Low-Abundance Protein Enrichment for Medical Applications: The Involvement of Combinatorial Peptide Library Technique.

The discovery of low- and very low-abundance proteins in medical applications is considered a key success factor in various important domains. To reach this category of proteins, it is essential to adopt procedures consisting of the selective enrichment of species that are present at extremely low concentrations. In the past few years pathways towards this objective have been proposed.

Combinatorial peptides: A library that continuously probes low-abundance proteins.

After a decade of experimental applications, it is the objective of this review to make a point on combinatorial peptide ligand libraries dedicated to low-abundance proteins from animals to plants and to microorganism proteomics. It is, thus, at the light of the recent technical developments and applications that we will examine the state of the art, its usage within the scientific community, and its openness to unexplored fields. The improvements of the methodology and its implementation in connection with analytical determinations of combinatorial peptide ligand library (CPLL)-treated samples are extensively reviewed and commented upon.

Detection of Plant Low-Abundance Proteins by Means of Combinatorial Peptide Ligand Library Methods.

The detection and identification of low-abundance proteins from plant tissues is still a major challenge. Among the reasons are the low protein content, the presence of few very high-abundance proteins, and the presence of massive amounts of other biochemical compounds. In the last decade numerous technologies have been devised to resolve the situation, in particular with methods based on solid-phase combinatorial peptide ligand libraries.

Low-abundance plant protein enrichment with peptide libraries to enlarge proteome coverage and related applications.

In plant tissues proteins are present in low amounts but in a very large number. To this peculiar situation many complex foreign components render protein extraction and purification very difficult. In the last several years interesting technologies have been described to improve the technical situation to the point that some methodologies allow reaching very low-abundance proteins and minor allergens.

Progress in farm animal proteomics: The contribution of combinatorial peptide ligand libraries.

The present review covers proteomics discoveries in farm animals using combinatorial peptide ligand libraries (CPLLs). These libraries enhance the identification of low-abundance proteins by compressing the dynamic range of the protein concentration. This technology can be applied in multiple biological fluids, such as plasma or serum, follicular and cerebrospinal fluids, urine, saliva, tears seminal fluid, milk whey and even lymph.

Novel low-abundance allergens from mango via combinatorial peptide libraries treatment: A proteomics study.

Mango allergy is a rare condition, which may cause severe hypersensitivity reactions, such as anaphylaxis, angioedema, asthma and contact dermatitis. By exploiting the combinatorial peptide ligand library (CPLL) technology, mango proteomes have been extracted and the presence of traces of allergens assessed via Western blot analysis two-dimensional maps. Upon reactive spot elution and mass spectrometry analyses, four major mango allergens could be identified for the first time and shown to be in common with three of the five known banana species.

Aptamer affinity ligands in protein chromatography.

The present review deals with the place of single chain oligonucleotide ligands (aptamers) in affinity chromatography applied to proteins. Aptamers are not the only affinity ligands available but they represent an emerging and highly promising route that advantageously competes with antibodies in immunopurification processes. A historical background of affinity chromatography from the beginning of the discipline to the most recent outcomes is first presented.

Protein biomarkers for early detection of diseases: The decisive contribution of combinatorial peptide ligand libraries.

Unlabelled: The present review deals with biomarker discovery, especially in regard to sample treatment via combinatorial peptide ligand libraries, perhaps the only technique at present allowing deep exploration of biological fluids and tissue extracts in search for low- to very-low-abundance proteins, which could possibly mark the onset of most pathologies. Early-stage biomarkers, in fact, might be the only way to detect the beginning of most diseases thus permitting proper intervention and care. The following cancers are reviewed, with lists of potential biomarkers suggested in various reports: hepatocellular carcinoma, ovarian cancer, breast cancer and pancreatic cancer, together with some other interesting applications.

DNA aptamer affinity ligands for highly selective purification of human plasma-related proteins from multiple sources.

Nucleic acid aptamers are promising ligands for analytical and preparative-scale affinity chromatography applications. However, a full industrial exploitation requires that aptamer-grafted chromatography media provide a number of high technical standards that remained largely untested. Ideally, they should exhibit relatively high binding capacity associated to a very high degree of specificity.

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

Unlabelled: 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.

Widening and diversifying the proteome capture by combinatorial peptide ligand libraries via Alcian Blue dye binding.

Combinatorial peptide ligand libraries (CPLLs) tend to bind complex molecules such as dyes due to their aromatic, heterocyclic, hydrophobic, and ionic nature that may affect the protein capture specificity. In this experimental work Alcian Blue 8GX, a positively charged phthalocyanine dye well-known to bind to glycoproteins and to glucosaminoglycans, was adsorbed on a chemically modified CPLL solid phase, and the behavior of the resulting conjugate was then investigated. The control and dye-adsorbed beads were used to harvest the human urinary proteome at physiological pH, this resulting in a grand total of 1151 gene products identified after the capture.

Mixed-bed affinity chromatography: principles and methods.

Mixed-bed chromatography is far from being a well-established technology within the panoply of bioseparation tools. Composed of an assembly of distinct sorbents that are mixed in a single bed, they have been mostly developed in the last decade for the reduction of dynamic concentration range where they allowed discovering many low-copy proteins within very complex proteomes. Other interesting preparative applications of mixed-bed chromatography have since been developed.

Sample treatment methods involving combinatorial peptide ligand libraries for improved proteomes analyses.

If used in an optimized manner, the technology of combinatorial peptide solid-phase libraries can easily improve the analytical determinations of proteomes by several factors. The discovery of novel species and of early stage biomarkers becomes thus reachable with a simple sample treatment. This report describes the most important point to consider (overloading and full recovery) along with a minimum scientific background and gives then detailed recipes to laboratory technicians.

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

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.

Plant proteomics methods to reach low-abundance proteins.

The question of low-abundance proteins from biological tissues is still a major issue. Technologies have been devised to improve the situation and in the last few years a method based on solid-phase combinatorial peptide ligand libraries has been extensively applied to animal extracts. This method has also been extended to plant extracts taking advantage of findings from previous experience.

Optimized sample treatment protocol by solid-phase peptide libraries to enrich for protein traces.

Combinatorial peptide ligand libraries have been extensively used for the enrichment of very low-abundance proteins, while concomitantly reducing the concentration of major species. A number of biological extracts have been reported with great success. Nevertheless, there are examples where the enrichment was not as good as expected.

Combinatorial peptide libraries to overcome the classical affinity-enrichment methods in proteomics.

The enrichment of targeted low-abundance proteins is possible by affinity adsorption using selected sorbents. Different categories of very dilute proteins are present in most of biological extracts so that specific affinity methods are unable to address their collective enrichment. Only recently an interesting approach has been proposed associating the affinity of multiple ligands used as a library mode under overloading much beyond the saturation of the affinity mixed bed.

Breakfast at Tiffany's? Only with a low-abundance proteomic signature!

Food science is a complex domain where modern analytical technologies interact with each other. Named as "Foodomics," this domain assembles a variety of investigational fields such as genomics, transcriptomics, proteomics, peptidomics, and metabolomics. All these technologies are at the service of several goals that are essentially dictated by fundamental understanding, safety, and consistency.

Allergomic study of cypress pollen via combinatorial peptide ligand libraries.

Although Cupressus sempervirens (Cups) pollen represents one of the main aeroallergens in southern Europe, only two Cups allergens have yet been identified and reported: Cup s 1 and Cup s 3. The aim of this study was to identify allergens in cypress pollen using an immuno-proteomic approach. A sequential pollen protein extraction was developed and supplemented by a combinatorial peptide ligand library (CPLL) treatment to select low-abundance species.

Mark Twain: how to fathom the depth of your pet proteome.

The present review highlights recent progresses in the technique of combinatorial peptide ligand libraries (CPPL), a methodology that has much to offer for the detection of low- to very-low abundance proteins (nanograms/mL scale and below) in any proteome. In particular, advances in exploration of the urinary, plasma and tissue proteomes are discussed and evaluated. It is shown that when treating biological fluids, such as plasma, with CPLLs, the detection sensitivity, which in the control only reaches 10 ng/mL, can be enhanced to as high as 10 pg/mL, with an increment of sensitivity of three orders of magnitude.

Carotid atherosclerotic plaques: proteomics study after a low-abundance protein enrichment step.

Atherosclerosis is one of the most important causes of cardiovascular and cerebrovascular events. Although phenotypic differentiation between stable and unstable plaques is currently possible, proteomic analysis of the atherosclerotic plaque could offer a global view of the atherosclerosis pathology. With the objective to highlight the detection of low-abundance proteins, we reduced the dynamic range of proteins by combinatorial peptide ligand library treatment of human carotid artery atherosclerotic plaques.

"The quest for biomarkers": are we on the right technical track?

The discovery phase of biomarkers of diagnostic or therapeutic interest started a decade ago with the very rapid development of proteomic investigations. In spite of the development of innovative technologies and multiple approaches, the "harvest" is still modest. Various reasons justified the encountered difficulties and most of them have been circumvented by specific sample treatments or dedicated analytical approaches.