Using Proteowizard is highly recommended.
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If you are using GUI of Proteowizard, please set the parameters according to the screenshot below.
Note: the “peak Picking” parameter has to be set as the first filtering condition to ensure the centroiding works properly. -
If you are using docker version of Proteowizard, please use the following command to run the conversion:
docker run -it --rm -e WINEDEBUG=-all -v /YOUR/ABSOLUTE/DATA/DIR/:/data chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert *.raw --mzML --filter "peakPicking true 1-" --filter "zeroSamples removeExtra" --filter "msLevel 1" --64 --zlib
Note: Please modify “*.raw” based the extension of your vendor MS files.