The error that you are getting is:
error reading spectrum controllerType=0 controllerNumber=1 scan=20342
This error is caused by a corrupted scan in the .raw file. If you look at that scan in Qualbrowser, you will see that the scan looks completely blank, but the reported total ion current of that spectrum is not zero.
What you need to do is use ProteoWizard msconvert.exe to create a .mzML file with that scan removed from it.
The commandline for msconvert.exe to skip over scan number 20342 would be something like:
msconvert.exe -v -z SureQuantRetinoid_Heavy+Light_Lumos_IC_NewMetNewSample-dilute1000x.raw --filter "peakPicking true 1-" --filter "index 1-20341 20343-"
(the -- filter "peakPicking true 1-" is there to tell msconvert to centroid the spectra. The other filter with the "index" is the one that causes it to skip over scan #20342)
It is possible that you may have more than one corrupt scan in the .raw file. If that is the case msconvert will give you a new error with a new scan number. Then, you will have to run msconvert with a different command line where the list of index ranges skips over this new scan number in addition to skipping over scan #20342.
When ProteoWizard reads a corrupted scan, that puts the process memory in a bad state, and it is necessary to exit Skyline in order to safely continue. This is why Skyline cannot simply skip over these corrupted scans, and they have to be removed before Skyline can process the file.
I hope this works for you. If you need more help, you can send us that problematic .raw file. You can upload that file here: