With the development of material sciences, the characterization of nanomaterials has become a critical issue in managing their fascinating size-dependent physical and chemical properties. Controlling these properties from synthesis to the application phase, and consequently to their fate as a worldwide environmental and societal concern, is becoming more and more necessary. In this context, nanometrology, seen as a step to the total control of quantum dot (QD) properties, should make real headway in the near future. From this perspective, we present a careful investigation of small (<6 nm) CdS QDs synthesized either by a thermal growth process or in a microwave oven, using organometallic precursors. We will show that mass spectrometry (MS) is a worthwhile alternative to traditional solid state methods such as transmission electron microscopy (TEM) for QD diameter measurements. Indeed, low ionization technique such as Matrix Assisted Laser Desorption Ionization coupled to Time Of Flight (MALDI-TOF) analyser overcomes the propensity of large molecules to fragment when severely ionized. Moreover, MS can confirm TEM direct geometric observations. Combined with TEM, it provides a reliable determination of the shape-related correcting factor as a fit parameter, improving the consistent results for QD diameters obtained from both techniques. Consequently, MALDI-TOF MS is suitable for nanomaterial analyses and, when combined with physical methods, brings new insight to the analysis of chemical composition, structure, and stability and gives another potential tool for the accurate metrology of QDs.