Dear David,
I recently suspect the causes of this problem with the MALDI DATA
option.
As I am using ProbID as the search engine, and use the SEQUEST
pipeline in TPP. Would this be a cause of the problem?
I use the out2XML program from the ProbID package but not the TPP one.
Also I found that the
Dear David,
I have updated the search parameter in ProbID and I have uploaded the
output files to
ftp://ftp.systemsbiology.net/incoming/melody_lam.rar
I have tried to use XTandem on this dataset and I can find about 300
proteins.
Thanks a lot for your help!
Regards,
Melody
On Oct 6, 1:10 am,
Hi David,
I've downloaded the code and build the subversion. However, the
problem still exists.
Here are some debug traces attached:
Key:
At XX\X\.h - It means the file name involved
My thoughts at indicated at the comment /* ?? */
Thanks again!
Regards,
Melody
At
Hi all,
Thanks a lot for you advices.
Here I post the output for running the peptideProphet at the command
line:
C:\Inetpub\wwwroot\ISB\data\probidoutput\ipimousexinteract -
Ninteract.pep.xml
-p0.05 -l7 -OAFm -I2 -I3 -I4 -I5 -I6 -I7 analysis100.xml
analysis125.xml analy
sis150.xml
Hi Melody,
I've tracked down and fixed the bug using the files you sent. My new
code is in the sashimi subversion code repository. Maybe someone can
build the PeptideProphetParser executable on windows and share that
with you until a new release is made available that includes this fix.
Hi all!
I have encountered the same problem. I am also using TPP v4.3.0 on
Windows XP.
The output file interact.prot.shtml and the stylesheet
interact.prot.xsl files are not found in the directory of the input
file interact.pep.xml.
However, by manually running the following line in the command
Also, consider upgrading to TPP 4.3.1, which contains several bug fixes.
-Natalie
On Sep 22, 2009, at 8:32 AM, Brian Pratt wrote:
If it's really the same problem, then it's not a surprise that those
files don't exist, since the protXML file didn't get created,
because the pepXML file
Hi everyone!
Here are some more supplementary information from the output screen of
TPP:
Command 1
c:\Inetpub\tpp-bin\ProteinProphet c:/Inetpub/wwwroot/ISB/data/
probidoutput/ipimouse/interact.pep.xml c:/Inetpub/wwwroot/ISB/data/
probidoutput/ipimouse/interact.prot.xml
I'll have a quick look at this.
Brian
On Thu, Sep 17, 2009 at 12:13 AM, YAN ms006z...@hotmail.com wrote:
Hi everyone!
Here are some more supplementary information from the output screen of
TPP:
Command 1
c:\Inetpub\tpp-bin\ProteinProphet c:/Inetpub/wwwroot/ISB/data/
It appears to have never been run though peptideProphet.
I should add a bit of logic to proteinProphet to catch that and issue a more
useful error message.
On Thu, Sep 17, 2009 at 10:52 AM, Brian Pratt brian.pr...@insilicos.comwrote:
I'll have a quick look at this.
Brian
On Thu, Sep 17,
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