The main window of RATIO. Upon loading of MS data, analytes are first automatically recognized and assigned (A). When necessary, manual assignment of analytes is performed in a different window. The experimental parameters are set by the user (B), then MDVM (C) and flux ratios (D) are calculated. Abnormal residuals indicate that the corresponding fragments are outlier, and they can be excluded (white) or reactivated (blue) by a single mouse click on the corresponding bar. Finally, the flux ratios, the MDVA and the MDVM are exported to a text file or Excel workbook (E).