Hi David!
I played with the fragment mass tolerance but I am still having the issue.
However I searched the problematic files with TPP's X!Tandem (instead of
GPM's) and it worked perfectly with Peptide Prophet! Is there a linux
version of it which I can use on the cluster or is it just usable
Thanks David!
Let me try lowering fragment mass error. I will let you know about the
outcome.
Well, we already had the Proteome Discoverer results and we really want to
create the spectral library asap, so I was given those results to use
instead of X!Tandem. and I have never worked with
The TPP is not tested to work with ProteomeDiscoverer pepXML. Sure you can
send me a sample file, but it may take some time to implement support for
this type of data. Comet is open source and easy to use out of the box.
Why don't you try that route?
-David
On Wed, Oct 12, 2016 at 3:24 PM, Ali
Dear David
Thank you very much! You were right, the problem was with X!Tandem. I
decided do the searches with Proteome Discoverer. I exported the results to
pep.xml (from .msf) using PD but now the results don't work with
PeptideProphet. I can open them in PepXMLViewer but as I said in another
My suspicion regarding the Tandem failure is the fragment mass tolerance.
I am observing fragment mass differences of much less than 0.05 daltons,
yet your Tandem search uses 0.5 daltons as the tolerance. Could GPM-tandem
be having a problem there? Can you try to lower the fragment mass
Hi Ali,
I searched your data with Comet and PeptideProphet got valid PSMs in the
analysis that failed to produce correct results from your GPM-version of
tandem on the same data. The problem in your dataset is the Tandem
search. Attached are the comet parameters I used to search your data.
Dear Waovoo
This is an old post but I thought may be you could help me. I have Proteome
Discoverer v2.0 exported pep.xml and it is not working with PeptideProphet.
How did you analyze your results with PeptideProphet?
Thank you very much,
Ali
On Wednesday, August 19, 2015 at 1:54:13 PM UTC-4,
