In this paper, studies on electrospray ionisation ion trap mass spectrometry of organophosphates are extended to a series of dimethyl methylphosphono and trimethyl phosphoro thionates and thiolates and some deuterated isotopomers. Of particular, interest is the comparison of the collision-induced fragmentation of ions from these compounds with those of the non-sulphur containing analogues reported previously. The thiono and thiolo isomeric structures of the sulphur containing ions analogous to I and II (see below) have very similar energies and undergo a ready interconversion. In the case of the phosphono compounds, the electronic structure calculations show that the methyl migration implicit in thiono-thiolo interconversion occurs directly and although methyl migration from P to the phosphonyl O or phosphonothionyl S can occur, the transition state (TS) energies are somewhat higher and, in the case of the migration to O, too high to take part in any of the subsequent collision induced fragmentations. With one exception, the mechanisms proposed for some of these fragmentations are supported by electronic structure calculations at the DFT-B3LYP level.