msconvert
msconvert is a command line tool for converting between various file formats.
Examples:
msconvert
(prints usage information)
msconvert data.RAW
(creates data.mzML in current directory)
msconvert data.RAW --mzXML
(creates data.mzXML in current directory)
msconvert *.RAW -o my_output_dir
(converts all files matching *.RAW to mzML, output files created in my_output_dir
)
msconvert data.RAW --zlib --filter "peakPicking true [2,3]"
(use zlib compression for binary data arrays, and use vendor centroiding for msLevels in [2,3])
msconvert data.RAW --filter "msLevel 2"
(only write ms2 scans)
msconvert data.RAW --filter "msLevel 2-"
(only write ms2 and higher scans)
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