A system is configured to perform capnometry/capnography, and/or other compositional analysis on a non-invasively ventilated subject. As such, the system determines amounts of a molecular species of gas (e.g., carbon dioxide, oxygen, etc.) excreted by the subject on a per-breath basis. Determinations of amounts of the molecular species of gas excreted are adjusted to reflect amounts of the molecular species of gas leaked from the non-invasive interface used to communicate with the airway of the subject.