Sample preparation and fractionation techniques for intact proteins for mass spectrometric analysis

Abstract The analysis of proteins in biological samples is highly desirable, given their connection to myriad biological functions and disease states, as well as the growing interest in the development of protein‐based pharmaceuticals. The introduction and maturation of “soft” ionization methods, such as electrospray ionization and matrix‐assisted laser desorption/ionization, have made mass spectrometry an indispensable tool for the analysis of proteins. Despite the availability of powerful instrumentation, sample preparation and fractionation remain among the most challenging aspects of protein analysis. This review summarizes these challenges and provides an overview of the state‐of‐the‐art in sample preparation and fractionation of proteins for mass spectrometric analysis, with an emphasis on those used for top‐down proteomic approaches. Biological fluids, particularly important for clinical and pharmaceutical applications and their characteristics are also discussed. While immunoaffinity‐based methods are addressed, more attention is given to non‐immunoaffinity‐based methods, such as precipitation, coacervation, size exclusion, dialysis, solid‐phase extraction, and electrophoresis. These techniques are presented in the context of a significant number of studies where they have been developed and utilized.