Breath-by-breath measurement of alveolar gas exchange must preserve mass balance and conform to a physiological definition of a breath.

Tidal breathing in awake humans is variable. This variability causes changes in lung gas stores that affect gas exchange measurements. To overcome this, several algorithms provide solutions for breath-by-breath alveolar gas exchange measurement; however, there is no consensus on a physiologically robust method suitable for widespread application. A recent approach, the 'independent-breath' (IND) algorithm, avoids the complexity of measuring breath-by-breath changes in lung volume by redefining what is meant by a 'breath'. Specifically, it defines a single breathing cycle as the time between equal values of the / (or / ) ratio, that is, the ratio of fractional concentrations of lung-expired O (or CO) and nitrogen (N). These developments imply that the end of one breath is not, by necessity, aligned with the start of the next. Here we demonstrate how the use of the IND algorithm fails to conserve breath-by-breath mass balance of O and CO exchanged between the atmosphere and tissues (and vice versa). We propose a new term, within the IND algorithm, designed to overcome this limitation. We also present the far-reaching implications of using algorithms based on alternative definitions of the breathing cycle, including challenges in measuring and interpreting the respiratory exchange ratio, pulmonary gas exchange efficiency, dead space fraction of the breath, control of breathing, and a broad spectrum of clinically relevant cardiopulmonary exercise testing variables. Therefore, we do not support the widespread adoption of currently available alternative definitions of the breathing cycle as a legitimate solution for breath-by-breath alveolar gas exchange measurement in research or clinical settings.