As an alternative to direct analysis of nucleic acids, mass spectrometry can also be used to detect nucleic acids indirectly through the use of cleavable mass tags, which avoids many of the limitations of direct analysis of nucleic acids while also offering numerous advantages such as ease of multiplexing, more robust detection of tag species and higher sensitivity and less demanding workup and sample preparation for analysis. Mass spectrometric analysis of mass tags, by ESI or MALDI also offers the possibility of accurate quantification through the use of isotopic tags. This capability of mass spectrometry has not really been exploited in genomic analysis but has been quite widely used in proteomic analysis (17) (18) (19) and is a key advantage of the mass spectrometric approach.