Converting raw data to mzML

We recommend using msconvert to convert raw data generated from the different instruments to mzML format. Files can be converted from a GUI or from the command line. To convert all the files with names ending in .RAW inside a directory from the command line the following command can be used:

msconvert *.RAW -o my_output_dir

If you are using a Waters instrument with lockspray correction, the scanEvent filter can be used to remove the signal from the lockspray.

msconvert *.RAW --filter "msEvent 1" -o my_output_dir

To perform feature detection, data must be provided in centroid format. This can be done using the peakPicking filter option:

msconvert data.RAW --filter "peakPicking cwt snr=1 peakSpace=0.01"

A snr=1 is recommended as noisy peaks will be removed during feature detection anyway. peakSpacing should be chosen according to the instrument used. For QTOF instruments a value of 0.01 is recommended, but for higher resolution instruments, such as orbitrap or FT-ICR, lower values may be used.