Background: Mycobacterium bovis bacillus Calmette-Guerin (BCG) is the only vaccine available against tuberculosis, and the strains used worldwide represent a family of daughter strains with distinct genotypic characteristics. To establish a Korean tuberculosis vaccine derived from BCG Pasteur 1173P2, genome sequencing of a BCG Korea was completed by Joung and coworkers (2013). Here, we report the proteomics data of BCG Korea, the strain that will be actually used in Korea for vaccine production. Methods: The tryptic peptides were loaded onto a fused silica microcapillary column (12 cm x 75 μm) packed with C18 reversed phase resin (5 μm, 100 A). The column was directly connected to an LTQ linear ion-trap mass spectrometer equipped with a nano-electrospray ion source. All spectra were acquired in data-dependent scan mode. The acquired LC-ESI-MS/MS fragment spectra were searched in the BioWorksBrowserTM with the SEQUEST search engine against NCBI non-redundant database including reverse database. The putative function of proteins, which were not listed in UniProtKB, was further analyzed using Pfam and gene ontology databases. Scaffold was used to validate MS/MS based peptide and protein identifications. Results: A total of 914 proteins were identified from LC-ESI-MS/MS analysis and their abundance was estimated by SWATH methods. Some predominant proteins, including fatty acid synthase, mycocerosic acid synthase, RNA polymerase, heat shock protein and peptide synthase which represent potential prominent antigens in the humoral and cellular immune response. Conclusions: The aim of this study was to construct a reference protein map for these proteins in BCG Korea. Especially, the SWATH is very straightforward and provides a promising approach owing to its strong reliability and reproducibility during the proteomic analysis. These results will be compared with the currently used BCG strains and basic information for the development of a novel vaccine.