The application of eigenstructure tracking analysis (ETA) and SIMPLISMA for the investigation of the protonation equilibria of a monomer and several polynucleotides is proposed. Both approaches have been applied in the pH and in the wavelength direction to the spectroscopic data matrices obtained in the study of each equilibrum. ETA provides information about the number of components in the,system, their evolution along the titration, and the local rank. SIMPLISMA also used to obtain the number of compounds in the system, the concentration profiles, and the unit spectrum of each compound. The results obtained with SIMPLISMA and those obtained previously with the alternating least-squares approach are compared.