Proton-transfer-reaction mass spectrometry (PTR-MS) has been widely used to study the emissions, distributions, and chemical evolution of volatile organic compounds (VOCs) in the atmosphere. The applications of PTR-MS have greatly promoted understanding of VOC sources and their roles in air-quality issues. In the past two decades, many new mass spectrometric techniques have been applied in PTR-MS instruments, and the performance of PTR-MS has improved significantly. This Review summarizes these developments and recent applications of PTR-MS in the atmospheric sciences. We discuss the latest instrument development and characterization work on PTR-MS instruments, including the use of time-of-flight mass analyzers and new types of ion guiding interfaces. Here we review what has been learned about the specificity of different product ion signals for important atmospheric VOCs. We present some of the recent highlights of VOC research using PTR-MS including new observations in urban air, biomass-burning plumes, forested regions, oil and natural gas production regions, agricultural facilities, the marine environment, laboratory studies, and indoor air. Finally, we will summarize some further instrument developments that are aimed at improving the sensitivity and specificity of PTR-MS and extending its use to other applications in atmospheric sciences, e.g., aerosol measurements and OH reactivity measurements.