invention include but are not limited to tandem mass spectrometry infrared multiphoton dissociation and pyrolytic gas chromatography mass spectrometry pgc ms in one embodiment of the invention the bioagent detection system operates continually in bioagent detection mode using pyrolytic gc ms without pcr for rapid detection of increases in biomass for example increases in fecal contamination of drinking water or of germ warfare agents to achieve minimal latency a continuous sample stream flows directly into the pgc ms combustion chamber when an increase in biomass is detected a pcr process is automatically initiated bioagent presence produces elevated levels of large molecular fragments from for example about 100 7 000 da which are observed in the pgc ms spectrum the observed mass spectrum is compared to a threshold level and when levels of biomass are determined to exceed a predetermined threshold the bioagent classification process described hereinabove combining pcr and ms preferably ft icr ms is initiated optionally alarms or other processes halting ventilation flow physical isolation are also initiated by this detected biomass level the accurate measurement of molecular mass for large dnas is limited by the adduction of cations from the pcr reaction to each strand resolution of the isotopic peaks from natural abundance 13 c and 15 n isotopes and assignment of the charge state for any ion the cations are removed by in line dialysis using a flow through chip that brings the solution containing the.