A brief experiment to determine whether there were any obvious size dependent effects on the efficiency of the cleavage of the TNT from the TNT-PNA conjugate during electrospray ionisation was carried out. In this experiment, pairs of TNT-PNA oligonucleotides of different lengths were mixed together in 1:1 concentrations. It might be expected that the larger TNT-PNA probes would fragment somewhat less easily due to their greater size and the consequent ability to dissipate kinetic energy from collisions over many more different modes of vibration. This would mean that the larger probes should be detected with less sensitivity. It turned out that the larger sequences gave slightly more sensitivity with the 16-mer being almost twice as sensitive as the 8-mer in this experiment. This result may reflect the mechanisms of cleavage and detection, which are dependent on protonation of the aspartic acid and the piperazine groups in the tags. The larger probes tend to adopt higher charge states (not shown), i.e. they are more heavily protonated and the availability of more free protons on the larger probe ions may facilitate the cleavage of the tags, masking steric effects. However, only three different size molecules were evaluated, and this will be explored more fully in future.