Final answer:
The most suitable method to separate the two subunits of the botulinum protein is size-exclusion chromatography, which separates proteins based on their size, allowing for the differential fractionation of the subunits.
Step-by-step explanation:
The easiest method to separate the two subunits of the botulinum protein for subsequent analytical purposes would be size-exclusion chromatography (D). This method relies on the size difference between protein subunits to fractionate them and is particularly useful in separating proteins of different sizes. Size-exclusion chromatography, unlike gas chromatography or mass spectrometry, is designed specifically for this purpose, as it allows for the separation of macromolecules in a sample according to their size. The technique involves a stationary phase with pores of different sizes that allow smaller molecules to enter, while larger molecules are excluded and elute earlier. This is an effective way to separate protein subunits without the need for conversion to volatile compounds as in gas chromatography or the need for ionization and analysis of molecular fragments as in mass spectrometry.