The Tandem2XML program will try to read each scan's retention time
from the mzXML and add it to the resulting pep.xml. If not it can't
find the mzXML file, it issues the warning and leaves out the
retention time.
This warning does imply that the standard TPP convention of expected
files and filen
Oh, whoops, silly me. Since it said that it couldn't open the file, I
assumed it never created the pepXML file. Thank you for those points
though.
So then what is it upset about? Is it trying to open the mzXML file in
addition to the output xml file?
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