Thank you for uploading your raw files.
It looks like the problem is that only some of your isolation windows are overlapping with other isolation windows.
That is, the isolation windows from [395-405] all the way up to [570-580] all overlap with their neighbors.
However, after that, the isolation windows from [570-580] to [900-910] do not overlap with their neighbors.
If you want to use msconvert to demultiplex this data, you are going to need to create two separate .mzML files with the two different types of scans in them, and then use msconvert again to merge those two mzML files into one mzML file.
So, the commands I would run are:
- Tell msconvert to create a file called "overlapped.mzML" containing the demultiplexed overlapping MS2 spectra
msconvert.exe CVL31974_DIA.raw --filter peakPicking --filter "mzPrecursors [400.43188,405.43417,410.43646,415.43872,420.44101,425.44327,430.44553,435.44781,440.4501,445.45236,450.45465,455.45691,460.4592,465.46146,470.46375,475.466,480.46829,485.47055,490.47284,495.4751,500.47739,505.47964,510.48193,515.48419,520.48645,525.48877,530.49103,535.49329,540.49554,545.49786,550.50012,555.50238,560.50464,565.50696,570.50922,575.51147]" --filter demultiplex --outfile overlapped.mzML
- Tell msconvert to create a file called "regular.mzML" which contains the MS1 spectra and the non-overlapping MS2 spectra
msconvert.exe --outfile regular.mzML --filter peakPicking --filter "mzPrecursors [0,575.51147,585.51605,595.52057,605.52515,615.52966,625.53424,635.53876,645.54333,655.54785,665.55243,675.55695,685.56152,695.56604,705.57062,715.57513,725.57971,735.58423,745.58881,755.59332,765.5979,775.60242,785.60699,795.61151,805.61609,815.62061,825.62518,835.6297,845.63428,855.63879,865.64337,875.64789,885.65247,895.65698,905.66156]" CVL31974_DIA.raw
- Tell msconvert to create a file called "merged.mzML" which contains the everything from "overlapped.mzML" and "regular.mzML":
msconvert.exe --outfile merged.mzML --merge --filter sortByScanTime overlapped.mzML regular.mzML