Combinatorial peptides: A library that continuously probes low‐abundance proteins

Abstract

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. Relevant examples covering few critical aspects describe the performance of the technology. Finally, a reflection on the technological future is attempted in particular by involving new concepts adapted to the limited availability of certain biological samples.

Recent developments and applications of capillary and microchip electrophoresis in proteomics and peptidomics (mid‐2018–2022)

“…In biological samples (e.g., blood plasma or serum), the presence of high abundant proteins often interferes with the analysis of lower abundant proteins. In this case, depletion of high‐abundance proteins or enrichment strategies for low‐abundance proteins [84] or their tryptic peptides has to be included in the sample preparation process. Immobilized metal affinity SPE‐CE‐MS method with Ni(II) sorbent allowed selective enrichment of His‐containing peptides from protein tryptic digests with preconcentration factors 25–100 [85].…”

Common Post-translational Modifications (PTMs) of Proteins: Analysis by Up-to-Date Analytical Techniques with an Emphasis on Barley

“…Although CPLL technology is currently used to track low abundance proteins, some research groups are still comparing the immunodepletion method with enrichment methods to obtain the best results. 54 Data-dependent acquisition (DDA) and data-independent acquisition (DIA) methods along with sequential window acquisition of all theoretical mass spectra (SWATH-MS) are also more widely used for protein identification and quantification. 55 iTRAQ, an advanced MS-based procedure, is also used for the relative and absolute quantification of proteins and their modification by the derivatization of primary NH 2 groups in intact proteins.…”

“…Eliminating high-abundance proteins is very efficient, but detecting low-abundance proteins remains limited due to their dilute presence. What seems interesting about reducing the number of high abundance proteins while increasing the number of low abundance proteins is the possibility of detecting more proteins and their PTMs . CPLL technology is characterized by three important principles: (1) a mixed set of affinity resins covering the largest spectrum of affinity ligands to statistically provide a partner ligand for each protein present in the samples, (2) the saturation effect of the capture due to a large number of sample overload, and (3) the exhaustiveness of protein recovery for full analysis.…”

“…What seems interesting about reducing the number of high abundance proteins while increasing the number of low abundance proteins is the possibility of detecting more proteins and their PTMs. 54 CPLL technology is characterized by three important principles: (1) a mixed set of affinity resins covering the largest spectrum of affinity ligands to statistically provide a partner ligand for each protein present in the samples, (2) the saturation effect of the capture due to a large number of sample overload, and (3) the exhaustiveness of protein recovery for full analysis. Although CPLL technology is currently used to track low abundance proteins, some research groups are still comparing the immunodepletion method with enrichment methods to obtain the best results.…”

Recent developments in capillary and microchip electroseparations of peptides (2021–mid‐2023)

“…Antimicrobial peptides are considered potential new antibiotics [2,4]. Peptides serve as biomarkers [5,6], and the combinatorial peptide libraries are employed for finding and identification of low-abundant proteins [7]. In the current era of proteomics, peptidomics, and metabolomics, the importance of peptides is even increasing as these methodologies are the major analytical tools for a study of molecular bases of biological processes, as well as for finding new biomarkers and drug targets [8,9].…”