Hydrogen ions vs protons 

"Hydrogen ion is recommended by the International Union of Pure and Applied Chemistry as a general term for all ions of hydrogen and its isotopes" - see Hydrogen ion. A Google search reveals that considerably more botanical articles use ions and ion flux in preference to protons. H+ denotes the provenance of the ion as being from Hydrogen, whereas proton is a sort of Deus ex machina with no hint as to where it originated.