Yes, it'll be implemented some day sooner than later just to avoid
this confusion for future users. Sorry you have to deal with the
mismatch ratios for the time being.
On Sat, Aug 6, 2011 at 8:15 PM, Oded <oded.kleif...@gmail.com> wrote:
> Hi Jimmy,
> Yes indeed it is the 13C isotope peaks option ("-p). If I set it to 0
> everything seems to be OK.
> Are there any plans implement it in the XPressPeptideUpdateParser.cgi
> as well?
> Thanks,
> Oded
>
> On Aug 6, 4:30 am, Jimmy Eng <jke...@gmail.com> wrote:
>> 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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