Application of a peptide-based PF2D platform for quantitative proteomics in disease biomarker discovery.

A peptide-based 2-D liquid phase fractionation (PF2D) system was used in a quantitative proteomic analysis of hepatocellular carcinoma. 2-D liquid maps of peptide specimens showed better resolution than those of proteins, leading to the identification of differentially expressed proteins. Peptide-based PF2D gave well-matched theoretical and experimental pI values and was proven to be a very efficient and versatile analytical tool for both large-scale profiling and quantification of phosphoproteins in disease biomarker discovery.