Commandline Arguments for Running msConvert CLI

Often Scaffold DIA users wish to run msConvert outside of Scaffold DIA. Reasons for this include taking advantage of times when instrument is still running but some raw files are already created; or wanting to run multiple msConvert processes in parallel.

When running msconvert.exe on Windows, Scaffold DIA calls the msConvert CLI with command structure:

msconvert.exe --mzML --mz64 --inten32 --filter "peakPicking vendor msLevel=1-" --filter "demultiplex optimization=overlap_only" --outfile test.mzML input.raw

Where --filter "demultiplex optimization=overlap_only" is used for staggered and overlapping windows. Omit this filter for non-overlapping windows:

msconvert.exe --mzML --mz64 --inten32 --filter "peakPicking vendor msLevel=1-" --outfile test.mzML input.raw

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