A bit late for a response, but I was also experimenting with QualScore and encountered the same issue, where I'm also getting NaN coefficients and 0 dtas.
After debugging the QualScore source code from
here, the issue seems to be with their custom mzXML parser class (org.isb.mzxml.MzXMLParser.java).
It looks like the bug occurs when the code tries to parse the encoded mz_intensity list of a scan from the MzXML file.
In the function MzXMLParser.convertMassList(), the code assumes that the mz and intensity values are encoded in a 32-bit single-precision binary floating-point format, which would work fine if that's the format of your MzXML file.
However, in my raw file at least, the mz_intensity values are encoded in 64-bit precision doubles, so the incorrect parsing ends up converting the mz and intensities to very small values, which is probably what led to the NaN coeffs and 0 dtas further down the line.
I couldn't figure out how to convert my mzXML file such that it encodes mz and intensity in 32-bit precisions instead of 64-bit (even the --mz32 --inten32 options from ProteoWizard's msconvert don't seem to do the job), which is probably the easier way to solve this issue.
So, I ended up modifying the source code to make it parse the file as 64 bits precision doubles instead, as shown in the screenshot below, which solved the NaN and 0 dta issue for me.
The modification was made in the convertMassList() function and the endElement() function, both under the MzXMLParser.java class mentioned above.
Hope this might help.
Best regards,
Yun-En Chung