Cancers are genetically and clinically very heterogeneous diseases; therefore, various proteomic studies have been trying to find biomarkers which can facilitate prognosis, diagnosis or treatment of these oncological diseases. The mass spectrometry is an eff ective tool for identification, quantitation, and characterization of biomolecules in the complex biological samples. The fi rst step suitable for selection of biomarkers called discovery proteomics provides a detailed analysis of the samples contributing to the identification of proteins, comparison of their presence in the samples, and selection of the convenient candidates for the prospective biomarkers. The next step of proteomics analysis is directed towards verification of chosen biomarkers with the approach called targeted proteomics. This technique evaluates presence and quantity of the proteins (biomarkers) in clinically precisely defined samples. This article focuses on the description of various approaches suitable for the quantitative analysis of the proteins connected with mass spectrometry.