Skyline and Panorama combine to provide a robust QC workflow for LCMS instrumentation used in proteomics experiments. AutoQC Loader, a utility application, uses SkylineRunner to invoke Skyline without user interface for automated data processing. AutoQC Loader can be run on an instrument control computer to capture new QC runs automatically, and add them to an existing Skyline document, where the information is archived for later use and transferred to Panorama. Panorama retains a full history of QC run performance, and presents users with interactive plots for key metrics including retention time and peak area. Additionally, users can add information about changes including instrumentation, maintenance, and reagents, which are overlaid on the plots, providing a convenient way to correlate cause and effect.