Two kinds of microorganisms with high detection rate in sprouts were identified by MALDI-TOF MS method as Raoultella ornithinolytica(33.3%) and Klebsiella pneumoniae(43.5%),respectively.The protein spectrums for the two microorganisms were analyzed by SARAMIS Premium,and 16 groups of characteristic peaks for R.ornithinolytica and 10 groups of characteristic peaks for K.pneumonia were identified.All peaks and weighted characteristic peaks were used for correlation analysis.The weighting for characteristic peaks could effect the correlation between different microorganisms and strengthen their resolutions.Through comparion by several methods,the two kinds of microorganisms are relatively similar in biochemical reactions.However,the 16SrDNA could isolate them,and their MS correlation trees were recognizable even though they intersected each other.The experimental results show that MALDI-TOF MS is capable of detecting the microorganisms in sprouts,and has certain advantages in their feature analysis and traceability research.MALDI-TOF MS/SARAMIS,as an open platform,could be expanded its applicable scope and improved its identified accuracy by the collection and optimization of microbial characteristics spectrums.