideParser
'jagan-J1772.pepprophet.xml' -s -lRK -F -r0.05
-mM147.035K136.10916R166.10941 - - - - 63 sec
/mnt/sanfs/APCF/APCF_WEB/tpp/bin/DatabaseParser 'jagan-J1772.pepprophet.xml'
/mnt/sanfs/APCF/APCF_WEB/tpp/bin/RefreshParser 'jagan-J1772.pepprophet.xml'
'/mnt/sanfs/APCF/databases/SwissProt/decoy_uniprot_sprot_generic.fasta' 19
sec
/mnt/sanfs/APCF/APCF_WEB/tpp/cgi-bin/PepXMLViewer.cgi -I
/mnt/sanfs/APCF-PROD/results/tpp/2011-01-31/jagan-J1772.pepprophet.xml 1 sec
job completed in 102 sec
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the
original Perl by A. Keller (TPP v4.4 JETSTREAM (unstable development
prerelease) rev 0, Build 201006071455 (linux))
(xml input) (ASAPRatio) (report Protein Length) (using degen pep info)
. . . reading in
/mnt/sanfs/APCF-PROD/results/tpp/2011-01-31/jagan-J1772.pepprophet.xml. . .
. . . read in 0 1+, 994 2+, 491 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min
prob 0.05
. . . importing ASAPRatio protein ratios . . . and pvalues . . .
Analyzing jagan-J1772.prot.xml ...
Stderr of TPP for jagan-J1772#script file generated by tpp-submit.pl.
Created at Mon Jan 31 15:07:13 2011
# ----------This ia a OMSSA->Prophets Job----------
#step -1: try and change protections on apcf output files
#step 0: update db with time of start of job running
ssh search.apcf.edu.au /var/www/APCF_WEB/APCF/job-start.pl jagan-J1772
#step 1: cd to the result dir so we can see mzXML file
cd /home/APCF/results/tpp/2011-01-31
/usr/bin/unzip /home/APCF/results/omssa/2011-01-31/jagan-J1771.zip
jagan-J1771/jagan-J1771.omx -d .;
/bin/mv jagan-J1771/jagan-J1771.omx .;
/bin/rm -rf jagan-J1771
/bin/ln jagan-J1771.omx jagan-J1772.omx;
/bin/ln: creating hard link `jagan-J1772.omx' to `jagan-J1771.omx': File
exists
/home/APCF/omssa-2.1.9.linux/omssa2pepXML -o jagan-J1772.pep.xml
jagan-J1772.omx;
# step 2: set the viewing for the input pepxml file
echo '' >jagan-J1772.pep.shtml
echo '' >>jagan-J1772.pep.shtml
echo '' >> jagan-J1772.pep.shtml
echo '' >> jagan-J1772.pep.shtml
echo '' >> jagan-J1772.pep.shtml
echo '' >> jagan-J1772.pep.shtml
echo '' >> jagan-J1772.pep.shtml
#step5: call peptideProphet
/home/APCF/tpp/bin/xinteract -Njagan-J1772.pepprophet.xml -eT -d'sp|decoy'
-p0.05 -l7 -x20 -R -OAP -A-s-lRK-F-r0.05-mM147.035K136.10916R166.10941----
jagan-J1772.pep.xml
PeptideProphet (TPP v4.4 JETSTREAM (unstable development prerelease) rev 0,
Build 201007011135 (linux)) AKeller@ISB
read in 3 1+, 3624 2+, 4366 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra.
Found 2186 Decoys, and 5807 Non-Decoys
WARNING: Mixture model quality test failed for charge (1+).
WARNING: Mixture model quality test failed for charge (4+).
WARNING: Mixture model quality test failed for charge (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
Warning: empty y range [0:0], adjusting to [0:1]
Warning: empty y range [0:0], adjusting to [0:1]
plot "jagan-J1772.pepprophet_IPPROB.tsv" using 2:1 title "iProphet" with
line lc 2 , x notitle with line lt 0 lc -1
^
"jagan-J1772.pepprophet_IPPROB.gp", line 16: warning: Skipping data file
with no valid points
- Building Commentz-Walter keyword tree...#rm jagan-J1772.dat
#step5A: call proteinProphet
/home/APCF/tpp/bin/ProteinProphet jagan-J1772.pepprophet.xml
jagan-J1772.prot.xml ASAP_PROPHET ;
INFO: mu=8.22677e-07, db_size=733092553
/home/APCF/tpp/bin/ProtProphModels.pl -i jagan-J1772.prot.xml;
------------------------------------------------------------------------------------------------------------------------------------------------------.
*
I am able to view ASAPRatio from the pepXML file generated after running
PeptideProphet without any issues.*
*I am also able to view pvalue curve from the ProteinXML Viewer but when I
click ASAPRatio pointer, I get an error message "error" without any details.
I wonder whether anyone has any idea what is going on here. I am here with
enclosing the snap-shot for your ready reference.
*
with regards,
--
Dr. Jagan Kommineni
Systems Administrator and Duty Programmer
Australian Proteomics Computational Facility
Ludwig Institute for Cancer Research,
6th Floor, Royal Melbourne Hospital,
Royal Parade, Parkville, Victoria
Ph:03 9341-3177.
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