Zheng et al. BMC Genomics 2011, 12:40 http://www.biomedcentral.com/1471-2164/12/40 BCG NCTC 5692. This work was supported by the National Natural Science Fund (grant no. 30800039) from the National Natural Science Foundation of China, Eleven-Fifth Mega-Scientific Project on infectious diseases, China (grant no. 2008ZX10003-005 and 2008ZX10003-009), and an intramural grant from the Institute of Pathogen Biology, Chinese Academy of Medical Sciences (grant no.2007IPB007). Authors’ contributions JZ performed collection of M. bovis BCG, samples preparation, the mass spectrometry experiments, data processing and bioinformatics analysis, and wrote the manuscript. CW and WL participated in the mass spectrometry experiments and data processing, and helped write the manuscript. LZ and LL contributed to samples preparation, the mass spectrometry experiments and bioinformatics analysis. WL carried out collection of M. bovis BCG and samples preparation. 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