You might try converting the ABSciex mzML to another mzML or mzXML with the latest version of
msconvert. The ABSciex file makes heavy use of referenceable param groups and there are a few bugs
(like an incorrect spectrumList count) in it which msconvert can compensate for.
Hope this helps,
Oded,
The Xpress values you see in the pep.xml file, which means those
viewed in the PepXML Viewer, are those that are most correct based on
your run settings. What you view in the XPressPeptideUpdateParser.cgi
ideally should correspond exactly to the same numbers but they don't
in the one case
