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
wrote:
> I wonder whether these is any way possible to generate mzXML file from MGF
> file to match the scan number as that of original sc
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 distri
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
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 protei
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 n
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;
-- -
/usr/local/tpp-4-4-0/bin/xinteract -Ninteract.pep.xml -p0 -eT -l7 -D/
var/www
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 th
Hi Adam, I am forwarding your question to the spctools-discuss newsgroup,
which is the best place to post such questions. Please continue this thread
there. The first troubleshooting step I would perform is to verify that
there are msLevel="2" spectra in your mzXML file. You can text search
through
Check InsPecT source directoy. You can find 'InspectToPepXML.py
script.
Taejoon
On Nov 8, 3:34 am, ChargedPeptide 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 from Inspect that
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 from Inspect that I'm not finding in the
documentation?
A small thing but a bit of a roadblock, I'd rather avoid trying to
code a converter on my o
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