I've used OMSSA and X!Tandem with ETD data. I get slightly different
results, but that's to be expected from different search engines. I
haven't tried X!Tandem Tornado yet, but in previous versions all you
had to do to search ETD data was specify c and z ions and exclude
a,b,x,y ions. See
Hello all-
I just discovered an issue with TPP's decoy database creation tool.
When I was adding a reverse sequence decoy database to my database,
many entries were deleted. When I went back to find out why, I
discovered that whoever had put together the database had left some
blank lines in it.
Documentation on how to modify a X!Tandem params file can be found
here: http://www.thegpm.org/TANDEM/api/index.html
On Oct 21, 2:43 am, Fournier beb...@msn.com wrote:
I would like to use X!Tandem with TPP to compare the results with
Sequest.
However, I can not create the file parameter
Do you mean search a specific database? The taxonomy file specifies
the location of a database.
The GUI automatically generates a taxonomy file based on the database
and location you specify.
If you're going to run things in command line, there are other things
you can do.
What are you trying to
your proteins of interest in a database for another
organism whose proteins should not give you any positive hits.
On Oct 21, 3:24 pm, James Broadbent james.broadb...@gmail.com wrote:
Thanks Kristian. I think my concept of databases and specifying
taxonomy is a little underdeveloped. I think what I
From the start menu, go to Control Panel, System, Advanced,
Environment Variables.
Near the end of the list is a variable called WEBSERVER_ROOT whose
value is c:\Inetpub\wwwroot
Change the c to the new drive letter. RESTART YOUR MACHINE. That
should fix it.
This was an issue on the
Do you have XCalibur installed on the machine? You have to have a
licensed version of Thermo's software installed on the machine you try
to convert on (something about their .dll libraries).
On Jul 24, 2:58 pm, Eileen Yue y...@ohsu.edu wrote:
Hello:
I tried to covert my raw file to mzxml file
Setting the time out to 0 causes the TPP to become unusable. Setting
a ridiculously large timeout works just fine.
On Jul 22, 12:52 pm, Joe Slagel jsla...@systemsbiology.org wrote:
Hi Kristian,
Deleting the line will result in Apache using the default value of 300
seconds for the timeout
Hey all-
I've seen this issue addressed in a few different threads, but I
thought I'd add my experience here.
I run Sequest searches on a Windows machine with TPP 4.2. I was
having a problem with the GUI stalling out after only completing three
or four of the searches I had queued up (that is,
Is there something I am doing wrong here? Ideally the command I would
like to run on all my files is:
xinteract -Ninteract.pep.xml -p0.05 -l9 -OAp -X-m0.15-nR,10-nK,8-L
Thanks!
Chris
On Apr 22, 3:18 pm, Luis Mendoza lmend...@systemsbiology.org wrote:
Hello Kristian,
Glad you were able
[mailto:spctools-disc...@googlegroups.com] On Behalf Of Kristian
Sent: Thursday, April 23, 2009 12:05 PM
To: spctools-discuss
Subject: [spctools-discuss] Re: Limit on number of pep.xml files that can be
analyzed with XInteract?
The globbing command doesn't seem to work for me.
When I enter
-Ndesiredfilename.pep.xml -p0.05 -l7 -Oip -X-m1.0-L -A-lC-r0.5
*.pep.xml
On Apr 22, 10:13 am, Kristian kristian.swearin...@gmail.com wrote:
I use petunia on a Windows machine, so there is no command line from
my end. I use the default settings. I'm not even sure what Eric's
post means.
Is there a line I can
I'm using the Petunia GUI of TPP 4.2.1 on a windows machine.
In the upper right corner of the results page (filenam.shtml), Protein
Prophet has button to Write Displayed Data Subset To File. When I
do this, a new page appears that says
data written to
...@systemsbiology.org wrote:
Hi Kristian,
Also, 4.2.1 contained many bug fixes. I'm not sure if this would have been
addressed, but it's always most efficient for us if you can try to replicate
the issue on the latest version.
-Natalie
On Thu, Apr 16, 2009 at 12:42 PM, Christine Vogel vogel
I'm using TPP 4.2.0 to analyze cleavable ICAT data from an LCQ. When
all replicates are done, I have 120 seperate .pep.xml files to combine
and analyze. With earlier versions of TPP (i.e. 3.4) I could analyze
them all at once with Xinteract, but with 4.2 the operation simply
aborts and fails
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