Update information. Low temperature storage, a widely used technique for extending shelf life of tomato (Solanum lycopersicum) fruits, also induces chilling injury and results in fruit quality loss and consumer dissatisfaction. Numerous studies have been performed to dissect the molecular mechanisms of the cold tolerance of tomato fruits, mainly with long-time cold treatments. However, the early signal events of cold response in fruits are largely unknown. In this study, we construct mass spectral libraries of proteome (corresponding to over 11,000 proteins) and phosphoproteome (corresponding to over 24,000 high-confidence phosphosites) of tomato fruits, and then perform data-independent acquisition (DIA) based comprehensive proteome and phosphoproteome profiling of tomato fruits at red-ripe stage upon cold treatment of 30 minutes.