Abstract: Method and apparatus for characterizing drug-modified polymers, macromolecules, proteins, antigens, antibodies or nanoparticles and quantitative determination of their impurity profile by two-dimensional liquid chromatography analysis. The first dimension is preferably size exclusion chromatography (SEC)—which is also known as gel permeation chromatography in case of non-aqueous samples (GPC)—for complete molecular weight analysis of nanoscale particles. It is not just included the application of separating small molecules from big molecules, but it is also the separation of different sorts of oligomers (e.g. monomers, dimers, trimers, tetramers). The second dimension is adapted for separating and characterizing small molecules which can be impurities or non-reacted modifiers with high-performance liquid chromatography (HPLC). Between the dimensions it is feasible to use solid phase extraction column(s) to collect small molecules, wash off or change solvent, or minimize broadening of their peaks.