Pre-analytical Purification Strategies for the Characterization of Food Protein Digestomes

In general, a food protein digestome is a very complex biomolecular system that may combine thousands of variously sized peptides, free amino acids, undigested proteins, degradation products of macro- and micronutrients other than proteins as well as relatively abundant enzymes and compounds of the digestive tract. The extraction and purification of peptides and proteins from a digestome, preparatory to peptidomic and proteomic analyses, is challenging and might run into various pitfalls. There are currently no standardized or harmonized protocols for the purification of protein digestion products, also because purification strategies should be adapted according to food composition, conditions of the digestive process, and purpose of the analysis. This chapter details the operative phases of several alternative procedures to sub-fractionate, purify, and prepare proteins and peptides of a digestome for the downstream mass spectrometry-based analysis.