A mainstream gas monitoring system and method that includes using a mainstream airway adapter and a gas sensing assembly associated with the airway adapter to measure an analyte of a gas flow through the adapter. A gas sensing portion outputs a signal indicative of the analyte in a gas flow in the mainstream airway adapter. A processing portion receives the signal from the gas sensing portion and determines an amount of the analyte in the gas flow based on the signal from the gas sensing portion. The processing portion determines whether the oxygen measurements are of sufficient quality for their intended use, such as for measuring oxygen consumption or metabolic estimations. Quality measurements may be used to improve accuracy of derived metabolic estimations. Methods are provided by which carbon dioxide measurements can be processed and substituted for direct oxygen measurement for all or part of a respiratory cycle.
