Fractionation techniques improve the proteomic analysis of human serum

Different fractionation steps have been developed to reduce the complexity of serum proteome and to allow the detection and the identification of single proteins. The nature of fractionation (performed either on denatured or native proteins), the efficiency of recovery, the capacity of directly identifying proteins or protein panels, the possibility of associating to other laboratory techniques influence the choice of the methods to be used in different experimental and clinical settings. In this review, the main fractionation techniques (such as electrophoresis, SELDI and liquid chromatography) are described for proteomic studies in clinical field, and their advantages and disadvantages are discussed on the basis of our experience. In particular, liquid-liquid fractionation performed by PF2D is discussed in detail because of its partial automation, its ability to improve mass spectrometry analysis of serum proteins and its potential application in clinical studies.