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,
OdedOn Aug 6, 4:30 am, Jimmy Eng <[email protected]> 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 <[email protected]> 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 <[email protected]> > > 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, [email protected] > > > <[email protected]> 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 <[email protected]> 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, [email protected] > > >>> <[email protected]> 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 > > >>> > -- > >>> > You received this message because you are subscribed to the Google > >>> > Groups "spctools-discuss" group. > >>> > To post to this group, send email to [email protected]. > >>> > To unsubscribe from this group, send email to > >>> > [email protected]. > >>> > For more options, visit this group > >>> > athttp://groups.google.com/group/spctools-discuss?hl=en. > > >> -- > >> You received this message because you are subscribed to the Google Groups > >> "spctools-discuss" group. > >> To post to this group, send email to [email protected]. > >> To unsubscribe from this group, send email to > >> [email protected]. > >> For more options, visit this group > >> athttp://groups.google.com/group/spctools-discuss?hl=en. > > > -- > > You received this message because you are subscribed to the Google Groups > > "spctools-discuss" group. > > To post to this group, send email to [email protected]. > > To unsubscribe from this group, send email to > > [email protected]. > > For more options, visit this group > > athttp://groups.google.com/group/spctools-discuss?hl=en. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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