I stumbled on this one on accident just now looking for a cool Shiny App I use online for generating pretty bar plots for Metabolomics data.
If you've got a Thermo instrument up to the mid-generational Q Exactives, you can probably find an old copy of Raw Meat somewhere. It was from a great little software company that some big corporation purchased and killed all their products.
RawBeans is the Python GUI app that I use that you can find multiple entries on the blog about.
If you prefer Shiny for whatever reason, RawHummus is next in line. It was designed for Metabolomics QC, but I don't see why you couldn't use it for any instrument experiment once you've converted your data to a universal format. You can read about it here. Or run an online instance of it here!