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.