Global proteome analysis in plants by means of peptide libraries and applications

Like in animals plant proteins are differently expressed by organ with, for instance, few high abundance species such as RuBisCO in leaves colonizing the analytical space. Contrary to animals, a very large number of plant proteins are present at particularly low concentrations and in the presence of an excessive amount of polysaccharides and other natural polymers. This situation renders the functional investigations particularly challenging since the understanding of plant expression and interaction commences with the particularly laborious proteome deciphering. This fact impacts the investigations on protein differential biosynthesis in response to various stresses of physical, chemical and biological nature. This review updates the technical situation of global protein analysis while making a point on profiling changes resulting from external aggressions throughout recently published data. Within this context the importance of the combinatorial peptide ligand library methodology as an approach for facilitating the differential expression analysis is highlighted.The present review covers in extenso the latest progresses made in plant proteomics analyses with the use of the combinatorial peptide ligand library (CPLL) methodology. It well documents the ability of the CPLL technology in greatly extending the coverage of such proteomes, particularly in regard to the discovery and identification of low-abundance proteins, whose signal is obscured not only by the high-abundance species, as typically occurring in animal proteomics, but also by the overwhelming presence of plant polymers, such as polysaccharides, polyphenols, fibers and the like. The review covers the proteomics analysis aspect of modifications contingent upon plant stresses of physical, chemical and biological nature, as well as the discovery of hidden allergens on fruits and vegetable and their undiscovered proteomes. A sure conclusion can be made: no matter what mass spectrometry experts say, pre-fractionation in plant proteomics is a must and among such tools CPLLs appear to exert a major role in plant proteome discoveries.