Technologies and methods for sample pretreatment in efficient proteome and peptidome analysis

Although great progresses have been made in proteomics during the last decade, proteomics is still in its infancy. Extreme complexity of proteome sample and large dynamic range of protein abundance overwhelm the capability of all currently available analytical platforms. Sample pretreatment is a good approach to reduce the complexity of proteome sample and decrease the dynamic range. In this article, we present an overview of different technologies and methods for sample pretreatment in efficient proteome and peptidome analysis. Methods for isolation of rare amino acid-containing peptides, terminal peptides, PTM peptides and endogenous peptides are reviewed. In addition, two automated sample pretreatment technologies, i.e. automated sample injection and on-line digestion, are also covered.