Check InsPecT source directoy. You can find 'InspectToPepXML.py
script.
Taejoon
On Nov 8, 3:34 am, ChargedPeptide malm.e...@gmail.com wrote:
Hello everyone, this one's a simple one, is there an established
script to get Inspect output into a pep.xml format or is there a
pep.xml output option
Jagan,
Hopefully searches run as in steps 1 through 4 have no issues with
visualizing the spectra.
Regarding points 6 and 7, I can't tell you definitely why there's a
difference in scan counts without knowing specifics of how the MGF was
created. If I had to guess, one thing that accounts for
Hi,
I've been struggling to run PeptideProphet on phenyx generated pepXML
files.
The error I get from PeptideProphet is read in no data. Full output
from the tool is as follows;
-- BEGIN COMMANDLINE OUTPUT-
/usr/local/tpp-4-4-0/bin/xinteract -Ninteract.pep.xml
Did you extract ALL the files from the pwiz-bin package to the same directory?
-Matt
On 11/5/2010 8:40 PM, tgreco wrote:
I was having same problem with msconvert as described above (on
windows 7 64-bit). I installed MSfilereader and newest Proteowizard
package (to tpp-bin) as suggested. But
Phenyx search results can only be processed with the semi-parametric
modeling based on decoys. Judging from name of your database, it does
have decoys in there. Now you must tell PeptideProphet to use the
semi-parametric model with xinteract option -OP and the decoy tag that
all your decoy
Thanks for your quick response.
I've modified my command to
/usr/local/tpp-4-4-0/bin/xinteract -Ninteract.pep.xml -p0 -eT -l7 -D/
var/www/ISB/data/Databases/OnMascot/SPHuman/
sphuman_20101013_DECOY.fasta -OdP -ddecoy 206_pepxml.xml
(also tried without the -Od option).
Unfortunately I still get
Dear Jimmy,
Thanks for your detailed information. It looks like file conversions from
RAW-mzXML with msconvert and mzXML-mgf with your mzXML2Search.exe
performed as expected.
I have used this mgf file to perform OMSSA search and then pepXML file has
generated with omssa2pepXML from OMSSA
As far as I'm aware, there's no tools that can do this. Hopefully others
can chime in if they know otherwise.
On Mon, Nov 8, 2010 at 7:59 PM, Jagan Kommineni
jagan.kommin...@gmail.comwrote:
I wonder whether these is any way possible to generate mzXML file from MGF
file to match the scan
