1.) Convert .raw to .mzML (MS) Put all 96 .raw files in a specific folder. Run the ThermoFischerParser (https://github.com/compomics/ThermoRawFileParser/releases) code (included in the Jupyter Notebook File) (change input and output dir as desired and change parser path to where your parser is stored)
2.) Convert .mzML to .csv (UV) Install RaMS for RStudio (https://github.com/wkumler/RaMS) Run following R code in RStudio
Change directory to where your .mzML files are stored
3.) Run Code Run ‘MSProcessing_072024_York.ipynb’ notebook. Note: requires a csv file with names of all files and the target masses.