Gel-Based and Gel-Free Sample Preparation for LC-MS/MS Analysis

Abstract

To understand the biological processes in health and disease, it would be useful to profile all the nucleic acids, glycans, lipids, proteins, and metabolites in a particular system. Unfortunately, no single analytical approach exists that is capable of analyzing all of these elements simultaneously. Rather, each unique sample type requires distinct methods for preparation and analysis: genomics for nucleic acids, glycomics for glycans, lipidomics for lipids, proteomics for proteins, and metabolomics for metabolites. In proteomic analyses, unique experimental designs frequently apply various degrees of fractionation, diverse gel-based or gel-free separation techniques, and a host of mass spectrometric analytical approaches. These issues are discussed in the introduction to encourage the broad community of scientists to develop a specific method for each unique experiment. At the same time, this chapter describes several special sample preparation methods for LC-MS/MS using electrospray ionization and a linear ion-trap mass spectrometer. The methods are optimized, reproducible, and as simple as possible, and they are capable of generating excellent results. However, optimization for each unique experiment is always a good idea.