Hello,
That is quite odd; Are you able to share a pepXML file so we can
troubleshoot?  You can contact me directly to arrange a file transfer.
Thanks,
--Luis


On Tue, Oct 18, 2022 at 12:21 PM 2kl...@gmail.com <2kl...@gmail.com> wrote:

> Hi all,
>
> I am using the TPP v6.1.0 Parhelion, Build 202108271510 for analyzing
> dimethylation following Comet (or MSFragger) search with the light label
> set as fixed and the heavy mass difference as variable. Xpress settings
> include mass tolerance of 20 ppmת a Minimum number of chromatogram points
> needed for quantitation:3 and Number of isotopic peaks to sum is set to 0.
>
> When I open the interact.pep.xml file with the viewer and filter the
> results based on probability, for some of the peptides there is a
> discrepancy between the ratio shown in the pepXML and the one in the
> XPressPeptideUpdateParser. The differences can be relatively large (for
> example, 0.1 versus 1.5)
>
> Similar results are obtained if the Number of isotopic peaks to sum is
> set to 1, 2 or 3.
>
> Can you please advise?
> Many thanks,
> OK
>
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