Oded,
The Xpress values you see in the pep.xml file, which means those
viewed in the PepXML Viewer, are those that are most correct based on
your run settings. What you view in the XPressPeptideUpdateParser.cgi
ideally should correspond exactly to the same numbers but they don't
in the one case mentioned previously. As discussed in this thread,
the option to sum signal from 13C isotope peaks was never implemented
in the XPressPeptideUpdateParser.cgi. So this cgi currently doesn't
sum isotope peaks in reconstructing chromatograms which accounts for
the ratio differences if Xpress was run with that option turned on.
If you don't use that option, I would hope that the Xpress peptide
ratios that you see are exactly the same across the various tools. If
this is not the case, tell me what options/settings you used in
running Xpress and I'll investigate.
I didn't test all possible settings but I did just run TPP 4.4.1
Xpress and can confirm that peptide ratios in PepXML Viewer are
exactly the same as shown in XPressPeptideUpdateParser.cgi.
- Jimmy
On Wed, Aug 3, 2011 at 10:27 PM, Oded oded.kleif...@gmail.com wrote:
Dear all,
I am using TPP for SILAC analysis of Obritrap X!tandem data (with K+8/R
+10).
I noticed some differences between the peptide Xpress values shown
thorough ProtXML viewer (XPressCGIProteinDisplayParser.cgi) and pepXML
viewer (PepXMLViewer.cgi) and those that appear in
XPressPeptideUpdateParser.cgi (which I assume are the correct ones).
These differences are usually not that big (i.e 1-5%) in some cases
can be totally off (i.e 0.1 vs 0.25).
I have got similar outputs with TPP 4.4.1 on a Mac (OS 10.6) and Win
XP.
I should mention that I run it all through the gui.
Any idea how to overcome it?
Many thanks,
Oded
-- Forwarded message --
From: Jimmy Eng jke...@gmail.com
Date: Dec 21 2010, 8:16 am
Subject: XPRESS discrepancy between PepXML viewer and XPRESS viewer
To: spctools-discuss
Oliver,
I finally had a chance to revert to 4.3.1 on two machines (linux
windows desktop), runXPRESSon an old ICAT dataset, and view the
ratios using new 4.4.1 XPressUpdateParser.cgi. On both systems I
don't see the inconsistent ratios being reported for this dataset.
Then I found some Orbi SILAC datasets which were run under 4.3.1.
Viewing the ratios chromatograms using the current 4.4.1 cgi viewer
shows the exact same ratios as calculated by 4.3.1XPRESS.
At this point, I can't replicate the discrepancy you're seeing. My
advice would be to run your analysis again and see if the discrepancy
remains. If you still see the problem, isolate a small dataset
(single lcms run) and send it to me (mzXML, pep.xml) along with
yourXPRESSrun parameters.
- Jimmy
On Mon, Dec 13, 2010 at 10:02 AM, oschill...@gmail.com
oschill...@gmail.com wrote:
Sorry for my late reply: the discrepancy occurs when viewing a TPP 4.3
analysis with TPP 4.4. We have now rolled back to TPP 4.3 to keep our
XPRESSanalysis consistent. Any advice on how to proceed in the
future?
Thanks
Oliver
On Nov 23, 5:46 pm, Jimmy Eng jke...@gmail.com wrote:
Oliver,
What parameters did you use to runXPRESS? The GUI showing elution
profiles has no current support for the isotope option (summed
intensities of first N isotope peaks) but otherwise should return the
same ratios as that shown in the pepXML file.
- Jimmy
On Mon, Nov 22, 2010 at 5:09 AM, oschill...@gmail.com
oschill...@gmail.com wrote:
Dear TPP community,
we notice a small discrepancy between theXPRESSvalues displayed in
the PepXML viewer tab (table withpeptidesequences etc) and the
XPRESStab (graphic display of elution peak). For almost all peptides,
we observe slightly differentXPRESSvalues in both tabs. For example,
apeptidehas anXPRESSvalue of 2.32:1 in the PepXML viewer and
2.27:1 in theXPRESSviewer.
Our impression is that this discrepancy occurs as of TPP 4.4.1 and
does not occur for TPP 4.3.x.
Can anyone please advice us on how to proceed here?
Thanks a lot
Oliver
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