The FIRe System measures changes in chlorophyll fluorescence that occur during a short (100 – 400 ?s) but intense (> 20,000 ?mol photons m-2 s-1) flash of light whereas the PAM approach measures the fluorescence induced by a weak modulated light source while using ‘saturating’ pulses of ~3000 – 10,000 ?mol photons m-2 s-1 to modify fluorescence yields.
The FIRe System also fundamentally differs from a PAM in that the FIRe fully reduces the primary electron acceptor, QA, allowing a simultaneous single closure (STF) event of all photosystem II (PSII) reaction centers whereas the PAM technique generates multiple photochemical charge separations (MTF) that fully reduces QA, the secondary acceptor, QB, and plastoquinone (PQ). By lengthening the measuring protocol the FIRe can also yield MTF data.
For a complete discussion on the mechanistic and practical differences between the two techniques see: Suggett, D.J., K. Oxborough, N.R. Baker, H.L. MacIntyre, T.M. Kana, & R.J. Geider. 2003. Fast repetition rate and pulse amplitude modulation chlorophyll a fluorescence measurements for assessment of photosynthesis electron transport in marine phytoplankton. European Journal of Phycology. 38: 371-84.