the selected ion is then fragmented using e g blackbody irradiation infrared multiphoton dissociation or collisional activation for example ions generated by electrospray ionization esi can be fragmented using ir multiphoton dissociation this activation leads to dissociation of glycosidic bonds and the phosphate backbone producing two series of fragment ions called the w series having an intact 3 u2032 terminus and a 5 u2032 phosphate following internal cleavage and the a base series having an intact 5 u2032 terminus and a 3 u2032 furan the second stage of mass analysis is then used to detect and measure the mass of these resulting fragments of product ions such ion selection followed by fragmentation routines can be performed multiple times so as to essentially completely dissect the molecular sequence of a sample if there are two or more targets of similar base composition or mass or if a single amplification reaction results in a product which has the same mass as two or more bioagent reference standards they can be distinguished by using mass modifying u201c tags u201d in this embodiment of the invention a nucleotide analog or u201c tag u201d is incorporated during amplification e g a 5 trifluoromethyl deoxythymidine triphosphate which has a different molecular weight than the unmodified base so as to improve distinction of masses such tags are described in for example pct wo97 33000 which is incorporated herein by reference in its entirety this further limits the number of possible base compositions consistent with any mass for example 5 trifluoromethyl deoxythymidine triphosphate can be used in place of dttp in a separate nucleic acid amplification reaction measurement of the mass shift between a conventional.