Using Proteowizard is highly recommended.
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.