Compatibility of plant protein extraction methods with mass spectrometry for proteome analysis

Different protein extraction methods have been developed for plant proteome analysis but their compatibility with mass spectrometry has rarely been tested. We evaluated four protein extraction methods, i.e., trichloroacetic acid (TCA)–acetone, phenol, direct iso-electric focusing (IEF) buffer, and Tris–HCl buffer, using tomato pollen for proteome analysis. The data presented show that the TCA–acetone and phenol protein extraction methods are superior to the other two tested methods for tomato pollen proteome analysis, in terms of two-dimensional gel electrophoresis (2-DE) gel separation, mass spectrometric analysis, and identification of proteins by peptide mass fingerprinting (PMF). These results highlight the importance of plant protein extraction method for subsequent MS analysis and protein identification.