Thank you for sending that data file.
Skyline is choking while trying to read the total ion current (TIC) chromatogram.
The TIC chromatogram has more points in it than the total number of spectra, which causes Skyline to crash when Skyline tries to figure out which of the TIC points came from MS1 or MS2 spectra.
You can work around this bug by using ProteoWizard MSConvert.exe to convert your .d folder to .mzML.
You will need to invoke MSConvert from the command-line, because you need to tell MSConvert to not try to read the chromatograms.
The command-line that I used was:
msconvert.exe --chromatogramFilter "index 100" 20231208_PepMix_300nL_09_1_1_4358.d
The '--chromatogramFilter "index 100"' is the thing that tells MSConvert not to read any chromatograms (specifically, it says to only read the 100th chromatogram, but, because there is no 100th chromatogram, it causes it to skip all of the chromatograms).
Thank you for reporting this bug. I will ask some of my coworkers and see if anyone can fix this bug.
-- Nick |