Ensuring food safety requires a rapid and reliable method for detecting food-borne pathogens.Mass spectrometry has been demonstrated as a powerful tool to classify purebacterial species. However, matrix interference from food backgrounds may lead to falseresults because of the suppression of microbial signals. It is useful to develop a method forbacterial enrichment and marker identification in food samples. Magnetic zirconia nanoparticleswere used to concentrate spiked microorganisms from apple juice/lettuce underspecific conditions (pH 4.5). Bacterial identification was achieved using nanoLCeMS.Selected reaction monitoring of bacteria-related peptides was applied for the first time toidentify bacteria including Staphylococcus aureus and Escherichia coli. This study presents anaccurate means for bacterial identification in food matrixes using MS. The analysis time isless than 90 min and the minimum concentration of E. coli detected was 5 _ 103 CFU/mL.The interaction between bacteria and the magnetic nanoparticles was electrostatic andnonspecific, in contrast to immunoassays which require specific antibodies. The targetedpeptide analysis focuses on the bacterial markers, thus significantly simplifying theanalysis and leading to an accurate identification of bacteria.