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 at http://groups.google.com/group/spctools-discuss?hl=en.
