Dataset with emission spectra of CdSe/CdS core/shell quantum dots (QDs) in a single nanoparticle mass spectrometer at trap temperatures from 50 to 300 K. Additional meta information and analysis scripts are included. From the gas phase emission spectra the temperature of the respective QDs is determined, using calibration data of QDs on a surface. A model for the QD temperature in the gas phase is refined based on the experimental results.