Hi Phil,
I have a 15 hek files searched with Mascot, X!Tandem and MSGF+ separately.
I am trying to create a library using TPP pipeline and SpectraST.
I have convert the results individually to pepxml using Mascot2XML,
Tandem2XML and Idconvert and then apply peptideprophet on each file. My
Hi Javan,
Many (many) years ago Thermo had a command line executable SEQUEST that
BioWorks called to run SEQUEST. Thermo put it inside hidden folders and
there were license key issues. You could not copy the EXE to another
machine and have it run. That scheme may have persisted for some of the
Javan,
You're not going to be able to run SEQUEST through the TPP unless you've
purchased the software from Thermo and have it installed on the same
computer that's running the TPP. It doesn't come with the TPP itself. And
support for the SEQUEST pipeline option should probably be removed
Confirm that you are using Comet's Percolator output which you can generate
by setting "output_percolatorfile = 1" in the search parameters. This will
create a tab-delimited text file with a ".pin" file extension. Note that
this is different than Comet's ".txt" output file which is a
Hello,
Is this running on your local machine? If so, you can see if Percolator is
still running by either opening the Task Manager (if on Windows) or
executing the "ps" command (in Linux).
Most likely, the command might have timed out due a very long running time,
and the interface (Petunia) is
Hello,
I exported a Comet search as a txt file to search with percolator and the
percolator has now been "running" for three days. When I try to kill the
job, it gives me "Unable to kill command 8760! ()." I'm guessing it's stuck
in a loop, but I was wondering what the best way of ending
