The details of the reaction are somewhat beyond the scope of this article; essentially, normal cytosine has a C=C double bond which is sensitive to addition of a sulfate group from the bisulphite ion; this sulfate group weakens the exocyclic amine group and leads to its hydrolytic loss, thereby replacing the -NH2 with =0, which defines the difference between cytosine and uracil bases.
For our purposes, the effect of bisulphite treatment on a methylated versus unmethylated DNA sequence can be summarized in Figure 1.
The bisulphite treatment has therefore (at least on paper) neatly distinguished the two forms--methylated and unmethylated--of our target sequences of interest, in the form of differing DNA template molecules suitable for a range of downstream analytical methods capable of determining which template we have.
In this version of the approach, following bisulphite modification, we'd use PCR with primers flanking the methylation site of interest to generate sufficient amounts of template for sequencing by either Sanger methods or pyrosequencing.
The answer is one could, if enough of a uniform DNA fragment containing the site of interest were available to feed into the mass spectrometer; however, generally this is not the case, so bisulphite treatment and PCR is needed to generate this uniform flanking fragment).