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The Earth Observing System (EOS) Microwave Limb Sounder (MLS) is an atmospheric remote sensing experiment led by the Jet Propulsion Laboratory of the California Institute of Technology. The objectives of the EOS MLS are to learn more about stratospheric chemistry and causes of ozone changes, processes affecting climate variability, and pollution in the upper troposphere. The EOS MLS is one of four instruments on the National Aeronautics and Space Administration (NASA) EOS Aura spacecraft launched on July 15, 2004, with an operational period extending at least 5 years after launch. This paper describes the architecture and capabilities of the Science Data Processing System (SDPS) for the EOS MLS. The SDPS consists of two major component—the Science Computing Facility and the Science Investigator-led Processing System. The Science Computing Facility provides the facilities for the EOS MLS Science Team to perform the functions of scientific algorithm development, processing software development, quality control of data products, and scientific analyses. The Science Investigator-led Processing System processes and reprocesses the science data for the entire mission and delivers the data products to the Science Computing Facility and to the Goddard Space Flight Center Earth Science Distributed Active Archive Center, which archives and distributes the standard science products. The Science Investigator-led Processing System is developed and operated by Raytheon Information Technology and Scientific Services of Pasadena under contract with Jet Propulsion Laboratory. [ABSTRACT FROM AUTHOR]