convert thermo raw file to a .mat in matlab

To convert a Thermo RAW file to a MATLAB .mat file, you can use the msconvert tool from the ProteoWizard package. Here's an example command to run in the command prompt:

main.m
msconvert <input_file>.raw -o <output_directory> --mzXML --32 --zlib --mzInterval 0.1- --filter "threshold count 1000 most-intense" --outfile <output_file>.mat
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This command will convert the input_file.raw to mzXML and use ProteoWizard's peak picking algorithm to filter out low-intensity peaks. It also specifies a mzInterval of 0.1, meaning the .mat file will use 0.1 Da-wide bins. Finally, it outputs the .mat file to the specified output_directory with the specified output_file name.

Note that ProteoWizard must be installed and added to your system's PATH environment variable for this command to work. Once the conversion is complete, you can load the .mat file into MATLAB using the "load" command.