Disclosed is a method of quantitatively analyzing a target protein population in a sample to be analyzed, the method including (a) treating a sample to be analyzed with an aptamer library specific to a target protein population present in the sample so as to form complexes between target proteins and aptamers binding specifically thereto, thereby forming a target protein-aptamer complex population, (b) isolating the complex population from unbound aptamers, and (c) analyzing the sequence of each aptamer of the complex population through a next-generation sequencing process so as to quantify each aptamer of the complex population, thereby quantifying each target protein in the complex population. The method of the present invention can be very useful in collectively quantifying proteins in an analytical sample.
