A proteome reference map and virulence factors analysis of Yersinia pestis 91001

► We covered 46% of the Yersinia pestis proteome using accurate mass spectrometer. ► The three techniques used showed different preferences toward Y. pestis proteins. ► Transcriptome analysis showed 56% overlap with the proteome results. ► Most of virulence-associated proteins were detected under the research condition. ► We provide a reference map of Y. pestis proteome for further researches.