Comparative Study of Three Methods of Sample Preparation for Proteomics Research

Abstract Protein sample preparation is a vital issue for proteomics research. Due to different physical and chemical properties of reagents used for sample preparation, the ability of different reagents to disrupt cell or tissue, as well as to solubilize a variety of proteins, is very different. In the present study, three sample preparation methods widely used in proteomics researches (Triton X-100 method, urea method and TRIzol method) were compared by using mass spectrometric method in analyzing proteins isolated from cultured 293T cells, followed by bioinformatics analyses. The results indicated that the number of the identified proteins extracted by Triton X-100 method was almost the same as that by urea method, whereas the number of the identified proteins extracted by TRIzol method was approximately 8 percent smaller than those by either Triton X-100 or urea method. A large difference was found among the protein categories identified by three extraction methods, and only 32 percent proteins were identified from samples by all three methods. The profiles of proteins prepared by three methods were compared and further analyzed using functional classification software. This study provides a rapid, effective and comprehensive tool for evaluating the sample preparation methods for proteomics study.