Sample Preparation Guide for Mass Spectrometry–Based Proteomics

Sample preparation is an integral, but sometimes neglected, part of a successful mass spectrometry (MS)-based proteomics experiment. Good sample preparation techniques require a profound understanding of the biological samples to be analyzed and of the liquid chromatography (LC)–MS process. Depending on the experiment, biological samples often contain components (buffers and salts, detergents, polyethylene glycols, lipids, chromatins, antibodies, and streptavidin) that are not necessarily compatible with the LC–MS-MS analysis. Thus, successful sample preparation starts with a proper experimental design. Whenever possible, electrospray ionization-MS incompatible components should be systematically replaced with compatible components, such as volatile salts and MS-friendly detergents. In addition, the removal of incompatible components should be advised when they cannot be avoided (for example, an insoluble membrane protein requires detergent for solubilization or streptavidin resin is needed to enrich biotin-labeled proteins and peptides). This review article summarizes successful sample preparation strategies that led to some of the highest peptide and protein identification rates reported in the literature