Oliver, I finally had a chance to revert to 4.3.1 on two machines (linux & windows desktop), run XPRESS on 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 4.3.1 XPRESS.
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 your XPRESS run 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 > XPRESS analysis 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 with peptide sequences etc) and the >> >XPRESStab (graphic display of elution peak). For almost all peptides, >> > we observe slightly differentXPRESSvalues in both tabs. For example, >> > a peptide has 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 spctools-disc...@googlegroups.com. >> > To unsubscribe from this group, send email to >> > spctools-discuss+unsubscr...@googlegroups.com. >> > 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 spctools-disc...@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com. > For more options, visit this group at > http://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 spctools-disc...@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
