A large number of hydrocarbons, halocarbons, and organic nitrates were quantified in whole air samples acquired for the NASA-sponsored GTE missions PEM-Tropics A and B. The samples were collected in electro-polished stainless steel canisters from two aircraft while flying over the Pacific Basin. Two nominally identical multicolumn multidetector gas chromatographic analytical systems were employed. Whole air samples were also used as working and calibrated standards and were collected specifically for this purpose. This paper describes the analytical procedure employed during PEM-Tropics B. Minor differences in the PEM-Tropics A system will also be discussed. More than 3,900 samples were analyzed for 34 gases during PEM-Tropics A, over 4,500 samples were analyzed for 58 gases during PEM-Tropics B. An overview is presented of the collection, analysis, and quantification of whole air samples during the PEM-Tropics missions, along with an analysis of the analytical precision achieved during these missions.