In addition, we demonstrate a novel MS/MS-based tandem nucleic acid mass tag (TNT) design and detection process that allows highly specific detection of TNTs in a complex background. The Tandem Nucleic acid mass Tag design also allows easy synthesis of large sets of isotopic tags supporting the development of multiplexed and quantitative assays. We demonstrate the quantitative nature of the TNT approach. Furthermore, we evaluate ESI-cleavable TNT-PNA conjugates as hybridization probes for the detection of target DNA sequences via the use of ESI-MS/MS.