Hi Ludovic,
I suspect a feature was added in a version between 4.1 and 4.3 or a
bug was fixed that changed the behavior of the tool under certain
execution paths through the code. With complex software it is often
difficult to pinpoint the exact change that caused the problem. The
new software
Hi David,
This is the final word on that topic...
I tracked down the guilty spectrum till the mzXML and the Thermo .raw
file => it is still there even in the thermo raw file acquired by the
Orbitrap(spectrum 10165 annotated as Charge=10 in the raw file!!).
So at the end, this was due to the Orbitr
Hi David,
Wow, thanks for having found this out. I had a look at the out files,
and there is indeed a weird 20100422_04_control_07.c.
10165.10165.10.out file in there (see the attached tgz file for
20100422_04_control_07.c). I had a quick look in the other files and
there is nothing strange like th
Hi Andreas,
I suspect this problem was only with your sequest search because of
the offending spectrum I pointed out. I've corrected the source of
PeptideProphet so it will in the future simply spit out a warning and
ignore spectra where the encoded charge doesn't match assumed charge.
For now yo
hey david,
there is another question, i would like to ask: when trying to trace the
problem we also analyzed these mzxml files with other programs such as
xtandem, mascot, and omssa. by looking at their results we did not oberserve
any suspicious behavior. hence, do you think the problem you descr
hey david,
many thanks for looking into it!
i was wondering if you could point me to a source where conditions such as
not using a '.' character in the file's basename are described because i was
not aware of that.
many thanks in advance,
andreas
On Wed, Jun 2, 2010 at 12:17 AM, David Shteynber
Hello Ludovic,
I think the problem might be in the pepXML generated in your pipeline.
The offending entry is in the file 20100422_04_control_07.c.pep.xml :
Looks like the assumed charge opf 1+ doesn't match the encoded charge
in the spectrum name (the number after the last dot "10" in this
Hello Ludovic,
Yes, I see that there is a difference in the output files. I think
the problem is that the output of probabilities and fvals is
misaligned from the spectra in the pep.xml file. You'll see that the
next spectrum has the correct value. This definitely points to a bug
in the 4.3 ver
Hi David,
No, I confirm again that I do find a difference upon running the
xinteract command with the files in different orders (I confirm I also
see those differences on TPP 4.3.1 installed on Unix and on
WindowsXP).
I have re-run the command on the same folder, on the same files, to
avoid any co
Hi Ludovic,
It is completely normal to expect some difference in the results
between version of the software since the models maybe slightly
different in new a version due to optimization, bug fixes and the
sort. Hopefully the new analysis is able to increase your correct
identifications at a set
Hi David,
TPP is installed in different servers in our Institute. I have re-
uploaded a new file (lgillet_interact-again.zip) for which the TPP
xinteract was performed on the same server and with different versions
of the TPP. You can see that the results are still very different,
even the scrambl
Hi Ludovic,
I was unable to duplicate the different results on different order of
input using the latest version of SVN tpp or version 4.3.1. I noticed
that your two analyses point to different locations. Are you sure
that the files at these locations are identical?
Thanks,
-David
On Wed, Ma
Hi David,
all my apologizes, the rar file got corrupted probably during the
upload (the original on my HD was fine).
I have uploaded again a zip file this time: lgillet_pepxml-again2.zip
I hope that works this time (after download, I can decompress it
back).
Thanks for having a look at this issue.
Hi Ludovic,
It seems the file you uploaded lgillet_pepxml_for_TPP4.3.rar is
corrupted. At least I am unable to open it. Please upload again.
Thanks,
-David
On Wed, May 19, 2010 at 2:54 AM, lgillet wrote:
> Hi David, Hi Natalie,
>
> I just posted the 4 pepxml files which give me the most striki
Hi David, Hi Natalie,
I just posted the 4 pepxml files which give me the most striking
differences in results between TPP-V4.0 and TPP-V4.3:
lgillet_pepxml_for_TPP4.3.rar. I also posted the results
(interact.pep.xml) which I obtain from running TPP-V4.0, TPP-V4.3 and
TPP-V4.3 on scrambled file ord
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