Xpress-related Discrepancy between pepXML and XPressPeptideUpdateParser.

[2kl...@gmail.com]

Hi everybody,In reference to my report from 2022 (https://groups.google.com/g/spctools-discuss/c/BHES_8aAWnA/m/d11lND0nBwAJ), we continue to observe discrepancies between the ratios displayed in the pepXML and those obtained after using the XPressPeptideUpdateParser to visualize the peaks. These discrepancies are sometimes significant (e.g., a ratio of 0.1 in the pepXML versus 1.5 in the XPressPeptideUpdateParser), and in certain instances, no ratio is reported in the pepXML, whereas a definite ratio is observed with the XPressPeptideUpdateParser.

We are currently utilizing TPP v6.3.2 Arcus, Build 202305092202-8951, and our analysis involves dimethylation following a Comet search. In this setup, the light label is set as fixed and the heavy mass difference as variable. Our Xpress settings are configured with a mass tolerance of 20 ppm, a minimum requirement of three chromatogram points for quantitation, and the number of isotopic peaks to sum is set to 0. It is noteworthy that altering the number of isotopic peaks to sum (whether set to 1, 2, or 3) does not affect the ratios in the pepXML, and similar results are obtained regardless of this setting.

Can you please advise?
Many thanks,
OK