Dear Natalie,
I have freshly installed TPP-4-1-1 and downloaded
7MIX_STD_110802_1.mzxml file from
http://sashimi.sourceforge.net/repository.html.
Thenafter,
Step 1. Ran tandem.exe program on 7MIX_STD_110802_1.mzxml and
generated jp.xml
Step 2. Ran the Tandem2xml program and converted jp.xml to c
Hello Ian,
I'm sorry that you're still having trouble. From your log, it looks like
you're still running with the new default minimum peptide length cutoff of
7. Or you're reprocessing results with that option, and it's sticking.
I'm seeing the " -
L'7'" flag in your output. Please try reruning
Dear Natalie and David,
I have examined the peptide IDs probabilities through pepXML viewer
and there are plenty of them with probability greater than 0.05. I
also ran xinteract specifying the -p0 flag, and again protein prophet
gives error. The command output is as follows:
[r...@localhost outp
You might have to rerun the tool specifying a minimum probability of 0
(-p0 xinteract flag)
On Mon, Dec 8, 2008 at 10:54 AM, Natalie Tasman
<[EMAIL PROTECTED]> wrote:
> Hi Ian,
>
> Can you please tell us how many peptide IDs actually pass a probability
> cutoff of 0.05 or greater (by using the pe
Hi Ian,
Can you please tell us how many peptide IDs actually pass a probability
cutoff of 0.05 or greater (by using the pepXML viewer)?
-Natalie
On Mon, Dec 8, 2008 at 9:23 AM, Ian <[EMAIL PROTECTED]> wrote:
>
> Hi Natalie,
> I am able to replicated the error with TPP 4-1-1. ProteinProphet qui
Hi Natalie,
I am able to replicated the error with TPP 4-1-1. ProteinProphet quits
abruptly. I have also tried to run xinteract with the -l1 (minimum
peptide length) option, but with no effect.
The following is the output for TPP 4-1-1:
[EMAIL PROTECTED] output_added]# ../bin/xinteract -Njp.xml
Hello Ian,
Can you replicate this with 4.1.1? You may also want to refer to the recent
posts about manually setting minimum peptide length back to 1.
Please let us know how it goes,
Natalie
On Fri, Nov 14, 2008 at 6:45 PM, Ian <[EMAIL PROTECTED]> wrote:
>
> Hi All,
> I am unable to get Pepti
