The most common method for proton MRS quantification is the linear combination of model basis spectra. Typically, these model spectra are simulated using density matrix formalism. Here we aimed to compare the quantification using two basis sets with full localization and real RF pulses and one basis set with non-localized ideal RF pulses. Statistically significant differences were found between metabolite concentrations quantified in LCModel with different basis sets. Whereas two models that used localized real RF pulses were not significantly different for the major metabolites, the ideal basis set differed in concentration for all metabolites except NAA.