Advances in chromatographic techniques and methods in shotgun proteome analysis

Shotgun proteomics is a high-throughput approach to proteome analysis whereby the protein mixture is digested and the peptides generated are separated by capillary liquid chromatography and sequenced by tandem mass spectrometry (MS). Due to the huge number of peptide species, separation prior to MS analysis plays an important role in shotgun proteomics. Overall sensitivity, dynamic range, throughput and general effectiveness of shotgun proteomic analysis largely depend on how well the peptide mixture is separated. In recent years, new separation techniques have been applied successfully to proteome analysis and have dramatically improved protein identification. We briefly review the recent development of chromatographic techniques and methods in shotgun proteome analysis, including the following three aspects: one-dimensional separation; multidimensional separation; and, automated proteome-analysis systems.