The unique optical properties, such as size-tunable absorption and emission, caused semiconductor nanocrystals to attract a great deal of interest for recent technological developments. For the evaluation of semiconductor nanocrystals as new materials for various applications like optoelectronic devices, knowledge of the structure-property relationships is indispensable, but still presents a challenge. Here, we address these challenges for thioglycolic acid-capped CdTe nanocrystals with a focus on the quantification of thiol ligands, identification of the ligand shell structure and their influence on the optical properties of these nanocrystals. We present the use of a simple analytical technique, the Ellman's test, and ICP-OES analysis for the study of the surface chemistry of these nanomaterials. Together with theoretical calculations, the results of these studies show the strong influence of the amount of Cd-thiolates present in the ligand shell on the concentration-dependent emission properties, thereby providing the basis for a better understanding of the chemical nature of the NC-ligand interface. In this context, the present work contributes to the establishment of a clearer picture and better control of the surface chemistry, which will provide the basis for the design of highly emitting nanocrystals and the prediction of their applicability.