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Stony corals form the foundation of coral reefs, which are of prominent ecological and economic significance. A robust workflow for investigating the coral proteome is essential in understanding coral biology. Here we investigated different preparative workflows and characterized the proteome of Platygyra carnosa, a common stony coral of the South China Sea. We found that a combination of bead homogenization with suspension trapping (S-Trap) preparation could yield more than 2700 proteins from coral samples. Annotation using a P. carnosa transcriptome database revealed that the majority of proteins were from the coral host cells (2140, 212, and 427 proteins from host coral, dinoflagellate, and other compartments, respectively). Label-free quantification and functional annotations indicated that a high proportion were involved in protein and redox homeostasis. Furthermore, the S-Trap method achieved good …