A food-borne pathogen, Salmonella Typhimurium, was detected and quantified in liquid food samples using NanoGene assay. The NanoGene assay is a recently developed gene quantification assay that employs DNA hybridization in solution and quantum dot nanoparticles. The invA gene was used as a functional gene target for the quantification of S. Typhimurium in liquid food samples (chicken broth, vegetable broth, and milk). We demonstrated quantification linearity with R2 = 0.91. However, a reduced sensitivity suggested that the NanoGene assay might have limited inhibitions to certain food compounds. Food compounds namely glucose, sucrose, l-lysine, casein, minerals, and oil were examined to further identify their respective inhibitory contribution. It was shown that the NanoGene assay was highly resistant to inhibition by carbohydrates. However, it was vulnerable to proteins, in particular casein hydrolysate.