The complexity of samples brings great challenges for proteome analysis. Therefore, in our recent study, much effort has been made to develop various new sample prepration methods.

To decrease the dyanmic range of proteins in abundance, protein fractionation with ampholine modified polymer microspheres was performed, by which the identified protein number from human plasma was doubled, and the detected low abundance protein (with concentration less than 100 ng/mL) number was increased from 4 (without fractionation) to 17. Such improvement should be contributed to the decreased intereferece of high abundance proteins.

To improve the identification of target proteins,  N-terminal peptide imprinted polyethersulfone (PES) beads for transferrin recognition were prepared by phase inversion self-assembly,which showed high selectivity to capture transferrin from human plasma. Besides, various hydrophilic monolithic materials were systhesized, to achieve the high selective enrichment of glycoproteins/peptides, which might play important roles in large-scale glycoproteome analysis.

To achieve on-line protein digestion, a novel immobilized enzymatic reactor (IMER), with trypsin attached to graphene oxide modified polymer particles, was developed, which demonstrated the high enzyme binding capacity and low non-specific adsorption, leading to the high digestion effiecieny. By such an IMER, an integrated platform for quantitative proteome analysis, composed of on-line protein digestion, labeling by ¹⁸O, peptide separation and identification by nano-2D-HPLC, was constructed, and successfully applied for the analysis of syngenetic mouse hepatocarcinoma ascites cell lines with different metastasis risks, by which both the precision and accuracy for proteome quantitation were improved obviously.

All these results demonstrated that the above-mentioned methods showed great protential to promote the in-depth study of proteomes.