Methods of quantitating extra-cellular vesicle surface markers are provided. Aspects of the methods include comparing: a mean fluorescence intensity of a surface marker of interest (surface marker MFI) of a labeled extra-cellular vesicle (EV) sample with a calibration plot obtained from a liposome calibration composition to quantitate the surface marker on extra-cellular vesicles of the EV sample. Also provided are compositions that find use in practicing embodiments of the invention.