A side-stream respiration monitoring system that is configured to generate an alignment signal and assess information that is derived in part from the alignment signal to align in a time domain the respiration flow and composition information. The system includes an analyzer that is fluidly connected to a flow sensor that is disposed in a respiration flow path. The system includes a controller that is configured to initiate delivery of the alignment signal to the flow sensor during a portion of at least one breath cycle. The controller is configured to determine a flow rate of respiration flow and at least a portion of a composition of the respiration flow on a breath-by-breath basis and temporally associate the respiration flow value and the determined portion(s) of the composition of the respiration flow as a function of information associated with the alignment signal generated by the analyzer.
