The present invention describes a method of selective peptide isolation for the identification and quantitative analysis of proteins in complex mixture. The method comprises the selective isolation from every protein of those peptides that neither contain arginine nor histidine (NHNR peptides), and the determination of the relative concentrations of one or several proteins in different samples from the ratio between the areas of the estimated theoretical spectra for the NHNR peptides labeled with different isotopes in each sample. The determination of the relative concentration of proteins is valid for any type of isotopic label of the NHNR peptides. The method avoids the separation and purification of the proteins present in a complex mixture, and the analysis of all peptides generated from the enzymatic digest of the samples. The method is applicable to the identification of proteins with vacunal, therapeutic and diagnostic aims.