how to convert a thermo raw file in matlab

To convert Thermo Raw files in Matlab, we can use the mzXML function provided by the ProteoWizard toolbox. This function is capable of reading and converting Thermo Raw files into mzXML format, which can be easily read into Matlab. Here's how you can do it:

1. First, make sure that you have installed the ProteoWizard toolbox in Matlab. You can download it from here: https://proteowizard.sourceforge.io/download.html

2. In Matlab, add the ProteoWizard folder to your path. You can do this by running the following command in the Command Window:

main.m
addpath('/path/to/ProteoWizard');
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Replace /path/to/ProteoWizard with the actual path to the ProteoWizard folder on your system.

3. Now, let's convert the Thermo Raw file to mzXML format. Assuming that your Thermo Raw file is named myfile.raw, run the following command in the Command Window:

main.m
mzXML('myfile.raw');
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This will create a new file named myfile.mzXML in the same directory as myfile.raw.

4. Finally, let's read the mzXML file into Matlab. We can use the mzxmlread function provided by the ProteoWizard toolbox. Here's how you can use it:

main.m
[data, headers] = mzxmlread('myfile.mzXML');
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This will read the mzXML file into the data variable and the headers into the headers variable. You can now use these variables to analyze the data as per your requirements.

Note: The ProteoWizard toolbox supports many other file formats as well, not just Thermo Raw files. You can use the same approach to convert and read other types of mass spectrometry data files too.