A key feature of the Tandem Nucleic acid mass Tag design is the ease with which large numbers of chemically identical, isotopomeric tags can be made (Figure 3) . Sets of TNT isotopes should have almost identical behaviour in analytical separations (17) and during the ionization process. This means that it should be possible to use these tags to accurately quantify their associated oligonucleotide sequences as the ratios of the intensities of the TNT isotopomer fragments should reflect the ratios of the concentrations of the probes in solution or hybridized on their targets ( Figure 5 ). To demonstrate this feature of the TNT design, various experiments were conducted. In these experiments, pairs of TNT-PNA conjugates are analysed by ESI-MS/MS, where the parent tag ions are cleaved from their probes in the ESI ion source using a cone voltage of 25 V. The cleaved parent tag ions are subsequently selected from background by gating both 387.3 and 388.3 ions with the first quadrupole of the Q-TOF instrument. The gated parent tag ions are then subjected to CID in the second quadrupole of the Q-TOF instrument using a collision energy of 25 V followed by mass separation and detection in the TOF analyser to determine the ratios of the tag pairs. In the first set of experiments, pairs of TNT-PNA oligonucleotide probes of the same length and sequence, but with different tags were mixed in a predefined ratio and diluted to determine how well the ratios are conserved as the concentration of probes is decreased. Results are shown in Figure 6 . It can be seen that the ratios of the isotopic TNT-PNA probes are conserved over the range of concentrations investigated.