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?
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