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In situ and laser remote measurements of gases and aerosols were made with airborne instrumentation to establish a baseline chemical signature of the atmosphere above the South Pacific Ocean during the NASA Global Tropospheric Experiment (GTE)/Pacific Exploratory Mission‐Tropics A (PEM‐Tropics A) conducted in August‐October 1996. This paper discusses general characteristics of the air masses encountered during this experiment using an airborne lidar system for measurements of the large‐scale variations in ozone (O3) and aerosol distributions across the troposphere, calculated potential vorticity (PV) from the European Centre for Medium‐Range Weather Forecasting (ECMWF), and in situ measurements for comprehensive air mass composition. Between 8°S and 52°S, biomass burning plumes containing elevated levels of O3, over 100 ppbv, were frequently encountered by the aircraft at altitudes ranging from 2 to 9 km. Air with elevated O3 was also observed remotely up to the tropopause, and these air masses were observed to have no enhanced aerosol loading. Frequently, these air masses had some enhanced PV associated with them, but not enough to explain the observed O3 levels. A relationship between PV and O3 was developed from cases of clearly defined O3 from stratospheric origin, and this relationship was used to estimate the stratospheric contribution to the air masses containing elevated O3 in the troposphere. The frequency of observation of the different air mass types and their average chemical composition is discussed in this paper.