Mass spectrometry has significantly extended its applicability in the area of characterization of protein structures. Electrospray ionization enables on-line coupling with liquid chromatography which has become a powerful tool for the characterization of peptide and protein mixtures. The most recent development of a nanoelectrospray source, using capillary forces for a particularly mild analyte transport and ionization into the mass spectrometer, opens a wide field for applications to protein structure analysis. In this paper, the analytical development of liquid chromatography-electrospray ionization mass spectrometry and nano-electrospray ionization mass spectrometry, adapted to an electrospray ionization quadrupole mass spectrometer and its application to the characterization of noncovalent protein complexes are described.