The present study was undertaken because ZnO is being used as affinity probes for enhancing the signal intensities of bacterial analytes. Since, ZnO is established for its bactericidal activity, it is vital that the threshold concentrations up to which ZnO does not show bactericidal activity and above which concentration the bactericidal activity of ZnO becomes pronounced is identified. The results showed that at concentrations below 10 g/L, such as 5 and 1 g/L ZnO NPs did not damage the E. coli cells much but improved the intensity of most of the peaks in the spectra. For the first time, this paper reports the use of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) for assessing the damage incurred on the bacterial cells. The results showed significant differences in spectral pattern confirming that MALDI-TOF MS was successful in evaluating the bactericidal activity. This paper is unique in that it presents the results of the comparative study conducted in assessing the capability of MALDI-TOF MS with the existing conventional plating technique which is generally used to estimate bactericidal activity. This study brings out the inadequacy of the conventional plating techniques used in microbiology to depict antibacterial activity. On the other hand, MALDI-MS analysis led to direct, simple, and rapid acquisition of data (5 min for each measurement) which promptly reflected the bactericidal activity.