A pressure support system comprising: a pressure generator configured to generate a pressurized flow of breathable gas for delivery to an airway of a subject; a gas delivery circuit configured to deliver the pressurized flow of breathable gas from the pressure generator to the airway of the subject; a first sensor configured to generate output signals conveying information related to the breathing phase of the subject; a second sensor configured to generate output signals conveying information related to the composition of gas at or near the airway of the subject; and one or more processors configured to execute computer program modules, the computer program modules comprising: a control module configured to control the pressure generator to adjust the pressurized flow of breathable gas such that pressure at or near the airway of the subject remains at or above an expiratory pressure level if the output signals generated by the first sensor indicate that the breathing of the subject is in an expiratory phase; a therapy pressure module configured to set the expiratory pressure level implemented by the control module during expiratory phases of the breathing of the subject, wherein the therapy pressure module is configured such that during most expiratory phases the expiratory pressure level is set at a predetermined baseline expiratory pressure level; and an exhalation composition module configured to determine a concentration of a gaseous molecular species in gas exhaled from the lungs of the subject, Characterized in that The therapy pressure module is further configured such that intermittently the expiratory pressure level (48,50) is lowered below the predetermined baseline expiratory pressure level; and In that the exhalation composition module is configured such that the determination of the concentration of the gaseous molecular species in gas exhaled from the lungs of the subject is made based on output signals generated by the second sensor during the intermittent expiratory phases for which the expiratory pressure level (48,50) is lowered below the predetermined baseline expiratory pressure level. a pressure generator configured to generate a pressurized flow of breathable gas for delivery to an airway of a subject; a gas delivery circuit configured to deliver the pressurized flow of breathable gas from the pressure generator to the airway of the subject; a first sensor configured to generate output signals conveying information related to the breathing phase of the subject; a second sensor configured to generate output signals conveying information related to the composition of gas at or near the airway of the subject; and one or more processors configured to execute computer program modules, the computer program modules comprising: a control module configured to control the pressure generator to adjust the pressurized flow of breathable gas such that pressure at or near the airway of the subject remains at or above an expiratory pressure level if the output signals generated by the first sensor indicate that the breathing of the subject is in an expiratory phase; a therapy pressure module configured to set the expiratory pressure level implemented by the control module during expiratory phases of the breathing of the subject, wherein the therapy pressure module is configured such that during most expiratory phases the expiratory pressure level is set at a predetermined baseline expiratory pressure level; and an exhalation composition module configured to determine a concentration of a gaseous molecular species in gas exhaled from the lungs of the subject, Characterized in that a control module configured to control the pressure generator to adjust the pressurized flow of breathable gas such that pressure at or near the airway of the subject remains at or above an expiratory pressure level if the output signals generated by the first sensor indicate that the breathing of the subject is in an expiratory phase; a therapy pressure module configured to set the expiratory pressure level implemented by the control module during expiratory phases of the breathing of the subject, wherein the therapy pressure module is configured such that during most expiratory phases the expiratory pressure level is set at a predetermined baseline expiratory pressure level; and an exhalation composition module configured to determine a concentration of a gaseous molecular species in gas exhaled from the lungs of the subject, Characterized in that The therapy pressure module is further configured such that intermittently the expiratory pressure level (48,50) is lowered below the predetermined baseline expiratory pressure level; and In that the exhalation composition module is configured such that the determination of the concentration of the gaseous molecular species in gas exhaled from the lungs of the subject is made based on output signals generated by the second sensor during the intermittent expiratory phases for which the expiratory pressure level (48,50) is lowered below the predetermined baseline expiratory pressure level.