Proteomic analysis has been widely used in elucidating the mechanism of diseases. As a classical proteomic approach, two-dimensional gel electrophoresis (2DGE) has been commonly applied in finding differentially expressed proteins through a first dimension of separation by the isoelectric point (pI) of proteins and a second dimension of separation according to the molecular weight (MW) of proteins. Compared to 2DGE, a recently developed commercial system from Beckman Coulter, the two-dimensional protein fractionation (PF2D), separates proteins according to the pI of proteins in the first dimension followed by a second dimension of separation according to the degree of protein hydrophobicity. As a liquid-based fractionation system, PF2D could facilitate the extraction and separation of broader protein categories and improve reproducibility and quantification as well as be less labor-intensive, which are usually identified as limitations of a gel-based 2DGE platform. This review evaluates the applications of the PF2D system and discusses the perspectives and advantages of PF2D in the investigation of cancer and genetic disorders and in protein mapping in human biological fluids and cell cultures. <alternatives> [...] </alternatives>
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