We developed convolutional-neural-networks(CNNs) for each individual metabolites capable of spectrally isolating target metabolite signal for quantification on simulated rat brain spectra at 9.4T. Although heuristically and empirically developed, a method of predicting measurement uncertainty is also proposed by exploiting the spectral isolation capability of the CNNs and the availability of big data. The quantitative accuracy of the proposed method was higher than that of the LC model. The measurement uncertainty predicted by the proposed method was highly correlated with the ground-truth error. The proposed method may be used for metabolite quantification with measurement uncertainty estimation in rat brain at 9.4T.