We present herein a joint physical/physico-chemical study and, more specifically, the first application of Matrix Assisted Laser Desorption Ionization coupled with Time of Flight Mass Spectrometry (MALDI-TOF-MS) to analyze small-sized ZnO quantum dots (QDs) (2.8-3.1 nm diameter range) synthesized by sol-gel chemistry and stabilized through an aminosilane coating. A careful investigation of the stability of ZnO QDs was initiated once these dots were dispersed in different media (water, biological buffer) for a period up to 3 weeks. Positive ion mode mass spectra MALDI-TOF-MS combined with optical spectrometry was used to monitor the stability of ZnO QDs when aging. Such a unique combination of MALDI-TOF-MS and physico-chemical techniques is likely to bring new insights into the structure analysis, the stability and consequently the potential toxicity of QDs.