The "Dark Side" of Food Stuff Proteomics: The CPLL-Marshals Investigate

Abstract

The present review deals with analysis of the proteome of animal and plant-derived food stuff, as well as of non-alcoholic and alcoholic beverages. The survey is limited to those systems investigated with the help of combinatorial peptide ligand libraries, a most powerful technique allowing access to low- to very-low-abundance proteins, i.e., to those proteins that might characterize univocally a given biological system and, in the case of commercial food preparations, attest their genuineness or adulteration. Among animal foods the analysis of cow's and donkey's milk is reported, together with the proteomic composition of egg white and yolk, as well as of honey, considered as a hybrid between floral and animal origin. In terms of plant and fruits, a survey is offered of spinach, artichoke, banana, avocado, mango and lemon proteomics, considered as recalcitrant tissues in that small amounts of proteins are dispersed into a large body of plant polymers and metabolites. As examples of non-alcoholic beverages, ginger ale, coconut milk, a cola drink, almond milk and orgeat syrup are analyzed. Finally, the trace proteome of white and red wines, beer and aperitifs is reported, with the aim of tracing the industrial manipulations and herbal usage prior to their commercialization.

Keywords: alcoholic beverages; animal foods; aperitifs; combinatorial peptide libraries; non-alcoholic beverages; plant foods; proteomics.

Figure 1

(A) Mechanism of action of combinatorial peptide ligand libraries. (B) Artistic rendering of combinatorial peptide ligand library (CPLL) beads with proteins docked on the hexapeptide baits.

Figure 2

Upper panel: Venn diagrams showing the total identifications of avocado proteins in either the control or in the CPLL treated samples (left diagrams). The Venn diagrams to the right display the relative contributions to the total IDs of the denatured vs. the native sample extractions. Lower panel: GO analysis of the proteins detected in various metabolic processes in the control vs. CPLL-treated samples. In the latter case, five additional metabolic processes can be described, which are not visible in the control sample and most likely represent low- to very-low abundance proteins, whose visibility has been substantially enhanced via the CPLL technology (modified from Esteve et al. [43]).

Figure 3

SDS-PAGE profiles of orgeat syrup (two tracks to the left) and of almond’s milk (right panel). Orgeat: CTRL = 100 μL of control orgeat solution before CPLL treatment. 2.2 E = 50 μL 2% SDS eluate of orgeat solution treated with a home-made-CPLL library at pH = 2.2. Almond’s milk: control (A-CTRL) and eluates from a 1:1 mixed library of PM and home-made-CPLLs at pH 7.2 (7A) and pH 9.3 (9A) values (modified from Fasoli et al. [48]).

Figure 4

SDS-PAGE of white-vine vinegar. Mr: molecular mass ladder. Laemmli discontinuous buffer. Gel: 8%–18% polyacrylamide gradient. Run: three hours at 300 V. Sample load: 25 µL containing ca. 50 µg protein. Staining with micellar Coomassie Brilliant Blue. The major protein (the whole genome shotgun sequence of line PN40024, scaffold_22, a protein belonging to the glycosyl hydrolase 32 family) is indicated with an arrow (modified from Di Girolamo et al. [52]).

Figure 5

Venn diagrams of the proteins identified in 10 different human cell lines. Each cell exhibited an average of 10,361 species, of which 8522 proteins represented a common set and the remaining a set specific for each cell line, as indicated (modified from Geiger et al. [65]).