Convert raw MS data
Raw mass spectrometry data need to be converted to centroid mzML or mxXML format for MassCube data processing.
We recommend to use MSConvert for file conversion.
Visit the official website to download ProteoWizard and install MSConvert.
Step 1. Set options
Check the boxes as shown in Fig. 1.
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Do NOT check Use zlib compression.
Step 2. Set the peak picking filter
Step 3. Add the peak picking filter
Step 4. Browse and load files
Step 5. Start conversion
By default, the converted files will be saved in the same directory as the raw files.