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The systematic study of all proteins, referred to as proteomics, is performed to identify the components of a particular proteome and analyze global changes in protein expression in response to different stimuli. Over the past two decades, mass spectrometry has become an important tool for the analysis of proteins (Aebersold and Mann, 2003; Yates, 2004). It is estimated that a cell contains at least 10 000-30 000 different proteins that span a wide range of sizes, relative abundance, acidity/basicity, and hydrophobicity (Badock et al., 2001). As is known, the low-abundance and high-abundance proteins differ in concentration over nine orders of magnitude (Omenn, 2004), which results in the high-abundance proteins impeding the investigation of middleor low-abundance proteins. The separation of the protein mixture into organelles or other multi-protein complex fractions prior to a proteomics analysis is usually the first step to increase the probability of detecting low-copy-number proteins (Rabilloud et al., 1998; Taylor et al., 2000; Cronshaw et al., 2002; Jiang et al., 2004; Gao et al., 2005). Efficient and highly resolving separation of the protein mixture into organelles or other multi-protein complex fractions prior to a mass spectrometry analysis is usually used as reducing the complexity of samples, which highly increases the probability of detecting low-copy-number proteins (Rabilloud et al., 1998; Taylor et al., 2000; Cronshaw et al., 2002; Jiang et al., 2004; Gao et al., 2005). Before the widespread use of shotgun methods, proteins were fractionated by 2D gel electrophoresis (2D-gel), a method that separates them according to pI and molecular weight (Harry et al., 2000; Gygi, et al., 2000; Motoyama & Yates, 2008). Although 2D-gel has excellent resolving power for intact proteins, the process is difficult to automate, laborious, and suffers from low throughput (Klose & Kobalz, 1995). The more fundamental drawbacks are the limited dynamic range and the exclusion of certain classes, such as low-abundance proteins (Gygi et al., 2000), integral membrane proteins (Braun et al., 2007), and proteins with extremes in isoelectric point (pI) and molecular weight (MW) (Corthals et al., 2000; Oh-Ishi et al., 2000). Another explored proteins pre-fractionation methods is multidimensional liquid chromatography technique combined ion-exchange chromatography and/or hydrophobic chromatography and/or reverse-phase chromatography, which has been a powerful

The Improvement of LC-MS/MS Proteomic Detection with Biomimetic Affinity Fractionation