DIA can't demultiplex

DIA can't demultiplex wendy white  2020-06-18 11:35:55
I made a DIA overlap method on the instrument- but when I use MS Convert GUI, it fails and reports this error:
Opening file "C:\Users\WHITEW01\Desktop\Histones\2020_0617_histones.raw" for read...
Calculating SHA1 checksum...
Writing "C:\Users\WHITEW01\Desktop\Histones\2020_0617_histones.mzML"...
Failed - System.Exception: SpectrumToIndices() Number of demultiplexing windows changed. Minimum window size or window boundary tolerance may be set too low.
   at pwiz.CLI.msdata.MSDataFile.write(MSData msd, String filename, WriteConfig config, IterationListenerRegistry iterationListenerRegistry)
   at MSConvertGUI.MainLogic.processFile(String filename, Config config, ReaderList readers, Map`2 usedOutputFilenames)
   at MSConvertGUI.MainLogic.Go(Config config, Map`2 usedOutputFilenames).
Nick Shulman responded:  2020-06-18 11:49:12
Someone else ran into this error a few months ago, and was able to work around it by passing a "minWindowSize" to the demultiplex filter. (You probably have to use the msconvert.exe command line tool in order to be able to specify this, instead of the GUI).

You can read about that other support request here:

This other person was running into the error because their DIA windows had margins that overlapped with each other, and specifying the minWindowSize would tell msconvert to ignore those margins and not treat them as DIA windows that needed to be deconvoluted into separate scans.

I am not sure whether this fix would work for your data. If not, you can try sending us your .raw file and we can see what can be done.
You can upload that .raw file here:
or if that file is already on Panorama you can just tell us where to find it.
-- Nick